Patent Application
20170088821
This invention relates generally to the field of virology and more particularly to Caliciviridae compositions and methods.
The Caliciviridae family of viruses are members of Class IV of the Baltimore scheme. The genome of these viruses is non-enveloped, non-segmented, positive-sense, single-stranded RNA. Caliciviruses are found in a large number of organisms such as humans, cattle, pigs, cats, chickens, reptiles, dolphins and amphibians.
Caliciviruses are not very well studied because until recently they could not be grown in culture, and there is no suitable animal model. Several research groups are pursuing in vitro culturing of particular caliciviruses, but it is a difficult virus family to study. What is needed are compositions and methods for culturing caliciviruses in vitro and use of in vitro culture methods for diagnosis, virus identification and vaccine development. What is needed are compositions comprising virus-permissive cell cultures.
Noroviruses (NoVs) are nonenveloped plus-strand RNA viruses that cause a majority of gastroenteritis outbreaks worldwide. They are also now recognized as one of the leading causes of severe childhood diarrhea in both industrialized and developing nations (1-3). The cellular tropism of human NoVs, and thus the development of a cultivation system for their in vitro propagation, has long eluded the NoV research community. Based on the enteric nature of NoVs, the most likely target of infection may be the intestinal epithelial cell (IEC). However, IECs have not been demonstrated to be permissive to human NoV (HuNoV) or murine NoV (MNV) infection in vitro (in spite of intensive efforts to infect this cell type with NoVs) although NoV particles can be transcytosed across a polarized epithelium (4-10). Infection of IECs cannot be entirely excluded since viral antigen has been detected in IECs of gnotobiotic pigs and calves infected with a HuNoV (11, 12) and in interferon-deficient mice infected with a MNV (13). The first clue to an alternative NoV cell tropism was provided by the discovery that MNVs productively infect professional antigen presenting cells (APCs) including dendritic cells (DCs) and macrophages (Mφs) (14). There is accumulating evidence that HuNoVs share this cell tropism: HuNoV antigen was detected in lamina propria cells of an intestinal biopsy from an infected volunteer (15); an inactivated HuNoV bound to lamina propria cells, but not IECs, when incubated with human intestinal tissue sections (16); chimpanzees infected with a HuNoV contain infected DCs, but not Mφs or IECs (17); and immunodeficient mice infected with a pool of HuNoVs contain antigen-positive Mφ-like cells in their spleens and livers (18). In spite of this wealth of in vivo supporting data, initial efforts to infect blood-derived monocytes with a HuNoV were unsuccessful (15).
Examples herein demonstrate that MNV strains replicate efficiently in B-cells both in vitro and in vivo. Mature B-cell infection is distinct from Mφ/DC infection-mature B-cells are infected in the absence of significant cytopathic effect and become persistently infected; this is in stark contrast to the rapid and lytic infection of other APCs in culture. Persistent B-cell infection affects the pathogenesis and immune response to NoVs and leads to the development of a successful HuNoV cultivation system, vaccines for Caliciviridae, methods of diagnosing Caliciviridae infections, methods of assaying for antiviral agents that are effective against viruses of Caliciviridae, and other applications that are disclosed herein. Thus, the disclosed invention provides compositions (including virus-permissive cell cultures) and methods for culturing caliciviruses in vitro and use of in vitro culture methods for diagnosis, virus identification and vaccine development.
Disclosed herein are compositions comprising a calicivirus-permissive cell culture infected with a calicivirus, such as norovirus. Such calicivirus-permissive cell cultures can be comprised of vertebrate cells, in particular B-cells. In some aspects, the vertebrate cells can be murine cells, while in other aspects, the vertebrate cells can be human cells or hybrid cells such as human-mouse fusion cells. In some aspects, a norovirus can be a murine norovirus, while in other aspects, a norovirus can be a human norovirus. Compositions may also comprise other calicivirus-permissive cells.
In an aspect, the present invention comprises methods of replicating a calicivirus, such as a norovirus, in vitro. Methods may comprise inoculating calicivirus-permissive cells with a calicivirus, such as a norovirus, and culturing the cells. In aspects, inoculating calicivirus-permissive cells may comprise infecting the cells with the calicivirus, such as a norovirus. In aspects, the methods can comprise inoculating vertebrate cells such as B-cells. In some aspects, the vertebrate cells can be murine cells, while in other aspects, the vertebrate cells can be human cells or hybrid cells such as human-mouse fusion cells. In some aspects, a calicivirus, such as a norovirus, can be a murine norovirus, while in other aspects, a norovirus can be a human norovirus. Compositions may also comprise other calicivirus-permissive cells.
An aspect disclosed herein comprises methods of detecting calicivirus, such as a norovirus, in a biological or diagnostic sample. For example, a method comprises contacting a cell culture comprising norovirus-permissive cells with a sample, and detecting norovirus viral replication in the cell culture. The sample may be a biological sample, such as a biological sample from a mammal suspected of infection with a calicivirus, such as a norovirus or a diagnostic sample. The mammal can be a human, a laboratory animal such as a rodent, a farm animal, or a companion animal. A biological or diagnostic sample can be a tissue sample, a blood sample, a vomitus sample, a sputum sample, a stool sample or a purified virus. Norovirus-permissive cells may comprise B-cells.
An aspect of the present invention comprises methods of detecting calicivirus, such as a norovirus, in a biological or diagnostic sample comprising performing a cytopathic or non-cytopathic assay, an antibody assay, a nucleic acid detection assay, or a protein detection assay. In an aspect, a cytopathic assay may comprise a dye exclusion assay, an enzyme release assay, a necrosis assay or an apoptosis assay. In an aspect, an antibody assay may comprise a monoclonal or a polyclonal antibody, such as an antibody directed against a norovirus polypeptide and any antigen detection system known in the art, such as a Western blot assay, an ELISA assay, an immunofluorescence assay, an immunoprecipitation assay or a radioimmunoassay. In an aspect, a nucleic acid detection assay may comprise an assay such as a polymerase chain reaction assay or a hybridization assay such as a Northern blot assay.
An aspect of the present invention comprises methods of determining the attachment of a norovirus to permissive target cells. In an aspect, this method may also comprise evaluation of compounds for their ability to inhibit attachment to permissive cells. Such compounds include polyclonal and monoclonal antibodies, anti-virals, biological additives, etc.
An aspect of the present invention comprises methods of identifying a compound having anti-viral activity effective against members of the Caliciviridae family. In an aspect, a method may comprise contacting the compound with a calicivirus-permissive cell culture infected with a calicivirus, such as a norovirus, and detecting inhibition of virus replication. A method may comprise contacting the compound with a calicivirus-permissive cell culture prior to virus infection and assessing for inhibition of infection. Detecting inhibition of viral replication may comprise detecting inhibition of viral nucleic acid synthesis or viral protein synthesis. In an aspect, detecting inhibition of virus replication may comprise performing a plaque assay or a focus forming assay on a calicivirus-permissive cell culture. In an aspect, an assay for identifying anti-viral compounds can be used for identifying compounds having anti-RNA virus activity, anti-single-stranded RNA virus activity, anti-positive strand single-stranded RNA virus activity, anti-positive strand single-stranded RNA activity, no DNA stage virus activity, anti-calicivirus activity, anti-norovirus activity or anti-norovirus attachment activity.
An aspect of the present invention comprises methods of adapting a calicivirus, such as a norovirus, to have a modified host range. In an aspect, a method may comprise serially passaging a norovirus population for three or more generations in calicivirus-permissive cell cultures. Serially passaging may comprise plaque-purifying or focus-forming purifying the calicivirus, such as a norovirus, and growing the plaque-purified or focus-forming purified calicivirus, such as a norovirus, in calicivirus-permissive host cells for three or more serial passages.
An aspect of the present invention comprises methods to test anti-norovirus antibodies for their ability to neutralize viral infection. In an aspect, a method may comprise mixing virus with an antibody and testing whether the antibody reduces infectivity of the virus. Such neutralizing antibodies could be useful vaccine candidates.
An aspect of the present invention comprises methods to generate attenuated viruses as vaccine candidates. In an aspect, a method may comprise passaging the virus through permissive cells numerous times such that the virus evolves to replicate efficiently in cell culture but acquires mutations in virulence genes that are needed during in vivo infections, thus producing an attenuated virus which may be used as a vaccine.
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication, with color drawing(s), will be provided by the Office upon request and payment of the necessary fee.
The present invention comprises compositions, methods and kits comprising members of the Caliciviridae family. Compositions comprise in vitro cell culture and attachment systems for members of the Caliciviridae family comprising B-cells, and methods for making and using such in vitro culture and attachment systems. Methods of the present invention comprise continuous culture or attachment of members of the Caliciviridae family, diagnostic methods, screening tests, detection of diseases or conditions associated with human or other animal infection by members of the Caliciviridae family, kits for accomplishing such methods or comprising compositions of the present invention, development of vaccines in the form of attenuated live viruses, and testing of virus-specific antibodies for neutralization capacity or passive immunity.
