Gene Presence/Absence Variation Analysis of Coronavirus Family Displays Its Pan-genomic Diversity

Overview

Journal Int J Biol Sci

Specialty Biology

Date 2021 Oct 21

PMID 34671195

Citations 2

Authors

Du Jiao

Xiaorui Dong

Yingyan Yu

Chaochun Wei

Affiliations

Soon will be listed here.

Abstract

SARS-CoV-2 belongs to the coronavirus family. Comparing genomic features of viral genomes of coronavirus family can improve our understanding about SARS-CoV-2. Here we present the first pan-genome analysis of 3,932 whole genomes of 101 species out of 4 genera from the coronavirus family. We found that a total of 181 genes in the pan-genome of coronavirus family, among which only 3 genes, the S gene, M gene and N gene, are highly conserved. We also constructed a pan-genome from 23,539 whole genomes of SARS-CoV-2. There are 13 genes in total in the SARS-CoV-2 pan-genome. All of the 13 genes are core genes for SARS-CoV-2. The pan-genome of coronaviruses shows a lower level of diversity than the pan-genomes of other RNA viruses, which contain no core gene. The three highly conserved genes in coronavirus family, which are also core genes in SARS-CoV-2 pan-genome, could be potential targets in developing nucleic acid diagnostic reagents with a decreased possibility of cross-reaction with other coronavirus species.

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References

Benvenuto D, Giovanetti M, Ciccozzi A, Spoto S, Angeletti S, Ciccozzi M . The 2019-new coronavirus epidemic: Evidence for virus evolution. J Med Virol. 2020; 92(4):455-459. PMC: 7166400. DOI: 10.1002/jmv.25688. View

Koonin E . Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet. 2005; 39:309-38. DOI: 10.1146/annurev.genet.39.073003.114725. View

Andersen K, Rambaut A, Lipkin W, Holmes E, Garry R . The proximal origin of SARS-CoV-2. Nat Med. 2020; 26(4):450-452. PMC: 7095063. DOI: 10.1038/s41591-020-0820-9. View

Vernikos G, Medini D, Riley D, Tettelin H . Ten years of pan-genome analyses. Curr Opin Microbiol. 2014; 23:148-54. DOI: 10.1016/j.mib.2014.11.016. View

Li Y, Zhou W, Yang L, You R . Physiological and pathological regulation of ACE2, the SARS-CoV-2 receptor. Pharmacol Res. 2020; 157:104833. PMC: 7194807. DOI: 10.1016/j.phrs.2020.104833. View

Tettelin H, Masignani V, Cieslewicz M, Donati C, Medini D, Ward N . Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A. 2005; 102(39):13950-5. PMC: 1216834. DOI: 10.1073/pnas.0506758102. View

Zhang T, Wu Q, Zhang Z . Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak. Curr Biol. 2020; 30(7):1346-1351.e2. PMC: 7156161. DOI: 10.1016/j.cub.2020.03.022. View

. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol. 2020; 5(4):536-544. PMC: 7095448. DOI: 10.1038/s41564-020-0695-z. View

Woo P, Lau S, Huang Y, Yuen K . Coronavirus diversity, phylogeny and interspecies jumping. Exp Biol Med (Maywood). 2009; 234(10):1117-27. DOI: 10.3181/0903-MR-94. View

10.

Ding W, Baumdicker F, Neher R . panX: pan-genome analysis and exploration. Nucleic Acids Res. 2017; 46(1):e5. PMC: 5758898. DOI: 10.1093/nar/gkx977. View

11.

McGinnis S, Madden T . BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 2004; 32(Web Server issue):W20-5. PMC: 441573. DOI: 10.1093/nar/gkh435. View

12.

Han Y, Du J, Su H, Zhang J, Zhu G, Zhang S . Identification of Diverse Bat Alphacoronaviruses and Betacoronaviruses in China Provides New Insights Into the Evolution and Origin of Coronavirus-Related Diseases. Front Microbiol. 2019; 10:1900. PMC: 6702311. DOI: 10.3389/fmicb.2019.01900. View

13.

Forni D, Cagliani R, Clerici M, Sironi M . Molecular Evolution of Human Coronavirus Genomes. Trends Microbiol. 2016; 25(1):35-48. PMC: 7111218. DOI: 10.1016/j.tim.2016.09.001. View

14.

Chan J, Yuan S, Kok K, To K, Chu H, Yang J . A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet. 2020; 395(10223):514-523. PMC: 7159286. DOI: 10.1016/S0140-6736(20)30154-9. View

15.

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

16.

Kumar S, Stecher G, Li M, Knyaz C, Tamura K . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018; 35(6):1547-1549. PMC: 5967553. DOI: 10.1093/molbev/msy096. View

17.

Liu P, Jiang J, Wan X, Hua Y, Li L, Zhou J . Correction: Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)?. PLoS Pathog. 2021; 17(6):e1009664. PMC: 8189448. DOI: 10.1371/journal.ppat.1009664. View

18.

Lu R, Zhao X, Li J, Niu P, Yang B, Wu H . Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020; 395(10224):565-574. PMC: 7159086. DOI: 10.1016/S0140-6736(20)30251-8. View

19.

So R, Chu D, Miguel E, Perera R, Oladipo J, Fassi-Fihri O . Diversity of Dromedary Camel Coronavirus HKU23 in African Camels Revealed Multiple Recombination Events among Closely Related Betacoronaviruses of the Subgenus Embecovirus. J Virol. 2019; 93(23). PMC: 6854494. DOI: 10.1128/JVI.01236-19. View

20.

Wang L, Luo Y, Zhao Y, Gao G, Bi Y, Qiu H . Comparative genomic analysis reveals an 'open' pan-genome of African swine fever virus. Transbound Emerg Dis. 2020; 67(4):1553-1562. DOI: 10.1111/tbed.13489. View