PROTECTION METHOD, PROTECTION SEQUENCE, COMPOSITION AND KIT FOR PREVENTING RNA DEGREADATION, AND USE THEREOF

TECHNICAL FIELD

The present invention relates to the technical field of in vitro nucleic acid detection, in particular to a protection method, protection sequence, composition and kit for preventing RNA degradation, and applications thereof.

REFERENCE TO AN ELECTRONIC SEQUENCE LISTING

The contents of the electronic sequence listing (Name: 2022 PROTECTION METHOD, PROTECTION SEQUENCE, COMPOSITION AND KIT FOR PREVENTING RNA DEGRADATION, AND USE THEREOF; Sequence Listing XML; Date of Creation: Dec. 27, 2022; Size: 8,000 bytes) is herein incorporated by reference in its entirety.

BACKGROUND OF THE INVENTION

Ribonucleic acid (RNA), a genetic information carrier present in biological cells and some viruses and viroids, has only single strands, is unstable, and is easily degraded by RNase. RNase is very active, and abundant in nature. In order to prevent the degradation of RNA by RNase and improve the yield of target RNA during experiments or tests, it is of great significance to research and develop various RNA extraction techniques and methods.

SUMMARY OF THE INVENTION

In order to solve the problems existing in the prior art, the present invention provides a protection method, protection sequence, composition and kit for preventing RNA degradation, and applications thereof, which further improve a protection effect on virus RNA.

The technical solutions employed in the present invention are summarized as follows: a protection method for preventing RNA degradation includes the following step: forming an RNA:DNA complex by efficient binding of a RNase protection sequence (RNase-AP) to target RNA, wherein such binding reduces an exposure area of RNA, so that RNase cannot effectively cleave the target RNA and prevent RNA degradation.

A binding position of the RNase protection sequence (RNase-AP) to the target RNA is an RNase recognition site on the target RNA.

A protection method for preventing RNA degradation includes the following step: forming a complex by binding of a RNase protection sequence (RNase-AP) to RNase, wherein the complex affects the activity of RNase, inhibits the ability of binding the RNase to the target RNA, and prevents the target RNA from being degraded.

A binding position of the RNase protection sequence (RNase-AP) to the RNase is an RNase recognition site on the RNase.

A protection method for RNA degradation includes the following step: binding a RNase protection sequence (RNase-AP) to target RNA to cause local structure changes in the target RNA, such that the efficiency of binding the RNase to the target RNA is reduced or the binding position is changed, and RNase cannot cleave and degrade the target RNA, preventing the target RNA from being degraded.

A binding position of the RNase protection sequence (RNase-AP) to the target RNA is an RNase recognition site on the target RNA.

An RNase protection sequence uses a sequence of a RNase recognition site as the RNase protection sequence.

An RNase protection sequence is applied in the preparation of a virus detection reagent.

A virus detection composition includes the RNase protection sequence.

A virus detection kit includes the virus detection reagent.

The present invention has the following beneficial effect: the present invention provides a protection method, protection sequence, composition and kit for preventing RNA degradation, and applications thereof, which further improve a protection effect on virus RNA. After the definite addition of the RNase AP protection sequence, a three-dimensional structure of the target protected RNA and the structural allosteric characteristics of RNA can achieve a better protection effect on RNA integrity, and a high detection rate can be obtained by one-time amplification, ensuring efficient enrichment of virus RNA and providing guarantee for subsequent reverse transcription and PCR amplification.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the fluorescence quantitative detection of plasmid cDNA at different concentrations, with a minimum detection copy number of 1 ag (15 copies)/μl.

FIG. 2 shows the repeatability detected by virus cDNA: RT-PCR (15 copies/ml), with 10 replicates of 1 ag plasmid cDNA and 10 replicates of negative control, without any false positive in 50 cycles of Q-PCR amplification.

FIG. 3 shows that a minimum detection copy number of a virus RNA standard during RT-PCR detection is 80 copies/ml.

FIG. 4 shows that a minimum detection copy number of a simulated sample of saliva added with the virus RNA standard is 80 copies/ml.

FIG. 5 shows the comparison of a detection effect of a commercial kit A and a detection effect of a commercial kit B as virus RNA standards in saliva samples.

FIG. 6 shows that common bacteria have no interference effect on the detection of COVID-19 virus RNA.

FIG. 7 shows that the CT value of ORF gene detected by an extracting solution of “Wenzhou Medical University” is lower than that of an extracting solution of the commercial extraction kit A.

FIG. 8 is a schematic diagram of a secondary structure of a 500 nt fragment of N gene before and after AP binding.

FIG. 9 is a schematic diagram of a secondary structure of a 500 nt fragment of ORFlab gene before and after AP binding.

DETAILED DESCRIPTION OF THE INVENTION

The experimental methods used in the following examples are conventional methods unless otherwise specified.

The SARS-CoV-2 novel coronavirus is now used, and the effect is further verified by the protection method against RNA degradation described in the present invention:

(I) Effective Recognition of SARS-CoV-2 Virus and Protection Effect and Mechanism of Novel Sample Treatment Solution on Virus RNA.

