Patent Grant
10557138
A computer readable form of a sequence listing is filed with this application by electronic submission and is incorporated into this application by reference in its entirety. The sequence listing is contained in the file named P34159US02_SEQ.txt, which is 9,785 bytes in size (measured in operating system MS windows) and was created on Jun. 10, 2016.
The present embodiments relate generally to compositions and methods for reducing the susceptibility of bees to infectious disease using RNA interference technology, and more particularly, to the use of RNA interference technology for reducing viral load and suppressing viral replication in the Varroa mite vector and in the bees.
Honeybees, Apis mellifera, are required for the effective pollination of crops and are therefore critical to world agriculture. Honeybees also produce economically important products, including honey and bees wax. The health and vigor of honeybee colonies are threatened by numerous parasites and pathogens, including viruses, bacteria, protozoa, and mites, each with characteristic modes of transmission.
In general, transmission of viruses can occur via two pathways: horizontal and vertical transmission. In horizontal transmission, viruses are transmitted among individuals of the same generation, while vertical transmission occurs from adults to their offspring. Transmission can occur through multiple routes in social organisms (for a detailed review see Chen Y P, et al (2006) Appl Environ Microbiol. 72(1):606-11). Recently, horizontal transmission of honeybee viruses has been documented in bee colonies, for example, transmission of deformed wing virus (DWV) and Kashmir Bee Virus (KBV) by the parasitic mite Varroa destructor, as well as some evidence of virus in honeybee eggs and young larvae, life stages not parasitized by Varroa mites.
Varroa (Varroa destructor) mites are the number one parasite of managed honey bees (Apis mellifera) and the biggest global threat to commercial beekeeping (Rosenkranz et al. 2010). Varroa mites parasitize pupae and adult bees and reproduce in the pupal brood cells. The mites use their mouths to puncture the exoskeleton and feed on the bee's hemolymph. These wound sites in the exoskeleton harbor bacterial infections, such as Melissococcus pluton, which causes European foulbrood. In addition, to their parasitic effects, Varroa mites are suspected of acting as vectors for a number of honey bee pathogens, including deformed wing virus (DWV), Kashmir bee virus (KBV), acute bee paralysis virus (ABPV) and black queen cell virus (BQCV), and may weaken the immune systems of their hosts, leaving them vulnerable to infections. Some bee viruses are known to replicate in the mite, thus dramatically increasing the viral load. If left untreated Varroa infestations typically result in colony-level mortality.
Currently, beekeepers use a plethora of methods to control Varroa levels that include various chemical miticides, most of which have lost efficacy and are toxic and/or leave residues in wax and honey. Other methods include application of oxalic or formic acid, monoterpenes (thymol) and a variety of other management practices, with highly variable outcomes, including toxicity to the treated colonies. Breeding of bees for resistance to Varroa, such as selection for Hygienic behavior which results in the removal of infested brood, has provided a limited practical success.
Current methods of treating Varroa infestations are proving to be ineffective as the mites develop resistance to existing miticides. In addition, the use of such miticides may introduce injurious chemicals into honey that is intended for human consumption.
The present embodiments relate to compositions and methods for controlling viral load and/or viral replication in Varroa mites and honeybees.
The present disclosure provides a method for reducing viral load or suppressing viral replication in a Varroa destructor mite or in a bee colony, the method comprising providing to the Varroa destructor mite or the bee colony a composition comprising an effective amount of at least one trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a sequence of at least 21 contiguous nucleotides of a bee viral gene, thereby reducing viral load or suppressing viral replication in the Varroa destructor mite or in the bee colony. In some embodiments, the virus is selected from the group consisting of: Acute Bee Paralysis Virus (ABPV), Deformed Wing Virus (DWV), Kashmir Bee Virus (KBV), Black Queen Cell Virus (BQCV), Sacbrood Virus (SBV), Chronic Bee Paralysis Virus (CPV), Cloudy Wing Virus (CWV), Israeli Acute Paralysis Virus (IAPV), Invertebrate iridescent virus type 6 (IIV-6), Varroa Destructor Virus (VDV-1), Kakugo Virus (KV), and Laker Sinai Virus (LSV).
The present disclosure also provides a composition for providing to a Varroa destructor mite, a bee, or a bee colony, comprising an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a sequence of at least 21 contiguous nucleotides of a bee viral gene. In some embodiments, the composition reduces viral load or suppresses viral replication in the Varroa destructor mite, the bee, or the bee colony. In some embodiments, the composition increases the tolerance of a bee or a bee colony to a disease caused by the bee virus.
In some embodiments, the trigger polynucleotide is single-stranded DNA (ssDNA), single-stranded RNA (ssRNA), double-stranded RNA (dsRNA), double-stranded DNA (dsDNA), or double stranded DNA-RNA hybrid.
In some embodiments, the trigger polynucleotide downregulates the viral gene. In some embodiments, the viral gene encodes a coat protein, RdRp, VP1, VP2, or helicase. In some embodiments, the trigger polynucleotide comprises a nucleic acid sequence having at least about 80%, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, or 99% sequence identity or complementarity, or having 100% sequence identity or complementarity to a sequence selected from the group consisting of SEQ ID NOs:1-21, or a fragment thereof. In some embodiments, the trigger polynucleotide comprises a mixture of 2, 3, 4, 5, 6, 7, 8, 9, or 10 different trigger polynucleotides, which target different viruses, or target different genes of the same virus, or target different fragments of a viral gene.
The present disclosure also provides a method for reducing viral load in a bee colony, the method comprising reducing viral load in a parasite of the bee colony by providing to the parasite a composition comprising an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a sequence of at least 21 contiguous nucleotides of a bee viral gene, thereby suppressing viral replication in the parasite and reducing the viral load in the bee colony. In some embodiments, the parasite is a Varroa destructor mite.
The present disclosure further provides a method for reducing the susceptibility of a bee to a disease caused by a bee virus, the method comprising providing to a parasite of the bee a composition comprising an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a sequence of at least 21 contiguous nucleotides of a bee viral gene, thereby suppressing viral replication in the parasite and reducing the susceptibility of the bee to a disease caused by the bee virus. In some embodiments, the disease is Colony Collapse Disorder (CCD). In some embodiments, the parasite is a Varroa destructor mite.
In some embodiments, the composition comprising an effective amount of the trigger polynucleotide is provided by spraying the Varroa mite, by directly feeding the Varroa mite, by directly feeding the bees in a bee colony, or any combination thereof.
In some embodiments, a method for reducing viral load in Varroa mites is provided. In some embodiments the bee virus is selected from the group consisting of: Acute Bee Paralysis Virus (ABPV), Deformed Wing Virus (DWV), Kashmir Bee Virus (KBV), Black Queen Cell Virus (BQCV), Sacbrood Virus (SBV), Chronic Bee Paralysis Virus (CPV), Cloudy Wing Virus (CWV), Israeli Acute Paralysis Virus (IAPV), Invertebrate iridescent virus type 6 (IIV-6), Varroa Destructor Virus (VDV-1), and Kakugo Virus (KV). According to some embodiments, a trigger polynucleotide comprising a nucleic acid sequence having essential identity or essential complementary to a sequence of at least 21 contiguous nucleotides of a bee viral gene is provided. According to some embodiments, there is provided a method for down-regulating expression of a viral gene in Varroa mites.
According to some embodiments, methods and compositions for preventing the spread of bee diseases, such as Colony Collapse Disorder through the application of RNA interference technology to Varroa mites directed to bee infectious organisms and agents, such as DWV, IAPV, Acute Bee Paralysis Virus and Kashmir Bee Paralysis Virus are provided.
According to some embodiments of the present invention there is provided a method for increasing the tolerance of a bee to a disease caused by a bee virus comprising providing an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a bee viral gene to a Varroa mite, thereby reducing the viral load in the Varroa mite and increasing the tolerance of the bee to the disease caused by the bee virus. In some embodiments, the nucleic acid is essentially identical or essentially complementary to a sequence of at least 21 contiguous nucleotides of the bee viral gene.
According to some embodiments of the present invention there is provided a method for increasing the tolerance of a bee colony to a disease caused by a bee virus comprising providing an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a bee viral gene to a Varroa mite, thereby reducing the viral load in the Varroa mite and increasing the tolerance of the bee colony to the disease caused by the bee virus. In some embodiments, the nucleic acid is essentially identical or essentially complementary to a sequence of at least 21 contiguous nucleotides of the bee viral gene.
In one aspect, the present disclosure provides a method for reducing viral load in a Varroa destructor mite, the method comprising providing or administering to the Varroa destructor mite a composition comprising an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a bee viral sequence, thereby suppressing viral replication in the Varroa destructor mite. In some embodiments, the bee viral sequence is a sequence of at least 21 contiguous nucleotides of a bee viral gene.
In one aspect, the present disclosure provides method of reducing viral load in a bee colony, the method comprising reducing viral load in a parasite of the bee colony by providing to the parasite a composition comprising an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a viral sequence, thereby suppressing viral replication in the parasite and reducing the viral load in the bee colony. In some embodiments, the parasite is Varroa destructor. In some embodiments, the bee viral sequence is a sequence of at least 21 contiguous nucleotides of a bee viral gene.
In one aspect, the present disclosure provides a method for reducing viral replication in a Varroa destructor mite, the method comprising administering to the Varroa destructor mite a composition comprising an effective amount of at least one trigger polynucleotide which comprises a nucleic acid sequence that downregulates expression of a bee viral gene in the Varroa destructor mite, thereby reducing viral replication in the Varroa destructor mite. In some embodiments, the nucleic acid sequence is a trigger polynucleotide that is essentially identical or essentially complementary to the viral gene or a fragment thereof. In some embodiments, the nucleic acid is essentially identical or essentially complementary to a sequence of at least 21 contiguous nucleotides of the bee viral gene.
In one aspect, the present disclosure provides for reducing viral replication in a bee colony, the method comprising reducing viral replication in a parasite of the bee colony by providing to the parasite a composition comprising an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a bee viral sequence, thereby suppressing viral replication in the parasite and reducing viral expression in the bee colony. In some embodiments, the parasite is Varroa destructor. In some embodiments, the bee viral sequence is a sequence of at least 21 contiguous nucleotides of a bee viral gene.
In one aspect, the present disclosure provides a method for reducing the susceptibility of a bee to a disease caused by a bee virus, the method comprising providing to a parasite of the bee a composition comprising an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a bee viral sequence, thereby suppressing viral replication in the parasite and reducing the susceptibility of the bee to a disease caused by the bee virus. In some embodiments, the parasite is Varroa destructor. In some embodiments, the disease is Colony Collapse Disorder (CCD). In some embodiments, the bee viral sequence is a sequence of at least 21 contiguous nucleotides of a bee viral gene.
According to some embodiments of the invention the bee is a honeybee.