Members of the Caliciviridae family include, but are not limited to, lagovirus, norovirus, sapovirus, vesivirus, recovirus and valovirus genera, from which species have been identified, such as Nebovirus, Norwalk virus, Sapporo virus, Vesicular exanthema of swine virus, rabbit hemorrhagic disease virus, and other Caliciviridae viruses such as St. Valerien-like viruses, chicken calicivirus and newly identified caliciviruses. Vesiviruses and certain sapoviruses (porcine) can already be cultured in vitro in feline and porcine kidney cells, respectively. Rabbit hemorrhagic disease virus is non-cultivable, similar to human noroviruses prior to the present invention. A new cluster of noroviruses has been proposed which has a number of canine caliciviruses. Additional proposed Caliciviridae genera include Bavovirus (chickens), Nacovirus (turkeys and chickens), and Secalivirus (found in sewage). These caliciviruses are contemplated by the present invention and though the disclosure is directed to noroviruses for clarity, this is not to be seen as limiting. As used herein, the term “norovirus” can refer to unmodified, wild-type norovirus, e.g., norovirus obtained from an individual with viral gastroenteritis, or may be an identified, purified, or laboratory standard norovirus. A host range-modified norovirus refers to norovirus modified, with regard to its host range, using well known viral laboratory methods, e.g., norovirus grown in vitro for multiple passages that grows in cells other than the original cells in which the virus grew.
In Vitro Cell Culture
Aspects of the present invention comprise an in vitro cell culture system for a calicivirus, such as norovirus. Methods and compositions for culturing norovirus are described herein. The methods and compositions described herein use well known laboratory techniques which can be found in laboratory manuals such as Sambrook, J., et al., Molecular Cloning: A Laboratory Manual, 3rd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 2001; Spector, D. L. et al., Cells: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1998; and Harlow, E., Using Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1999.
An in vitro cell culture system for human norovirus is disclosed herein and comprises norovirus-permissive host cells, which are human B-cells. A cell culture system for murine norovirus is disclosed herein and comprises norovirus-permissive host cells, which are murine B-cells. As used herein, a “norovirus-permissive cell” is a cell in which a norovirus replicates following infection with live norovirus. Both murine and human in vitro cell culture systems for calicivirus, such as norovirus, may comprise B-cells in an in vitro cell culture system, or an in vitro cell culture system may comprise a co-culture of B-cells and intestinal epithelial cells in a transwell in vitro cell culture system. See
As disclosed herein, an in vitro cell culture system may further comprise HBGA-like carbohydrates or one or more sources of HBGA-like carbohydrates. The HBGA-like carbohydrates may be added directly to the in vitro cell culture system. The HBGA-like carbohydrates may be mixed with a biological or diagnostic sample and the resulting mixture added to the in vitro cell culture system. The HBGA-like carbohydrates may be mixed with a filtered biological or diagnostic sample and the resulting mixture added to the in vitro cell culture system. The HBGA-like carbohydrates may be mixed with a purified virus sample and the resulting mixture added to the in vitro cell culture system.
As used herein, a “B-cell” or B-lymphocyte is a type of lymphocyte in the humoral immunity of the adaptive immune system. B-cells can be distinguished from other lymphocytes, such as T cells and natural killer cells (NK cells), by the presence of a protein on the B-cell's outer surface known as a B-cell receptor (BCR). This specialized receptor protein allows a B-cell to bind to a specific antigen. In birds, B-cells mature in the bursa of Fabricius. In mammals, immature B-cells are formed in the bone marrow. In vivo, the principal functions of B-cells are to make antibodies against antigens, to perform the role of antigen-presenting cells (APCs), and to develop into memory B-cells after activation by antigen interaction. A B-cell is not in the macrophage or dendritic cell lineage of hematopoietic system cells.
As used herein, “norovirus replication” can be understood to include various stages in norovirus life cycle, such as, for example, binding or attachment of a norovirus to a host cell, entry into the host cell, trafficking, processing, genome release, translation, transcription, assembly, and release. Norovirus replication can also be detected by measuring norovirus protein activity, for example polyprotein protease activity, viral RNA polymerase activity, VPG activity and NTPase activity. For example, measurement of an increased accumulation of viral RNA or viral protein in infected cells can be considered an indication of viral replication, although an increase in virus particle production is not measured. Any of the aspects of norovirus replication and reproduction may be used, for example, in a test of an anti-viral agent, anti-viral activity can be detected by detecting inhibition of a norovirus protein activity, such as inhibition of polyprotein protease activity, viral RNA polymerase activity, VPG activity or NTPase activity, or by detecting inhibition of a norovirus protein accumulation, such as inhibition of polyprotein protease accumulation, viral RNA polymerase accumulation, VPG accumulation or NTPase accumulation.
Aspects of the present invention comprise use of an in vitro cell culture system for a calicivirus, such as norovirus, in methods such as diagnostic methods, development of assays for detection or quantification of viral attachment or replication, selection of mutant viruses with desirable properties, identification of mutant viruses, screening of potential anti-viral compounds, and development of vaccines. In an aspect, the vertebrate cells can be murine cells, human cells, or other cells. Cells in the in vitro culture can be, for example, B-cells or a co-culture of B-cells and intestinal epithelial cells as disclosed herein. In an aspect, a calicivirus can be a norovirus that is a murine norovirus or a human norovirus, such as a Norwalk virus.
An in vitro cell culture system for a calicivirus, such as norovirus, may comprise bacteria comprising carbohydrates that mimic human histo-blood group antigens (HBGAs) or one or more biological sources for HBGAs, isolated HBGA-like carbohydrates or porcine gastric mucin. As used herein, HBGA-like carbohydrates include bacteria expressing HBGA-like carbohydrates, other biological sources of HBGA-like carbohydrates, such as human cells, or isolated HBGA-like carbohydrates (isolated from a biological source such a cell or a bacteria), or synthetic HBGA-like carbohydrates made by synthetic methods in a laboratory, or porcine gastric mucin. HBGA-like carbohydrates may be used herein interchangeably with bacteria that express HBGA-like carbohydrates or other natural or synthetic sources of HBGAs such as porcine gastric mucin, and those of skill in the art are able to determine the meaning from such use.
As shown herein, human noroviruses can infect and replicate in human B-cells when using virus-positive stool samples as a source of virus. When the stool sample was filtered through a 0.2 micron filter, which removes bacteria in the stool but not small viruses like noroviruses, infectivity was ablated (see
HBGA, HBGA-expressing bacteria and HBGA containing porcine gastric mucin) restores attachment of norovirus to the target cell (see
It is known that bacteria, including certain commensal bacteria, express carbohydrates that are indistinguishable from human HBGAs (22-25). Though not wishing to be bound by any particular theory, from the findings herein, it is currently believed that human noroviruses can bind these HBGA-like carbohydrates on commensal bacteria in the gut lumen and this is used for viral infection of B-cells. It is theorized that any bacteria expressing the correct HBGA-like carbohydrate for a given human norovirus strain will facilitate viral infection. The types of bacteria known to express HBGA-like carbohydrates are diverse and include Enterobacter, Escherichia, Shigella, and Helicobacter. There are likely many other commensal bacteria (e.g. strict anaerobes) that express HBGA-like molecules.
It is known that people generate antibodies directed to non-self HBGAs (isoantibodies that mediate blood transfusion reactions). Though not wishing to be bound by any particular theory, it is currently believed that these antibodies are secreted into the gut lumen where the antibodies bind and exclude commensal bacteria expressing non-matched carbohydrates. So a person's HBGA expression profile will shape his or her microbiota through exclusion of bacteria expressing non-matched HBGA-like carbohydrates. Though not wishing to be bound by any particular theory, it is currently believed that the correlation between a person's HBGA genetics and his or her susceptibility to specific human norovirus strains may be due to HBGA expression.
Methods of the present invention comprising an in vitro cell culture system may further comprise adding HBGA-like carbohydrates or one or more sources of HBGA-like carbohydrates. The HBGA-like carbohydrates may be added directly to an in vitro cell culture system. The HBGA-like carbohydrates may be mixed with a biological or diagnostic sample and the resulting mixture added to the in vitro cell culture system. The HBGA-like carbohydrates may be mixed with a filtered biological or diagnostic sample and the resulting mixture added to the in vitro cell culture system. The HBGA-like carbohydrates may be mixed with a purified virus sample and the resulting mixture added to the in vitro cell culture system.
A method comprises determining the susceptibility of a subject to norovirus infection comprising identifying the HBGA of the subject and testing a norovirus for its binding to that HBGA. If the virus binds the HBGA of the subject, the subject is susceptible to that norovirus strain. In an aspect, a method comprises obtaining from a subject a sample comprising bacteria or HBGA-like carbohydrates, such as a fecal sample, adding the sample to an ELISA assay described herein to determine the type of HBGA present in the sample, and determining the norovirus susceptibility of the subject.
Replicating a Virus in vitro
In an aspect, the present invention comprises methods of replicating a norovirus in vitro. A method may comprise inoculating norovirus-permissive cells with a norovirus, and culturing the cells. In an aspect, the cells may be human cells and the norovirus is a human norovirus. Inoculating norovirus-permissive cells may comprise infecting the cells with a norovirus. In an aspect, a method may comprise inoculating vertebrate cells, which can be B-cells or co-cultures of B-cells and intestinal epithelial cells. In an aspect, the vertebrate cells can be murine cells, human cells, or other cells. Cells in the in vitro culture can be, for example, B-cells or a co-culture of B-cells and intestinal epithelial cells as disclosed herein. In an aspect, a calicivirus can be a norovirus that is a murine norovirus or a human norovirus, such as a Norwalk virus.