Primer sequences of new RNA protection sites are designed for a target gene of the novel coronavirus.

In addition, a composition ratio, a compound reagent concentration, a salt ion concentration, PH, etc. of various components for lysis/protection in a sample treatment solution are optimized, and a novel lysis solution reaction system is completed to further improve the protection effect of the lysis/protection solution on virus RNA. After the definite addition of an effective protection agent, a three-dimensional structure of a target protected virus RNA and the structural allosteric properties of the virus RNA are clarified, and the effective recognition of SARS-CoV-2 virus and the protection effect and mechanism of the sample treatment solution in this project kit on virus RNA are studied.

1. The composition ratio of the sample treatment solution is: 1 mmol/L 2-(N-morpholine) ethanesulfonic acid, 100 mmol/L NaCl, 100 mmol/L KCl, 10 mmol/L Tris-HCl, 5 mol/L guanidine hydrochloride, 1% Triton X-100, 0.1 mg/ml proteinase K, and 0.1 mg/ml kieselguhr, as well as 20 nM of a specially designed N gene protection sequence 1 (anchor primer, AP, protection sequence information is detailed in Part II, AP-WHN-1) and 20 nM of a specifically designed ORFlablab protection sequence (AP-WHORF1ab-1, protection sequence information is detailed in Part II).

2. Mechanism of action: first, AP binds to SARS-CoV-2 virus RNA to cause local structural changes in virus RNA, so that the efficiency of binding of RNase to virus RNA is reduced or the binding position is changed, and RNase cannot cleave and degrade virus RNA. Secondly, RNase-AP first binds efficiently to virus SARS-CoV-2 virus RNA to form a RNA: DNA complex, and such competitive binding reduces RNA exposure areas and prevents RNases from being effectively cleaved. Finally, RNase-AP may bind to RNAase to form a complex, and such binding competition inhibits the ability to bind to virus RNA and affects the RNase activity.

(II) Optimization on Specificity of Primers/Probes: The Specificity of the Kit is Improved, the False Positive Rate is Effectively Reduced, and the Detection Rate is Increased; and with Reference to the Structure of the Novel Coronavirus, Novel Specific Primers/Probes are Designed to Cope with Possible Mutations of the Current Virus.

By designing a probe with dual gene targets of ORFlablab and N genes against the SARS-CoV-2 virus and performing simultaneous detection, the specificity of the detection of targeted cancer RNA is achieved. The primer design to other regions of ORFlab is added to realize the detection of multiple genes and sites, and effectively increase the detection rate of the kit. Meanwhile, the homology of different types of coronaviruses is analyzed in detail, combined with the latest research results of the 2019 novel coronavirus in structural biology and bioinformatics, to cope with the possible mutations of the 2019 novel coronavirus against a new primer probe designed for its highly conserved region, thereby realizing the immediate update of the detection kit, and ensuring the detection accuracy.

Through bioinformatic analysis, we first designed specific protection sequences for N gene (gene coordinates 2889-2997, FIG. 9A) and ORFlablab gene (gene coordinates 28548-28763, FIG. 8A) of SARS-CoV-2, see AP-WHORF1ab-1 and AP-WHN-1 in Table 1.

TABLE 1

Detected

fragment
Protection

Gene
size
primer

Name
coordinates
(nt)
sequence

ORF1ablab
2889-2997
105
AP-WHORFlab-1:

gtcctcactgccg

tcttgttgaccaa

cagtttgttgact

N
28548-28763
215
AP-WHN-1:

cctcttctcgttc

ctcatcacgtagt

cgcaacagttcaa

1. Bioinformatic structure prediction of SARS-CoV-2 virus RNA after binding of RNA to RNase-AP (FIGS. 8B and 9B), and prediction study of binding of SARS-CoV-2 virus RNA to RNase (FIGS. 1C and 2C) are performed.

1) First, we call RPIseq random forest and support vector machine algorithms to evaluate the binding characteristics of the protection sequence to human RNase. By scoring the affinity of RNase RNASE1-7 and a core sequence of N gene (ORFlab gene), it is found that RNASE1, RNASE3, and RNASE7 have a strong binding probability to the core sequence of N gene (ORFlab gene), which may serve as their potential target. catRAPID is called to predict a possible binding position of RNASE1-7 to the core sequence of N gene (ORFlab gene), and it is found that the protection sequence position can interact with RNase.

Further, a minimum free energy prediction algorithm and RNAstructure are used to predict the RNA secondary structure before and after the binding of the protection sequence to the core sequence of N gene (ORFlab gene) of the virus, respectively. Further, a local alignment algorithm RNAsmc for the RNA secondary structure is used to compare the structural similarity. The results show that the core sequence of N gene (ORFlab gene) RNA before and after the binding to the protection sequence has a structural similarity score of 7.70 (on a scale of 1-10) for N gene and of 9.12 for ORFlab gene, which indicates that the protection sequence has a great influence on the overall structural state of the core sequence of N gene (ORFlab gene). To further validate the effect of primers on N gene (ORFlab gene), a PSMAliven structure alignment tool is used to quantify the effects of the binding region on the RNA structure of the core sequence of N gene (ORFlab gene) (FIGS. 8B and 9B). A PSMAlign result score of 0 indicates no change in structure, on the contrary, the higher the score, the more significant the difference. After calculation, the structural similarity of the core sequence RNA of N gene before and after the binding to the protection sequence is scored as 148 for N gene (18 for ORFlab gene), which indicates that the protection sequence has a great influence on the structure of N gene. In addition, this result is consistent with an evaluation result on RNAsmc, and the structural changes of the core sequence RNA of N gene (ORFlab gene) may cause abnormal molecular interaction.