According to some embodiments of the invention the honeybee is a forager.
According to some embodiments of the invention the honeybee is a hive bee.
Several embodiments relate to a composition comprising an effective amount of one or more trigger polynucleotides comprising a nucleic acid sequence that is essentially identical or essentially complementary to a sequence of at least 21 contiguous nucleotides of a bee viral gene. In some embodiments, the virus is selected from the group consisting of: Acute Bee Paralysis Virus (ABPV), Deformed Wing Virus (DWV), Kashmir Bee Virus (KBV), Black Queen Cell Virus (BQCV), Sacbrood Virus (SBV), Chronic Bee Paralysis Virus (CPV), Cloudy Wing Virus (CWV), Israeli Acute Paralysis Virus (IAPV), Invertebrate iridescent virus type 6 (IIV-6), Varroa Destructor Virus (VDV-1), Kakugo Virus (KV), and Lake Sinai Virus (LSV). In some embodiments, the virus is IAPV. In some embodiments, the virus is DWV. In some embodiments, the viral gene encodes a coat protein, RdRp, VP1, VP2, or helicase. In some embodiments, the trigger polynucleotide comprises a nucleic acid sequence having at least about 80%, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, or 99% sequence identity or complementarity, or having 100% sequence identity or complementarity to a sequence selected from the group consisting of SEQ ID NOs:1-21, or a fragment thereof. In some embodiments, the trigger polynucleotide comprises a mixture of 2, 3, 4, 5, 6, 7, 8, 9, or 10 different trigger polynucleotides, which target different viruses, or target different genes of the same virus, or target different fragments of a viral gene. In some embodiments, the composition comprises one or more trigger polynucleotides comprising a nucleic acid sequence having at least about 80%, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, or 99% sequence identity or complementarity, or having 100% sequence identity or complementarity to a DWV sequence and one or more trigger polynucleotides comprising a nucleic acid sequence having at least about 80%, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, or 99% sequence identity or complementarity, or having 100% sequence identity or complementarity to a IAPV sequence. Several embodiments relate to a composition comprising an effective amount of one or more trigger polynucleotides comprising a nucleic acid having at least about 80%, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, or 99% sequence identity or complementarity, or having 100% sequence identity or complementarity to a nucleic acid sequence selected from the group consisting of SEQ ID NOs:11, 13, 14, 17, and 18. Several embodiments relate to a composition comprising an effective amount of one or more trigger polynucleotides comprising a nucleic acid having at least about 80%, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, or 99% sequence identity or complementarity, or having 100% sequence identity or complementarity to a nucleic acid sequence selected from the group consisting of SEQ ID NOs:12, 15, 16, 19, and 20. In some embodiments, the trigger polynucleotide is single-stranded DNA (ssDNA), single-stranded RNA (ssRNA), double-stranded RNA (dsRNA), double-stranded DNA (dsDNA), or double stranded DNA-RNA hybrid. In some embodiments, the composition comprises one or more trigger polynucleotides and one or more excipients. In some embodiments, the excipient comprises one or more substance selected from: a sugar, a solvent, a protein, a bee food, and any combination thereof. In some embodiments, the sugar is selected from: fructose, glucose, sucrose, trehalose, lactose, galactose, ribose and any combination thereof. In some embodiments, the bee food is selected from: honey, pollen, Wheast, soybean flour, yeast, yeast product, and any combination thereof. In some embodiments, the composition is a bee-ingestible composition selected from the group consisting of a liquid bee-ingestible composition and a solid bee-ingestible composition. In some embodiments, the liquid bee-ingestible composition is a sugar syrup. In some embodiments, the solid bee-ingestible composition is a cake or dry mix.
Unless defined otherwise, technical and scientific terms as used herein have the same meaning as commonly understood by one of ordinary skill in the art. One skilled in the art will recognize many methods can be used in the practice of the present disclosure. Indeed, the present disclosure is in no way limited to the methods and materials described. Any references cited herein are incorporated by reference in their entireties. For purposes of the present disclosure, the following terms are defined below.
As used herein, the term “about” refers to ±10%.
As used herein, the singular form “a”, “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a compound” or “at least one compound” may include a plurality of compounds, including mixtures thereof.
Unless otherwise stated, nucleic acid sequences in the text of this specification are given, when read from left to right, in the 5′ to 3′ direction. It is understood that any Sequence Identification Number (SEQ ID NO) disclosed in the instant application can refer to either a DNA sequence or a RNA sequence, depending on the context where that SEQ ID NO is mentioned, even if that SEQ ID NO is expressed only in a DNA sequence format or a RNA sequence format. Further, disclosure of a nucleic acid sequence discloses the sequence of its reverse complement, as one necessarily defines the other, as is known by one of ordinary skill in the art. Where a term is provided in the singular, the inventors also contemplate aspects of the invention described by the plural of that term.
Bees are susceptible to a myriad of viral infections. To date, 24 bee viruses have been identified. Most are positive strand RNA viruses, which contain RNA-dependant RNA polymerase (RdRp). Two phylogenetic families of bee viruses with two main structural formats have been identified. See
According to some embodiments, RNA interference technology is used to reduce the viral load in Varroa destructor mites and in bees. Varroa mites parasitize pupae and adult bees and reproduce in the pupal brood cells. The mites use their mouths to puncture the exoskeleton and feed on the bee's hemolymph. Polynucleotide agents administered to the bees to treat Varroa mite infestations presented in the bee's hemolymph thereby becoming available to the mite (see U.S. Patent Publication 2012/0258646).
In several embodiments of the present disclosure, RNA interference technology is used to reduce viral replication in Varroa destructor mites and in bees. In several embodiments of the present disclosure, RNA interference technology is used to reduce or prevent transmission of bee viruses from a bee or bee larvae to a Varroa destructor mite which feeds on the bee or bee larvae. In several embodiments of the present disclosure, RNA interference technology is used to reduce or prevent transmission of bee viruses from a Varroa destructor mite to a bee or bee larvae that the mite parasitizes.
In some embodiments of the present disclosure, RNA interference technology is used to reduce viral load in a bee. In some embodiments, RNA interference technology is used to reduce viral load in a bee colony.
In some embodiments of the present disclosure, RNA interference technology is used to reduce viral replication in a bee. In some embodiments, RNA interference technology is used to reduce viral replication in a bee colony.
RNA interference refers to the process of sequence-specific post-transcriptional gene silencing in animals mediated by small RNAs. The corresponding process in plants is commonly referred to as post-transcriptional gene silencing or RNA silencing and is also referred to as quelling in fungi. While not being limited to any particular theory, the process of post-transcriptional gene silencing is thought to be an evolutionarily-conserved cellular defense mechanism used to prevent the expression of foreign genes and is commonly shared by diverse flora and phyla. Such protection from foreign gene expression may have evolved in response to the production of double-stranded RNAs (dsRNAs) derived from viral infection or from the random integration of transposon elements into a host genome via a cellular response that specifically destroys homologous single-stranded RNA or viral genomic RNA. In aspects according to the present disclosure, a nucleic acid composition results in RNA interference in a target organism. In certain aspects the nucleic acid composition results in RNA interference in Varroa destructor when present on the host organism, the bee or bee larvae.
The phrase “Varroa destructor mite” refers to the external parasitic mite that attacks honey bees Apis cerana and Apis mellifera. The mite can be at an adult stage, feeding off the bee, or at a larval stage, inside the honey bee brood cell.
In some embodiments of the present disclosure, a bee virus is selected from the group consisting of: Acute Bee Paralysis Virus (ABPV), Deformed Wing Virus (DWV), Kashmir Bee Virus (KBV), Black Queen Cell Virus (BQCV), Sacbrood Virus (SBV), Chronic Bee Paralysis Virus (CPV), Cloudy Wing Virus (CWV), Israeli Acute Paralysis Virus (IAPV), Invertebrate iridescent virus type 6 (IIV-6), Varroa Destructor Virus (VDV-1), Kakugo Virus (KV), and Lake Sinai Virus (LSV).
In some embodiments of the present disclosure, the bee virus is a positive strand RNA virus. In some embodiments, the bee virus is a negative strand RNA virus. In some embodiments, the bee virus is DWV. In some embodiments, the bee virus is IAPV. In some embodiments, the bee virus is LSV.
As used herein, a measurement of “viral load,” “viral levels,” and “viral expression” refers to the detection of the sense strand of a bee virus sequence, and they are used interchangeably in the present disclosure. A number of detection methods are known in the art, including but not limited to, quantitative PCR (Q-PCR) and the QuantiGene® assay. In some embodiments, viral load or viral expression is measured as median fluorescence intensity (MFI) and normalized with MFI of housekeeping genes to represent the presence of the virus in a bee, a bee colony, or Varroa mites. In some embodiments, viral load is a measure of the severity of an active viral infection.
As used herein, a measurement of “viral replication” refers to the detection of the negative strand of a bee virus sequence. In some embodiments, viral replication is measured as median fluorescence intensity (MFI) and normalized with MFI of housekeeping genes to represent the replication of the virus in a bee, a bee colony, or Varroa mites. In some embodiments, viral replication is a measure of the severity of an active viral infection.
As used herein, the term “viral titer” refers to the concentration of viruses in a sample. In some embodiments, the viral load is measured by the viral titer. A number of methods are known in the art for calculating the viral titer, and they are emcompassed by this application.
As used herein, the term “host” or “host organism” refers to an organism that harbors a parasite and provides nourishment to the parasite. A “parasite” is an organism that has a non-mutual symbiotic relationship with a host organism and benefits at the expense of the host organism. In some embodiments, the host organism is a bee. In some embodiments, the parasite is a Varroa mite.
As used herein, the term “bee” refers to both an adult bee and pupal cells thereof. According to one aspect, the bee is in a hive. An adult bee is defined as any of several winged, hairy-bodied, usually stinging insects of the superfamily Apoidea in the order Hymenoptera, including both solitary and social species and characterized by sucking and chewing mouthparts for gathering nectar and pollen. Examples of bee species include, but are not limited to, Apis, Bombus, Trigona, Osmia and the like. In one aspect, bees include, but are not limited to bumblebees (Bombus terrestris), honeybees (Apis mellifera) (including foragers and hive bees) and Apis cerana. The present disclosure provides for, and includes, methods and compositions for treating insects as either a host or as a parasite.
According to one aspect, a bee is part of a colony. The term “colony” refers to a population of bees comprising dozens to typically several tens of thousands of bees that cooperate in nest building, food collection, and brood rearing. A colony normally has a single queen, the remainder of the bees being either “workers” (females) or “drones” (males). The social structure of the colony is maintained by the queen and workers and depends on an effective system of communication. Division of labor within the worker caste primarily depends on the age of the bee but varies with the needs of the colony. Reproduction and colony strength depend on the queen, the quantity of food stores, and the size of the worker force. Honeybees can also be subdivided into the categories of “hive bees”, usually for the first part of a workers lifetime, during which the “hive bee” performs tasks within the hive, and “forager bee”, during the latter part of the bee's lifetime, during which the “forager” locates and collects pollen and nectar from outside the hive, and brings the nectar or pollen into the hive for consumption and storage. The present disclosure provides for, and includes, methods and compositions for treating insects colonies.
