Detection of single nucleotide polymorphisms (SNPs) in a SARS-CoV-2 virus strain in Vietnam

Authors

  • Tran Xuan Thach Institute of Biotechnology, VAST, Vietnam
  • Bui Thi Thuy Duong Institute of Biotechnology, VAST, Vietnam https://orcid.org/0000-0003-1002-7517
  • Le Van Truong Institute of Biotechnology, VAST, Vietnam
  • Nguyen Thi Hoa Institute of Biotechnology, VAST, Vietnam
  • Pham Thi Lanh Institute of Biotechnology, VAST, Vietnam
  • Nguyen Thai Uy Institute of Biotechnology, VAST, Vietnam
  • Le Quynh Mai The National Institute of Hygiene and Epidemiology, Ha Noi, Vietnam
  • Dang Duc Anh
  • Dinh Duy Khang Institute of Biotechnology, VAST, Vietnam
  • Dong Van Quyen Institute of Biotechnology, VAST, Vietnam

DOI:

https://doi.org/10.15625/2615-9023/15846

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of a pandemic of acute respiratory disease in humans. This pandemic has now spread worldwide and caused more than 2,000,000 deaths by 15 January 2021. The complexity and the ongoing pandemic of coronavirus SARS-CoV-2 make it difficult to control the disease. Sequence analysis on some open reading frames (ORFs) of a SARS-CoV-2 virus strain isolated in Vietnam in February 2020 (SARS-CoV-2/NIHE/human/2020/VIE strain) revealed some single nucleotide polymorphisms (SNPs) that only appeared in the Vietnamese strain in comparison to those of the isolates in other countries, including: (1) a change in ORF8-Nucleocapsid (accession number MT127114.1) at nucleotide (nt) 691 (CTC in SARS-CoV-2/NIHE/human/2020/VIE strain, TTC in all other isolates) but it does not change the encoded amino acid, (2) ORF3a-EM-ORF6-ORF7a region (accession number MT127115.1) has four-point changes, three of which lead to changes in the amino acid sequences, being nt 479 (GTA encoding  Valine changed into TTA encoding Leucine), nt 575 (CGC encoding Arginine changed to GGC encoding Glycine) in the M gene, and nt 1126 (GTG encoding Valine changed to GAG encoding Glutamic acid) in ORF6. Taken together, the results provided useful information for the SARS-CoV-2 diagnostic kit and vaccine development.

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Author Biography

Tran Xuan Thach, Institute of Biotechnology, VAST, Vietnam

References

Aftab, S. O., Ghouri, M. Z., Masood, M. U., Haider, Z., Khan, Z., Ahmad, A., & Munawar, N., 2020. Analysis of SARS-CoV-2 RNA-dependent RNA polymerase as a potential therapeutic drug target using a computational approach. Journal of Translational Medicine, 18(1), 1−15.

Ahmed S. F., Quadeer A. A., McKay M. R., 2020. Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies. Viruses, 12(3): 254.

Alsaadi E. A., Jones I. M., 2019. Membrane binding proteins of coronaviruses. Future Virology, 14(4): 275−286.

Bonaccorsi R., Pullman A., Scrocco E., Tomasi J., 1972. The molecular electrostatic potentials for the nucleic acid bases: adenine, thymine, and cytosine. Theoretica Chimica Acta, 24(1): 51−60.

Caly L., Druce J. D., Catton M. G., Jans D. A., Wagstaff K. M., 2020. The FDA-approved drug ivermectin inhibits the replication of SARS-CoV-2 in vitro. Antiviral Research., https://doi.org/ 10.1016/j.antiviral.2020.104787

Chen L., Liu W., Zhang Q., Xu K., Ye G., Wu W., Liu Y., 2020. RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak. Emerging Microbes Infections, 9(1): 313−319.

Chu D. K., Pan Y., Cheng S. M., Hui K. P., Krishnan P., Liu Y., Poon L. L., 2020. Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia. Clinical Chemistry, 66(4): 549−555.

Corman V. M., Landt O., Kaiser M., Molenkamp R., Meijer A., Chu D. K., ..., Drosten C., 2020. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance., 25(3): 2000045.

Cui J., Li F., Shi Z. L., 2019. Origin and evolution of pathogenic coronaviruses. Nature Reviews Microbiology, 17(3): 181−192.

Elfiky A. A., 2020. SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: An in silico perspective. Journal of Biomolecular Structure and Dynamics. https://doi.org/ 10.1080/07391102. 2020.1761882

Enjuanes L., DeDiego M. L., Álvarez E., Deming D., Sheahan T., Baric R., 2008. Vaccines to prevent severe acute respiratory syndrome coronavirus-induced disease. Virus Research, 133(1): 45−62.

