The onsite next generation sequencing(NGS)of Ebola virus(EBOV)genomes during the 2013–2016 Ebola epidemic in Western Africa provides an opportunity to trace the origin,transmission,and evolution of this virus.Herein,...The onsite next generation sequencing(NGS)of Ebola virus(EBOV)genomes during the 2013–2016 Ebola epidemic in Western Africa provides an opportunity to trace the origin,transmission,and evolution of this virus.Herein,we have diagnosed a cohort of EBOV patients in Sierra Leone in 2015,during the late phase of the outbreak.The surviving EBOV patients had a recovery process characterized by decreasing viremia,fever,and biochemical parameters.EBOV genomes sequenced through the longitudinal blood samples of these patients showed dynamic intra-host substitutions of the virus during acute infection,including the previously described short stretches of 13 serial TNC mutations.Remarkably,within individual patients,samples collected during the early phase of infection possessed Ts at these nucleotide sites,whereas they were replaced by Cs in samples collected in the later phase,suggesting that these short stretches of TNC mutations could emerge independently.In addition,up to a total of 35 nucleotide sites spanning the EBOV genome were mutated coincidently.Our study showed the dynamic intra-host adaptation of EBOV during patient recovery and gave more insight into the complex EBOV-host interactions.展开更多
In response to the current coronavirus disease 2019(COVID-19)pandemic,it is crucial to understand the origin,transmission,and evolution of severe acute respiratory syndrome coronavirus 2(SARS-Co V-2),which relies on c...In response to the current coronavirus disease 2019(COVID-19)pandemic,it is crucial to understand the origin,transmission,and evolution of severe acute respiratory syndrome coronavirus 2(SARS-Co V-2),which relies on close surveillance of genomic diversity in clinical samples.Although the mutation at the population level had been extensively investigated,how the mutations evolve at the individual level is largely unknown.Eighteen time-series fecal samples were collected from nine patients with COVID-19 during the convalescent phase.The nucleic acids of SARS-CoV-2 were enriched by the hybrid capture method.First,we demonstrated the outstanding performance of the hybrid capture method in detecting intra-host variants.We identified 229 intra-host variants at 182 sites in 18 fecal samples.Among them,nineteen variants presented frequency changes>0.3 within 1-5 days,reflecting highly dynamic intrahost viral populations.Moreover,the evolution of the viral genome demonstrated that the virus was probably viable in the gastrointestinal tract during the convalescent period.Meanwhile,we also found that the same mutation showed a distinct pattern of frequency changes in different individuals,indicating a strong random drift.In summary,dramatic changes of the SARS-CoV-2 genome were detected in fecal samples during the convalescent period;whether the viral load in feces is sufficient to establish an infection warranted further investigation.展开更多
Human respiratory syncytial virus(RSV)is a severe threat to children and a main cause of acute lower respiratory tract infections.Nevertheless,the intra-host evolution and inter-regional diffusion of RSV are little kn...Human respiratory syncytial virus(RSV)is a severe threat to children and a main cause of acute lower respiratory tract infections.Nevertheless,the intra-host evolution and inter-regional diffusion of RSV are little known.In this study,we performed a systematic surveillance in hospitalized children in Hubei during 2020–2021,in which 106 RSV-positive samples were detected both clinically and by metagenomic next generation sequencing(mNGS).RSV-A and RSV-B groups co-circulated during surveillance with RSV-B being predominant.About 46 high-quality genomes were used for further analyses.A total of 163 intra-host nucleotide variation(iSNV)sites distributed in 34 samples were detected,and glycoprotein(G)gene was the most enriched gene for iSNVs,with non-synonymous substitutions more than synonymous substitutions.Evolutionary dynamic analysis showed that the evolutionary rates of G and NS2 genes were higher,and the population size of RSV groups changed over time.We also found evidences of inter-regional diffusion from Europe and Oceania to Hubei for RSV-A and RSV-B,respectively.This study highlighted the intra-host and inter-host evolution of RSV,and provided some evi-dences for understanding the evolution of RSV.展开更多
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supported by the Megaproject for Infectious Disease Research of China(2016ZX10004222-003)the research of Ebola pathogen from the National Natural Science Foundation of China(NSFC,81590763)+4 种基金National Key Research and Development Program of China(2016YFC1200200 to Y.Shu)the Distinguished Young Scientist Program of the NSFC(81525017 to Y.Shu)the Excellent Young Scientist Program of the NSFC(81822040 to W.J.Liu)the Taishan Scholar Project of Shandong Province(ts201511056 to W.Shi)G.F.Gao is a primary principal investigator of the NSFC Innovative Research Group(81621091).