As used herein, the term “parasite” refers to both adult and immature forms of organisms that directly benefit at the expense of another, host, organism, for example by feeding on the blood or fluids of the host, living intracellularly in a host organism cell, or living within a body of a host organism. The present disclosure provides for, and includes, methods and compositions for treating parasites. In an aspect, the parasite is Varroa destructor.
As used herein, the phrase “RNA silencing” refers to a group of regulatory mechanisms (e.g. RNA interference (RNAi), transcriptional gene silencing (TGS), post-transcriptional gene silencing (PTGS), quelling, co-suppression, and translational repression) mediated by RNA molecules which result in the inhibition or “silencing” of the expression of a corresponding viral gene. RNA silencing has been observed in many types of organisms, including plants, animals, and fungi. In aspects according the present disclosure, nucleic acid compositions provide for RNA silencing. In certain aspects, the nucleic acid compositions provide for silencing of viral genes in a bee parasite.
The present disclosure provides a method for reducing viral load or suppressing viral replication in a Varroa destructor mite or in a bee colony, the method comprising providing to the Varroa destructor mite or the bee colony a composition comprising an effective amount of at least one trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a sequence of at least 21 contiguous nucleotides of a bee viral gene, thereby reducing viral load or suppressing viral replication in the Varroa destructor mite or in the bee colony. In some embodiments, the virus is selected from the group consisting of: Acute Bee Paralysis Virus (ABPV), Deformed Wing Virus (DWV), Kashmir Bee Virus (KBV), Black Queen Cell Virus (BQCV), Sacbrood Virus (SBV), Chronic Bee Paralysis Virus (CPV), Cloudy Wing Virus (CWV), Israeli Acute Paralysis Virus (IAPV), Invertebrate iridescent virus type 6 (IIV-6), Varroa Destructor Virus (VDV-1), Kakugo Virus (KV), and Laker Sinai Virus (LSV).
The present disclosure also provides a composition for providing to a Varroa destructor mite, a bee, or a bee colony, comprising an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a sequence of at least 21 contiguous nucleotides of a bee viral gene. In some embodiments, the composition reduces viral load or suppresses viral replication in the Varroa destructor mite, the bee, or the bee colony. In some embodiments, the composition increases the tolerance of a bee or a bee colony to a disease caused by the bee virus.
In some embodiments, the trigger polynucleotide is single-stranded DNA (ssDNA), single-stranded RNA (ssRNA), double-stranded RNA (dsRNA), double-stranded DNA (dsDNA), or double stranded DNA-RNA hybrid.
In some embodiments, the trigger polynucleotide downregulates the viral gene. In some embodiments, the viral gene encodes a coat protein, RdRp, VP1, VP2, or helicase. In some embodiments, the trigger polynucleotide comprises a nucleic acid sequence having at least about 80%, 85%, 88%, 90%, 92%, 95%, 96%, 97%, 98%, or 99% sequence identity or complementarity, or having 100% sequence identity or complementarity to a sequence selected from the group consisting of SEQ ID NOs:1-21, or a fragment thereof. In some embodiments, the trigger polynucleotide comprises a mixture of 2, 3, 4, 5, 6, 7, 8, 9, or 10 different trigger polynucleotides, which target different viruses, or target different genes of the same virus, or target different fragments of a viral gene.
The present disclosure also provides a method for reducing viral load in a bee colony, the method comprising reducing viral load in a parasite of the bee colony by providing to the parasite a composition comprising an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a sequence of at least 21 contiguous nucleotides of a bee viral gene, thereby suppressing viral replication in the parasite and reducing the viral load in the bee colony. In some embodiments, the parasite is a Varroa destructor mite.
The present disclosure further provides a method for reducing the susceptibility of a bee to a disease caused by a bee virus, the method comprising providing to a parasite of the bee a composition comprising an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a sequence of at least 21 contiguous nucleotides of a bee viral gene, thereby suppressing viral replication in the parasite and reducing the susceptibility of the bee to a disease caused by the bee virus. In some embodiments, the disease is Colony Collapse Disorder (CCD). In some embodiments, the parasite is a Varroa destructor mite.
In some embodiments, the composition comprising an effective amount of the trigger polynucleotide is provided by spraying the Varroa mite, by directly feeding the Varroa mite, by directly feeding the bees in a bee colony, or any combination thereof.
In one aspect, the present disclosure provides a method for reducing viral load or suppressing viral replication in a Varroa destructor mite, the method comprising providing to the Varroa destructor mite a composition comprising an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a viral sequence, thereby suppressing viral replication or reducing viral load in the Varroa destructor mite.
In one aspect, the present disclosure provides a method for reducing viral load or suppressing viral replication in a bee or a bee colony, the method comprising providing to the bee or bee colony a composition comprising an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a viral sequence, thereby suppressing viral replication or reducing viral load in the bee or bee colony.
In one aspect, the present disclosure provides a method of reducing viral load or suppressing viral replication in a bee or a bee colony, the method comprising reducing viral load or suppressing viral replication in a parasite of the bee or bee colony by providing to the parasite a composition comprising an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a viral sequence, thereby suppressing viral replication in the parasite and reducing the viral load in the bee colony. In some embodiments, the parasite is Varroa destructor.
In one aspect, the present disclosure provides a method for reducing viral load or suppressing viral replication in a Varroa destructor mite, the method comprising administering to the Varroa destructor mite a composition comprising an effective amount of at least one trigger polynucleotide which comprises a nucleic acid sequence that downregulates expression of a viral gene in the Varroa destructor mite, thereby reducing viral load or suppressing viral replication in the Varroa destructor mite. In some embodiments, the nucleic acid sequence is a trigger polynucleotide that is essentially identical or essentially complementary to the viral gene or a fragment thereof.
In one aspect, the present disclosure provides for reducing viral load or suppressing viral replication in a bee colony, the method comprising reducing viral load or suppressing viral replication in a parasite of the bee colony by providing to the parasite a composition comprising an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a viral sequence, thereby suppressing viral replication in the parasite and reducing viral expression in the bee colony. In some embodiments, the parasite is Varroa destructor.
In one aspect, the present disclosure provides a method for reducing the susceptibility of a bee to a disease caused by a bee virus, the method comprising providing to a parasite of the bee a composition comprising an effective amount of a trigger polynucleotide comprising a nucleic acid sequence that is essentially identical or essentially complementary to a viral sequence, thereby suppressing viral replication in the parasite and reducing the susceptibility of the bee to a disease caused by the bee virus. In some embodiments, the parasite is Varroa destructor. In some embodiments, the disease is Colony Collapse Disorder (CCD).
As used herein, the term “trigger” or “trigger polynucleotide” refers to a bioactive polynucleotide molecule that is substantially homologous or complementary to a polynucleotide sequence of a target gene or an RNA expressed from the target gene or a fragment thereof and functions to suppress the expression of the target gene or produce a knock-down phenotype. Trigger polynucleotides are capable of inhibiting or “silencing” the expression of a target gene. Trigger polynucleotides are generally described in relation to their “target sequence.” Trigger polynucleotides may be single-stranded DNA (ssDNA), single-stranded RNA (ssRNA), double-stranded RNA (dsRNA), double-stranded DNA (dsDNA), or double-stranded DNA/RNA hybrids. Trigger polynucleotides may comprise naturally-occurring nucleotides, modified nucleotides, nucleotide analogues or any combination thereof. In some embodiments, a trigger polynucleotide may be incorporated within a larger polynucleotide, for example in a pri-miRNA molecule. In some embodiments, a trigger polynucleotide may be processed into a small interfering RNA (siRNA). In an aspect, the trigger polynucleotide is capable of inhibiting the expression of a viral gene. In another aspect, the trigger polynucleotide is capable of being used in methods to inhibit the expression of a viral gene and thereby reduce the viral load of a host organism. In certain aspects, the viral gene is a DWV, VDV-1, IAPV, ABPV, KBV, or LSV gene and the host organism is Varroa destructor.
As used herein, the term “target sequence” or “target gene” refers to a nucleotide sequence that occurs in a gene or gene product against which a trigger polynucleotide is directed. In this context, the term “gene” means a locatable region of genomic sequence, corresponding to a unit of inheritance, which includes regulatory regions, such as promoters, enhancers, 5′ untranslated regions, intron regions, 3′ untranslated regions, transcribed regions, and other functional sequence regions that may exist as native genes or transgenes in a plant genome.
Depending upon the circumstances, the term target sequence or target gene can refer to the full-length nucleotide sequence of the gene or gene product targeted for suppression or the nucleotide sequence of a portion of the gene or gene product targeted for suppression.
As used herein, the term “derived from” refers to a specified nucleotide sequence that may be obtained from a particular specified source or species, albeit not necessarily directly from that specified source or species.
As used herein, the terms “sequence”, “nucleotide sequence” or “polynucleotide sequence” refer to the nucleotide sequence of a DNA molecule, an RNA molecule or a portion thereof.
The term “polynucleotide” refers to any polymer of mononucleotides that are linked by internucleotide bonds. Polynucleotides may be composed of naturally-occurring ribonucleotides, naturally-occurring deoxyribonucleotides, analogs of naturally-occurring nucleotides (e.g., enantiomeric forms of naturally-occurring nucleotides), or any combination thereof. Where a polynucleotide is single-stranded, its length can be described in terms of the number of nucleotides. Where a polynucleotide is double-stranded, its length can be described in terms of the number of base pairs.
As used herein, the term “non-transcribable polynucleotide” refers to a polynucleotide that does not comprise a complete polymerase II transcription unit.
The term “gene expression” refers to the process of converting genetic information encoded in genomic DNA into RNA (e.g., mRNA, rRNA, tRNA, or snRNA) through transcription of the gene via the enzymatic action of an RNA polymerase, and into protein, through translation of mRNA. Gene expression can be regulated at many stages in the process.
In the embodiments described herein, viral sequences are selected as targets for trigger polynucleotides. In some embodiments, target sequences are selected for including low G/C content as these have proven to be more effective in mediating gene silencing as compared to those with G/C content higher than 55%. In some embodiments, several target sites are selected along the length of the target gene.