2) RNAComposer is further used to predict a 3D structure of the core region of N gene (ORFlab gene), and HDOCK SERVER is used to predict an interaction region of RNase RNASE1-7 and the core sequence of N gene (ORFlab gene) (FIGS. 8C and 9C). The results show that the optimal interaction position of the core sequence of N gene (ORFlab gene) and RNase changes significantly after binding to the protection sequence, which further indicates that the structural changes of the core sequence RNA of N gene (ORFlab gene) may cause abnormal molecular interaction. The results show that RNase 1-7 has a strong probability of binding to the core region of N gene (ORFlab gene), can bind to N gene (ORFlab gene) at the protection sequence, and has a greater impact on the structure of N gene (ORFlab gene) after binding of the protection sequence to N gene (ORFlab gene). In addition, the optimal interaction position of the core sequence of N gene (ORFlab gene) and RNase changes significantly, which indicates that the structural changes of the core sequence RNA of N gene (ORFlab gene) may cause abnormal molecular interaction.

(III) SARS-CoV-2 Virus is Inactivated by Using the Sample Treatment Solution of the Kit, which is Developed into a Novel Virus RNA Preservation Solution by Studying the Components and Proportioning Process of the Sample Treatment Solution in the Kit; and its Biosafety of the Sample Treatment Solution in Clinical Testing is Investigated.

By improving the compatibility of the sample treatment solution of the kit with the kit, the virus is directly inactivated using a specific reagent, and the effects of its minimum and optimal concentrations on the detection sensitivity and specificity of the kit are investigated. The advantages and disadvantages between the sample treatment solution of this kit and the current RNA preservation solution, e.g., in terms of a preservation time, preservation conditions and preservation effects are compared and analyzed. It is proposed to use the sample treatment solution of this kit for the preservation of clinical pest specimens (viruses, bacteria, etc.), and its inactivation effect on the virus must be clarified. For the 2019 novel coronavirus, the virus inactivation effects are achieved by incubating at 60° C. for 5, 10, 20, and 30 minutes under different temperature conditions, thereby avoiding infection problems of detection personnel.

The sample treatment solution of this kit contains 5 mol/L guanidine hydrochloride, which can destroy the structure of a glycosylated coat protein of SARS-CoV-2 virus at room temperature and has an inactivation effect on SARS-CoV-2 virus. This kit has no degradation effect on standard RNA when standard RNA is incubated at 60° C. for 5, 10, 20, and 30 minutes. In addition, this kit has found in clinical tests that RNA of SARS-CoV-2 virus can still be extracted after 30 minutes of incubation at 60° C. In this way, this kit has a dual inactivation effect of guanidine salt and 60° C. warm bath (the Guidelines of the National Health Commission has specified that SARS-CoV-2 virus can be inactivated at 56° C. for 30 min).

By adding SARS-CoV-2 virus plasmid DNA and virus RNA standard to saliva, this kit has a minimum detection sensitivity of 15 copies/ml (cDNA) and 80 copies/ml (RNA standard; the clinical kit has a minimum detection sensitivity of −500 copies/ml at present) respectively, and has higher detection sensitivity.

The test results of this kit in 252 clinically confirmed COVID-19 positive cases show that the kit from Wenzhou Medical University has a better protection effect on RNA integrity under the action of AP of a single gene (N gene), and a high detection rate (80%) can be obtained by means of one-time amplification.

This kit detects the interference of common flora (including Streptococcus pneumoniae, Streptococcus pyogenes, Klebsiella pneumoniae, Candida albicans, Staphylococcus aureus, Haemophilus influenzae and Aspergillus fumigatus) on a detection system. It is found that common bacteria have no interference effect on the detection of SARS-CoV-2 virus RNA.

(4) The Protection Effect of Virus RNA is Improved and the Detection of Complex Samples is Achieved.

The sample treatment solution of this kit can be used to treat a variety of samples, increase the ability of the sample treatment solution to virus lysis and virus RNA release in complex samples, and improve the protection effect on virus RNA. Meanwhile, the adaptation conditions of this kit are optimized, the corresponding components in a washing solution are improved to effectively remove the interference of other components in complex samples, and the efficient enrichment of virus RNA is ensured to provide guarantee for subsequent reverse transcription and PCR amplification.

