{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:33Z","timestamp":1772138013273,"version":"3.50.1"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2022,1,22]],"date-time":"2022-01-22T00:00:00Z","timestamp":1642809600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100006662","name":"NIHR","doi-asserted-by":"publisher","award":["2017122"],"award-info":[{"award-number":["2017122"]}],"id":[{"id":"10.13039\/100006662","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"NSFC","doi-asserted-by":"publisher","award":["31822055"],"award-info":[{"award-number":["31822055"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31900155"],"award-info":[{"award-number":["31900155"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32041010"],"award-info":[{"award-number":["32041010"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["XDA19090118"],"award-info":[{"award-number":["XDA19090118"]}],"id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["XDB29010102"],"award-info":[{"award-number":["XDB29010102"]}],"id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Since the start of the SARS-CoV-2 pandemic in late 2019, several variants of concern (VOC) have been reported to have increased transmissibility. In addition, despite the progress of vaccination against SARS-CoV-2 worldwide, all vaccines currently in used are known to protect only partially from infection and onward transmission. We combined phylogenetic analysis with Bayesian inference under an epidemiological model to infer the reproduction number (Rt) and also trace person-to-person transmission. We examined the impact of phylogenetic uncertainty and sampling bias on the estimation. Our result indicated that lineage B had a significantly higher transmissibility than lineage A and contributed to the global pandemic to a large extent. In addition, although the transmissibility of VOCs is higher than other exponentially growing lineages, this difference is not very high. The probability of detecting onward transmission from patients infected with SARS-CoV-2 VOCs who had received at least one dose of vaccine was approximate 1.06% (3\/284), which was slightly lower but not statistically significantly different from a probability of 1.21% (10\/828) for unvaccinated individuals. In addition to VOCs, exponentially growing lineages in each country should also be account for when tailoring prevention and control strategies. One dose of vaccination could not efficiently prevent the onward transmission of SARS-CoV-2 VOCs. Consequently, nonpharmaceutical interventions (such as wearing masks and social distancing) should still be implemented in each country during the vaccination period.<\/jats:p>","DOI":"10.1093\/bib\/bbab594","type":"journal-article","created":{"date-parts":[[2021,12,23]],"date-time":"2021-12-23T07:12:39Z","timestamp":1640243559000},"source":"Crossref","is-referenced-by-count":5,"title":["SARS-CoV-2 transmissibility compared between variants of concern and vaccination status"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7897-8581","authenticated-orcid":false,"given":"Liang","family":"Wang","sequence":"first","affiliation":[{"name":"Institute of Microbiology, Chinese Academy of Sciences"}]},{"given":"Xavier","family":"Didelot","sequence":"additional","affiliation":[{"name":"School of Life Sciences and Department of Statistics, University of Warwick"}]},{"given":"Yuhai","family":"Bi","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, Chinese Academy of Sciences"}]},{"given":"George F","family":"Gao","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, Chinese Academy of Sciences"}]}],"member":"286","published-online":{"date-parts":[[2022,1,22]]},"reference":[{"key":"2022031506295585100_ref1","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1016\/S0140-6736(20)30419-0","article-title":"A distinct name is needed for the new coronavirus","volume":"395","author":"Jiang","year":"2020","journal-title":"Lancet"},{"key":"2022031506295585100_ref2","doi-asserted-by":"crossref","first-page":"eabg3055","DOI":"10.1126\/science.abg3055","article-title":"Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England","volume":"372","author":"Davies","year":"2021","journal-title":"Science"},{"key":"2022031506295585100_ref3","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1038\/s41586-021-03470-x","article-title":"Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England","volume":"593","author":"Volz","year":"2021","journal-title":"Nature"},{"key":"2022031506295585100_ref4","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1126\/science.abh2644","article-title":"Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil","volume":"372","author":"Faria","year":"2021","journal-title":"Science"},{"key":"2022031506295585100_ref5","doi-asserted-by":"crossref","DOI":"10.2807\/1560-7917.ES.2021.26.24.2100509","article-title":"Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021","volume":"26","author":"Campbell","year":"2021","journal-title":"Euro