Continuous Culture of Norovirus
Aspects of the present invention comprise a norovirus-permissive cell culture infected with a norovirus. A norovirus permissive cell culture can be maintained using routine cell culturing techniques well known to skilled artisans. A norovirus-permissive cell culture may comprise vertebrate cells, such as B-cells, or a co-culture of B-cells and intestinal epithelial cells. In an aspect, the vertebrate cells can be murine cells, human cells, or other cells. Cells in the in vitro culture can be, for example, B-cells or a co-culture of B-cells and intestinal epithelial cells as disclosed herein. In an aspect, a calicivirus can be a norovirus that is a murine norovirus or a human norovirus, such as a Norwalk virus.
In an aspect, a method for continuous culture of norovirus comprises a) contacting a norovirus to cells in a transwell in vitro cell culture system comprising a transwell culture vessel comprising intestinal epithelial cells grown on a transwell membrane and B-cells in the lower chamber, wherein the B-cells are located on the basal side of the intestinal epithelial cells; b) allowing the norovirus to replicate; and c) passaging the norovirus produced in the culture vessel to a subsequent in vitro culture vessel comprising a transwell culture vessel comprising intestinal epithelial cells grown on a transwell membrane and B-cells in the lower chamber, wherein the B-cells are located on the basal side of the intestinal epithelial cells. Passaging the norovirus produced or the norovirus infected cells may be repeated one or more times. In an aspect, the cells can be murine cells, human cells, or other cells. Cells in the in vitro culture can be, for example, B-cells or a co-culture of B-cells and intestinal epithelial cells as disclosed herein. In an aspect, a calicivirus can be a norovirus that is a murine norovirus or a human norovirus, such as a Norwalk virus.
In an aspect, a method for continuous culture of norovirus comprises a) contacting a norovirus to B-cells; b) allowing the norovirus to replicate; and c) passaging the norovirus produced in the culture vessel to a subsequent in vitro culture vessel comprising B-cells. Passaging the norovirus produced or the norovirus infected cells may be repeated one or more times. In an aspect, the cells can be murine cells, human cells, or other cells. Cells in the in vitro culture can be, for example, B-cells or a co-culture of B-cells and intestinal epithelial cells as disclosed herein. In an aspect, a calicivirus can be a norovirus that is a murine norovirus or a human norovirus, such as a Norwalk virus.
Method for Norovirus Detection
In an aspect, the invention comprises methods of detecting a member of the Caliciviridae family, such as a norovirus, in a biological or diagnostic sample. A method may comprise contacting an in vitro cell culture comprising norovirus-permissive cells, such as B-cells, with the sample, and detecting norovirus viral replication or attachment in the cell culture. A biological sample may be a diagnostic sample, such as a diagnostic sample from an animal suspected of infection with a member of the Caliciviridae family, such as a norovirus. The animal may be a mammal, for example, a human, a laboratory animal such as a rodent, for example a mouse, a rat, or a guinea pig, a farm animal such as a rabbit, cow or a sheep, or a companion animal such as a cat or dog. A biological/diagnostic sample may also be drinking water or a food item such as fresh fruits and vegetables, raw or processed seafoods or agents such as irrigation waters, or additives used to harvest or produce a food item. A biological/diagnostic sample may also be a tissue sample, a blood sample, vomitus, or a stool sample. A tissue sample can be from any tissue or body fluid (blood sample, vomitus, stool sample, saliva, sputum, etc.) that is suspected of infection with a member of the Caliciviridae family, such as a norovirus, such as, for example, liver, kidney, brain, blood, or saliva. In an aspect, the permissive cells can be murine cells, human cells, or other cells. Cells in the in vitro culture can be, for example, B-cells or a co-culture of B-cells and intestinal epithelial cells as disclosed herein. In an aspect, a calicivirus can be a norovirus that is a murine norovirus or a human norovirus, such as a Norwalk virus.
In an aspect, a method for calicivirus detection comprises a) contacting a biological or diagnostic sample (e.g., a diagnostic sample from a subject) or a biological/diagnostic sample pre-mixed with an HBGA-like or HBGA containing compound to an in vitro cell culture system comprising B-cells as disclosed herein, or to an in vitro cell culture system comprising a transwell culture vessel comprising intestinal epithelial cells grown on a transwell membrane and B-cells in the lower chamber, wherein the B-cells are located on the basal side of the intestinal epithelial cells; and b) after a predetermined time, testing the supernatant and/or the B-cells for calicivirus replication.
In an aspect, a method for norovirus detection comprises a) contacting a biological or diagnostic sample from a subject or a biological or diagnostic sample pre-mixed with an HBGA-like or HBGA containing compound to an in vitro cell culture system comprising B-cells as disclosed herein, or to an in vitro cell culture system comprising a transwell culture vessel comprising intestinal epithelial cells grown on a transwell membrane and B-cells in the lower chamber, wherein the B-cells are located on the basal side of the intestinal epithelial cells; and b) after a predetermined time, testing the supernatant and/or the B-cells for norovirus replication.
In an aspect, further steps of a method for calicivirus, such as a norovirus, detection, comprise a) identifying the calicivirus, such as a norovirus, found in an in vitro cell culture system. Identifying may comprise genetically identifying the virus found. The sample may be obtained from a subject suspected of infection with a member of the Caliciviridae family, such as a norovirus. The subject may be for example, a human, a rodent, a cow, a pig, a rabbit, a cat, a dog, a chicken, a reptile, a dolphin or an amphibian. A sample may be a stool sample, a vomitus sample, a tissue sample, blood sample or food item (as discussed above). Detection may be by any means known to those of skill in the art, including, but not limited to, those disclosed herein, such as a virus detection assay such as a cytopathic assay, an antibody assay, a nucleic acid detection assay or a protein detection assay. A cytopathic assay may be a dye exclusion assay, an enzyme release assay or an apoptosis assay. An antibody assay may comprise a Western blot assay, an ELISA assay, an immunofluorescence assay, an immunoprecipitation assay or a radioimmunoassay. A nucleic acid detection assay can be a polymerase chain reaction (PCR) assay or a hybridization assay. In an aspect, a method of detecting a member of the Caliciviridae family, such as a norovirus, in a biological or diagnostic sample can comprise detecting a host cell change that results from viral infection. An in vitro cell culture system as disclosed herein, comprising B-cells, may be used for detecting a host cell change in the B-cells. A host cell change can be, for example, a change in morphology, molecular composition, or cytopathicity. For example, a method for detecting a member of the Caliciviridae family, such as a norovirus, in a biological or diagnostic sample can comprise performing a cytopathic assay, an antibody assay, a protein detection assay or a nucleic acid detection assay. A cytopathic assay can be, in some configurations, a dye exclusion assay, an enzyme release assay, a necrosis assay, or an apoptosis assay. A dye exclusion assay can be, in non-limiting example, a trypan blue exclusion assay, or a fluorescent dye exclusion assay such as a propidium iodide exclusion assay. In some configurations, an antibody assay can use a monoclonal or a polyclonal antibody, such as a monoclonal antibody directed against a viral polypeptide. Any antigen detection system known in the art, such as a Western blot assay, an ELISA assay, an immunofluorescence assay, an immunoprecipitation assay or a radioimmunoassay, can be used to detect the presence and/or quantity of a norovirus. A protein detection assay may comprise, in non-limiting example, a gel electrophoresis assay, a column chromatography assay, and an enzyme assay. A nucleic acid detection assay can be an assay such as a polymerase chain reaction assay or a hybridization assay such as a Northern blot assay, or others known to those of skill in the art.
In an aspect, a method of using an in vitro cell culture system disclosed herein comprises a method of detecting the presence of a disease or condition due to norovirus in a subject comprising obtaining a tissue or body fluid sample from a subject, and contacting an in vitro cell culture vessel disclosed herein, for example, an in vitro culture system comprising B-cells. In an aspect, a method comprises contacting an in vitro cell culture system comprising a transwell culture vessel comprising intestinal epithelial cells grown on a transwell membrane and B-cells in the lower chamber, wherein the B-cells plus HBGA-containing compound or bacteria are located on the basal side of the intestinal epithelial cells and wherein the tissue or body fluid sample from the subject contacts the intestinal epithelial cells or the supernatant of the well comprising the intestinal epithelial cells. The presence of a disease or condition is indicated by detection of norovirus replication in the B-cells.
In an aspect, a method of using an in vitro culture system disclosed herein comprises a method for diagnosing calicivirus, such as a norovirus, in a subject having symptoms associated with calicivirus, such as a norovirus, infection comprising assaying a biological or diagnostic sample from a subject having symptoms associated with calicivirus, such as a norovirus, infection for the presence of calicivirus, such as a norovirus. In an aspect, a method comprises contacting the biological or diagnostic sample with or without HBGA containing compounds or bacteria with an in vitro cell culture system comprising B-cells as disclosed herein. In an aspect, a method comprises contacting the biological or diagnostic sample with an in vitro cell culture system comprising a transwell culture vessel comprising intestinal epithelial cells grown on a transwell membrane and B-cells mixed with HBGA containing compounds or bacteria in the lower chamber, wherein the B-cells are located on the basal side of the intestinal epithelial cells and wherein the tissue or body fluid sample from the subject contacts the intestinal epithelial cells or the supernatant of the well comprising the intestinal epithelial cells. Diagnosis of the viral infection comprises detection of the calicivirus such as norovirus comprises identifying the virus by methods known to those of skill in the art.
