DEVELOPMENT OF A PROTOCOL FOR WHOLE GENOME SEQUENCING OF THE SARS-COV-2 VIRUS
DOI:
https://doi.org/10.26577/eb.2022.v92.i3.08Abstract
Whole-genome sequencing of the SARS-CoV-2 virus during the pandemic has become an essential part of the epidemiological control of the spread of coronavirus infection. This made it possible to get actual data of circulating genetic variants and mutational changes of SARS-CoV-2 during the pandemic. The obtained results provided an opportunity for researchers to collect additional data to evaluate the virulence, infectivity, and the likelihood of evading an immune response when using vaccines and therapeutic monoclonal antibodies. There are different technological approaches for whole-genome sequencing of SARS-CoV-2, but multiplex PCR amplification is used most often due to ease of implementation and cost-effectiveness. When performing research on viral genome sequencing, researchers need to optimize existing sequencing protocols with available reagents or develop new approaches. This study is devoted to the development of a protocol for whole-genome sequencing of the SARS-CoV-2 virus based on the use of RT-PCR amplification using 39 primer pairs in 3 reaction mixtures. The protocol made it possible to obtain 15 complete genome data of the SARS-CoV-2 and can probably be used for large-scale studies on viral genome sequencing.
References
Yang X, Yu Y, Xu J, Shu H, Xia JA, Liu H, et al. Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study // Lancet Resp Med. – 2020. – Vol. 8. - P. 475–81. doi: 10.1016/S2213-2600(20)30079-5
Li, Z., Guan, X., Mao, N., Luo, H., Qin, Y., He, N., & Gao, G. F. Antibody seroprevalence in the epicenter Wuhan, Hubei, and six selected provinces after containment of the first epidemic wave of COVID-19 in China // The Lancet Regional Health-Western Pacific. -2021. – Vol. 8. 100094.
of the International, C. S. G. The species Severe acute respiratory syndrome- related coronavirus: classifying 2019-nCoV and naming it SARS- CoV-2 // Nat. Microbiol. –2020. –Vol. 5. – P. 536-544.
Corman V. M., Muth D. Niemeyer D. Hosts and sources of endemic human coronaviruses // Adv. Virus Res. – 2018. – Vol. 100. – P. 163-188.
Annan A., Baldwin H.J., Corman V.M., Klose S.M., Owusu M., Nkrumah E.E., et al. Human betacoronavirus 2c EMC/2012-related viruses in bats, Ghana and Europe // Emerg. Infect. Dis. – 2013. – Vol. 19. – P. 456-459.
https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19---22-february-2022
Taubenberger, J.K., Kash, J.C. Influenza virus evolution, host adaptation, and pandemic formation // Cell Host Microbe. - 2010, – Vol. 7. - P. 440–451.
World Health Organization. Summary table of SARS cases by country, 1 November 2002-7 August 2003. Weekly Epidemiological Record // Relevé épidémiologique hebdomadaire. -2003. – Vol. 78(35). – P. 310-311.
Zaki A.M., van Boheemen S., Bestebroer T.M., Osterhaus A.D., Fouchier R.A. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia // N. Engl. J. Med. – 2012. – Vol. 367. – P. 1814-1820.
Reusken C.B., Haagmans B.L., Muller M.A., Gutierrez C., Godeke G.J., Meyer B., et al. Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study // Lancet Infect. Dis. – 2013. – Vol.13. –P. 859-866.
Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, et al. Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell 182: 812–827. e819. pmid:32697968
Zhang L, Jackson CB, Mou H, Ojha A, Peng H, et al. (2020) SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity // Nature communications. – 2020. – Vol.11. – P. 1–9.
Yurkovetskiy L, Wang X, Pascal KE, Tomkins-Tinch C, Nyalile TP, et al. Structural and functional analysis of the D614G SARS-CoV-2 spike protein variant // Cell . -2020. – Vol.183. –p. 739–751.
Lu R., Zhao X., Li J., et al., Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding // Lancet. – 2020. – Vol. 395. – P. 565-574.