1. This kit can be used to treat a variety of SARS-CoV-2 samples, such as nasal swabs, pharyngeal swabs, sputum, urine, feces, conjunctival sac swabs and tears. It is founded in clinical testing:

Site 1
Site 2
Site 3

Total cases
57
115
75

Age
4-79 (52.74)
1-93 (44.90)
1-85 (39.74)

Sex
Male 31 (54.39%)
Male 58 (50.43%)
Male 38 (50.66%)

Female 26 (45.61%)
Female 57 (49.57%)
Female 37 (49.33%)

Specimen type
Sputum 37 (64.91%)
Sputum 38 (33.04%)
Nasal swabs 22 (29.33%)

Pharyngeal swab 10 (17.54%)
Pharyngeal swab 18 (15.65%)
Sputum 11 (14.67%)

Feces 7 (12.28%)
Feces 15 (13.04%)
Pharyngeal 41 (54.67%)

Nasal swab 3 (5.26%)
Sputum/pharyngeal 44 (38.26%)
unknown 1 (1.33%)

Detection rate
70.18%
80.87%
78.67%

Mean CT value
31.72
27.75
32.27

2. Treatment of special samples:

- 1) Feces: picking a small amount of sample and put it in the sample treatment solution, incubating at 60° C. for 30 minutes, centrifuging at 12000 rpm for 1 minute, and putting the supernatant onto the column for extraction. This kit can inactivate the virus on the one hand at this step; and effectively lyse the virus to release SARS-CoV-2 virus RNA on the other hand, and AP in the sample treatment solution immediately exerts its protection role.
- 2) Urine: first, centrifuging a collected clinical urine specimen, centrifuging at 12000 rpm for 2 minutes, taking 200-300 ul of urine from the lower layer, and adding 500 ul of sample treatment solution. This step will further concentrate epithelial cells in the urine and degrade all for sample treatment. This step is critical for handling abnormalities in small amount of samples.

(5) Primers and Probes of the Kit.

This kit sets a specific protection region for the protection sequence region, SARS-CoV-2.

N protection
cctcttctcgttcctcatc

sequence
acgtagtcgcaacagttca

a

WHN1-F2
5 to CAAGCCTCTTCTCG

TTCCT-3′

WHN1-R2
5′-GCAGCAGATTTCTTAG

TGACAG-3′

N-probe
5′-FAM-ATTCAACTCCAG

GCAGCAGTAG-BHQ1-3′

ORF1ab
gtcctcactgccgtcttgt

protection
tgaccaacagtttgttgac

sequence
t

WHO1-F2
5′-GCCACTTCTGCTGCTC

TTC-3′

WHO1-R2
5′-tgattgtcctcactgc

cgtc-3′

ORF1ab probe
5′-VIC-CAACCTGAAGAA

GAGCAAGAA-MGB-3′

Detection Steps:

- 1. Preparation before the experiment: it is necessary to ensure that experimental facilities are available, and the temperature of a metal bath and a water bath must be calibrated and verified.
- 2. Sample treatment

1. Sample treatment*
Treating the sample with a sample treatment solution

(about 800 μl) containing a sample at 60° C. for 10 min,

putting a supernatant onto a column, centrifuging at

12000 rpm for 30 s, and discarding effluent

2. Rinsing
Adding 60 μl of rinsing solution, centrifuging at 12000 rpm

for 30 s, and discarding effluent

Adding 400 μl of rinsing solution, centrifuging at 12000 rpm

for 45 s, discarding effluent, and then performing air

centrifugation for 2 min to remove residual ethanol

3. Elution**
Transferring the adsorption column to a new 1.5 ml

centrifuge tube, adding 45 μl of eluent, performing heat

preservation at 60° C. for 3 min, and centrifuging at 12000

rpm for 2 min.

4. Reverse transcription
Taking 8 μl of eluted sample solution after centrifugation,

adding 7 μl of NP reaction solution, and reacting at 42° C. for

10 min

5. PCR amplification
Adding 15 μl of PCR reaction solution and putting on the

machine

Negative control: ddH₂O;

Positive control: 3 μl (full-length plasmid of N gene);

Steps 4 and 5 are performed according to the above treatment procedures.

*Feces specimens need to be centrifuged at 12000 rpm for 1 min, and the supernatant is taken and incubated at 60° C. for 10 min for subsequent experiments.

**Eluant should be treated in a warm bath at 60° C. for 10-15 minutes before use.

- 3. PCR amplification

The following procedure is performed on a fluorescent quantitative PCR instrument: setting of cyclic parameters (please refer to instrument operating instructions for setting)

Number

Steps
Temperature
Time
of cycles

1
Pre-denaturating
95° C.
3
min
1

2
Denaturating
95° C.
10
s
45 cycles

Annealing
58° C.
35
s

In step 2, fluorescence detection is performed at 58° C. to determine whether fluorophore FAM and quenching group MGB exist, and ROX correction is not selected if there is no MGB option.

*The principle of threshold setting is that a threshold line exceeds a highest point of the negative control and is at the beginning of the exponential amplification period of the positive control.

Quality Control

The quality control procedure is to monitor the detection of negative control and positive control at the same time. The detection result is valid if the negative and positive control results comply with the cases specified by the interpretation of test results.

Interpretation of Test Results:

- Negative (−): no Ct value or Ct value≥45
- Positive (+): Ct value≤40.
- To be reviewed: 40<Ct value<45, and a positive result is determined if Ct value <45 after review again.

