Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks.A significant gap remains for the possible role of pangolins as a reser...Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks.A significant gap remains for the possible role of pangolins as a reservoir of SARS-CoV-2 related coronaviruses(SC2r-CoVs).Here,we screened SC2r-CoVs in 172 samples from 163 pangolin individuals of four species,and detected positive signals in muscles of four Manis javanica and,for the first time,one M.pentadactyla.Phylogeographic analysis of pangolin mitochondrial DNA traced their origins from Southeast Asia.Using in-solution hybridization capture sequencing,we assembled a partial pangolin SC2r-CoV(pangolin-CoV)genome sequence of 22895 bp(MP20)from the M.pentadactyla sample.Phylogenetic analyses revealed MP20 was very closely related to pangolin-CoVs that were identified in M.javanica seized by Guangxi Customs.A genetic contribution of bat coronavirus to pangolin-CoVs via recombination was indicated.Our analysis revealed that the genetic diversity of pangolin-CoVs is substantially higher than previously anticipated.Given the potential infectivity of pangolin-CoVs,the high genetic diversity of pangolin-CoVs alerts the ecological risk of zoonotic evolution and transmission of pathogenic SC2r-CoVs.展开更多
The pandemic due to the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the etiological agent of coronavirus disease 2019(COVID-19),has caused immense global disruption.With the rapid accumulation of SARS-...The pandemic due to the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the etiological agent of coronavirus disease 2019(COVID-19),has caused immense global disruption.With the rapid accumulation of SARS-CoV-2 genome sequences,however,thousands of genomic variants of SARSCoV-2 are now publicly available.To improve the tracing of the viral genomes’evolution during the development of the pandemic,we analyzed single nucleotide variants(SNVs)in 121,618 high-quality SARS-CoV-2 genomes.We divided these viral genomes into two major lineages(L and S)based on variants at sites 8782 and 28144,and further divided the L lineage into two major sublineages(L1 and L2)using SNVs at sites 3037,14408,and 23403.Subsequently,we categorized them into 130 sublineages(37 in S,35 in L1,and 58 in L2)based on marker SNVs at 201 additional genomic sites.This lineage/sublineage designation system has a hierarchical structure and reflects the relatedness among the subclades of the major lineages.We also provide a companion website(www.covid19evolution.net)that allows users to visualize sublineage information and upload their own SARS-CoV-2 genomes for sublineage classification.Finally,we discussed the possible roles of compensatory mutations and natural selection during SARS-CoV-2’s evolution.These efforts will improve our understanding of the temporal and spatial dynamics of SARS-CoV-2’s genome evolution.展开更多
基金This work was supported by the National Key Research and Development Projects of the Ministry of Science and Technology of China,National Key Research and Development Program of China(2021YFC0863300)Ministry of Agriculture of China(2016ZX08009003-006)+1 种基金Key Program of Chinese Academy of Sciences(KJZD-SW-L11)Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(the Large Research Infrastructure Funding)。
文摘Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks.A significant gap remains for the possible role of pangolins as a reservoir of SARS-CoV-2 related coronaviruses(SC2r-CoVs).Here,we screened SC2r-CoVs in 172 samples from 163 pangolin individuals of four species,and detected positive signals in muscles of four Manis javanica and,for the first time,one M.pentadactyla.Phylogeographic analysis of pangolin mitochondrial DNA traced their origins from Southeast Asia.Using in-solution hybridization capture sequencing,we assembled a partial pangolin SC2r-CoV(pangolin-CoV)genome sequence of 22895 bp(MP20)from the M.pentadactyla sample.Phylogenetic analyses revealed MP20 was very closely related to pangolin-CoVs that were identified in M.javanica seized by Guangxi Customs.A genetic contribution of bat coronavirus to pangolin-CoVs via recombination was indicated.Our analysis revealed that the genetic diversity of pangolin-CoVs is substantially higher than previously anticipated.Given the potential infectivity of pangolin-CoVs,the high genetic diversity of pangolin-CoVs alerts the ecological risk of zoonotic evolution and transmission of pathogenic SC2r-CoVs.
基金supported by the National Natural Science Foundation of China(91731301 and U1902201)the Ministry of Science and Technology of the People’s Republic of China(2020YFC0847000)the Light of West China Program of the Chinese Academy of Sciences.
文摘The pandemic due to the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the etiological agent of coronavirus disease 2019(COVID-19),has caused immense global disruption.With the rapid accumulation of SARS-CoV-2 genome sequences,however,thousands of genomic variants of SARSCoV-2 are now publicly available.To improve the tracing of the viral genomes’evolution during the development of the pandemic,we analyzed single nucleotide variants(SNVs)in 121,618 high-quality SARS-CoV-2 genomes.We divided these viral genomes into two major lineages(L and S)based on variants at sites 8782 and 28144,and further divided the L lineage into two major sublineages(L1 and L2)using SNVs at sites 3037,14408,and 23403.Subsequently,we categorized them into 130 sublineages(37 in S,35 in L1,and 58 in L2)based on marker SNVs at 201 additional genomic sites.This lineage/sublineage designation system has a hierarchical structure and reflects the relatedness among the subclades of the major lineages.We also provide a companion website(www.covid19evolution.net)that allows users to visualize sublineage information and upload their own SARS-CoV-2 genomes for sublineage classification.Finally,we discussed the possible roles of compensatory mutations and natural selection during SARS-CoV-2’s evolution.These efforts will improve our understanding of the temporal and spatial dynamics of SARS-CoV-2’s genome evolution.
