We analyzed variations in the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)genome during a flight-related cluster outbreak of coronavirus disease 2019(COVID-19)in Shenzhen,China,to explore the characteri...We analyzed variations in the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)genome during a flight-related cluster outbreak of coronavirus disease 2019(COVID-19)in Shenzhen,China,to explore the characteristics of SARS-CoV-2 transmission and intra-host single nucleotide variations(iSNVs)in a confined space.Thirty-three patients with COVID-19 were sampled,and 14 were resampled 3-31 days later.All 47 nasopharyngeal swabs were deep-sequenced.iSNVs and similarities in the consensus genome sequence were analyzed.Three SARS-CoV-2 variants of concern,Delta(n=31),Beta(n=1),and C.1.2(n=1),were detected among the 33 patients.The viral genome sequences from 30 Delta-positive patients had similar SNVs;14 of these patients provided two successive samples.Overall,the 47 sequenced genomes contained 164 iSNVs.Of the 14 paired(successive)samples,the second samples(T2)contained more iSNVs(median:3;95%confidence interval[95%CI]:2.77-10.22)than did the first samples(T1;median:2;95%CI:1.63-3.74;Wilcoxon test,P=0.021).38 iSNVs were detected in T1 samples,and only seven were also detectable in T2 samples.Notably,T2 samples from two of the 14 paired samples had additional mutations than the T1 samples.The iSNVs of the SARS-CoV-2 genome exhibited rapid dynamic changes during a flight-related cluster outbreak event.Intra-host diversity increased gradually with time,and new site mutations occurred in vivo without a population transmission bottleneck.Therefore,we could not determine the generational relationship from the mutation site changes alone.展开更多
基金the National Natural Science Foundation of China(grant number 82161148009)the Non‐profit Central Research Institute Fund of the Chinese Academy of Medical Science(grant number APL211276910010201002008)+4 种基金the Shenzhen Science and Technology Innovation Commission Key project(grant number JSGG20200225152648408)the Shenzhen Key Medical Discipline Construction Fund(grant number SZXK064)the Key Project of Shenzhen Science and Technology Innovation Commission(grant number KCXFZ2020020110061900)the First Fighting the Epidemic Project of Shenzhen(grant number JSGG 20210901145004012)the key project of Beijing Natural Science Foundation(grant number Z190017).
文摘We analyzed variations in the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)genome during a flight-related cluster outbreak of coronavirus disease 2019(COVID-19)in Shenzhen,China,to explore the characteristics of SARS-CoV-2 transmission and intra-host single nucleotide variations(iSNVs)in a confined space.Thirty-three patients with COVID-19 were sampled,and 14 were resampled 3-31 days later.All 47 nasopharyngeal swabs were deep-sequenced.iSNVs and similarities in the consensus genome sequence were analyzed.Three SARS-CoV-2 variants of concern,Delta(n=31),Beta(n=1),and C.1.2(n=1),were detected among the 33 patients.The viral genome sequences from 30 Delta-positive patients had similar SNVs;14 of these patients provided two successive samples.Overall,the 47 sequenced genomes contained 164 iSNVs.Of the 14 paired(successive)samples,the second samples(T2)contained more iSNVs(median:3;95%confidence interval[95%CI]:2.77-10.22)than did the first samples(T1;median:2;95%CI:1.63-3.74;Wilcoxon test,P=0.021).38 iSNVs were detected in T1 samples,and only seven were also detectable in T2 samples.Notably,T2 samples from two of the 14 paired samples had additional mutations than the T1 samples.The iSNVs of the SARS-CoV-2 genome exhibited rapid dynamic changes during a flight-related cluster outbreak event.Intra-host diversity increased gradually with time,and new site mutations occurred in vivo without a population transmission bottleneck.Therefore,we could not determine the generational relationship from the mutation site changes alone.
