Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis

Gao，Rongsui1; Zu，Wenhong1; Liu，Yang1; Li，Junhua2; Li，Zeyao3; Wen，Yanling1; Wang，Haiyan1; Yuan，Jing4; Cheng，Lin1; Zhang，Shengyuan1; Zhang，Yu5; Zhang，Shuye6; Liu，Weilong1; Lan，Xun7; Liu，Lei1; Li，Feng8; Zhang，Zheng1,9,10

2021

10.1080/21505594.2021.1911477

Virulence   影响因子和分区

2150-5594

2150-5608

New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies’ composition varies with time during the early onset of symptoms, which implicates viral evolution during infection. Network analysis of co-occurring SNPs revealed the most abundant non-synonymous SNP 22,638 in the S glycoprotein RBD region and 28,144 in the ORF8 region. Furthermore, SARS-CoV-2 variations differ in an individual’s respiratory tissue (nose, throat, BALF, or sputum), suggesting independent compartmentalization of SARS-CoV-2 populations in patients. The positive selection analysis of the SARS-CoV-2 genome uncovered the positive selected amino acid G251V on ORF3a. Alternative allele frequency spectrum (AAFS) of all variants revealed that ORF8 could bear alternate alleles with high frequency. Overall, the results show the quasispecies’ profile of SARS-CoV-2 in the respiratory tract in the first two months after the outbreak.

epitopes host adaptation intra-host single nucleotide variation (iSNV) quasispecies SARS-CoV-2 selective pressure Single nucleotide polymorphism (SNP)

SCI

英语

第一 ; 通讯

WOS:000653994500001

2-s2.0-85106704577

Scopus

1.Institute for Hepatology,National Clinical Research Center for Infectious Disease,Shenzhen Third People’s Hospital,the Second Affiliated Hospital,School of Medicine,Southern University of Science and Technology,Shenzhen,China
2.Shenzhen Key Laboratory of Unknown Pathogen Identification,BGI-Shenzhen,Shenzhen,China
3.School of Life Sciences,Tsinghua University,Beijing,China
4.Department of Infectious Diseases,Shenzhen Third People’s Hospital,National Clinical Research Center for Infectious Disease,Shenzhen,China
5.National Supercomputing Center in Shenzhen (Shenzhen Cloud Computing Center),Shenzhen,China
6.Shanghai Public Health Clinical Center,Institute of Biomedical Sciences,Fudan University,Shanghai,China
7.Department of Basic Medical Sciences at School of Medicine,Tsinghua University,Tsinghua-Peking Center for Life Sciences,Tsinghua University,Beijing,China
8.Guangzhou Eighth People’s Hospital,Guangzhou Medical University,Guangzhou,China
9.Shenzhen Research Center for Communicable Disease Diagnosis and Treatment of Chinese Academy of Medical Science,Shenzhen,China
10.Guangdong Key Laboratory for Anti-infection Drug Quality Evaluation,Shenzhen,China

Gao，Rongsui,Zu，Wenhong,Liu，Yang,et al. Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis[J]. Virulence,2021,12(1):1209-1226.

Gao，Rongsui.,Zu，Wenhong.,Liu，Yang.,Li，Junhua.,Li，Zeyao.,...&Zhang，Zheng.(2021).Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis.Virulence,12(1),1209-1226.

Gao，Rongsui,et al."Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis".Virulence 12.1(2021):1209-1226.