In an aspect, a method of using an in vitro culture system disclosed herein comprises assaying a biological or diagnostic sample for the presence of a calicivirus such as norovirus comprising assaying a biological or diagnostic sample, with or without HBGA containing compounds or bacteria mixed therewith, from a subject for the presence of a calicivirus, such as a norovirus. In an aspect, a method comprises contacting the biological or diagnostic sample with an in vitro cell culture system comprising B-cells as disclosed herein. In an aspect, a method comprises contacting the biological or diagnostic sample with an in vitro cell culture system comprising a transwell culture vessel comprising intestinal epithelial cells grown on a transwell membrane and B-cells in the lower chamber, wherein the B-cells are located on the basal side of the intestinal epithelial cells and wherein the tissue or body fluid sample from the subject contacts the intestinal epithelial cells or the supernatant of the well comprising the intestinal epithelial cells. The biological/diagnostic sample can be mixed with or without HBGA containing compounds or bacteria prior to contacting the biological/diagnostic sample with the cell culture system. Detection of the norovirus comprises identifying the norovirus by methods known to those of skill in the art. In an aspect, the cells can be murine cells, human cells, or other cells. Cells in the in vitro culture can be, for example, B-cells or a co-culture of B-cells and intestinal epithelial cells as disclosed herein. In an aspect, a calicivirus can be a norovirus that is a murine norovirus or a human norovirus, such as a Norwalk virus.
In an aspect, a method of using an in vitro culture system disclosed herein comprises a method for testing the ability of antibodies generated in a calicivirus infection, such as antibodies to the norovirus particle, to neutralize infectivity or attachment of a norovirus or other calicivirus. Without an in vitro cell culture cell culture system, such as those disclosed herein, currently used tests rely on a surrogate assay which tests whether an antibody inhibits binding to a putative attachment receptor as a measure of virus neutralization. However, there is no evidence that inhibition of binding to this receptor correlates with neutralization of infection. The culture systems disclosed herein allow for direct measurement of antibody activity. For example, a method for testing antibodies for neutralization of a norovirus comprises contacting a particular type of norovirus with antibodies isolated from a subject infected with that type of norovirus to affect binding of the antibody to the norovirus to form an antibody/norovirus complex. In an aspect, a method comprises contacting the antibody/norovirus complex with an in vitro cell culture system comprising B-cells as disclosed herein. In an aspect, a method comprises contacting the antibody/norovirus complex with an in vitro cell culture system comprising a transwell culture vessel comprising intestinal epithelial cells in the upper chamber and B-cells in the lower chamber, wherein the B-cells are located on the basal side of the intestinal epithelial cells and wherein the antibody/norovirus complex contacts the intestinal epithelial cells or the supernatant of the well comprising the intestinal epithelial cells. A further step comprises detection of the norovirus attachment to, or infection of, the B-cells. If the virus cannot bind to the B-cells, or the B-cells are not infected, the antibody was a neutralizing antibody and if the B-cells are infected with norovirus, the antibody was not a neutralizing antibody. In an aspect, the cells can be murine cells, human cells, or other cells. Cells in the in vitro culture can be, for example, B-cells or a co-culture of B-cells and intestinal epithelial cells as disclosed herein. In an aspect, a calicivirus can be a norovirus that is a murine norovirus or a human norovirus, such as a Norwalk virus.
A Kit
In an aspect, the present invention comprises kits for performing methods disclosed herein or kits comprising norovirus-permissive cells, such as B-cells. In an aspect, a kit comprising an in vitro cell culture system comprising B-cells as disclosed herein. In an aspect, a kit comprises an in vitro cell culture vessel comprising a transwell in vitro cell culture system comprising intestinal epithelial cells grown on a transwell membrane and B-cells in the lower chamber, wherein the B-cells are located on the basal side of the intestinal epithelial cells. In an aspect, a kit comprising an in vitro attachment system comprising B-cells as disclosed herein. A kit may further comprise instructions, media, other cells, positive and negative controls, and other components known to those of skill in the art. In an aspect, the cells can be murine cells, human cells, or other cells. Cells in the in vitro culture can be, for example, B-cells or a co-culture of B-cells and intestinal epithelial cells as disclosed herein. In an aspect, a calicivirus can be a norovirus that is a murine norovirus or a human norovirus, such as a Norwalk virus.
Detecting Anti-Viral Compounds
In an aspect, the present invention comprises methods of identifying a compound having anti-viral activity against a virus of the Caliciviridae family. “Anti-viral activity,” as used herein, may comprise inhibiting viral activity at any stage in a virus' life cycle. Anti-viral activity may also comprise inhibiting binding of a virus to a cell or inhibiting cellular uptake of the virus. Anti-viral activity may comprise, in non-limiting example, inhibition of viral replication, inhibition of viral gene expression, or inhibition of a viral protein accumulation or activity Inhibition of a viral protein accumulation or activity can comprise, in non-limiting example, inhibition of a member of the Caliciviridae family, such as a norovirus, polyprotein protease accumulation, inhibition of norovirus RNA polymerase accumulation, inhibition of VPG accumulation, inhibition of NTPase accumulation, inhibition of norovirus polyprotein protease activity, inhibition of norovirus RNA polymerase activity, inhibition of VPG activity, or inhibition of NTPase activity. Standard methods well known in the art for measuring or detecting viral protein accumulation or activity can be used, for example, enzyme assays and antibody assays.
In an aspect, a method for identifying a compound having anti-viral activity may comprise contacting a candidate potential anti-viral compound with a calicivirus-permissive cell culture infected with a member of the Caliciviridae family, such as a norovirus, and detecting inhibition of viral replication or attachment to B-cells. For example, a method may comprise contacting a candidate potential anti-viral compound with a norovirus-permissive cell culture infected with a norovirus, and detecting inhibition of norovirus replication. In certain aspects, a candidate anti-viral compound can be added to a calicivirus infected culture, such as an infected norovirus-permissive culture, at a concentration of from about 1 picomolar to about 100 millimolar, or from about 1 nanomolar to about 100 micromolar. Detecting inhibition of viral replication in some embodiments may comprise detecting inhibition of viral nucleic acid synthesis or viral protein synthesis. In an aspect, detecting inhibition of viral replication may comprise performing a plaque assay on the cell culture. A plaque assay may comprise determining a titer of virus accumulated in a plaque formed by infected cells in the presence of the candidate anti-viral molecule. A focus forming assay may comprise determining a titer of virus accumulated in the presence of the candidate anti-viral molecule. In these configurations, assays for identifying anti-viral compounds can be used for identifying compounds inhibiting viral attachment to B-cells or having anti-RNA virus activity, anti-single-stranded RNA virus activity, anti-positive strand single-stranded RNA virus activity, anti-positive strand single-stranded RNA activity, no DNA stage virus activity, anti-calicivirus activity, or anti-norovirus activity. In an aspect, anti-viral activity can be detected by detecting differences between infected cells contacted with a candidate anti-viral agent and control (not infected) cells. Such differences can comprise, in non-limiting example, gene expression differences, antigenic differences, enzyme activity differences, dye-staining differences, or morphological differences (as revealed by light microscopy or electron microscopy). In an aspect, anti-viral activity can be detected by performing a cytopathic effects (CPE) inhibition assay in which the anti-viral activity reduces or prevents norovirus-induced CPE. In an aspect, the cells can be murine cells, human cells, or other cells. Cells in the in vitro culture can be, for example, B-cells or a co-culture of B-cells and intestinal epithelial cells as disclosed herein. In an aspect, a calicivirus can be a norovirus that is a murine norovirus or a human norovirus, such as a Norwalk virus.
In an aspect, a method for screening for an active agent to inhibit norovirus attachment, replication or infection comprises a) contacting a candidate active agent (compound) with the cells or the supernatant of an in vitro culture system comprising B-cells, as disclosed herein, or an in vitro cell culture vessel comprising a transwell cell culture system comprising intestinal epithelial cells grown on a transwell membrane and B-cells in the lower chamber, wherein the B-cells are located on the basal side of the intestinal epithelial cells; b) adding a calicivirus, such as a norovirus, to the in vitro culture system; c) allowing the norovirus to replicate; and d) detecting the inhibition of virus replication in the supernatant of the B-cells compared to virus replication in the supernatant of B-cells not contacted with the candidate active agent and/or detecting the attachment of virus to the B-cells compared to virus attachment to B-cells not contacted with the candidate active agent. In an aspect, the cells can be murine cells, human cells, or other cells. Cells in the in vitro culture can be, for example, B-cells or a co-culture of B-cells and intestinal epithelial cells as disclosed herein. In an aspect, a calicivirus can be a norovirus that is a murine norovirus or a human norovirus, such as a Norwalk virus.