(1) Inactivation of Virus Samples

The high-precision novel coronavirus (SARS-Cov-2) detection kit is based on a development technology of a predecessor cancer early detection kit (RNA detection), and the biosafety risk of collected samples has been technically optimized and improved in the early stage; and on this basis, the compatibility of existing technologies in pharyngeal swabs, nasal secretions and feces has been studied. A reagent is used to treat the sample with guanidine salt, the virus is inactivated after the sample is incubated at 600° C. for 30 minutes, and the subsequent study will shorten the time to 10 minutes.

(2) Detection Stability of Kit

By effectively identifying multiple sites and forming complexes in RNA samples released by cleavage, a triple PCR or multiplex PCR method is used to simultaneously detect multiple gene fragments such as an open reading frame and N gene of coronavirus (SARS-Cov-2) to avoid the existence of false negative caused by virus mutation. The recognition of RNA sequences in multiple sites protects the RNA integrity, avoids RNA degradation problems caused by sample treatment, and solves the problem of false positive through the optimization of primers and probes, so that the system can determine positive detected at any gene locus of novel coronavirus as positive for initial screening. Multi-target genes are used for protection, and a plurality of gene sequences is detected while the mutation of the virus needs to be considered, thereby preventing missed detection caused by mutation.

Easy degradation of RNA: this kit has released RNA into the sample treatment solution at the same time as the sample acquisition, the sample treatment solution can protect the RNA integrity very effectively while efficiently identifying the released RNA sample at multiple sites and forming complexes, and effective RNA protection is also designed in subsequent detection operations and verified in multiple developed products.

Sensitivity and specificity of the kit: during sample treatment, the RNA sample has been specifically and effectively identified at multiple target gene loci to form a compound, which stably targets novel coronavirus RNA, and multi-target RNA amplification is achieved by selective reverse transcription and enrichment of specific RNA complex; the self-designed primers and probes are significantly superior to probe and primer sequences published by the National Center for Disease Control (bioinformatic analysis has found that no secondary structure such as a hairpin-like structure exists); and by designing primers and probes for dual gene targets of the ORFlab and N genes and detecting both sites at the same time, the sensitivity and specificity of the kit will be greatly improved.

The present invention has the following advantages.

- (1) A unique reaction system of innovative lysate and kit: the sample treatment solution can directly store collected virus samples, the sample treatment solution containing guanidine salt which can effectively and rapidly inactivate the virus. At the same time, self-designed materials may also be added to the sample treatment solution, a three-dimensional structure of the target protected RNA and the structural allosteric properties of RNA make the target gene specifically recognized and protected, thereby increasing the sensitivity and specificity of detection.
- (2) A unique reaction system of the kit: the combined use of the innovative lysate and reagent makes this detection kit have four characteristics: high sensitivity (100 times higher than Shanghai “ZJ Bio-Tech Co., Ltd. (Liferiver)”), high specificity, high speed (40-45 minutes from sample preparation to results) and dual direct inactivation of the virus to avoid infection of detection personnel.
- (3) Effective treatment of unique sample treatment solution for complex samples (feces and sputum): the sputum sample has been verified in the technology development, the treatment effect on the clinical sample is very satisfactory in the early stage of technology development, and a product, i.e., a lung cancer early detection kit (Guo Xie Zhu Zhun: 20173403247), has been developed using the reagent before optimization. We can apply the existing sample treatment method to clinical applications in samples such as feces.
- (4) Rapid sample preparation to detection (40 minutes): the kit currently developed by our team includes four detection steps: release, identification (5 min)—washing (1 min)—elution (2 min)—signal amplification (35 min). Results can be obtained within 45 minutes for pharyngeal swab samples. If used with an automatic nucleic acid extractor, this time can be shortened to 40 minutes.

Conclusion:

- (1) By adding COVID-19 virus plasmid DNA and virus RNA standard to saliva, this kit has a minimum detection sensitivity of 15 copies/ml (cDNA) and 80 copies/ml (RNA standard; the clinical kit has a minimum detection sensitivity of about 500 copies/ml at present) respectively.

(2) The detection results in clinical 252 COVID-19 positive cases show that the kit from Wenzhou Medical University has a better protection effect on RNA integrity (N gene locus), and a high detection rate (80%) can be obtained by means of one-time amplification.