Wan Y., Shang J., Graham R., et al. Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus // J. Virol. – 2020. – Vol. 94. doi: 10.1128/JVI.00127-20
de Groot R.J., Baker S.C., Baric R., Enjuanes L., Gorbalenya A.E., Holmes K.V., et al. Family Coronaviridae. Virus Taxonomy: Classification and Nomenclature of Viruses // Ninth Report of the International Committee on Taxonomy of Viruses. London. – 2012. – P. 806-828.
Wan Y., Shang J., Graham R., et al. Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus // J. Virol. – 2020. – Vol. 94(7). e00127-20.
Sun J., He W.T., Wang L., et al., COVID-19: epidemiology, evolution, and cross-disciplinary perspectives // Trends. Mol. Med. – 2020. – Vol. 26. – P. 483-495.
Neurath M.F. Covid-19 and immunomodulation in IBD // Gut. – 2020. – Vol. 69. – P. 1335–1342.
Masters P.S. The molecular biology of coronaviruses. advances in virus research // Academic Press. – 2006. – Vol. 66. – P. 193-292.
Manning, J. E., Bohl, J. A., Lay, S., Chea, S., Sovann, L., Sengdoeurn, Y., & Karlsson, E. A. Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia // Biorxiv. -2020. doi: 10.1101/2020.03.02.968818
Chrzastek, K., Tennakoon, C., Bialy, D., Freimanis, G., Flannery, J., & Shelton, H. A random priming amplification method for whole genome sequencing of SARS-CoV-2 and H1N1 influenza A virus // bioRxiv - 2021. doi: https://doi.org/10.1101/2021.06.25.449750
Itokawa, K., Sekizuka, T., Hashino, M., Tanaka, R., & Kuroda, M. A proposal of alternative primers for the ARTIC Network’s multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing // BioRxiv. - 2020. doi: https://doi.org/10.1101/2020.03.10.985150
Resende, P. C. et. al. SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms // BioRxiv. - 2020. doi: https://doi.org/10.1101/2020.04.30.069039
Mukanov K. K., Shevtsov A. B. Berdimuratova K. T, Amirgazin A. O, Kuibagarov М. А, Lutsay V. B. Optimization of PCR purification using silica-coated magnetic beads // Eurasian Journal of Applied Biotechnology. – 2020. – №. 1. – P. 81-89.
Andrews S. et al. FastQC: a quality control tool for high throughput sequence data. – 2010.
Ewels P. et al. MultiQC: summarize analysis results for multiple tools and samples in a single report //Bioinformatics. – 2016. – Т. 32. – №. 19. – C. 3047-3048.
Li H. Seqtk—Toolkit for Processing Sequences in FASTA/Q Formats; 2008.
Octavia, S., Ang, M. L., Van La, M., Zulaina, S., Saat, Z. A. A. S., Tien, W. S., Lin, R. T. Retrospective genome-wide comparisons of Salmonella enterica serovar Enteritidis from suspected outbreaks in Singapore // Infection, Genetics and Evolution. – 2018. – P. 229-233.
Quick, J., Loman, N. J., Duraffour, S., Simpson, J. T., Severi, E., Cowley, L., Carroll, M. W. Real-time, portable genome sequencing for Ebola surveillance // Nature. – 2016. – Vol. 530(7589). – P. 228-232.
Plante, J. A., Liu, Y., Liu, J., Xia, H., Johnson, B. A., Lokugamage, K. G., Shi, P. Y. Spike mutation D614G alters SARS-CoV-2 fitness // Nature. – 2021. – Vol. 592(7852). – P. 116-121.
Shastri, J., Parikh, S., Aggarwal, V., Agrawal, S., Chatterjee, N., Shah, R. & Pandey, R. Severe SARS-CoV-2 breakthrough reinfection with delta variant after recovery from breakthrough infection by alpha variant in a fully vaccinated health worker // Frontiers in Medicine. – 2021. – P. 1379.
Sekizuka T, Itokawa K, Kageyama T, Saito S, Takayama I, Asanuma H, Nao N, Tanaka R, Hashino M, Takahashi T, et al. Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak // Proc Natl Acad Sci USA. -2020. – Vol. 117. – P. 20198–20201.