In an aspect, the present invention may comprise methods of adapting norovirus to have a modified host range. For example, a method may comprise serially passaging a norovirus population for three or more generations in norovirus-permissive cell cultures. Serially passaging may comprise plaque-purifying a norovirus and growing the plaque-purified norovirus in norovirus-permissive host cells for two serial passages, three serial passages, or more serial passages. Serially passaging may comprise performing a focus forming assay to identify infected cells by immunostaining instead of cytopathic effect; the norovirus purified in this way will be grown in norovirus-permissive host cells for two serial passages, three serial passages, or more serial passages. In an aspect, adapting the host range-modified norovirus to growth in a vaccine production-approved cell line can comprise infecting the approved cell line with host range-modified norovirus, and growing the virus. Methods for producing a vaccine against a virus using a virus exhibiting reduced virulence through serial passage adaptation (Sabin, A. B., Ann. N.Y. Acad. Sci. 61: 924-938, 1955) or through genetic engineering (e.g., by altering codons) are well known to skilled artisans. In an aspect, an in vitro cell culture system may comprise B-cells as disclosed herein. In an aspect, an in vitro cell culture vessel may comprise a transwell in vitro cell culture system comprising intestinal epithelial cells grown on a transwell membrane and B-cells in the lower chamber, wherein the B-cells are located on the basal side of the intestinal epithelial cells. Cells in the in vitro culture can be, for example, B-cells or a co-culture of B-cells and intestinal epithelial cells as disclosed herein. In an aspect, a calicivirus can be a norovirus that is a murine norovirus or a human norovirus, such as a Norwalk virus.
Reduced Virulence Virus/Vaccine
In an aspect, the present invention may comprise a method for preparing a reduced virulence norovirus, comprising a) passaging norovirus in an in vitro cell culture system disclosed herein; and b) selecting a reduced virulence norovirus, wherein the virulence is reduced compared to wild-type or non-adapted norovirus. In an aspect, an in vitro cell culture system may comprise B-cells as disclosed herein. In an aspect, an in vitro cell culture vessel may comprise a transwell culture vessel comprising intestinal epithelial cells grown on a transwell membrane and B-cells in the lower chamber, wherein the B-cells are located on the basal side of the intestinal epithelial cells. Cells in the in vitro culture can be, for example, B-cells or a co-culture of B-cells and intestinal epithelial cells as disclosed herein. In an aspect, a calicivirus can be a norovirus that is a murine norovirus or a human norovirus, such as a Norwalk virus. In an aspect, the present invention comprises a norovirus vaccine comprising a therapeutically effective amount of a reduced virulence norovirus.
The invention can be further understood by reference to the examples which follow.
Cell lines. The M12 (26), WEHI-231 (27), and BJAB (28) B-cell lines were cultured in RPMI with 10% fetal bovine serum; M12 and WEHI-231 media was supplemented with 50 μM β-mercaptoethanol. RAW264.7, CMT-93, 293T, and HT-29 cell lines were cultured in DMEM with 10% fetal bovine serum. Media for all experiments contained 100 U/mL penicillin and 100 μg/mL streptomycin. For co-culturing human IECs and B-cells, HT-29 cells were grown to confluency on hanging wells. Polarization was confirmed prior to infections using fluorescein-conjugated dextran 3000 Da (FITC-dextran) exclusion. Specifically, 4 μg/mL FITC-dextran was loaded into the apical chamber. At 45 min. post-incubation, basal supernatants were collected and analyzed for fluorescent signal using a Synergy BioTek plate reader. Basal supernatants with fluorescence maxima less than 10% of the signal detected in a control well with no HT-29 cells were considered to be polarized. BJAB-cells were then cultured in the basal chamber.
Viruses. Recombinant MNV-1 and MNV-3 that have been previously described (19) were used for all experiments. In brief, virus stocks were generated by transfecting 5 μg infectious clone per 106 293T cells, freeze-thawing cells after 1 d, and infecting RAW264.7 cells with 293T lysates at MOI 0.05. RAW264.7 lysates were generated when>90% of cells displayed CPE and were purified through a 25% sucrose cushion. Titers of all MNV stocks were determined using a standard TCID50 assay (29). For HuNoV infections, a stool sample that tested positive for the GII.4-Sydney strain was provided by the Centers for Disease Control (CDC); this stool sample tested negative for GI and GIV HuNoVs, sapovirus, astrovirus, rotavirus, and enteric adenovirus. We also performed pilot studies with two de-identified stool samples testing positive for the GII.4-Sydney strain that were obtained from Shands Hospital associated with the University of Florida. Stool samples were not processed prior to inoculation of cells unless otherwise indicated. Titers of HuNoV stocks were determined by quantitative RT-PCR (RT-qPCR) using established genogroup-specific primer sets (30) (see below for details).
MNV infections and growth curves. Cells were infected at MOI 5 unless otherwise indicated and incubated for 1 h on ice. Cells were then washed to remove unbound virus and incubated at 37° C. At the indicated times post-infection, culture supernatants were collected and virus titers determined using a standard TCID50 assay (29).
Cell viability assays. Cells were incubated with propidium iodide (BD Pharmingen) at a final concentration of 2.5 μg/mL for 5 min. at room temperature. Flow cytometric analysis was performed on a FACSCalibur instrument (BD Biosciences) and the CellQuest Pro software was used to analyze data. Data are reported as the percentage of cells that did not incorporate dye (% viable cells).
Western blotting. Cells were lysed in lx Laemmli sample buffer, and proteins were separated by SDS-PAGE and transferred to polyvinylidene fluoride (PVDF) membranes. Previously described antibodies to the MNV-1 protease-polymerase (ProPol) nonstructural proteins (31), the VP1 major capsid protein (32), and the VP2 minor capsid protein (19) as well as a mouse anti-actin antibody (EMD Millipore) were used sequentially to probe the PVDF membranes for MNV studies. The blots were stripped using Restore PLUS Western Blot Stripping Buffer (Thermo Scientific) in between antibody incubations. A previously described antibody to a genogroup II HuNoV NS6 peptide (18) was used to probe membranes for HuNoV studies.
MNV immunofluorescence assay. Cells were fixed in 4% paraformaldehyde in phosphate buffered saline (PBS) and deposited onto glass slides using a Cytopro Cytocentrifuge (Wescor Inc.). Cells were then permeabilized with 0.1% Triton X-100/4% PFA in PBS and stained with anti-ProPol antibody (31) at a 1:1000 dilution followed by an Alexa Fluor 594-conjugated secondary antibody (Invitrogen). Antibodies were diluted in 1% bovine serum albumin in PBS. Nuclei were stained with mounting media containing DAPI (Vector Laboratories, Inc.). Stained cells were imaged with a Zeiss Axioplan-2 Upright Fluorescent Microscope. To determine infectivity frequencies, three random 40X fields were counted per sample and the data averaged.
MNV persistence assays. M12 cells were infected at MOI 5 and plated at 3×105 cells/mL. At 2 dpi, cells were washed extensively to remove extracellular virus and re-plated at 3×105 cells/mL. This procedure was repeated every 2 d. The culture supernatant and cells were collected at every fifth passage for viral detection using the described TCID50 assay and IFA, respectively.
Mice, virus infections, and in vivo tissue titer determination. Wild-type B6 mice (Jackson #00064) and Ighm™/Cgn mice (also known as μMT, Jackson #002288), which lack B-cells, were bred and housed in animal facilities at the University of Florida under specific-pathogen-free conditions. 129S6/SvEv Stat1™/Rds (Taconic #2045; referred to as Stat1−/−) mice were bred and housed in animal facilities at the University of Michigan under specific-pathogen-free conditions. Six- to ten-week old, sex-matched mice were used in all experiments. Virus infections were performed perorally (p.o.) with 25 μL inoculum, unless otherwise indicated. For neutral red-labeled MNV-1 infections, virus was administered through oral gavage with 100 μL inoculum and infections were carried out in the dark. For determining in vivo tissue titers, specified tissues were dissected from perfused mice, weighed, and homogenized in media by bead beating using 1.0 mm zirconia/silica beads (BioSpec Products, Inc.). Plaque assays of tissue samples have been described (14, 33). For titering tissues from mice inoculated with neutral red-labeled MNV-1, tissues were homogenized in the dark. One portion of each homogenate was titered in the dark (total titer) while a second portion was exposed to light for 30 min. and titered in a parallel plaque assay (light-insensitive titer representing replicated virus).
Magnetic separation of cells. Groups of B6 mice (n=8) were inoculated p.o. with mock inoculum or 107 TCID50 units MNV-1 or MNV-3. At 1 dpi, Peyer's patches were dissected and pooled single cell suspensions were prepared by grinding through a 70-μm strainer. B-cells were positively selected from bulk Peyer's patch cells using the EasySep Mouse CD19 Positive Selection Kit and EasySep magnet (STEMCELL Technologies Inc.). The purity of separated B-cells was measured by flow cytometric analysis and determined to be >97% in each experiment.