- (i) Taizhou Enze Medical Center (57 cases) (CT values need to be re-statistically analyzed): the CT value of ORF gene detected by the extracting solution from “Wenzhou Medical University” is significantly lower than that of an extracting solution from “ZJ Bio-Tech Co., Ltd.”, and the detected CT value of ORF gene is decreased by an average of 2.27 cycles, indicating that the sensitivity is improved by about 10 times (p=0.0001 paired with t-test, n=33), while the sensitivities of N gene and E gene are also reduced (p=0.0074 and p=0.6894).
- (ii) Wenzhou CDC (59 cases): the CT values of N and E genes detected by extracting solution+amplification solution from “Wenzhou Medical University” are significantly lower than those of other clinical kits (decreased by 3.74 cycles for N gene, p=0.0001; decreased by 2.0 cycles for E gene, p=0.002, n=59);
- (ii) Zhejiang CDC (54 cases): the CT values of N and E genes detected by extracting solution+amplification solution from “Wenzhou Medical University” are significantly lower than those of other clinical kits (decreased by 3.79 cycles for N gene, p<0.0001; decreased by XX cycles for E gene, p=0.002, n=59);
- (iv) the 1^stAffiliated Hospital and 2nd Affiliated Hospital of Wenzhou Medical University (54 mild cases): these cases are detected out by extracting solution from “Wenzhou Medical University”+amplification solution from “ZJ Bio-Tech Co., Ltd.”, including 4 cases, accounting for 7.4% (4/54), which become positive again after turning negative;
- (v) the 1st Affiliated Hospital of Wenzhou Medical University (11 cases): the detection rate from urine is 36.36% (4/11);
- (vi) the positive rate of COVID-19 (N gene) detected by this kit at one time: 70.18% (40/57) in Taizhou; 80.87% (97/115) in Wenzhou CDC: N gene; and 78.67% (59/75) in Zhejiang CDC: N gene. The 2^ndAffiliated Hospital of Wenzhou Medical University: 54 cases of clinical mild/ordinary type (turning positive in convalescent phase): 4 cases, 7.4% (4/54).

(3) Therefore, this kit can treat various types of specimens, such as nasal/pharyngeal swabs, sputum, saliva, feces and urine, etc., and trace virus specimens that may exist such as tears and conjunctival sac swabs are being verified.

A detailed progress report is as follows:

- (1) Ethics: approved by the ethics committee of Eye Hospital of Wenzhou Medical University.
- (2) The COVID-19 pseudovirus cDNA/RNA test indicates that the kit from Wenzhou Medical University has a minimum detection copy number of about 15 copies/ml (for cDNA standard) and 80 copies/ml (for RNA standard), showing higher sensitivity than that of the current clinical kit, and can detect lower viral titers in patient samples and effectively reduce the false negative rate.
- 2.1. Minimum detection copy number for COVID-19 pseudoviral plasmid cDNA: pseudoviral plasmid cDNA (provided by Xiamen Zeesan Biotech Co., Ltd.) is added to the simulated sample of sputum/saliva, and after the entire lysis/extraction and RT-PCR reaction steps, it is obtained that the minimum copy number of plasmid cDNA of this kit is about 1 ag (15 copies)/μl (FIG. 1) (the current clinical kit has the minimum copy number of about 500 copies/ml).
- 2.2. Repeatability of minimum copy number in detection of COVID-19 pseudoviral plasmid cDNA: pseudoviral plasmid DNA having a minimum detection copy number of 15 copies/ml (10 replicate tubes) is added to the simulated sample of sputum/saliva, and after the entire lysis/extraction and RT-PCR reaction steps, this kit has good repeatability in the case of the minimum copy number (FIG. 2).
- 2.3. Verification of the minimum detection copy number in the RT-PCR reaction step with COVID-19 virus RNA standard: the novel coronavirus RNA standard (provided by National Institute of Metrology, China) is added to the simulated samples of the RT-PCR reaction system (FIG. 3) and saliva (FIG. 4), to verify that the minimum detection copy number of the RT-PCR reaction step is 80 copies/ml (about 500 copies/ml for the current clinical kit).
- 2.4. Parallel comparison studies have found that: 8380 copies/ul of novel coronavirus RNA standard (provided by National Institute of Metrology, China) is added to the simulated sample of sputum/saliva, the RT-PCR reaction steps of the kits from “Wenzhou Medical University” and “ZJ Bio-Tech Co., Ltd.” are compared, wherein the CT value detected in “Wenzhou Medical University” is 20, with high intensity of fluorescence signals; and the CT value detected in “ZJ Bio-Tech Co., Ltd.” is 26, with low intensity of fluorescence signals.
- 2.5. Common bacteria have no interference effect on the detection of COVID-19 virus RNA
- The extracting solution (from Wenzhou Medical University)+RT-PCR amplification system (from ZJ Bio-Tech Co., Ltd.) is applied to detect the interference effects of common flora (including Streptococcus pneumoniae, Streptococcus pyogenes, Klebsiella pneumoniae, Candida albicans, Staphylococcus aureus, Haemophilus influenzae and Aspergillus fumigatus) on the detection system. The experimental results (3 replicates of nucleic acid extracted from bacteria) show that the expected amplification appears in the strong positive and weak controls (red), while interfering bacteria show no amplification (green).

(3) Statistics of clinical COVID-19 patient sample collection:

Participating
Pharyngeal
Nasal
Sputum/
Tear/conjunctival

Feces/anal

In

units
swab
swab
saliva
sac swab
Urine
swab
Negative
total

1^stAffiliated
0
0

43
20
10
0
84

Hospital of

Wenzhou

Medical

University

2^ndAffiliated
6
0
0
11
0
0
70
86

Hospital of

Wenzhou

Medical

University

Taizhou Enze
10
3
37
0
0
7
0
57

Medical

Center

Wenzhou
44
18
38
0

15
0
58

Epidemic

Disease

Prevention

and Control

Center

Zhejiang
41
22
11
0
0
0
0

Epidemic

Disease

Prevention

and Control

Center

Eye Hospital
0

0
0
0
0
150
150

of Wenzhou

Medical

University

3.2. Study on the effects of lysis/protection solution from Wenzhou Medical University on stable protection of COVID-19 virus RNA