In some embodiments, the trigger polynucleotide comprises a nucleotide sequence that is essentially complementary or essentially identical to a viral gene or a fragment thereof. In some embodiments, the trigger polynucleotide comprises a nucleic acid that is essentially complementary or essentially identical to a sequence of at least 21 contiguous nucleotides of a bee viral gene. In some embodiments, the trigger polynucleotide comprises a nucleic acid that is essentially complementary or essentially identical to a sequence of at least 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 contiguous nucleotides of a bee viral gene. In some embodiments, the viral gene encodes a coat protein, RdRp, Viral Protein 1 (VP1), VP2, or Helicase. In some embodiments, the trigger polynucleotide comprises a nucleotide sequence that is essentially complementary or essentially identical to a DWV or a IAPV gene, or a fragment thereof. In some embodiments, the trigger polynucleotide comprises a nucleotide sequence that is essentially complementary or essentially identical to a LSV gene or a fragment thereof. In some embodiments, the trigger polynucleotide comprises a nucleotide sequence that is essentially complementary or essentially identical to an Acute Bee Paralysis gene or a fragment thereof. In some embodiments, the trigger polynucleotide comprises a nucleotide sequence that is essentially complementary or essentially identical to a Kashmir Bee Virus gene or a fragment thereof. In some embodiments, the trigger polynucleotide comprises a nucleotide sequence that is essentially complementary or essentially identical to a Black Queen Cell Virus gene or a fragment thereof. In some embodiments, the trigger polynucleotide comprises a nucleotide sequence that is essentially complementary or essentially identical to a Chronic Paralysis Virus gene or a fragment thereof. In some embodiments, the trigger polynucleotide comprises a nucleotide sequence that is essentially complementary or essentially identical to a Cloudy Wing Virus gene or a fragment thereof.
Multiple bee-pathogen sequences can be designed to include sequences suitable for producing trigger polynucleotides effective against more than one bee virus. Such multiple bee-pathogen dsRNA can be of the long or short variety, and may include sequences corresponding to homologous sequences within a class of bee viruses. Further, multiple sequences can be designed to include two or more dsRNA sequences of the same bee-pathogen.
By “essentially identical” or “essentially complementary,” it is meant that the bioactive polynucleotide trigger (or at least one strand of a double-stranded polynucleotide or portion thereof, or a portion of a single strand polynucleotide) hybridizes under physiological conditions to the endogenous gene, an RNA transcribed there from, or a fragment thereof, to effect regulation or suppression of the endogenous gene. For example, in some embodiments, a bioactive polynucleotide trigger has 100 percent sequence identity or at least about 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 percent sequence identity when compared to a sequence of 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60 or more contiguous nucleotides in the target gene or RNA transcribed from the target gene. In some embodiments, a bioactive polynucleotide trigger has 100 percent sequence complementarity or at least about 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 percent sequence complementarity when compared to a sequence of 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60 or more contiguous nucleotides in the target gene or RNA transcribed from the target gene. In some embodiments, a bioactive polynucleotide trigger has 100 percent sequence identity with or complementarity to one allele or one family member of a given target gene (coding or non-coding sequence of a gene). In some embodiments, a bioactive polynucleotide trigger has at least about 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 percent sequence identity with or complementarity to multiple alleles or family members of a given target gene. In some embodiments, a bioactive polynucleotide trigger has 100 percent sequence identity with or complementarity to multiple alleles or family members of a given target gene.
As used herein, nucleic acid sequence molecules are said to exhibit “complete complementarity” when every nucleotide of one of the sequences read 5′ to 3′ is complementary to every nucleotide of the other sequence when read 3′ to 5′. A nucleotide sequence that is completely complementary to a reference nucleotide sequence will exhibit a sequence identical to the reverse complement sequence of the reference nucleotide sequence.
It will be appreciated that a trigger polynucleotide, for example dsRNA, of the present disclosure need not be limited to those molecules containing only natural nucleotides, but further encompasses chemically-modified nucleotides and non-nucleotides. Trigger polynucleotide agents of the present disclosure may also include base modifications or substitutions. As used herein, “unmodified” or “natural” bases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified bases include but are not limited to other synthetic and natural bases such as 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3-deazaadenine. Further bases include those disclosed in U.S. Pat. No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, pages 858-859, Kroschwitz, J. I., ed. John Wiley & Sons, 1990, those disclosed by Englisch et al., Angewandte Chemie, International Edition, 1991, 613, and those disclosed by Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, pages 289-2, Crooke, S. T. and Lebleu, B., ed., CRC Press, 1993. Such bases are particularly useful for increasing the binding affinity of the oligomeric compounds of the disclosure. These include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2° C. (Sanghvi Y S et al. (1993) Antisense Research and Applications, CRC Press, Boca Raton 276-278) and are presently preferred base substitutions, even more particularly when combined with 2′-O-methoxyethyl sugar modifications.
Following synthesis, the trigger polynucleotides of the present disclosure may optionally be purified. For example, polynucleotides can be purified from a mixture by extraction with a solvent or resin, precipitation, electrophoresis, chromatography, or a combination thereof. Alternatively, trigger polynucleotides may be used with no, or a minimum of, purification to avoid losses due to sample processing. The trigger polynucleotides may be dried for storage or dissolved in an aqueous solution. The solution may contain buffers or salts to promote annealing, and/or stabilization of the duplex strands.
As used herein, the terms “homology” and “identity” when used in relation to nucleic acids, describe the degree of similarity between two or more nucleotide sequences. The percentage of “sequence identity” between two sequences is determined by comparing two optimally aligned sequences over a comparison window, such that the portion of the sequence in the comparison window may comprise additions or deletions (gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity. A sequence that is identical at every position in comparison to a reference sequence is said to be identical to the reference sequence and vice-versa. An alignment of two or more sequences may be performed using any suitable computer program. For example, a widely used and accepted computer program for performing sequence alignments is CLUSTALW v1.6 (Thompson, et al. Nucl. Acids Res., 22: 4673-4680, 1994).
As used herein, a “control organism” means an organism that does not contain the trigger polynucleotide, or other nucleic acid that provides for control of a viral infection or viral replication. Control organisms are generally from same species and of the same developmental stage which is grown under the same growth conditions as the treated organism. Similarly, a “control colony” means a colony of organisms that do not contain the trigger polynucleotide or other nucleic acid that provides for control of viral infection or viral replication. Control colonies of organisms are generally from same species and of the same developmental stage which are grown under the same growth conditions as the treated colony of organisms.
As used herein, the term “treating” includes abrogating, substantially inhibiting, slowing or reversing the progression of a condition, substantially ameliorating clinical or aesthetical symptoms of a condition or substantially preventing the appearance of clinical or aesthetical symptoms of a condition. In an aspect according to the present disclosure, a composition may be used to treat an organism or colony of organisms for viral infection. In an aspect, a dsRNA composition may be used to treat a host organism or a parasite for viral infection. In an aspect, the host organism is a bee and the parasite is the mite, Varroa destructor. In an aspect, the present disclosure provides a method for treating Colony Collapse Disorder (CCD).
As used herein, the terms “improving,” “improved,” “increasing,” and “increased” refer to at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or greater increase in an organism or colony population, in increased productivity of an organism or colony (e.g., increased honey productions), increase growth rate of an organism or colony, or increased reproductive rate as compared to a control organism or colony. The present disclosure provides for methods of improving the health of an organism or colony by providing an antiviral composition.
As used herein, “viral load”, also known as “viral burden,” “viral titer”, “viral level” or “viral expression” in some embodiments, is a measure of the severity of a viral infection, and can be calculated by estimating the amount of virus in an infected organism, an involved body fluid, or an affected colony. It can also be calculated by estimating or measuring the amount of the sense strand of a bee virus sequence in an infected organism, an involved body fluid, or an affected colony.
As used herein, “a reduction” of the level of an agent such as a protein or mRNA means that the level is reduced relative to an organism or colony lacking a trigger polynucleotide, for example a dsRNA molecule, capable of reducing the agent. Also as used herein, “a reduction” in reference to viral load, means that the viral load is reduced relative to an organism or colony lacking a nucleic acid or other dsRNA molecule capable of reducing the viral load. The present disclosure provides for, and includes, methods and compositions for reducing the level of a viral protein or viral gene expression and reducing the viral load. The present disclosure also provides for methods and compositions for reducing the level of a viral replication in a Varroa mite or in a bee.
As used herein, the term “at least a partial reduction” of the level of an agent such as a protein or mRNA means that the level is reduced at least 25% relative to an organism or colony lacking a trigger polynucleotide, for example a dsRNA molecule, capable of reducing the agent. Also as used herein, “at least a partial reduction” in reference to viral load, means that the level is reduced at least 25% relative to an organism or colony lacking a nucleic acid or other dsRNA molecule capable of reducing the viral load. The present disclosure provides for, and includes, methods and compositions for at least partially reducing the level of a viral protein or viral gene expression and at least partially reducing the viral load.
As used herein, “a substantial reduction” of the level of an agent such as a protein or mRNA means that the level is reduced relative to an organism or colony lacking a trigger polynucleotide, for example a dsRNA molecule, capable of reducing the agent, where the reduction of the level of the agent is at least 75%. Also as used herein, “a substantial reduction” in reference to viral load, means that the viral load is reduced at least 75% relative to an organism or colony lacking a nucleic acid or other dsRNA molecule capable of reducing the viral load. The present disclosure provides for, and includes, methods and compositions for substantially reducing the level of a viral protein or viral gene expression and substantially reducing the viral load.
As used herein, “an effective elimination” of an agent such as a protein or mRNA is relative to an organism or colony lacking trigger polynucleotide, for example a dsRNA molecule, capable of reducing the agent, where the reduction of the level of the agent is greater than 95%. A trigger polynucleotide, preferably a dsRNA molecule, is preferably capable of providing at least a partial reduction, more preferably a substantial reduction, or most preferably effective elimination of another agent such as a viral protein or viral gene expression, or a virus, wherein the agent leaves the level of expression of a host gene, essentially unaffected, substantially unaffected, or partially unaffected. Also as used herein, “an effective elimination” in reference to viral load, means that the viral load is reduced at least 95% relative to an organism or colony lacking a nucleic acid or other dsRNA molecule capable of reducing the viral protein, viral gene expression or viral load. The present disclosure provides for, and includes, methods and compositions for the effective elimination of a viral protein or viral gene expression and effectively eliminating viral infection.
As used herein, the terms “suppress,” “repress,” and “downregulate” when referring to the expression or activity of a nucleic acid molecule in an organism are used equivalently herein and mean that the level of expression or activity of the nucleic acid molecule in a cell of an organism or a colony after applying a method of the present disclosure is lower than its expression or activity in the cell of an organism or a colony before applying the method, or compared to a control organism or colony lacking a nucleic acid molecule of the disclosure. The present disclosure provides for, and includes, methods and compositions for suppressing, repressing and down-regulating the level of a viral protein or viral gene expression and suppressing, repressing and down-regulating the level viral infection in an organism or colony. The present disclosure also provides for methods and compositions for suppressing, repressing and down-regulating the level of a viral replication in an organism or colony. In some embodiments, the organism is a Varroa mite. In some embodiments, the organism is a bee. In some embodiments, the colony is a bee colony.