MNV quantitative RT-PCR. RNA was extracted from purified Peyer's patch cells using the E.Z.N.A MicroElute Total RNA Kit (Omega Bio-Tek Inc.) and cDNA was synthesized using the ImProm-II Reverse Transcription System (Promega). Quantitative PCR was performed on each cDNA sample in triplicate. Primers for the MNV genome were sense 5′-CTTTGGAACAATGGATGCTG-3′ (SEQ ID NO: 1) and antisense 5′-CGCCATCACTCATCCTCAT-3′(SEQ ID NO: 2). Serial dilutions of a plasmid with the viral target sequence were used to generate a standard curve for the purpose of determining viral genome copy numbers in each sample.
Antibiotic depletion of the murine intestinal microbiota. The intestinal microbiota was depleted by oral gavage of a standard antibiotic cocktail, as previously described (34, 35). In brief, mice were orally gavaged daily for five days with 10 mg each of vancomycin (Fisher Scientific), ampicillin (Acros Organics), metronidazole (Acros Organics), and neomycin (Sigma). After the fifth day of gavage, antibiotics were added to the drinking water at a concentration of 1 g/L for ampicillin, metronidazole, and neomycin and 500 mg/L for vancomycin. Fresh fecal samples were collected from mice after the fifth day of oral gavage, homogenized, plated on brain-heart infusion (BHI) agar plates with 10% sheep blood, and incubated under anaerobic conditions at 37° C. for 2 d followed by aerobic conditions at 37° C. for 1 d to confirm efficient microbial depletion. Mice were maintained on the antibiotic- or PBS-containing water for the duration of the experiment, and infections were only performed after antibiotic-treated mice were verified to be free of detectable culturable bacteria.
HuNoV infections and genome copy number determination. The indicated numbers of viral genome copy numbers were applied directly to BJAB cells; or in the apical chamber of a hanging well containing polarized HT-29 cells grown on the membrane and BJAB cells in the lower chamber. Cultures were incubated at 37° C. for the indicated times, at which point the contents of the entire well (direct infections) or the entire basal chamber contents (co-culture) were freeze/thawed two times and the cell lysate used for RNA extraction and RT-qPCR detection of viral genome copy number. Published primers NK2PF (5′-ATGTTYAGRTGGATGAGATTCTC) (SEQ ID NO: 3) and NK2PR (5′-TCGACGCCATCTTCATTCAC) (SEQ ID NO: 4) were used to amplify genogroup II viruses at a final concentration of 200 nM each (30). Two pl of undiluted cDNA was added to each reaction and each sample was run in triplicate. Samples were amplified on a iCycler iQ (Bio-Rad) with SYBR Green Master Mix (Thermo Scientific) under the following cycling conditions: 95° C. for 10 min. followed by 41 cycles of 95° C. for 15s, 58° C. for 30 s, and 72° C. for 30 s. Serial dilutions of a plasmid with the viral target sequence provided by Park et al. (30) were used to generate a standard curve for the purpose of determining viral genome copy numbers in each sample. In certain experiments, aliquots of HuNoV stocks were inactivated with 200,000 μJ cm−2 UV for 25 min. prior to inoculation; aliquots of HuNoV stocks were incubated with 10 μg/mL anti-VP1 antibody (Abcam, catalog # ab92976) for 1 h at 37° C. prior to inoculation of BJAB cells to test for antibody-mediated virus neutralization; and stocks were filtered through a 0.2 μm membrane prior to inoculation.
HuNoV immunofluorescence assay. The protocol described for MNV IFAS was used with the following modifications. After permeabilization, cells were blocked with 5% normal goat serum. A Tyramide Signal Amplification Kit (Invitrogen) was then used according to manufacturer's protocol. Briefly, cells were stained with anti-VP1 mouse monoclonal antibody (Abcam; catalog #ab80022) at a 1:25 dilution followed by anti-mouse IgG-HRP and Alexa Fluor 594-conjugated tyramide.
HuNoV passaging studies. A passage 0 (P0) virus stock was prepared by infecting BJAB cells with 5×105 viral genome equivalents of the GII.4-Sydney HuNoV-positive stool for 2 h, washing the cells extensively to remove unbound virus, subjecting 3 dpi cultures to two freeze-thaw cycles, pelleting and discarding cellular debris, and aliquoting supernatant. 5×105 genome equivalents of this P0 stock were then applied to naïve B-cells and infections analyzed as described above.
HuNoV persistence studies. BJAB cells were inoculated with 5×105 viral genome equivalents of the GII.4-Sydney HuNoV-positive stool. At 3 dpi, cells were washed three times to remove extracellular virus and re-plated at 5×105 cells/mL. This procedure was repeated every 3 d. At each passage, one well was harvested for viral genome copy number determination.
HuNoV:bacteria incubation studies. Enterobacter cloacae was purchased from ATCC (ATCC 13047). Escherichia coli DH5-alpha from our common laboratory stock was used. Bacteria were inoculated into nutrient broth (NB) and incubated overnight at 37° C. Overnight cultures were serially diluted in NB to achieve the indicated concentrations and incubated at 65° C. for 40 min. for the purpose of heat inactivation. Inactivation was confirmed by plating on nutrient agar and inoculating into NB. For HuNoV studies, heat-inactivated bacteria were pre-incubated with virus for 1 h at 37° C. prior to inoculation onto cells. Lysates of heat-killed E. cloacae and E. coli were probed for H-type HBGA expression by western blotting with anti-H IgM antibody (Santa Cruz). Synthetic blood type H HBGA (GlycoTech product number 08-019; expected size of 238 kDa) was run in parallel as a positive control. The H-type antigen expressed by E. cloacae is ca. 63 kDa.
HuNoV attachment assay. A source of HuNoV is incubated with duplicate wells of BJAB-cells at 4° C. for the indicated amount of time. One sample is harvested without cell washing as an indication of input genome copy numbers; and one sample is centrifuged at 730 rcf (730 g) for 7.5 min. to pellet the cells with attached virus. The supernatant is removed and the pellet resuspended in cold PBS, and this wash is repeated two times. RNA is then extracted from both washed and unwashed sample, quantitative RT-PCR performed to determine viral genome copy numbers, and the amount of attachment determined by dividing genomes in washed sample by genomes in unwashed sample.
HuNoV antibody neutralization assays. A source of HuNoV is pre-incubated with a virus-specific antibody at 37° C. for 1 h and the sample is then tested in either attachment or infection assays, as described above. Serial dilutions of the antibody should be tested.
To test whether MNVs infect B-cells in culture, two murine B-cell lines called M12 and WEHI cells were infected with either MNV-1 or MNV-3 at MOI 5. The RAW 264.7 murine Mφ cell line known to be highly permissive to MNV infection was tested as a positive control (14). An IEC line CMT-93 was tested as a negative control since it has been shown that MNVs fail to infect IECs in vitro (9). As expected, RAW 264.7 cells produced ca. 108 TCID50 units per mL of each virus by 24 hpi whereas CMT-93 cells produced no detectable progeny virus through 96 h (
The extent of cell death induced by each virus in the two B-cell lines was next compared to RAW 264.7 cells. As expected based on the lytic nature of MNV infection in RAW 264.7 cells (14), there was nearly 100% loss of RAW 264.7 cell viability in cultures infected with either virus at 48 hpi (
To further investigate the efficiency of MNV replication in B-cells, the kinetics of viral protein production was assessed using western blotting. The viral RNA-dependent RNA polymerase (RdRp), the major capsid protein VP1, and the minor structural protein VP2 were first detected in WEHI cells at 24 hpi (
The infectivity of each MNV strain in RAW 264.7, M12, and WEHI cells was determined using IFA with a polyclonal antibody directed to the nonstructural protease-RdRp proteins (ProPol). As expected, nearly all RAW 264.7 cells infected with MNV-1 or MNV-3 at MOI 5 contained viral antigen at 24 hpi (
Specifically, viral antigen-positive cells and total cells based on DAPI stain were both counted in three random 40X fields per condition at the indicated time points. The entire experiment was repeated twice and all data per condition averaged.
Because MNV infection of M12 cells was associated with minimal CPE, it was examined whether the cultures were capable of clearing infection or instead became persistently infected. To address this, M12 cells were infected with MNV-1 or MNV-3 at MOI 5 for 48 h. Cells were then washed extensively to remove extracellular virus and re-plated at a low cell density. This was repeated every 48 h for a total of 25 passages. In all passages tested, a comparable amount of supernatant-associated virus ranging from 2×106-3×107 TCID50 units per mL for MNV-1 and 3×106-2×107 TCID50 units per mL for MNV-3 was detected, demonstrating persistent M12 infection by both virus strains (
It has previously been reported that MNV-3 distal ileum titers are reduced in B-cell−/− mice compared to wild-type mice at 24 hpi (19). To gain further insight into the significance of putative in vivo B-cell infection, titers of MNV-1 (
Discussion pertaining to MNV infection of B-cells: It was demonstrated that MNV-1 and MNV-3 infected both an immature (WEHI) and a mature (M12) B-cell line. Infection of immature B-cells was more efficient than infection of mature B-cells in terms of overall progeny virus production, kinetics of replication, and viral protein production (
The low infectivity of M12 infection correlated with an apparent absence of CPE (
The distinct nature of M12 cell infection correlated with the ability of MNVs to establish persistence in this cell line. This persistent infection was associated with ongoing progeny virion production since 106-107 TCID50 units per mL of supernatant-associated virus were detected throughout 25 passage events (
Finally, it is confirmed that B-cells are MNV targets during enteric infections. There appears to be intestinal specificity to the cell tropism of MNVs with B-cells being targeted in the small intestine (e.g., distal ileum) but not the large intestine (e.g., colon). Indeed, Peyer's patch B-cells contained significant numbers of viral genomes at the peak of acute infections, correlating with decreased viral titers in RAG1−/− and B-cell−/− mice compared to wild-type mice at this time point (
Overall it is concluded that MNVs efficiently infect multiple B-cell lines in vitro and Peyer's patch B-cells in vivo. The nature of infection is distinct from infection of other known cellular targets of MNVs such as Mφs and DCs. Of particular importance, mature B-cells display minimal CPE; support a low frequency of MNV infectivity; and are persistently infected in vitro which can have significant implications on NoV pathogenesis in vivo.