In order to detect that the innovative lysis/protection solution can specifically and effectively identify multiple COVID-19 target gene loci and form complexes to stably protect COVID-19 virus RNA, the cooperative unit (Taizhou Enze Hospital) compares the RNA extracted from the lysis/protection solutions from the “Wenzhou Medical University” and “ZJ Bio-Tech Co., Ltd.” kits in 33 positive specimens, and the nucleic acid detection kit from “ZJ Bio-Tech Co., Ltd.” is used for RT-PCR amplification detection. The results of clinical experiments show that:

- (1) The results of clinical experiments show that the positive rate of COVID-19N gene detection is 95%, the positive rate of E gene detection is 100%, and the positive rate of ORF/RDRP gene detection is 100%. This indicates that the kit has a better protection effect on RNA integrity (multiple gene loci) and enables the detection of multiple genes for one-time amplification to improve the detection rate and accuracy of the samples (Table 1).

Extraction

Inpatient/outpatient

Detection
Extraction and detection from
and detection

number
Gender
Age
Specimen type
results
ZJ
from WMU

50151329
Male
56
Sputum
Positive(+)
RDRP26.2932/E25.83/N26.29
RDRP

25.79/E

25.85/N 26.7

50151142
Male
75
Sputum
Positive(+)
RDRP35.21/34.45/34.91
RDRP

37.35/E 0/N

39.57

50151377
Female
67
Pharyngeal
Positive(+)
RDRP38.05/E37.48/39.02
RDRP

swab

35.74/E

37.03/N

34.96

50151088
Male
55
Feces
Positive(+)
RDRP37.68/E37.09/N38.70
RDRP

37.65/E

36.94/N 36.8

50151536
Female
77
Nasopharyngeal
Positive(+)
rdrp33.3/E35/N33.07
RDRP

swab

28.11/E

29.25/N

27.32

50151345
Male
64
Sputum
Positive(+)
rdrp32.9/E30.3/N38.6
RDRP

32.87/E

32.7/N 31.86

50151329
Male
56
Sputum
Positive(+)
RDRP30.38/E29.53/N30.21
RDRP

29.47/E

29.12/N

28.46

50151379
Male
55
Nasopharyngeal
Positive
RdRP38.97/E38.9/N37
RDRP 0/E

swab

39.71/N

37.71

50151118
Female
65
Nasopharyngeal
Positive
RdRP 35.25/E 35.21/N 33.51
RDRP

swab

35.15/E

34.33/N

33.95

50151406
Male
33
Sputum
Positive(+)
rdrp35.6/E34.6/N33.5
RDRP

31.58/E

32.11/N

30.69

50150887
Male
34
Sputum
Positive
RDRP33.9/E29.9/N 30.8
RDRP 32.81/E

32.58/N

32.3

50151409
Female
51
Sputum
To be
E36, N35.9
RDRP 0/E

reviewed

36.29/N

43.69

50150812
Male
50
Sputum
Positive(+)
rdrp37.4/E35.5/N35
RDRP

35.07/E

34.2/N 33.9

50151541
Female
48
Sputum
Positive(+)
rdrp36.99/E35.6/N35.6
RDRP 0/E

0/N 35.14

50151270
Female
44
Pharyngeal
Positive
RDRP 35.22/E31.68/N 32.97
RDRP

swab

35.15/E

32.35/N

31.75

50151536
Female
77
Sputum
Positive(+)
RDRP29.8/E28.0/E29.2
RDRP

21.43/E

22.17/N

23.09

50151307
Female
68
Sputum
To be
E37.9/N38.7
RDRP

reviewed

31.38/E

31.94/N

31.83

50150765
Female
56
Sputum
Positive(+)
RDRP35.6/E32.7/N33.3
RDRP

35.26/E

34.32/N 33.9

50151436
Female
30
Sputum
Positive(+)
RDRP37.46/E34.5/N36.36
RDRP

35.25/E

34.54/N

34.06

50150798
Male
43
Sputum
Positive(+)
rdrp36.34/E33.1/N33.03
RDRP

37.03/E

34.43/N

35.89

50151142
Male
75
Sputum
Positive(+)
RDRP38.66/E35.7/N37.5
RDRP

38.95/E

39.82/N

28.03

50151345
Male
64
Sputum
Positive(+)
rdrp34.91/E33.9/N32.53
RDRP

37.08/E

37.22/N

36.98

9000548489
Female
43
Pharyngeal
Negative
RdRP 41.7/E 36.56/N 36.9
RDRP

swab

35.91/E

35.84/N

36.04

50150798
Male
43
Pharyngeal
Positive
RdRP38.30/E 38.14/N 35.78
Non-standard

swab

curve

50151020
Female
26
Pharyngeal
Positive(+)
RdRP 38.79/E 37.07/N 37.71
RDRP

swab

33.87/E

34.02/N

34.27

50150887
Male
34
Pharyngeal
Positive(+)
RdRP 31.61/E 28.56/N 28.78
RDRP

swab

28.86/E

28.92/N

28.44

50151237
Male
70
Pharyngeal
Positive
RDRP38.01/E35.94/N35.38
RDRP

swab

33.6/E

35.07/N

34.09

50151166
Male
44
Pharyngeal
Positive
RdRP 32.53/E 31.16/N 35.41
RDRP

swab

33.74/E

33.65/N

33.64

50151065
Male
51
Sputum
Positive(+)
RDRP37.70/E37.12/N37.94
RDRP

29.08/E

28.45/N

28.47

50150954
Female
41
Pharyngeal
Positive
RdRP 33.77/E 32.98/N 39.01
RDRP

swab

32.3/E

32.56/N

32.68

50151017
Male
38
Pharyngeal
Positive
RdRP 39.91/E 39.93/N 38.21
Non-standard

swab

curve

50151406
Male
33
Faeces
Positive
RDRP33.12/E30.88/N32.29
RDRP

23.98/E

25.39/N

24.04

50151406
Male
33
Sputum
Positive
RDRP35.53/E32.72/N34.12
Non-standard

curve