The terms “suppressed,” “repressed” and “downregulated” as used herein are synonymous and mean herein lower, preferably significantly lower, expression or activity of the targeted nucleic acid molecule. Also as used herein, “suppressed,” “repressed” and “downregulated” in reference to viral infection or viral load, means that the level of infection or viral load is lower, preferably significantly lower relative to an organism or colony lacking a nucleic acid or other dsRNA molecule capable of reducing viral gene expression. The present disclosure provides for, and includes, methods and compositions for suppressing, repressing and down-regulating the expression or activity of a viral protein or viral gene and suppressing, repressing and down-regulating the infectivity of viruses.
In some embodiments, the trigger polynucleotide is single-stranded DNA (ssDNA), single-stranded RNA (ssRNA), double-stranded RNA (dsRNA), double-stranded DNA (dsDNA), or double-stranded DNA/RNA hybrid. In some embodiments, the trigger polynucleotide is dsRNA.
In some embodiments, the trigger polynucleotide comprises a nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity, or having 100% sequence identity to a sequence selected from the group consisting of SEQ ID NOs: 1-21, or a fragment thereof. In some embodiments, the trigger polynucleotide comprises a nucleic acid sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence complementarity, or having 100% sequence complementarity to a sequence selected from the group consisting of SEQ ID NOs: 1-21, or a fragment thereof. In some embodiments, the trigger polynucleotide composition comprises a nucleic acid sequence having essential identity or essential complementarity to a sequence consisting of at least 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 contiguous nucleotides from a sequence selected from SEQ ID NOs: 1-21.
In certain aspects, the present disclosure provides a dsRNA composition comprising a nucleotide sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity or complementarity to a sequence selected from the group consisting of SEQ ID NOs: 1 to 21, or a fragment thereof. In certain aspects, the dsRNA composition comprises a nucleotide sequence having 100% identity or complementarity to a sequence selected from SED ID NOs: 1-21, or a fragment thereof. In another aspect, the present disclosure provides a DNA encoding at least one dsRNA precursor comprising a nucleotide sequence having 100% identity or complementarity to a sequence selected from the group consisting of SEQ ID NOs: 1 to 21, or a fragment thereof, or having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity or complementarity to a sequence selected from SEQ ID NOs: 1 to 21, or a fragment thereof. In yet another aspect, the present disclosure provides a recombinant DNA encoding at least one dsRNA precursor comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1 to 21, or a fragment thereof, a heterologous promoter and a transcription terminator sequence are provided. In another aspect, the present disclosure provides a recombinant DNA encoding at least one dsRNA precursor comprising a nucleotide sequence having at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity or complementarity to a sequence selected from the group consisting of SEQ ID NOs: 1 to 21, or a fragment thereof, and further comprising a heterologous promoter and a transcription terminator.
In several embodiments, the present disclosure provides a composition comprising at least one trigger polynucleotide. In some embodiments, the composition comprises a mixture of at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 different trigger polynucleotides. In some embodiments, the composition comprises a mixture of 2, 3, 4, 5, 6, 7, 8, 9, or 10 different trigger polynucleotides. In some embodiments, the trigger polynucleotides can target different viruses. In some embodiments, the trigger polynucleotides can target different genes of the same virus. In some embodiments, the trigger polynucleotides can target different fragments of a viral sequence or a viral gene.
It will be appreciated that the trigger polynucleotides, for example dsRNA, can be delivered to the pest or parasite in a great variety of ways. According to one aspect, the trigger polynucleotides are delivered directly to the parasite (e.g. by spraying a mite infested hive). The trigger polynucleotides, or constructs encoding same may enter the mites' bodies by diffusion. In another aspect, the trigger polynucleotides are indirectly delivered via a host organism (e.g., by providing a bee food comprising the trigger polynucleotide to a bee). In an aspect, the parasite is Varroa destructor. In one aspect, the host organism is a bee.
It will be appreciated that since many parasites use their mouths to puncture the host arthropod exoskeleton and feed on the arthropod's hemolymph, the present disclosure contemplates delivering the trigger polynucleotides, for example dsRNA, of the present disclosure to the host arthropod, whereby they become presented in the host arthropod hemolymph thereby becoming available to the parasite. Thus, according to another aspect, the nucleic acid agents are delivered indirectly to the parasite (for example to a mite via a host bee). In certain aspects, the pest or parasite is Varroa destructor and the host arthropod is a bee.
According to one aspect, the trigger polynucleotides, for example dsRNA, are delivered to the infested hosts by spraying. The trigger polynucleotides, for example dsRNA, or constructs encoding same may enter the host's bodies by diffusion. In certain aspects, the pest or parasite is Varroa destructor and the host arthropod is a bee.
According to another aspect, the trigger polynucleotides, for example dsRNA, are delivered to the host via its food. The present inventors consider that following ingestion of the trigger polynucleotides of the present disclosure, the trigger polynucleotides can be presented, for example, in a host arthropod in the host's hemolymph, whereby it becomes available to the parasite, for example a Varroa mite.
In one aspect, the polynucleotides of the present disclosure can be synthesized in vitro and added to the food. For example double stranded RNA can be synthesized by adding two opposing promoters (e.g. T7 promoters) to the ends of the gene segments, wherein the promoter is placed immediately 5′ to the gene and the promoter is placed immediately 3′ to the gene segment in the opposite orientation. The dsRNA can then be transcribed in vitro with the T7 RNA polymerase.
Non-limiting examples of sequences for synthesizing dsRNA according to aspects of the present disclosure are provided in SEQ ID NOs: 1-21. Full length or a fragment of these sequences can be used as the template.
This application provides and discloses compositions comprising a trigger polynucleotide and an excipient substance. In an aspect, the excipient can be a combination of one or more inactive components. In some aspects, the excipient comprises a sugar. Examples of sugars include hexoses, disaccharides, trisaccharides and higher sugars. Excipient sugars include, for example, fructose, glucose, sucrose, trehalose, lactose, galactose, ribose. In other aspects the excipient comprises a sugar and a solvent. In other aspects, the excipient comprises a protein. In an aspect, the protein is a soy protein. In other aspects the excipient is pollen. In aspects according to the present disclosure, the excipient is a bee food.
In some embodiments, the excipient comprises one or more substance selected from: a sugar, a solvent, a protein, a bee food, and any combination thereof. In some embodiments, the sugar is selected from: fructose, glucose, sucrose, trehalose, lactose, galactose, ribose and any combination thereof. In some embodiments, the bee food is selected from: honey, pollen, Wheast, soybean flour, yeast, yeast product, and any combination thereof.
Bee feeding is common practice amongst bee-keepers, for providing both nutritional and other, for example, supplemental needs. Bees typically feed on honey and pollen, but have been known to ingest non-natural feeds as well. Bees can be fed various foodstuffs including, but not limited to Wheast (a dairy yeast grown on cottage cheese), soybean flour, yeast (e.g. brewer's yeast, torula yeast) and yeast products products-fed singly or in combination and soybean flour fed as a dry mix or moist cake inside the hive or as a dry mix in open feeders outside the hive. Also useful is sugar, or a sugar syrup. The addition of 10 to 12 percent pollen to a supplement fed to bees improves palatability. The addition of 25 to percent pollen improves the quality and quantity of essential nutrients that are required by bees for vital activity. Cane or beet sugar, isomerized corn syrup, and type-50 sugar syrup are satisfactory substitutes for honey in the natural diet of honey bees. The last two can be supplied only as a liquid to bees. Liquid feed can be supplied to bees inside the hive by, for example, any of the following methods: friction-top pail, combs within the brood chamber, division board feeder, boardman feeder, etc. Dry sugar may be fed by placing a pound or two on the inverted inner cover. A supply of water must be available to bees at all times. In one aspect, pan or trays in which floating supports—such as wood chips, cork, or plastic sponge—are present are envisaged. Detailed descriptions of supplemental feeds for bees can be found in, for example, USDA publication by Standifer, et al. 1977, entitled “Supplemental Feeding of Honey Bee Colonies” (USDA, Agriculture Information Bulletin No. 413).
In some embodiments, bee feeding comprises providing a bee-ingestible composition selected from the group consisting of a liquid bee-ingestible composition and a solid bee-ingestible composition to the host bee.
In aspects according to the present disclosure a trigger polynucleotide, for example a dsRNA, is combined with an excipient. In an aspect, the trigger polynucleotide, for example dsRNA, can be provided as a ratio of trigger polynucleotide to excipient. In an aspect, the ratio is one part trigger polynucleotide to 4 parts excipient. In an aspect the ratio of trigger polynucleotide to excipient is 1:1, 1:2, 1:5, or 1:10. In other aspects, the ratio of trigger polynucleotide to excipient is 1:20, 1:25, 1:30, 1:40, or more. In an aspect, ratio of trigger polynucleotide to excipient is 1:50. In aspects according to the present disclosure, the ratio can be determined as a volume to volume (v/v) ratio, a weight:weight (w/w) ratio, or a weight:volume (w/v) ratio. In certain aspects, the ratio is expressed as a volume to volume (v/v) ratio, a weight:weight (w/w) ratio, or a weight:volume (w/v) ratio.
In aspects according to the present disclosure, the composition can comprise a weight of trigger polynucleotide, for example dsRNA, combined with an excipient. In an aspect, the trigger polynucleotide comprises a percentage of the total weight of the composition. In an aspect, the trigger polynucleotide comprises about 0.1% by weight of the composition. In an aspect, the trigger polynucleotide comprises about 0.2% by weight of the composition. In an aspect, the trigger polynucleotide comprises about 0.3% by weight of the composition. In another aspect, the trigger polynucleotide comprises about 0.4% by weight of the composition. In an aspect, the trigger polynucleotide comprises up to 0.5% by weight of the composition. In an aspect, the trigger polynucleotide comprises up to 0.6% by weight of the composition. In an aspect, the trigger polynucleotide comprises up to 0.7% by weight of the composition. In an aspect, the trigger polynucleotide comprises up to 0.8% by weight of the composition. In another aspect, the trigger polynucleotide comprises up to 1.0% by weight of the composition. In other aspects, the trigger polynucleotide comprises up to 1.5% by weight of the composition. In yet other aspects, the trigger polynucleotide comprises up to 2.0% by weight, or 2.5% by weight of the composition.
