4.7 Article

Gene Presence/Absence Variation analysis of coronavirus family displays its pan-genomic diversity

期刊

INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
卷 17, 期 14, 页码 3717-3727

出版社

IVYSPRING INT PUBL
DOI: 10.7150/ijbs.58220

关键词

COVID-19; SARS-CoV-2; Genome; Diversity; Pangenomics

资金

  1. Cross-institute Innovation Foundation of Shanghai Jiao Tong University [YG2017ZD01]
  2. Innovation Foundation of Translational Medicine of Shanghai Jiao Tong University School of Medicine [TM202001, 15ZH4001, TM 201617, TM 201702]
  3. Shanghai Science and Technology Committee [20DZ2201900, 18411953100]

向作者/读者索取更多资源

The study revealed that the coronavirus family has 181 genes, with only 3 being highly conserved. The SARS-CoV-2 pan-genome consists of 13 core genes, showing a lower level of diversity compared to other RNA viruses. The three highly conserved genes in the coronavirus family and the core genes in the SARS-CoV-2 pan-genome could be potential targets for developing nucleic acid diagnostic reagents with reduced mutation potential.
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

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