(2) The CT values of three gene fragments (ORF, E and N) detected by the extracting solutions from “Wenzhou Medical University” and “ZJ Bio-Tech Co., Ltd.” are compared. The results show that the CT value of the ORF gene detected by the extracting solution from “Wenzhou Medical University” is significantly lower than that of the extracting solution from “ZJ Bio-Tech Co., Ltd.” (p=0.0067, N gene, p=0.057; E gene, p=0.761, paired with t-test, n=33, see FIG. 7), the CT value of the ORF gene is reduced by an average of 3 cycles, and the copy number of detected COVID-19RNA by pseudoviral standard curve conversion is increased by about 10 times.

3.4. Clinical compliance rate

- (vi) The positive rate of COVID-19 (N gene) detected by this kit at one time: 70.18% (40/57) in Taizhou; 80.87% (97/115) in Wenzhou CDC: N gene; and 78.67% (59/75) in Zhejiang CDC: N gene. The 1st Affiliated Hospital of Wenzhou Medical University: 54 cases of clinical mild/ordinary type (turning positive in convalescent phase): 4 cases, 7.4% (4/54).

3.5. The extracting solution from “Wenzhou Medical University” can treat a variety of complex COVID-19 patient samples:

Participating
Pharyngeal
Nasal

Tear/conjunctival

Feces/anal

In

units
swab
swab
Sputum/saliva
sac swab
Urine
swab
Negative
total

1^stAffiliated
0
0

43
20
10
0
84

Hospital of

Wenzhou

Medical

University

2^ndAffiliated
6
0
0
11
0
0
70
86

Hospital of

Wenzhou

Medical

University

Taizhou Enze
10
3
37
0
0
7
0
57

Medical

Center

Wenzhou
44
18
38
0

15
0
58

Epidemic

Disease

Prevention

and Control

Center

Zhejiang
41
22
11
0
0
0
0

Epidemic

Disease

Prevention

and Control

Center

Eye Hospital
0

0
0
0
0
150
150

of Wenzhou

Medical

University

3.6. COVID-19 Virus Inactivation and Safety

The sample treatment solution of this kit contains guanidine salt, which has an inactivation effect on the virus (which has been confirmed in existing reports). In addition, the sample treatment stage can achieve an effect of inactivation of the virus at 60° C. for 30 min. Virus inactivation can effectively reduce the exposure risk of detection personnel, protect the safety of operators, and reduce the risk of infection in testing laboratories.

3.7. Rapid Sample Preparation to Detection (40 Min):

This kit includes four detection steps: release, identification (5 min)—washing (1 min)—elution (2 min)—signal amplification (35 min). Results can be obtained within 45 minutes for pharyngeal swab samples. If used with an automatic nucleic acid extractor, this time can be shortened to 40 minutes.

3.8. Detection Sensitivity

By adding COVID-19 virus plasmid DNA and virus RNA standards, it is found in ex vivo experiments that this kit has the minimum detection sensitivities of 15 copies/ml (cDNA) and 80 copies/ml, respectively, with a low detection line. In addition, clinical detection in 1st Affiliated Hospital and 2nd Affiliated Hospital of Wenzhou Medical University has found that among 54 patients recovering from COVID-19, there are patients who are positive after turning negative clinically. Therefore, this kit has high detection sensitivity.

The materials, reagents, etc. used in the following examples unless otherwise specified, may be obtained commercially.

Notes to technical personnel: although the present invention has been described in accordance with the above specific examples, the inventive idea of the present invention is not limited to the present invention, and any modification using the idea of the present invention will be included in the protection scope of this patent.

The above is only preferred examples of the present invention, the protection scope of the present invention is not limited to the above examples, all technical solutions belonging to the ideas of the present invention are within the protection scope of the present invention. It should be noted that those of ordinary skill in the art may also make several improvements and modifications without departing from the principles of the present invention, which should be considered as the protection scope of the present invention.

PROTECTION METHOD, PROTECTION SEQUENCE, COMPOSITION AND KIT FOR PREVENTING RNA DEGREADATION, AND USE THEREOF

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