The present disclosure provides for, and includes, compositions having from 0.1% to 5% by weight trigger polynucleotide. In other aspects, a composition comprises from 0.1 to 4%, 0.1 to 3%, 0.1 to 2%, 0.1 to 1%, 0.1 to 2%, 0.1 to 3%, or 0.1 to 4% by weight trigger polynucleotide. In an aspect, a composition comprises from 0.2% to 5% by weight trigger polynucleotide. In other aspects, a composition comprises from 0.2 to 4%, 0.2 to 3%, 0.2 to 2%, 0.2 to 1%, 0.2 to 2%, 0.2 to 3%, or 0.2 to 4% by weight trigger polynucleotide. In other aspects, a composition comprises up to 1%, up to 2%, up to 3%, up to 4%, or up to 5% trigger polynucleotide. In other aspects, a composition comprises up to 7.5%, up to 10%, or up to 15% trigger polynucleotide.
The present disclosure provides for, and includes, compositions having from 0.01 to 20 mg/ml trigger polynucleotide. In some aspects, a composition comprises from 0.01 to 0.1 mg/ml, 0.01 to 1.0 mg/ml, 0.01 to 2.0 mg/ml, 0.01 to 2.5 mg/ml, 0.01 to 5 mg/ml, 0.01 to 10 mg/ml, 0.01 to 15 mg/ml, or 0.01 to 20 mg/ml trigger polynucleotide. In other aspects, a composition comprises from 0.1 to 1.0 mg/ml, 0.1 to 2.0 mg/ml, 0.1 to 2.5 mg/ml, 0.1 to 5 mg/ml, 0.1 to 10 mg/ml, 0.1 to 15 mg/ml, or 0.1 to 20 mg/ml trigger polynucleotide. In certain aspects, a composition comprises at least 0.01 μg/ml trigger polynucleotide. In certain aspects, a composition comprises at least 0.1 μg/ml trigger polynucleotide. In certain other aspects, a composition comprises at least 1.0 μg/ml trigger polynucleotide. In yet other aspects, a composition comprises at least 10 μg/ml trigger polynucleotide. In yet other aspects, a composition comprises at least 15 μg/ml trigger polynucleotide. In yet other aspects, a composition comprises at least 20 μg/ml trigger polynucleotide. In an aspect, a composition comprises from 0.01 to 0.5 mg/ml trigger polynucleotide. In an aspect, a composition comprises from 0.5 to 10 mg/ml trigger polynucleotide. In other aspects, a composition comprises from 0.5 to 1.0 mg/ml, 0.5 to 2.0 mg/ml, 0.5 to 2.5 mg/ml, 0.5 to 5 mg/ml, 0.5 to 10 mg/ml, 0.5 to 15 mg/ml, or 0.5 to 20 mg/ml trigger polynucleotide. In an aspect, a composition comprises from 1.0 to 10 mg/ml trigger polynucleotide. In other aspects, In other aspects, a composition comprises from 0.01 to 0.02 mg/ml, 0.02 to 0.03 mg/ml, 0.03 to 0.04 mg/ml, 0.04 to 0.05 mg/ml, 0.05 to 0.06 mg/ml, 0.06 to 0.07 mg/ml, 0.07 to 0.08 mg/ml, 0.08 to 0.09 mg/ml, 0.09 to 0.1 mg/ml, 0.1 to 0.2 mg/ml, 0.2 to 0.3 mg/ml, 0.3 to 0.4 mg/ml, 0.4 to 0.5 mg/ml, 0.5 to 0.6 mg/ml, 0.6 to 0.7 mg/ml, 0.7 to 0.8 mg/ml, 0.8 to 0.9 mg/ml, 0.9 to 1.0 mg/ml, 1.0 to 2.0 mg/ml, 1.0 to 2.5 mg/ml, 2.0 to 3.0 mg/ml, 3.0 to 4.0 mg/ml, 4.0 to 5.0 mg/ml, 5.0 to 6.0 mg/ml, 6.0 to 7.0 mg/ml, 7.0 to 8.0 mg/ml, 8.0 to 9.0 mg/ml, 9.0 to 10.0 mg/ml, 10.0 to 12.0 mg/ml, 12.0 to 13.0 mg/ml, 13.0 to 14.0 mg/ml, 14.0 to 15.0 mg/ml, 15.0 to 16.0 mg/ml, 16.0 to 17.0 mg/ml, 17.0 to 18.0 mg/ml, 18.0 to 19.0 mg/ml, 19.0 to 20.0 mg/ml, 1.0 to 5 mg/ml, 1.0 to 10 mg/ml, 1.0 to 15 mg/ml, or 1.0 to 20 mg/ml trigger polynucleotide. In some aspects, a composition comprises about 0.1 μg/ml, about 0.2 μg/ml, about 0.5 μg/ml, about 1.0 μg/ml, about 2.0 μg/ml, about 5.0 μg/ml, about 10 μg/ml, about 0.02 mg/ml, about 0.05 mg/ml, about 0.1 mg/ml, about 0.125 mg/ml, about 0.2 mg/ml, about 0.25 mg/ml, about 0.3 mg/ml, about 0.4 mg/ml, about 0.5 mg/ml, about 0.6 mg/ml, about 0.7 mg/ml, about 0.8 mg/ml, about 0.9 mg/ml, about 1.0 mg/ml, about 1.5 mg/ml, about 2.0 mg/ml, about 2.5 mg/ml, about 3.0 mg/ml, about 3.5 mg/ml, about 4.0 mg/ml, about 4.5 mg/ml, about 5.0 mg/ml, about 5.5 mg/ml, about 6.0 mg/ml, about 6.5 mg/ml, about 7.0 mg/ml, about 7.5 mg/ml, about 8.0 mg/ml, about 8.5 mg/ml, about 9.0 mg/ml, about 9.5 mg/ml, about 10 mg/ml, about 11 mg/ml, about 12 mg/ml, about 13 mg/ml, about 14 mg/ml, about 15 mg/ml, about 16 mg/ml, about 17 mg/ml, about 18 mg/ml, about 19 mg/ml, or about 20 mg/ml trigger polynucleotide.
In some aspects, a composition comprises from about 1 mg to about 2000 mg trigger polynucleotide per bee colony. In certain aspects, a composition comprises from about 1 mg to about 100 mg, from about 1 mg to about 200 mg, from about 1 mg to about 300 mg, from about 1 mg to about 400 mg, from about 1 mg to about 500 mg, from about 1 mg to about 600 mg, from about 1 mg to about 700 mg, from about 1 mg to about 800 mg, from about 1 mg to about 900 mg, from about 1 mg to about 1000 mg, from about 1 mg to about 1200 mg, from about 1 mg to about 1500 mg, from about 1 mg to about 1800 mg, from about 10 mg to about 100 mg, from about 10 mg to about 200 mg, from about 10 mg to about 300 mg, from about 10 mg to about 400 mg, from about 10 mg to about 500 mg, from about 10 mg to about 600 mg, from about 10 mg to about 700 mg, from about 10 mg to about 800 mg, from about 10 mg to about 900 mg, from about 10 mg to about 1000 mg, from about 10 mg to about 1200 mg, from about 10 mg to about 1500 mg, from about 10 mg to about 1800 mg, or from about 10 mg to about 2000 mg trigger polynucleotide per bee colony. In other aspects, a composition comprises about 1 mg, about 5 mg, about 10 mg, about 15 mg, about 20 mg, about 25 mg, about 30 mg, about 35 mg, about 40 mg, about 45 mg, about 50 mg, about 60 mg, about 70 mg, about 80 mg, about 90 mg, about 100 mg, about 125 mg, about 150 mg, about 175 mg, about 200 mg, about 250 mg, about 300 mg, about 350 mg, about 400 mg, about 450 mg, about 500 mg, about 550 mg, about 600 mg, about 650 mg, about 700 mg, about 750 mg, about 800 mg, about 850 mg, about 900 mg, about 950 mg, about 1000 mg, about 1100 mg, about 1200 mg, about 1300 mg, about 1400 mg, about 1500 mg, about 1600 mg, about 1700 mg, about 1800 mg, about 1900 mg, or about 2000 mg trigger polynucleotide per bee colony.
The present disclosure provides for, and includes, methods for reducing the viral load of an organism. In some embodiments, the organism is a parasite. In an aspect, the viral load refers to the number of viruses per individual host. In an aspect, the viral load refers to the average number of viruses per 100 host organisms. In an aspect, the viral load refers to the number of viruses per colony of parasite hosts. In another aspect, the viral load is determined by measuring the viral expression in a host, such as a bee or a Varroa mite. In aspects according to the present disclosure the parasite is Varroa destructor and the host is the honey bee, Apis mellifera.
In one aspect, the methods of reducing viral infection comprises providing an effective amount of a trigger, for example dsRNA, composition to a host organism on which a parasite feeds. In another aspect, the methods of reducing viral infection comprises providing an effective amount of a trigger, for example dsRNA, composition directly to a parasitic organism. In aspects according to the present disclosure the parasite is Varroa destructor and the host is the honey bee, Apis mellifera. An effective amount of a composition of the present disclosure results in a decrease in viral infection in the host and/or parasite over a period of time. In an aspect, a decrease in viral infection can be measured within one day or within two days of providing an effective amount of a trigger, for example dsRNA, composition. In an aspect, viral infection can be measured after two days. In an aspect, viral infection can be measured after 3 days. In other aspects, viral infection can be measured after 4 days, after 5 days, after 6 days, after 7 days, after 1 week, after two weeks, after 3 weeks, or after a month. In another aspect, viral infection can be measured more than one time, for example, every day, every 2 days, every 3 days, every 4 days, every 5 days, every 6 days, every 7 days, every week, every two weeks, every three weeks, once a week, twice a week, three times a week, once a month, twice a month, or three times a month. In certain aspects, according to the present disclosure, a decrease in viral infection can be measured and compared to an untreated control host organism, parasite, or colony. In aspects according to the present disclosure the parasite is Varroa destructor and the host is the honey bee, Apis mellifera.
In one aspect, the methods of reducing viral replication comprises providing an effective amount of a trigger, for example dsRNA, composition to a host organism on which a parasite feeds. In another aspect, the methods of reducing viral replication comprises providing an effective amount of a trigger, for example dsRNA, composition directly to a parasitic organism. In aspects according to the present disclosure the parasite is Varroa destructor and the host is the honey bee, Apis mellifera. An effective amount of a composition of the present disclosure results in a decrease in viral gene expression in the host and/or parasite over a period of time. In an aspect, a decrease in viral gene expression can be measured within one day or within two days of providing an effective amount of a trigger, for example dsRNA, composition. In an aspect, viral replication can be measured after two days. In an aspect, viral replication may be measured after 3 days. In other aspects, viral replication can be measured after 4 days, after 5 days, after 6 days, after 7 days, or after 1 week, after two weeks, after 3 weeks, or after a month. In another aspect, viral replication can be measured more than one time, for example, every day, every 2 days, every 3 days, every 4 days, every 5 days, every 6 days, every 7 days, every week, every two weeks, every three weeks, once a week, twice a week, three times a week, once a month, twice a month, or three times a month. In certain aspects, according to the present disclosure, a decrease in viral replication can be measured and compared to an untreated control host organism, parasite, or colony. In aspects according to the present disclosure the parasite is Varroa destructor and the host is the honey bee, Apis mellifera.
