The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has evolved rapidly into new variants throughout the pandemic.The Omicron variant has more than 50 mutations when compared with the original wild-type str...The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has evolved rapidly into new variants throughout the pandemic.The Omicron variant has more than 50 mutations when compared with the original wild-type strain and has been identified globally in numerous countries.In this report,we analyzed the mutational profiles of several variants,including the per-site mutation rate,to determine evolutionary relationships.The Omicron variant was found to have a unique mutation profile when compared with that of other SARS-CoV-2 variants,containing mutations that are rare in clinical samples.Moreover,the presence of five mouse-adapted mutation sites suggests that Omicron may have evolved in a mouse host.Mutations in the Omicron receptor-binding domain(RBD)region,in particular,have potential implications for the ongoing pandemic.展开更多
The severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2)pandemic resulted in significant societal costs.Hence,an in‐depth understanding of SARS‐CoV‐2 virus mutation and its evolution will help determine th...The severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2)pandemic resulted in significant societal costs.Hence,an in‐depth understanding of SARS‐CoV‐2 virus mutation and its evolution will help determine the direction of the COVID‐19 pandemic.In this study,we identified 296,728 de novo mutations in more than 2,800,000 high‐quality SARS‐CoV‐2 genomes.All possible factors affecting the mutation frequency of SARS‐CoV‐2 in human hosts were analyzed,including zinc finger antiviral proteins,sequence context,amino acid change,and translation efficiency.As a result,we proposed that when adenine(A)and tyrosine(T)bases are in the context of AM(M stands for adenine or cytosine)or TA motif,A or T base has lower mutation frequency.Furthermore,we hypothesized that translation efficiency can affect the mutation frequency of the third position of the codon by the selection,which explains why SARS‐CoV‐2 prefers AT3 codons usage.In addition,we found a host‐specific asymmetric dinucleotide mutation frequency in the SARS‐CoV‐2 genome,which provides a new basis for determining the origin of the SARS‐CoV‐2.Finally,we summarize all possible factors affecting mutation frequency and provide insights into the mutation characteristics and evolutionary trends of SARS‐CoV‐2.展开更多
文摘The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has evolved rapidly into new variants throughout the pandemic.The Omicron variant has more than 50 mutations when compared with the original wild-type strain and has been identified globally in numerous countries.In this report,we analyzed the mutational profiles of several variants,including the per-site mutation rate,to determine evolutionary relationships.The Omicron variant was found to have a unique mutation profile when compared with that of other SARS-CoV-2 variants,containing mutations that are rare in clinical samples.Moreover,the presence of five mouse-adapted mutation sites suggests that Omicron may have evolved in a mouse host.Mutations in the Omicron receptor-binding domain(RBD)region,in particular,have potential implications for the ongoing pandemic.
基金This study was supported by funding from the Foundation of the Committee on Science and Technology of Tianjin(19YFZCSN00080)the State Key Research and Development Plan(2019YFC1605004)the National Key Programs for Infectious Diseases of China(2017ZX10303405‐001).
文摘The severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2)pandemic resulted in significant societal costs.Hence,an in‐depth understanding of SARS‐CoV‐2 virus mutation and its evolution will help determine the direction of the COVID‐19 pandemic.In this study,we identified 296,728 de novo mutations in more than 2,800,000 high‐quality SARS‐CoV‐2 genomes.All possible factors affecting the mutation frequency of SARS‐CoV‐2 in human hosts were analyzed,including zinc finger antiviral proteins,sequence context,amino acid change,and translation efficiency.As a result,we proposed that when adenine(A)and tyrosine(T)bases are in the context of AM(M stands for adenine or cytosine)or TA motif,A or T base has lower mutation frequency.Furthermore,we hypothesized that translation efficiency can affect the mutation frequency of the third position of the codon by the selection,which explains why SARS‐CoV‐2 prefers AT3 codons usage.In addition,we found a host‐specific asymmetric dinucleotide mutation frequency in the SARS‐CoV‐2 genome,which provides a new basis for determining the origin of the SARS‐CoV‐2.Finally,we summarize all possible factors affecting mutation frequency and provide insights into the mutation characteristics and evolutionary trends of SARS‐CoV‐2.
