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SARS-CoV-2 SNV Genotyping Test Technology |
WANG Tao-xue1,2,3,LIU Qian1,2,3,QI Hao1,2,3,*() |
1. School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China 2. Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China 3. Collaborative Innovation Center of Chemical Science and Engineering, Syn Bio Research Platform, Tianjin University, Tianjin 300072, China |
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Abstract The global pandemic of the COVID-19 has had a major impact on the entire human society, and human beings are facing challenges such as fiscal stimulus, financial stress, and debt restructuring. Before the emergence of specific therapeutic drugs and methods, large-scale population screening and isolation has become the most effective method for epidemic management. However, the new strain of coronavirus this time has shown a very high genetic variability, with a statistical mutation rate of more than 2.3‰ as of March 31st, 2022. So far, new highly infectious virus strains have been emerging, and the number of mutant strains officially warned by the World Health Organization has reached 7. Therefore, in the next virus prevention and control and research, we not only need to detect SARS-CoV-2, but also need to explore accurate and practical single nucleotide variation (SNV) genotyping techniques, especially for large-scale population screening. It is not only necessary to obtain information on the SRAS-CoV-2, but also to accurately and quickly distinguish variant strains with higher infectivity and virulence. This paper briefly introduces the infection and mutation mechanism of the virus, and focuses on the classification and review of the existing main SARS-CoV-2 SNV genotyping techniques, hoping to provide insight into the development of new detection technologies.
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Received: 21 April 2022
Published: 07 September 2022
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Corresponding Authors:
Hao QI
E-mail: haoq@tju.edu.cn
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[1] |
Li B S, Deng A P, Li K B, et al. Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant. Nature Communications, 2022, 13: 460.
doi: 10.1038/s41467-022-28089-y
|
|
|
[2] |
Boni M F, Lemey P, Jiang X W, et al. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nature Microbiology, 2020, 5(11): 1408-1417.
doi: 10.1038/s41564-020-0771-4
|
|
|
[3] |
Hou W. Characterization of codon usage pattern in SARS-CoV-2. Virology Journal, 2020, 17(1): 138.
doi: 10.1186/s12985-020-01395-x
|
|
|
[4] |
Wu C R, Liu Y, Yang Y Y, et al. Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceutica Sinica B, 2020, 10(5): 766-788.
doi: 10.1016/j.apsb.2020.02.008
|
|
|
[5] |
Sanjuán R, Domingo-Calap P. Mechanisms of viral mutation. Cellular and Molecular Life Sciences, 2016, 73(23): 4433-4448.
pmid: 27392606
|
|
|
[6] |
Sevajol M, Subissi L, Decroly E, et al. Insights into RNA synthesis, capping, and proofreading mechanisms of SARS-coronavirus. Virus Research, 2014, 194: 90-99.
doi: 10.1016/j.virusres.2014.10.008
pmid: 25451065
|
|
|
[7] |
Smith E C, Denison M R. Coronaviruses as DNA wannabes: a new model for the regulation of RNA virus replication fidelity. PLoS Pathogens, 2013, 9(12): e1003760.
doi: 10.1371/journal.ppat.1003760
|
|
|
[8] |
Song H D, Tu C C, Zhang G W, et al. Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102(7): 2430-2435.
|
|
|
[9] |
Su Y C F, Bahl J, Joseph U, et al. Phylodynamics of H1N1/2009 influenza reveals the transition from host adaptation to immune-driven selection. Nature Communications, 2015, 6: 7952.
doi: 10.1038/ncomms8952
|
|
|
[10] |
Kirchdoerfer R N, Ward A B. Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors. Nature Communications, 2019, 10: 2342.
doi: 10.1038/s41467-019-10280-3
pmid: 31138817
|
|
|
[11] |
Korber B, Fischer W M, Gnanakaran S, et al. Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell, 2020, 182(4): 812-827.e19.
doi: S0092-8674(20)30820-5
pmid: 32697968
|
|
|
[12] |
Meng B, Kemp S A, Papa G, et al. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Cell Reports, 2021, 35(13): 109292.