In one aspect, the methods of reducing a viral load comprises providing an effective amount of a trigger, for example dsRNA, composition to a host organism on which a parasite feeds. In another aspect, the methods of reducing a viral load comprises providing an effective amount of a trigger, for example dsRNA, composition directly to a parasitic organism. In aspects according to the present disclosure the parasite is Varroa destructor and the host is the honey bee, Apis mellifera. An effective amount of a composition of the present disclosure results in a decrease in the viral load in the host and/or parasite over a period of time. In an aspect, a decrease in viral load is measured within one day or within two days of providing an effective amount of a trigger, for example dsRNA, composition. In an aspect, the viral load can be measured after two days. In an aspect, the viral load can be measured after 3 days. In other aspects, the viral load can be measured after 4 days, after 5 days, after 6 days, after 7 days, after 1 week, after two weeks, after three weeks, or after a month. In another aspect, the viral load can be measured more than one time, for example, every day, every 2 days, every 3 days, every 4 days, every 5 days, every 6 days, every 7 days, every week, every two weeks, every three weeks, once a month, twice a month, or three times a month. In certain aspects, according to the present disclosure, a decrease in the viral load can be measured and compared to an untreated control host organism, parasite, or colony. In aspects according to the present disclosure the parasite is Varroa destructor and the host is the honey bee, Apis mellifera.
In some aspects according to the present disclosure, a reduction in viral load or a reduction in viral infection after a period of time means a decrease in viral titer. In an aspect, viral titer is decreased by about 10%, 20%, 30% or more between measurements. In another aspect, viral titer is decreased by about 40% or more between measurements. In another aspect, viral titer is decreased by about 50% or more between measurements. In another aspect, viral titer is decreased by about 60% or more between measurements. In another aspect, viral titer is decreased by about 70% or more between measurements. In another aspect, viral titer is decreased by about 80% or more between measurements. In another aspect, viral titer is decreased by about 90% or more between measurements. In some embodiments, the viral titer in a host organism or a parasite provided with an effective amount of a trigger polynucleotide is decreased by at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% compared with the viral titer in a host organism or a parasite that is not provided with the trigger polynucleotide. In some embodiments, the viral titer is measured within 1 day, within 2 days, after 2 days, after 3 days, after 4 days, after 5 days, after 6 days, after 7 days, or after 1 week, after 2 weeks, after 3 weeks, or after a month of providing the trigger polynucleotide. In some embodiments, the viral titer is measured more than once. In some embodiments, the viral titer is measured every day, every 2 days, every 3 days, every 4 days, every 5 days, every 6 days, every 7 days, every week, every two weeks, every three weeks, once a month, twice a month, or three times a month. In one aspect, the host organism is a bee. In one aspect, the parasite is Varroa destructor.
In some aspects according to the present disclosure, a reduction in viral load or a reduction in viral infection after a period of time means a decrease in viral expression. In an aspect, viral expression is decreased by about 10%, 20%, 30% or more between measurements. In another aspect, viral expression is decreased by about 40% or more between measurements. In another aspect, viral expression is decreased by about 50% or more between measurements. In another aspect, viral expression is decreased by about 60% or more between measurements. In another aspect, viral expression is decreased by about 70% or more between measurements. In another aspect, viral expression is decreased by about 80% or more between measurements. In another aspect, viral expression is decreased by about 90% or more between measurements. In some embodiments, the viral expression in a host organism or a parasite provided with an effective amount of a trigger polynucleotide is decreased by at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% compared with the viral expression in a host organism or a parasite that is not provided with the trigger polynucleotide. In some embodiments, the viral expression is measured within 1 day, within 2 days, after 2 days, after 3 days, after 4 days, after 5 days, after 6 days, after 7 days, or after 1 week, after 2 weeks, after 3 weeks, or after a month of providing the trigger polynucleotide. In some embodiments, the viral expression is measured more than once. In some embodiments, the viral expression is measured every day, every 2 days, every 3 days, every 4 days, every 5 days, every 6 days, every 7 days, every week, every two weeks, every three weeks, once a month, twice a month, or three times a month. In one aspect, the host organism is a bee. In one aspect, the parasite is Varroa destructor.
In some aspects according to the present disclosure, a reduction in viral load or a reduction in viral infection after a period of time means a decrease in viral replication. In an aspect, viral replication is decreased by about 10%, 20%, 30% or more between measurements. In another aspect, viral replication is decreased by about 40% or more between measurements. In another aspect, viral replication is decreased by about 50% or more between measurements. In another aspect, viral replication is decreased by about 60% or more between measurements. In another aspect, viral replication is decreased by about 70% or more between measurements. In another aspect, viral replication is decreased by about 80% or more between measurements. In another aspect, viral replication is decreased by about 90% or more between measurements. In some embodiments, the viral replication in a host organism or a parasite provided with an effective amount of a trigger polynucleotide is decreased by at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% compared with the viral replication in a host organism or a parasite that is not provided with the trigger polynucleotide. In some embodiments, the viral replication is measured within 1 day, within 2 days, after 2 days, after 3 days, after 4 days, after 5 days, after 6 days, after 7 days, or after 1 week, after 2 weeks, after 3 weeks, or after a month of providing the trigger polynucleotide. In some embodiments, the viral replication is measured more than once. In some embodiments, the viral replication is measured every day, every 2 days, every 3 days, every 4 days, every 5 days, every 6 days, every 7 days, every week, every two weeks, every three weeks, once a month, twice a month, or three times a month. In one aspect, the host organism is a bee. In one aspect, the parasite is Varroa destructor.
In aspects according to the present disclosure, a reduction in viral load after a period of time results in a decrease in bee mortality. In an aspect, bee mortality is decreased by 10%, 20%, 30% or more between measurements. In another aspect, bee mortality is decreased by 40% or more between measurements. In another aspect, bee mortality is decreased by 50% or more between measurements. In another aspect, bee mortality is decreased by 60% or more between measurements. In another aspect, bee mortality is decreased by 70% or more between measurements. In another aspect, bee mortality is decreased by 80% or more between measurements. In another aspect, bee mortality is decreased by 90% or more between measurements. In some embodiments, bee mortality in a bee colony provided with an effective amount of a trigger polynucleotide is decreased by at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% compared with bee mortality in a bee colony that is not provided with the trigger polynucleotide. In some embodiments, bee mortality is measured within 1 day, within 2 days, after 2 days, after 3 days, after 4 days, after 5 days, after 6 days, after 7 days, or after 1 week, after 2 weeks, after 3 weeks, or after a month of providing the trigger polynucleotide. In some embodiments, bee mortality is measured more than once. In some embodiments, bee mortality is measured every day, every 2 days, every 3 days, every 4 days, every 5 days, every 6 days, every 7 days, every week, every two weeks, every three weeks, once a month, twice a month, or three times a month.
In aspects according to the present disclosure, an effective amount of trigger polynucleotide, for example dsRNA, can be provided periodically or continually. In an aspect, an effective amount of a trigger, for example dsRNA, composition can be provided once, twice or three times a day. In other aspects, an effective amount of a trigger, for example dsRNA, composition can be provided once a day. In another aspect, an effective amount of a trigger, for example dsRNA, composition can be provided one or more times every other day. In an aspect, an effective amount of a trigger, for example dsRNA, composition can be provided every two days, every three days, every four days, every five days, every six days, or once a week. In an aspect, an effective amount of a trigger, for example dsRNA, composition can be provided continuously to an organism in need, for example by providing a continuous source of food. In one aspect, an effective amount of a trigger, for example dsRNA, composition can be provided continuously as a bee-ingestible composition. In one aspect, an effective amount of a trigger, for example dsRNA, composition can be provided to a host organism. In another aspect, an effective amount of a trigger, for example dsRNA, composition can be provided directly to a parasitic organism. In aspects according to the present disclosure the parasite is Varroa destructor and the host is the honey bee, Apis mellifera.
The present disclosure provides for methods of reducing the viral load of a honey bee colony comprising providing a bee colony an effective amount of a trigger, for example dsRNA, composition. An effective amount of a trigger polynucleotide composition of the present disclosure results in a reduction of viral gene expression and viral replication over a period of time. In an aspect, a reduction of viral replication or viral expression is measured within one day or within two days of providing an effective amount of a trigger, for example dsRNA, composition. In an aspect, the reduction of viral replication or viral expression can be measured after two days. In an aspect, the reduction of viral replication or viral expression can be measured after 3 days. In other aspects, the reduction of viral replication or viral expression can be measured after 4 days, after 5 days, after 6 days, after 7 days, after 1 week, after two weeks, after three weeks, or after a month. In another aspect, the reduction of viral replication or viral expression can be measured more than one time, for example every day, every 2 days, every 3 days, every 4 days, every 5 days, every 6 days, every 7 days, every week, every two weeks, every three weeks, once a month, twice a month, or three times a month. In certain aspects, according to the present disclosure, a reduction of viral replication or viral expression can be measured and compared to an untreated control host organism, parasite, or colony.
In an aspect, the present disclosure provides for methods and compositions for reducing the susceptibility of bees to viral infection. In other aspects, the present disclosure provides for methods and compositions to prevent viral infection of colonies of bees. In another aspect, the present disclosure provides methods for reducing the viral infection of honeybees transmitted by the mite Varroa destructor.
The following Examples are presented for the purposes of illustration and should not be construed as limitations.
To test the effect of dsRNA targeting bee viruses in Varroa, the mites were placed on diet plates supplemented with a mix of dsRNA triggers. A non-specific dsRNA having no sequence identity above 19 bp to Varroa genes was used as a non-specific control (SCRAM; SEQ ID NO:24). Varroa mites were collected, RNA extracted and DWV or IAPV expression analyzed using quantitative reverse transcription PCR (Q-PCR).
First, an artificial diet was prepared as follows in Table 1:
In one experiment, the dsRNA trigger mix contained a mixture of SEQ ID NOs: 1-10 from the following dsRNA sequences:
After plates cooled down, 15 Varroa mites were placed on each plate. Then the plates were sealed with absorbance paper, parafilm and incubated for 72 h in an incubator at 29° C. Following 72 h on LB agar containing treatment, dead/alive mites were counted. As shown in
Both live and dead Varroa were collected for RNA extraction and bee virus levels and replication were analyzed by Q-PCR or QuantiGene® Plex 2.0 (RNA assay platform from Affymetrix).