Fehr A. R., Perlman S., 2015. Coronaviruses: an overview of their replication and pathogenesis. Coronaviruses. https://doi.org/10.1007/978-1-4939-2438-7_1

Gao J., Lu G., Qi J., Li Y., Wu Y., Deng Y., Gao G. F., 2013. Structure of the fusion core and inhibition of fusion by a heptad repeat peptide derived from the S protein of Middle East respiratory syndrome coronavirus. Journal of Virology, 87(24): 13134−13140.

Gronau I., Moran S., 2007. Optimal implementations of UPGMA and other common clustering algorithms. Information Processing Letters, 104(6): 205−210.

Hillen, H. S., Kokic, G., Farnung, L., Dienemann, C., Tegunov, D., & Cramer, P., 2020. Structure of replicating SARS-CoV-2 polymerase. Nature, 584(7819): 154−156.

Maache M., Komurian F., Rajoharison A., Perret M., Berland J. L., Pouzol S., Paranhos G., 2006. False-positive results in a recombinant severe acute respiratory syndrome-associated coronavirus (SARS-CoV) nucleocapsid-based western blot assay were rectified by the use of two subunits (S1 and S2) of spike for detection of antibody to SARS-CoV. Clinical and Vaccine Immunology, 13(3): 409−414.

Masters P. S., 2006. The molecular biology of coronaviruses. Advances in Virus Research, 66: 193−292.

Miorin, L., Kehrer, T., Sanchez-Aparicio, M. T., Zhang, K., Cohen, P., Patel, R. S., ... & García-Sastre, A., 2020. SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling. Proceedings of the National Academy of Sciences, 117(45): 28344−28354.

Neuman B. W., Kiss G., Kunding A. H., Bhella D., Baksh M. F., Connelly S., Buchmeier, M. J., 2011. A structural analysis of M protein in coronavirus assembly and morphology. Journal of Structural Biology, 174(1): 11−22.

Pachetti M., Marini B., Benedetti F., Giudici F., Mauro E., Storici, P., Ippodrino R., 2020. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. Journal of Translational Medicine, 18: 1−9.

Plant E. P., Pérez G. C., Jacobs J. L., Mukhopadhyay B., Hennig M., Dinman J. D., 2005. A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal. PLoS Biol., 3(6): e172.

Sheikh A., Al-Taher A., Al-Nazawi M., Al-Mubarak A. I., Kandeel M., 2020. Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design. Journal of Virological Methods, 277: 113806. https://doi.org/ 10.1016/j.jviromet.2019.113806

Siddell S. G., Ziebuhr J., Snijder E. J., 2005. Coronaviruses, toroviruses, and arteriviruses Topley and Wilson's Microbiology and Microbial Infections., pp. 823−856.

Sohail M. S., Ahmed S. F., Quadeer A. A., McKay M., 2020. In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives. Available at SSRN., http://dx.doi.org/10.2139/ssrn.3720371

Tan Y. J., Lim S. G., Hong W., 2005. Characterization of viral proteins encoded by the SARS-coronavirus genome. Antiviral Research., 65(2): 69−78.

Thompson J. D., Higgins D. G., Gibson T. J., 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research., 22(22): 4673−4680.

Weiwei H., Qinghua Y., Liqi Z., Haofei L., Shanshan Z., Qi G., Qian Y., 2014. Complete genomic sequence of the coronavirus transmissible gastroenteritis virus SHXB isolated in China. Archives of Virology, 159(9): 2295−2302.

Yuen C. K., Lam J. Y., Wong W. M., Mak L. F., Wang X., Chu H., Kok K. H., 2020. SARS-CoV-2 nsp13, nsp14, nsp15 and orf6 function as potent interferon antagonists. Emerging Microbes Infections, 9(1): 1418−1428.

Zhao P., Cao J., Zhao L. J., Qin Z. L., Ke J. S., Pan W., Qi Z. T., 2005. Immune responses against SARS-coronavirus nucleocapsid protein induced by DNA vaccine. Virology, 331(1): 128−135.

Ziebuhr J., 2004. Molecular biology of severe acute respiratory syndrome coronavirus. Current Opinion in Microbiology, 7(4): 412−419.

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Published

30-06-2021

How to Cite

Thach, T. X., Duong, B. T. T., Truong, L. V., Hoa, N. T., Lanh, P. T., Uy, N. T., Mai, L. Q., Anh, D. D., Khang, D. D., & Quyen, D. V. (2021). Detection of single nucleotide polymorphisms (SNPs) in a SARS-CoV-2 virus strain in Vietnam. Academia Journal of Biology, 43(2), 95–105. https://doi.org/10.15625/2615-9023/15846

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