doi: 10.1016/j.celrep.2021.109292
|
|
|
[13] |
Calistri P, Amato L, Puglia I, et al. Infection sustained by lineage B.1.1.7 of SARS-CoV-2 is characterised by longer persistence and higher viral RNA loads in nasopharyngeal swabs. International Journal of Infectious Diseases: Official Publication of the International Society for Infectious Diseases, 2021, 105: 753-755.
|
|
|
[14] |
Davies N G, Abbott S, Barnard R C, et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science, 2021, 372(6538): eabg3055.
doi: 10.1126/science.abg3055
|
|
|
[15] |
Collier D A, de Marco A, Ferreira I A T M, et al. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature, 2021, 593(7857): 136-141.
doi: 10.1038/s41586-021-03412-7
|
|
|
[16] |
Moustafa A M, Bianco C, Denu L, et al. Comparative analysis of emerging B.1.1.7+E484K SARS-CoV-2 isolates. Open Forum Infectious Diseases, 2021, 8(7): ofab300.
doi: 10.1093/ofid/ofab300
|
|
|
[17] |
Garcia-Beltran W F, Lam E C, St Denis K, et al. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell, 2021, 184(9): 2372-2383.e9.
doi: 10.1016/j.cell.2021.03.013
pmid: 33743213
|
|
|
[18] |
Faria N R, Mellan T A, Whittaker C, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science, 2021, 372(6544): 815-821.
doi: 10.1126/science.abh2644
pmid: 33853970
|
|
|
[19] |
Radvak P, Kwon H J, Kosikova M, et al. SARS-CoV-2 B.1.1.7 (alpha) and B.1.351 (beta) variants induce pathogenic patterns in K18-hACE2 transgenic mice distinct from early strains. Nature Communications, 2021, 12(1): 6559.
doi: 10.1038/s41467-021-26803-w
pmid: 34772941
|
|
|
[20] |
Greaney A J, Loes A N, Crawford K H D, et al. Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host & Microbe, 2021, 29(3): 463-476.e6.
|
|
|
[21] |
Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Global Challenges, 2017, 1(1): 33-46.
doi: 10.1002/gch2.1018
|
|
|
[22] |
McMahan K, Giffin V, Tostanoski L H, et al. Reduced pathogenicity of the SARS-CoV-2 Omicron variant in hamsters. Med, 2022, 3(4): 262-268.e4.
doi: 10.1016/j.medj.2022.03.004
|
|
|
[23] |
Chan M C. HKUMed finds Omicron SARS-CoV-2 can infect faster and better than Delta in human Bronchus but with less severe infection in lung. Brazilian Journal of Implantology and Health Sciences, 2022, 4(1): 50-54.
doi: 10.36557/2674-8169.2022v4n1p50-54
|
|
|
[24] |
Gazali F M, Nuhamunada M, Nabilla R, et al. Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. Heliyon, 2021, 7(9): e07936.
doi: 10.1016/j.heliyon.2021.e07936
|
|
|
[25] |
Aoki A, Mori Y, Okamoto Y, et al. Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. Journal of Infection and Chemotherapy: Official Journal of the Japan Society of Chemotherapy, 2021, 27(9): 1336-1341.
doi: 10.1016/j.jiac.2021.06.007
|
|
|
[26] |
Diaz-Garcia H, Guzmán-Ortiz A L, Angeles-Floriano T, et al. Genotyping of the major SARS-CoV-2 clade by short-amplicon high-resolution melting (SA-HRM) analysis. Genes, 2021, 12(4): 531.
doi: 10.3390/genes12040531
|
|
|
[27] |
Zhao Y N, Lee A N, Composto K, et al. A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. Emerging Microbes & Infections, 2021, 10(1): 994-997.
|
|
|
[28] |
Sitjar J, Liao J D, Lee H, et al. Challenges of SERS technology as a non-nucleic acid or-antigen detection method for SARS-CoV-2 virus and its variants. Biosensors & Bioelectronics, 2021, 181: 113153.