To test the effect of dsRNA targeting bee viruses on viral load (IAPV or DWV) in honeybees and Varroa mites in a minihive environment, the honeybees are placed on a diet supplemented with one or more dsRNA triggers (e.g., SEQ ID NOs: 1-10 and 21) targeting bee virus genes. A non-specific dsRNA having no sequence identity above 19 bp to Varroa genes is used as a non-specific control (SCRAM, e.g., SEQ ID NOs:22, 23, or 24). The blank control contains no dsRNA.
Bee hives with high viral load and Varroa load are identified. Minihives are then assembled with 400-600 bees (2 cups) from the identified high Varroa mite and high viral load hives, foundation frames, and queen in queen-cell with a few escort-bees. The queen cell is sealed with candy. While filling the hives, time zero samples of bees and Varroa are collected (1 cup of bees from each hive). The samples are frozen (−70° C.), Varroa mites are collected from frozen cups and samples of bees and Varroa are prepared for Q-PCR or QuantiGene® analysis. The viral loads in the honey bees and the Varroa mites are determined at the initial time point.
The Mini-hives are fed with 66% sucrose solution and protein-cakes and placed in a net house under dark cover for 24 hrs to improve queen habitation. Following queen habitation, the dark cover is removed and the bees are fed with a sugar solution containing a mix of dsRNA targeting multiple bee viruses (concentration of 1 μg/bee to 10 μg/bee).
Samples of bees are collected, 10 bees from each hive every 4-5 days. The collected bees are analyzed by QG (QuantiGene® Plex 2.0 RNA assay platform from Affymetrix) to determine viral load. Viral load is decreased in bees fed dsRNA targeting bee viruses compared to bees fed a diet supplemented with non-specific dsRNA.
Varroa are collected from each hive every 4-5 days by sugar shake: one cup of bees from each minihive and two spoons of sugar powder are placed into a container with a punched sealer. The cup is shaken and turned top to bottom—the Varroa mites fall through the holes in the sealer and bees stay in the cup. Bees are returned into the minihive and Varroa are analyzed by QG (QuantiGene® Plex 2.0 RNA assay platform from Affymetrix) to determine viral load. Viral load is decreased in Varroa collected from bees fed dsRNA targeting bee viruses compared to Varroa collected from bees fed a diet supplemented with non-specific dsRNA.
Quantigene®, a quantitative, non-amplification-based nucleic acid detection analysis, is performed on total lysate from frozen honey bees or Varroa mite samples to measure viral expression and viral replication. The oligonucleotide probes used for the QuantiGene® Plex 2.0 assay are designed and supplied by Affymetrix, using the sense strand of bee virus sequences as template or negative strand for replicating virus. Housekeeping gene probes are designed from sequences of Apis mellifera Actin, Ribosomal protein subunit 5 (RPS5) and Ribosomal protein 49 (RP49). The QuantiGene® assay is performed according to the manufacturer's instructions (Affymetrix, Inc., User Manual, 2010) with the addition of a heat denaturation step prior to hybridization of the sample with the oligonucleotide probes. Samples in a 20 μL volume are mixed with 5 μl of the supplied probe set in the well of a PCR microplate followed by heating for 5 minutes at 95° C. using a thermocycler. Heat-treated samples are maintained at 46° C. until use. The 25 μl samples are transferred to an Affymetrix hybridization plate for overnight hybridization. Before removing the plate from the thermocycler, 75 μl of the hybridization buffer containing the remaining components are added to each sample well. The PCR microplate is then removed from the thermocycler and the content of each well (˜100 μl) is transferred to the corresponding well of a Hybridization Plate (Affymetrix) for overnight hybridization. After signal amplification, median fluorescence intensity (MFI) for each sample is captured on a Luminex 200 machine (Luminex Corporation).
To test the effect of dsRNA targeting DWV or IAPV in honeybees and Varroa mites, honeybees were placed on a diet supplemented with a mixture of dsRNA triggers selected from SEQ ID NOs: 5-9 targeting DWV, and SEQ ID NOs: 1-4 and 10 targeting IAPV. A non-specific dsRNA having no sequence identity above 19 bp to Varroa genes was used as a control (SCRAM; SEQ ID NO:22 or 23).
Bee hives with high viral load and Varroa load were identified.
The Mini-hives were fed with 66% sucrose solution and protein-cakes and placed in a net house under dark cover for 24 hrs to improve queen habitation. After 2 days of acclimatization, bees were fed with a sugar solution only (CON), a sugar solution containing non-specific control dsRNA (SCR), or a sugar solution containing a mixture of dsRNAs targeting multiple bee viruses (SEQ ID NOs: 1-10; MIX) at concentration of 1 μg/bee to 10 μg/bee.
10 bees from each hive were collected every 4-5 days after hives were infected. The collected bees were analyzed by QuantiGene® as described in Example 2 to determine viral replication as median fluorescence intensity (MFI).
This is another example of the Varroa direct feeding experiment as described in Example 1. To test the effect of dsRNA targeting bee viruses in Varroa, the mites were placed on diet plates supplemented with a mix of dsRNA triggers. A non-specific dsRNA having no sequence identity above 19 bp to Varroa genes was used as a non-specific control (SEQ ID NO: 22 or 23). The blank control contained no dsRNA. Varroa mites were collected, RNA extracted and DWV or IAPV expression analyzed using QuantiGene® analysis Plex 2.0 (RNA assay platform from Affymetrix).
First, an artificial diet was prepared as follows in Table 3:
The dsRNA trigger mix contained a mixture of SEQ ID NOs: 2-6 and 8-10 (125 μg/ml from each).
After plates cooled down, 15 Varroa mites were placed on each plate. Then the plates were sealed with absorbance paper, parafilm and incubated for 72 h in an incubator at 29° C. Live Varroa were collected for RNA extraction and bee viruses levels and replication were analyzed with QuantiGene® Plex 2.0 (RNA assay platform from Affymetrix).
To test the effect of dsRNA targeting bee viruses on DWV viral load and replication in honeybees in a bee box environment (lab conditions), the honeybees were brought from commercial hives in the field and placed in bee boxes fed with 66% sugar syrup supplemented with either individual dsRNA triggers selected from SEQ ID NOs: 5, 6, 8, and 9 targeting DMV (T1=SEQ ID NO:5, T2=SEQ ID NO:6, T3=SEQ ID NO:8, and T4=SEQ ID NO:9) or a mixture of these dsRNA triggers. A non-specific dsRNA (SEQ ID NO:22 or 23) having no sequence identity above 19 bp to honeybee's genes was used as a non-specific control. The blank control contained no dsRNA.
Bee hives with high viral load were identified. Bee boxes were then assembled with 5 bees from the identified high viral load. While filling the boxes, time zero samples of bees were collected. The samples were frozen (−70° C.). The viral loads in the honey bees were determined at the initial time point.
The bee boxes were fed with 66% sucrose solution. Following 2 days of acclimatization, bees were fed with a sugar solution containing the individual or mixture of dsRNAs targeting DMV (concentration of 1 μg/bee to 10 μg/bee), containing the non-specific dsRNA control, or containing no dsRNA. After 3 more days, bees were fed again with the same sugar solutions.
24 bees from each group of treatment were collected after 4 and 10 days from the second treatment. The collected bees were analyzed by QuantiGene® Plex 2.0 to determine viral load and viral replication.
To test the effect of dsRNA targeting bee viruses on IAPV viral load and replication in honeybees in a bee box environment (lab conditions), the honeybees were brought from commercial hives in the field and placed in bee boxes fed with 66% sugar syrup supplemented with either individual dsRNA triggers selected from SEQ ID NOs: 2-4 and 10 targeting IAPV (T5=SEQ ID NO:2, T6=SEQ ID NO:3, T7=SEQ ID NO:4, and T8=SEQ ID NO:10) or a mixture of these dsRNA triggers. A non-specific dsRNA (SEQ ID NO:22 or 23) having no sequence identity above 19 bp to honeybee's genes was used as a non-specific control. The blank control contained no dsRNA.
Bee hives with high viral load were identified. Bee boxes were then assembled with 5 bees from the identified high viral load. While filling the boxes, time zero samples of bees were collected. The samples were frozen (−70° C.). The viral loads in the honey bees were determined at the initial time point.
The bee boxes were fed with 66% sucrose solution. Following 2 days of acclimatization, bees were fed with a sugar solution containing the individual or mixture of dsRNAs targeting DMV (concentration of 1 μg/bee to 10 μg/bee), containing the non-specific dsRNA control, or containing no dsRNA. After 3 more days, bees were fed again with the same sugar solutions.
24 bees from each group of treatment were collected after 4 and 10 days from the second treatment. The collected bees were analyzed by QuantiGene® Plex 2.0 to determine viral load and viral replication.
To test the effect of dsRNA targeting bee viruses on LSV viral load and replication in honeybees in a bee box environment (lab conditions), the honeybees were brought from commercial hives in the field and placed in bee boxes fed with 66% sugar syrup supplemented with a mixture of five dsRNA triggers selected from SEQ ID NOs: 11-20. Two dsRNA trigger mixes were tested. Mix A contained SEQ ID NOs:11, 13, 14, 17, and 18 and Mix B contained SEQ ID NOs:12, 15, 16, 19, and 20, having the following dsRNA sequences:
A non-specific dsRNA (SEQ ID NO:22 or 23) having no sequence identity above 19 bp to honeybee's genes was used as a control. The blank control contained no dsRNA.
Bee hives with high viral load were identified. Bee boxes were then assembled with 5 bees from the identified high viral load. While filling the boxes, time zero samples of bees were collected. The samples were frozen (−70° C.). The viral loads in the honey bees were determined at the initial time point.
The bee boxes were fed with 66% sucrose solution. Following 2 days of acclimatization, bees were fed with a sugar solution containing the individual or mixture of dsRNAs targeting DMV (concentration of 1 μg/bee to 10 μg/bee), containing the non-specific dsRNA control, or containing no dsRNA. After 3 more days, bees were fed again with the same sugar solutions.
24 bees from each group of treatment were collected after 4 and 10 days from the second treatment. The collected bees were analyzed by QuantiGene® Plex 2.0 to determine viral load.
This application is a U.S. National Stage Application of PCT/US2014/069353, filed on Dec. 9, 2014, which claims the benefit of U.S. Provisional Application No. 62/069,142, filed on Oct. 27, 2014, and also claims the benefit of U.S. Provisional Application No. 61/913,917, filed on Dec. 10, 2013, which are incorporated by reference in their entirety herein.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2014/069353 | 12/9/2014 | WO | 00 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2015/089078 | 6/18/2015 | WO | A |
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| Number | Date | Country | |
|---|---|---|---|
| 20170037407 A1 | Feb 2017 | US |
| Number | Date | Country | |
|---|---|---|---|
| 62069142 | Oct 2014 | US | |
| 61913917 | Dec 2013 | US |