文摘The onsite next generation sequencing(NGS)of Ebola virus(EBOV)genomes during the 2013–2016 Ebola epidemic in Western Africa provides an opportunity to trace the origin,transmission,and evolution of this virus.Herein,we have diagnosed a cohort of EBOV patients in Sierra Leone in 2015,during the late phase of the outbreak.The surviving EBOV patients had a recovery process characterized by decreasing viremia,fever,and biochemical parameters.EBOV genomes sequenced through the longitudinal blood samples of these patients showed dynamic intra-host substitutions of the virus during acute infection,including the previously described short stretches of 13 serial TNC mutations.Remarkably,within individual patients,samples collected during the early phase of infection possessed Ts at these nucleotide sites,whereas they were replaced by Cs in samples collected in the later phase,suggesting that these short stretches of TNC mutations could emerge independently.In addition,up to a total of 35 nucleotide sites spanning the EBOV genome were mutated coincidently.Our study showed the dynamic intra-host adaptation of EBOV during patient recovery and gave more insight into the complex EBOV-host interactions.
基金supported by grants from National Key R&D Program of China(2020YFC0848900)the Strategic Priority CAS Project(XDB38000000)Chinese Academy of Sciences and the National Major Science and Technology Project for Control and Prevention of Major Infectious Diseases in China(2018ZX10305409,2018ZX10301401,2018ZX10732401)
文摘In response to the current coronavirus disease 2019(COVID-19)pandemic,it is crucial to understand the origin,transmission,and evolution of severe acute respiratory syndrome coronavirus 2(SARS-Co V-2),which relies on close surveillance of genomic diversity in clinical samples.Although the mutation at the population level had been extensively investigated,how the mutations evolve at the individual level is largely unknown.Eighteen time-series fecal samples were collected from nine patients with COVID-19 during the convalescent phase.The nucleic acids of SARS-CoV-2 were enriched by the hybrid capture method.First,we demonstrated the outstanding performance of the hybrid capture method in detecting intra-host variants.We identified 229 intra-host variants at 182 sites in 18 fecal samples.Among them,nineteen variants presented frequency changes>0.3 within 1-5 days,reflecting highly dynamic intrahost viral populations.Moreover,the evolution of the viral genome demonstrated that the virus was probably viable in the gastrointestinal tract during the convalescent period.Meanwhile,we also found that the same mutation showed a distinct pattern of frequency changes in different individuals,indicating a strong random drift.In summary,dramatic changes of the SARS-CoV-2 genome were detected in fecal samples during the convalescent period;whether the viral load in feces is sufficient to establish an infection warranted further investigation.
基金National Key Research and Development Program of China(2018YFC1603803)National Natural Science Foun-dation of China(31970548)+2 种基金Knowledge Innovation Program of Wuhan-Basi Research(2022020801010519)Health Commission of Hubei Province(WJ 2021M262)Natural Science Fund of Hubei Province(2021CFA012).
文摘Human respiratory syncytial virus(RSV)is a severe threat to children and a main cause of acute lower respiratory tract infections.Nevertheless,the intra-host evolution and inter-regional diffusion of RSV are little known.In this study,we performed a systematic surveillance in hospitalized children in Hubei during 2020–2021,in which 106 RSV-positive samples were detected both clinically and by metagenomic next generation sequencing(mNGS).RSV-A and RSV-B groups co-circulated during surveillance with RSV-B being predominant.About 46 high-quality genomes were used for further analyses.A total of 163 intra-host nucleotide variation(iSNV)sites distributed in 34 samples were detected,and glycoprotein(G)gene was the most enriched gene for iSNVs,with non-synonymous substitutions more than synonymous substitutions.Evolutionary dynamic analysis showed that the evolutionary rates of G and NS2 genes were higher,and the population size of RSV groups changed over time.We also found evidences of inter-regional diffusion from Europe and Oceania to Hubei for RSV-A and RSV-B,respectively.This study highlighted the intra-host and inter-host evolution of RSV,and provided some evi-dences for understanding the evolution of RSV.
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.