doi: 10.1016/j.bios.2021.113153
|
|
|
[29] |
Zavyalova E, Ambartsumyan O, Zhdanov G, et al. SERS-based aptasensor for rapid quantitative detection of SARS-CoV-2. Nanomaterials (Basel, Switzerland), 2021, 11(6): 1394.
|
|
|
[30] |
Awada C, Abdullah M M B, Traboulsi H, et al. SARS-CoV-2 receptor binding domain as a stable-potential target for SARS-CoV-2 detection by surface-enhanced Raman spectroscopy. Sensors (Basel, Switzerland), 2021, 21(13): 4617.
doi: 10.3390/s21134617
|
|
|
[31] |
Kowalczyk A, Krajczewski J, Kowalik A, et al. New strategy for the gene mutation identification using surface enhanced Raman spectroscopy (SERS). Biosensors and Bioelectronics, 2019, 132: 326-332.
doi: S0956-5663(19)30222-2
pmid: 30897539
|
|
|
[32] |
Hernandez M M, Banu R, Gonzalez-Reiche A S, et al. Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach. Journal of Medical Virology, 2022, 94(4): 1606-1616.
doi: 10.1002/jmv.27510
|
|
|
[33] |
Stelzl E, Kessler H H, Mustafa H G, et al. Alternative detection of SARS-CoV-2 RNA by a new assay based on mass spectrometry. Clinical Chemistry and Laboratory Medicine, 2021, 59(12): 1998-2002.
doi: 10.1515/cclm-2021-0483
|
|
|
[34] |
World Health Organization/Europe. Methods for the detection and characterisation of SARS-CoV-2 variants: first update.[2021-12-20]. WHO/EURO:2021-2148-41903-62832.
|
|
|
[35] |
Suzuki O, Dong O M, Howard R M, et al. Characterizing the pharmacogenome using molecular inversion probes for targeted next-generation sequencing. Pharmacogenomics, 2019, 20(14): 1005-1020.
doi: 10.2217/pgs-2019-0057
pmid: 31559919
|
|
|
[36] |
Lu R J, Zhao X, Li J, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet (London, England), 2020, 395(10224): 565-574.
doi: 10.1016/S0140-6736(20)30251-8
|
|
|
[37] |
Borkakoty B, Bali N K. TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. Indian Journal of Medical Microbiology, 2021, 39(1): 73-80.
doi: 10.1016/j.ijmmb.2021.01.003
|
|
|
[38] |
Sandoval Torrientes M, Castelló Abietar C, Boga Riveiro J, et al. A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. Journal of Virological Methods, 2021, 294: 114143.
doi: 10.1016/j.jviromet.2021.114143
|
|
|
[39] |
Perchetti G A, Zhu H Y, Mills M G, et al. Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. Journal of Medical Virology, 2021, 93(10): 5931-5941.
doi: 10.1002/jmv.27155
pmid: 34170525
|
|
|
[40] |
Iijima T, Ando S, Kanamori D, et al. Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). PLoS One, 2022, 17(3): e0265748.
doi: 10.1371/journal.pone.0265748
|
|
|
[41] |
Liang Y H, Lin H Q, Zou L R, et al. CRISPR-Cas12a-based detection for the major SARS-CoV-2 variants of concern. Microbiology Spectrum, 2021, 9(3): e0101721.
doi: 10.1128/Spectrum.01017-21
|
|
|
[42] |
Stanley K K, Szewczuk E. Multiplexed tandem PCR: gene profiling from small amounts of RNA using SYBR Green detection. Nucleic Acids Research, 2005, 33(20): e180.
doi: 10.1093/nar/gni182
pmid: 16314310
|
|
|
[43] |
Corman V M, Landt O, Kaiser M, et al. Detection of 2019 novel coronavirus(2019-nCoV) by real-time RT-PCR. Eurosurveillance, 2020, 25(3):23-30.