106 genome equivalents of a stool sample collected from a GII.4 HuNoV-infected human patient were added directly to human B-cells, either unfiltered or filtered through a 0.2 micron membrane. At 0, 3, and 5 days post-infection (dpi), cells and supernatants were collected, the cells were frozen/thawed to release intracellular virus, cell debris was spun out, and RNA was extracted from lysate. Quantitative RT-PCR was then performed using primers specific to the virus. In
In this experiment, human intestinal epithelial cells (IECs; HT-29 cell line) were cultured on the membrane of a transwell, confirmed to be confluent using a FITC-dextran diffusion assay, and human BJAB cells were added to the lower chamber (as shown in
Based on our observations that filtration of a HuNoV-positive stool sample ablates viral infectivity (see
To probe the mechanism by which HBGA facilitate HuNoV infection of B-cells, we next performed attachment assays. As was observed for B-cell infections, filtration of the GII.4-positive stool ablated viral attachment to the surface of BJAB cells while pre-incubation of filtered stool with synthetic H completely restored attachment (
Discussion pertaining to HuNoV infection of B-cells and commensal bacteria as a co-factor for NoV infections. Our identification of B-cells as a target for HuNoV infection represents the first identification of a permissive cell type in vitro for these critical human pathogens. When a GII.4-Sydney HuNoV-positive stool sample was applied to the human B-cell line BJAB, we detected significant albeit modest increases in viral genome copy number. As expected, viral genome replication was completely ablated by UV treatment and a polyclonal α-VP1 antibody fully neutralized infectivity. Further confirming viral replication in these cells, we detected nonstructural and structural protein. Most importantly, lysates from the infected cells supported infection of naïve BJAB cells, demonstrating productive infection of progeny virions. Similar to MNV infection of M12 cells, we failed to detect CPE in HuNoV-infected BJAB cultures microscopically or using trypan blue exclusion (data not shown). Although both MNV and HuNoV infection of certain B-cell lines is thus apparently noncytopathic, GII.4-Sydney HuNoV did not establish persistence in BJAB cells as MNVs did in M12 cells.
Filtration of the GII.4-Sydney HuNoV-positive stool sample through a 0.2-μm membrane significantly reduced viral genome replication in direct B-cell infection and in the transwell system, revealing a filterable co-factor for HuNoV infection of B-cells. Because we used unprocessed stool as a source of virus, we reasoned that the most likely candidate for a filterable co-factor was commensal bacteria. H antigen-expressing E. cloacae stimulated viral infection of B-cells in a dose-dependent manner whereas H antigen-negative Escherichia coli and free lipopolysaccharide (LPS) failed to stimulate infection. The bacteria used in these experiments were heat-killed prior to incubation with the filtered stool inoculum so bacterial viability is not required for its stimulatory activity. Providing further evidence that the HBGA specifically stimulates infection, synthetic H antigen also rescued infectivity of filtered virus inoculum. Although we do not yet know the precise mechanism by which a HBGA (either free or bacterial-bound) stimulates HuNoV infection of B-cells, we determined that it facilitates viral binding to the surface of B-cells.
Antibiotic depletion of the intestinal microbiota prior to MNV-1 and MNV-3 infections resulted in significant reductions in acute virus titers. These data strongly argue that NoVs have evolved common strategies to use bacterial ligands to enhance their infectivity although the strategies used by MNVs and HuNoVs are likely not identical. For example, MNVs can efficiently infect macrophages, dendritic cells, and B-cells in vitro in the absence of bacteria. Moreover, mice do not express HBGAs so MNVs must use distinct bacterial ligands. Regardless, the mouse model will be invaluable in dissecting the general in vivo relevance of these interactions to overall NoV infection. Based on our collective data, we have generated a working model of NoV infection whereby virus binds commensal bacteria in the gut lumen via a bacterial carbohydrate, the virus-bacteria or virus-glycan complex is transcytosed across the intestinal epithelium, and the bacterial glycan stimulates viral infection of underlying immune cells (65).
The availability of a HuNoV cultivation system will enable the development of tools/systems for investigating mechanisms of viral replication methods for measuring immune correlates of protection (e.g., antibody neutralization assays), development of live attenuated viral vaccine candidates, and testing of putative antiviral compounds in vitro. In fact, our finding that a polyclonal α-VP1 antibody could fully neutralize viral infectivity provides proof-of-principle that this new cell culture system can be used to assess true neutralizing activity of α-HuNoV antibodies.
From Frozen Stock: Vial removed from LN2 freezer was thawed in a 37° C. water bath until cells were just thawed. Cells were added to 9 ml of RPMI and centrifuged at 1100 rpm for 10 min. Medium was aspirated and pellet was re-suspended in 1 ml of RPMI with 50% FBS. A small aliquot (10 μl) was taken and used to determine cell concentration. Culture was then seeded into wells of a 6 well plate at a density between 5-7×105 cells per well. Additional RPMI with 50% FBS was added to the wells to bring the final volume to 2 ml. Plate was incubated at 37° C.
1st Passage: The culture was checked 3 days after initial plating. A growing, healthy culture formed clumps of cells. Initially, smaller clumps (10-20 cells) were seen, but after 1-2 days of additional incubation at 37° C., larger clumps (40+) cells began to form. When the culture concentration reached 1-2×106 cells/ml, it was split. Seed 5×105 cells per well of a 6 well plate. Added additional RPMI with 1% FBS to bring final volume to 2 ml. Plate was incubated at 37° C.
Subsequent Passaging: On average, a culture reached 1×106 cells per well after 3-4 days of culture. When seeded at 5×105 cells per well, cells can be incubated for up to 5 days. Cells can be passaged after 3-4 days of incubation.
From Frozen Stock: Vials of cells were thawed in a 37° C. water bath until cells were just thawed. Cells were added to 9 ml of DMEM and centrifuged at 1100 rpm for 10 min. Medium was aspirated and pellet was resuspended in 1 ml DMEM. The cells were seeded into a T-25 flask with 7 mL DMEM. The flask was incubated at 37° C. Media was changed every 4-5 days until culture was 80-90% confluent. 1st Passage: When culture was 80-90% confluent, the cell layer was rinsed with 1X PBS to remove all traces of serum which contains trypsin inhibitor. 2 mL of trypsin was added and cells were observed under an inverted microscope until the cell layer was dispersed (usually within 5 to 15 minutes). Cells that are difficult to detach may be placed at 37° C. to facilitate dispersal.
6.0 to 8.0 mL of complete growth medium was added and cells aspirated by gently pipetting. Cells were counted and appropriate aliquots of the cell suspension were added to new culture vessels. At this point the culture was expanded to T-75 flasks. The recommended inoculum is 1×104 viable cells/cm2. Cultures were incubated at 37° C., 5% CO2.
Subsequent Passaging: When the flask reached 80-90% confluency, cells were rinsed and treated with trypsin as above. Cells were split at 1:4 to 1:8. Cultures were incubated at 37° C., 5% CO2.
Seeding to Hanging Wells: When a flask of cells was 80-90% confluency, the cells were rinsed with PBS, treated with trypsin and resuspended in DMEM as above. 1 ml of DMEM was added to the wells of a 12 well plate. Aseptically, hanging wells were transferred to the 12 well plate and 200 μl of DMEM. 5×104 cells per hanging well were seeded and final volume was brought to lml with DMEM. The plate was incubated at 37° C., 5% CO2. Media above and below the hanging well was changed every 3-4 days. Once the cells in the well were 100% confluent for one week, they were tested for polarization of cells using the dextran-FITC assay.
Virus Prep
Frozen stool samples obtained from CDC were incubated in a 37° C. water bath until just thawed and then distributed into 50 μl aliquots and stored at −80° C. One aliquot was removed and used to titer the virus stocks.
Experimental Design
BJABs: Cells from multiple culture wells were combined into a 50 ml conical tube. The tube was gently mixed and the cell concentration determined. Wells of a 12-well plate were then seeded with 2.5×105 cells. The culture was then brought up to a final volume of 1300 μl using RMPI (10% FBS). Cultures used had been passed no less than 3 days prior to the start of the experiments.
HT-29s: Using aseptic technique, old media was removed from the hanging wells and transfered to the well of a 12 well plate seeded with BJABs. 200 μl of DMEM was added.
Virus: An aliquot (50 μl) of virus was removed from −80° C. storage and incubated in a water bath until just thawed. The virus was then placed on ice until use, then seeded onto the apical side of the hanging wells. Plates were incubated at 37° C.
