SARS-CoV-2 Genomic Characterization and Evolution in China

Overview

Journal Heliyon

Specialty Social Sciences

Date 2023 Aug 28

PMID 37636456

Authors

Peng Zhang

Dongzi Liu

Lei Ji

Fenfen Dong

Affiliations

Soon will be listed here.

Abstract

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) affected global health worldwide due to its high contagiousness. During the viral spread, many mutations occurred within the virus genome. China has adopted nonpharmaceutical intervention (NPI) to contain COVID-19 outbreaks. In order to understand the evolution and genomic variation of SARS-CoV-2 in China under this policy, a total of 524 sequences downloaded from Global Initiative on Sharing All Influenza Data (GISAID) between 2019 and 2022 were included in this study. The time-scaled evolutionary analysis showed that these sequences clustered in three groups (Group A-C). Group B and C accounted for the majority of the sequences whose divergence times were around 2020 and distributed in multiple regions. Group A was mainly composed of G variants, which were mainly isolated from several regions. Moreover, we found that 191 sites had mutations with no less than 3 times, including 30 amino acids that were deleted. Finally, we found that spike and nucleocapsid genes underwent positive selection evolution, indicating that the mutations within spike and nucleocapsid genes increased the SARS-CoV-2 contagiousness. Hence, this study preliminarily elucidates the evolutionary characteristics and genomic mutations of SARS-CoV-2 under the implementation of the NPI policy in China, providing scientific basis for further understanding the control effect of the NPI policy on the epidemic.

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References

Suchard M, Lemey P, Baele G, Ayres D, Drummond A, Rambaut A . Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 2018; 4(1):vey016. PMC: 6007674. DOI: 10.1093/ve/vey016. View

Ma J, Chen Y, Wu W, Chen Z . Structure and Function of N-Terminal Zinc Finger Domain of SARS-CoV-2 NSP2. Virol Sin. 2021; 36(5):1104-1112. PMC: 8365134. DOI: 10.1007/s12250-021-00431-6. View

Zou J, Kurhade C, Xia H, Liu M, Xie X, Ren P . Cross-neutralization of Omicron BA.1 against BA.2 and BA.3 SARS-CoV-2. Nat Commun. 2022; 13(1):2956. PMC: 9135681. DOI: 10.1038/s41467-022-30580-5. View

Dearlove B, Lewitus E, Bai H, Li Y, Reeves D, Joyce M . A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Proc Natl Acad Sci U S A. 2020; 117(38):23652-23662. PMC: 7519301. DOI: 10.1073/pnas.2008281117. View

Li Z, Chen Q, Feng L, Rodewald L, Xia Y, Yu H . Active case finding with case management: the key to tackling the COVID-19 pandemic. Lancet. 2020; 396(10243):63-70. PMC: 7272157. DOI: 10.1016/S0140-6736(20)31278-2. View

Delbue S, DAlessandro S, Signorini L, Dolci M, Pariani E, Bianchi M . Isolation of SARS-CoV-2 strains carrying a nucleotide mutation, leading to a stop codon in the ORF 6 protein. Emerg Microbes Infect. 2021; 10(1):252-255. PMC: 7894437. DOI: 10.1080/22221751.2021.1884003. View

Davies N, Jarvis C, Edmunds W, Jewell N, Diaz-Ordaz K, Keogh R . Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. Nature. 2021; 593(7858):270-274. PMC: 9170116. DOI: 10.1038/s41586-021-03426-1. View

Washington N, Gangavarapu K, Zeller M, Bolze A, Cirulli E, Schiabor Barrett K . Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. Cell. 2021; 184(10):2587-2594.e7. PMC: 8009040. DOI: 10.1016/j.cell.2021.03.052. View

Yurkovetskiy L, Wang X, Pascal K, Tomkins-Tinch C, Nyalile T, Wang Y . Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Cell. 2020; 183(3):739-751.e8. PMC: 7492024. DOI: 10.1016/j.cell.2020.09.032. View

10.

Benedetti F, Snyder G, Giovanetti M, Angeletti S, Gallo R, Ciccozzi M . Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1. J Transl Med. 2020; 18(1):329. PMC: 7457216. DOI: 10.1186/s12967-020-02507-5. View

11.

Wang Q, Zhang Y, Wu L, Niu S, Song C, Zhang Z . Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2. Cell. 2020; 181(4):894-904.e9. PMC: 7144619. DOI: 10.1016/j.cell.2020.03.045. View

12.

Cleemput S, Dumon W, Fonseca V, Karim W, Giovanetti M, Alcantara L . Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes. Bioinformatics. 2020; 36(11):3552-3555. PMC: 7112083. DOI: 10.1093/bioinformatics/btaa145. View

13.

Zhou P, Yang X, Wang X, Hu B, Zhang L, Zhang W . A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; 579(7798):270-273. PMC: 7095418. DOI: 10.1038/s41586-020-2012-7. View

14.

Obeid D, Alsanea M, Alnemari R, Al-Qahtani A, Althawadi S, Mutabagani M . SARS-CoV-2 genetic diversity and variants of concern in Saudi Arabia. J Infect Dev Ctries. 2022; 15(12):1782-1791. DOI: 10.3855/jidc.15350. View

15.

Lu S, Ye Q, Singh D, Cao Y, Diedrich J, Yates 3rd J . The SARS-CoV-2 nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein. Nat Commun. 2021; 12(1):502. PMC: 7820290. DOI: 10.1038/s41467-020-20768-y. View

16.

Plante J, Liu Y, Liu J, Xia H, Johnson B, Lokugamage K . Spike mutation D614G alters SARS-CoV-2 fitness. Nature. 2020; 592(7852):116-121. PMC: 8158177. DOI: 10.1038/s41586-020-2895-3. View

17.

Rambaut A, Drummond A, Xie D, Baele G, Suchard M . Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7. Syst Biol. 2018; 67(5):901-904. PMC: 6101584. DOI: 10.1093/sysbio/syy032. View

18.

Harvey W, Carabelli A, Jackson B, Gupta R, Thomson E, Harrison E . SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021; 19(7):409-424. PMC: 8167834. DOI: 10.1038/s41579-021-00573-0. View

19.

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

20.

Salzberger B, Buder F, Lampl B, Ehrenstein B, Hitzenbichler F, Holzmann T . Epidemiology of SARS-CoV-2. Infection. 2020; 49(2):233-239. PMC: 7543961. DOI: 10.1007/s15010-020-01531-3. View