|
|
|
[44] |
Nörz D, Grunwald M, Olearo F, et al. Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. Journal of Clinical Virology, 2021, 141: 104894.
doi: 10.1016/j.jcv.2021.104894
|
|
|
[45] |
Neopane P, Nypaver J, Shrestha R, et al. SARS-CoV-2 variants detection using TaqMan SARS-CoV-2 mutation panel molecular genotyping assays. Infection and Drug Resistance, 2021, 14: 4471-4479.
doi: 10.2147/IDR.S335583
pmid: 34737587
|
|
|
[46] |
Suo T, Liu X J, Feng J P, et al. ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens. Emerging Microbes & Infections, 2020, 9(1): 1259-1268.
|
|
|
[47] |
Craw P, Balachandran W. Isothermal nucleic acid amplification technologies for point-of-care diagnostics: a critical review. Lab on a Chip, 2012, 12(14): 2469-2486.
doi: 10.1039/c2lc40100b
|
|
|
[48] |
Li Y, Li S Y, Wang J, et al. CRISPR/cas systems towards next-generation biosensing. Trends in Biotechnology, 2019, 37(7): 730-743.
doi: 10.1016/j.tibtech.2018.12.005
|
|
|
[49] |
Kellner M J, Koob J G, Gootenberg J S, et al. SHERLOCK: nucleic acid detection with CRISPR nucleases. Nature Protocols, 2019, 14(10): 2986-3012.
doi: 10.1038/s41596-019-0210-2
pmid: 31548639
|
|
|
[50] |
Ding X, Yin K, Li Z, et al. All-in-one dual CRISPR-Cas12a (AIOD-CRISPR) assay: a case for rapid, ultrasensitive and visual detection of novel coronavirus SARS-CoV-2 and HIV virus. BioRxiv: the Preprint Server for Biology, 2020.DOI: 10.1101/2020.03.19.998724.
doi: 10.1101/2020.03.19.998724
|
|
|
[51] |
Azhar M, Phutela R, Kumar M, et al. Rapid and accurate nucleobase detection using FnCas9 and its application in COVID-19 diagnosis. Biosensors and Bioelectronics, 2021, 183: 113207.
doi: 10.1016/j.bios.2021.113207
|
|
|
[52] |
Guo L, Sun X H, Wang X G, et al. SARS-CoV-2 detection with CRISPR diagnostics. Cell Discovery, 2020, 6: 34.
doi: 10.1038/s41421-020-0174-y
pmid: 32435508
|
|
|
[53] |
Broughton J P, Deng X D, Yu G X, et al. CRISPR-Cas12-based detection of SARS-CoV-2. Nature Biotechnology, 2020, 38(7): 870-874.
doi: 10.1038/s41587-020-0513-4
pmid: 32300245
|
|
|
[54] |
Ponce-Rojas J C, Costello M S, Proctor D A, et al. A fast and accessible method for the isolation of RNA, DNA, and protein to facilitate the detection of SARS-CoV-2. Journal of Clinical Microbiology, 2021, 59(4): e02403-e02420.
|
|
|
[55] |
Wang Y X, Xue T, Wang M J, et al. CRISPR-Cas13a cascade-based viral RNA assay for detecting SARS-CoV-2 and its mutations in clinical samples. Sensors and Actuators B, Chemical, 2022, 362: 131765.
doi: 10.1016/j.snb.2022.131765
|
|
|
[56] |
Wang Y X, Zhang Y, Chen J B, et al. Detection of SARS-CoV-2 and its mutated variants via CRISPR-Cas13-based transcription amplification. Analytical Chemistry, 2021, 93(7): 3393-3402.
doi: 10.1021/acs.analchem.0c04303
|
|
|
[57] |
Hale R, Crowley P, Dervisevic S, et al. Development of a multiplex tandem PCR (MT-PCR) assay for the detection of emerging SARS-CoV-2 variants. Viruses, 2021, 13(10): 2028.
doi: 10.3390/v13102028
|
|
|
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