At designated time points, cells were harvested and distributed into microcentrifuge tubes for further analysis. Supernatants were removed from the apical side of hanging wells, then the well was removed and the media and cells on the basolateral side were removed. Finally 1 ml of PBS was added to the hanging well and the HT-29 cells were scraped off and transferred. All aliquots were stored at −80° C.
Sample Analysis
RNA extraction: Sample aliquots (500 μl) were removed from −80° C. and thawed in a 37° C. water bath. Once thawed, samples were returned to −80° C. This process was repeated 1 more time (for a total of 3 freeze/thaw cycles).
After the final thaw, 1 ml of Trizol was added to the culture and incubated at room temperature for 5 min. Then 200 μl of chloroform was added and the sample was vortexed and incubated at room temperature for 3 min. Samples were then centrifuged at 12,000× g for 15 min. The aqueous phase was put into a fresh tube and 10 μg of glycerol was added to each sample. After mixing, 500 μl of isopropanol was added and then the samples were incubated at room temperature for 10 min at 4° C. at 12,000× g. The sample was centrifuged again for 10 min (at 4° C.). Isopropanol was removed and pellet was washed with 75% ethanol. Samples were centrifuged again for 5 min at 7,500× g. Ethanol was removed and pellet allowed to air dry for 5-10 min. Then pellet was re-suspended in 30 μl of pre-warmed (70° C.) RNase/DNase free water.
cDNA amplification: The Superscript kit (Invitrogen # 11752-050) was used per the manufacturer's instructions. 500 ng of RNA was added to the sample reactions.
qPCR: Sybr green (Fisher Scientific # FERK0243) was used according to the manufacturer's instructions. Primers NK2PF (5′-ATGTTYAGRTGGATGAGATTCTC) (SEQ ID NO: 3) and NK2PR (5′-TCGACGCCATCTTCATTCAC) (SEQ ID NO: 4) were used to amplify GII viruses at a final concentration of 200 nM each. Primers used for GI viruses were NK1PF (5′-GCYATGTTCCGYTGGATG) (SEQ ID NO: 5) and NK1PR (5′-GTCCTTAGACGCCATCATCAT) (SEQ ID NO: 6) at the concentrations mentioned above. 2 μl of undiluted cDNA was added to each sample well and each sample was run in triplicate. Samples were amplified on a Biorad iCycler under the following cycling conditions: 95° C. for 10 min followed by 41 cycles of 95° C. for 15s, 58° C. for 30 s, and 72° C. for 30 s. Melt curve was generated at 65° C. for 10 s for 61 cycles.
As an alternative, a one step RT-qPCR using the AgPath One-Step RT-PCR Kit (Ambion) can be used. In this alternative technique, a master mix can be set up and the reaction performed according to the manufacture's instructions (adding 150 ng of RNA per PCR well). The following primers and probes can be use with the following cycling program:
Cycling program:
10 min at 42° C. (RT step)
10 min at 95° C.
45 cycles of:
Collect fluorescence data during the “60 s at 60° C.” step.
Media
RPMI (50%)
RPMI (Fisher Scientific cat# MT10040CM)
50% FBS
1× Pen/strep
RPMI (10%)
RPMI (Fisher Scientific cat# MT10040CM)
10% FBS
1× Pen/strep
None of the RPMI media for BJABs contain BME.
BJAB culturing:
From Frozen Stock: Vials of cells were thawed in a 37° C. water bath until cells were just thawed. Cells were added to 9 ml of RPMI and centrifuged at 1100 rpm for 10 min. Medium was aspirated and pellet was re-suspended in lml of RPMI with 50% FBS. A small aliquot (10 μl) was taken and used to determine cell concentration. Culture was then seeded into wells of a 6 well plate at a density between 5-7×105 cells per well. Additional RPMI with 50% FBS was added to the wells to bring the final volume to 2 ml and the plate was incubated at 37° C.
1st Passage: The culture was checked 3 days after initial plating. A growing, healthy culture begins to form clumps of cells. Initially, smaller clumps (10-20 cells) were seen, but after 1-2 days of additional incubation at 37° C., larger clumps (40+) cells began to form. When the culture concentration reaches 1-2×106 cells/ml, the culture was split. 5×105 cells per well were seeded into a six well plate. Additional RPMI with 1% FBS was added to bring final volume to 2 ml and the plate incubated at 37° C. Subsequent Passaging: Subsequent Passaging: On average, a culture reached 1×106 cells per well after 3-4 days of culture. When seeded at 5×105 cells per well, cells can be incubated for up to 5 days. Cells can be passaged after 3-4 days of incubation.
Virus Prep
Stool samples obtained from CDC were incubated in a 37° C. water bath until just thawed and then distributed into 50 μl aliquots and stored at −80° C. One aliquot was removed and used to titer the virus stocks.
Experimental Design
BJABs: Cells from multiple culture wells were combined into a 50 ml conical tube. The tube was gently mixed and the cell concentration determined. Wells of a 12-well plate were then seeded with 2.5×105 cells. The culture was then brought up to a final volume of 1300 μl using RMPI (10% FBS). Alternatively, wells of a 48-well plate can be seeded with 6.45×104 cells per well and the culture volume brought up to 1000 μl using RMPI. Cultures used had been passaged no fewer than 3 days prior to the start of the experiments.
Virus: An aliquot (50 μl) of virus was removed from −80° C. storage and incubated in a water bath until just thawed. The virus was then placed on ice and 450 μl of RPMI (10% FBS) was added to the vial. Virus was seeded into wells at a concentration of 1×105-1×106 genome copies per well. Plates were incubated at 37° C. At 1 hr, 3 and 5 days post infection, cells from one well were harvested and distributed into microcentrifuge tubes in 2-500 μl and 1-300 μl aliquots. Aliquots were stored at −80° C.
Alternatively, cells can be infected in a 1.5 mL microcentrifuge tube seeded 6.45×104 BJAB cells per reaction. In this infection technique, frozen stool is removed from −80° C. storage, thawed and diluted 1:10 in 10% RPMI. 1×105-1×106 genome copies of virus per reaction is added to the BJAB cells. The mixture is incubated for 2 hrs and then centrifuged at 730 rcf (730 g) for 7.5 min and the supernatent removed. The pellet is resuspended in 50-100 μl of RPMI per reaction and distributed among an appropriate number of wells. The total volume of each well is brought up to 1000 μl.
RNA extraction: Sample aliquots (500 μl) were removed from −80° C. and thawed in a 37° C. water bath. Once thawed, samples were returned to −80° C. This process was repeated 1 more time (for a total of 3 freeze/thaw cycles).
After the final thaw, 1 ml of Trizol was added to the culture and incubated at room temperature for 5 min. Then 200 μl of chloroform was added and the sample was vortexed and incubated at room temperature for 3 min. Samples were then centrifuged at 12,000× g for 15 min. The aqueous phase was put into a fresh tube and 10μg of glycerol was added to each sample. After mixing, 500 μl of isopropanol was added and then the samples were incubated at room temperature for 10 min at 4° C. at 12,000× g. The sample was centrifuged again for 10 min (at 4° C.). Isopropanol was removed and pellet was washed with 75% ethanol. Samples were centrifuged again for 5 min at 7,500× g. Ethanol was removed and pellet allowed to air dry for 5-10 min. The pellet was then re-suspended in 30 μl of pre-warmed (70° C.) RNase/DNase free water.
cDNA amplification: The Superscript kit (Invitrogen # 11752-050) was used per the manufacturer's instructions. 500 ng of RNA was added to the sample reactions.
qPCR: Sybr green (Fisher Scientific # FERK0243) was used according to the manufacturer's instructions. Primers NK2PF (5′-ATGTTYAGRTGGATGAGATTCTC) (SEQ ID NO: 3) and NK2PR (5′-TCGACGCCATCTTCATTCAC) (SEQ ID NO: 4) were used to amplify GII viruses at a final concentration of 200 nM each. Primers used for GI viruses were NK1PF (5′-GCYATGTTCCGYTGGATG) (SEQ ID NO: 5) and NK1PR (5′-GTCCTTAGACGCCATCATCAT) (SEQ ID NO: 6) at the concentrations mentioned above. 2 μl of undiluted cDNA was added to each sample well and each sample was run in triplicate. Samples were amplified on a Biorad iCycler under the following cycling conditions: 95° C. for 10 min followed by 41 cycles of 95° C. for 15 s, 58° C. for 30 s, and 72° C. for 30 s. Melt curve was generated at 65° C. for 10 s for 61 cycles.
As an alternative, a one step RT-qPCR using the AgPath One-Step RT-PCR Kit (Ambion) can be used. In this alternative technique, a master mix can be set up and the reaction performed according to the manufacture's instructions (adding 150 ng of RNA per PCR well). The following primers and probes can be use with the following cycling program:
Cycling program:
10 min at 42° C. (RT step)
10 min at 95° C.
45 cycles of:
Collect fluorescence data during the “60 s at 60° C.” step.
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The present application claims the benefit of U.S. Provisional Application Ser. No. 61/992,040, filed May 12, 2014, which is hereby incorporated by reference herein in its entirety, including any figures, tables, or drawings.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US15/30361 | 5/12/2015 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 61992040 | May 2014 | US |