Surveill"},{"key":"2022031506295585100_ref6","doi-asserted-by":"crossref","first-page":"2201","DOI":"10.1016\/j.cell.2021.02.033","article-title":"Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera","volume":"184","author":"Supasa","year":"2021","journal-title":"Cell"},{"key":"2022031506295585100_ref7","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1056\/NEJMc2104974","article-title":"Effectiveness of the BNT162b2 Covid-19 vaccine against the B.1.1.7 and B.1.351 variants","volume":"385","author":"Abu-Raddad","year":"2021","journal-title":"N Engl J Med"},{"key":"2022031506295585100_ref8","doi-asserted-by":"crossref","first-page":"2384","DOI":"10.1016\/j.cell.2021.03.036","article-title":"SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies","volume":"184","author":"Hoffmann","year":"2021","journal-title":"Cell"},{"key":"2022031506295585100_ref9","doi-asserted-by":"crossref","first-page":"2348","DOI":"10.1016\/j.cell.2021.02.037","article-title":"Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera","volume":"184","author":"Zhou","year":"2021","journal-title":"Cell"},{"key":"2022031506295585100_ref10","doi-asserted-by":"crossref","first-page":"4220","DOI":"10.1016\/j.cell.2021.06.020","article-title":"Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum","volume":"184","author":"Liu","year":"2021","journal-title":"Cell"},{"key":"2022031506295585100_ref11","doi-asserted-by":"crossref","first-page":"2331","DOI":"10.1016\/S0140-6736(21)01290-3","article-title":"Neutralising antibody activity against SARS-CoV-2 VOCs B.1.617.2 and B.1.351 by BNT162b2 vaccination","volume":"397","author":"Wall","year":"2021","journal-title":"Lancet"},{"key":"2022031506295585100_ref12","doi-asserted-by":"crossref","first-page":"1379","DOI":"10.1038\/s41591-021-01413-7","article-title":"Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals","volume":"27","author":"Kustin","year":"2021","journal-title":"Nat Med"},{"key":"2022031506295585100_ref13","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1016\/S1473-3099(20)30981-6","article-title":"Household transmission of SARS-CoV-2 and risk factors for susceptibility and infectivity in Wuhan: a retrospective observational study","volume":"21","author":"Li","year":"2021","journal-title":"Lancet Infect Dis"},{"key":"2022031506295585100_ref14","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2022031506295585100_ref15","doi-asserted-by":"crossref","first-page":"vev003","DOI":"10.1093\/ve\/vev003","article-title":"RDP4: detection and analysis of recombination patterns in virus genomes","volume":"1","author":"Martin","year":"2015","journal-title":"Virus Evol"},{"key":"2022031506295585100_ref16","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1038\/nmeth.2109","article-title":"jModelTest 2: more models, new heuristics and parallel computing","volume":"9","author":"Darriba","year":"2012","journal-title":"Nat Methods"},{"key":"2022031506295585100_ref17","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1002\/gch2.1018","article-title":"Data, disease and diplomacy: GISAID's innovative contribution to global health","volume":"1","author":"Elbe","year":"2017","journal-title":"Glob Chall"},{"key":"2022031506295585100_ref18","doi-asserted-by":"crossref","first-page":"vey016","DOI":"10.1093\/ve\/vey016","article-title":"Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10","volume":"4","author":"Suchard","year":"2018","journal-title":"Virus Evol"},{"key":"2022031506295585100_ref19","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1093\/molbev\/mss243","article-title":"Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics","volume":"30","author":"Baele","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2022031506295585100_ref20","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior summarization in Bayesian phylogenetics using tracer 1.7","volume":"67","author":"Rambaut","year":"2018","journal-title":"Syst Biol"},{"key":"2022031506295585100_ref21","doi-asserted-by":"crossref","first-page":"3363","DOI":"10.1093\/molbev\/msaa163","article-title":"Bayesian evaluation of temporal signal in measurably evolving populations","volume":"37","author":"Duchene","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2022031506295585100_ref22","first-page":"997","article-title":"Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks","volume":"34","author":"Didelot","year":"2017","journal-title":"Mol Biol Evol"},{"key":"2022031506295585100_ref23","article-title":"Meta-analysis of the SARS-CoV-2 serial interval and the impact of parameter uncertainty on the COVID-19 reproduction number","author":"Challen","year":"2020","journal-title":"medRxiv"},{"key":"2022031506295585100_ref24","article-title":"Epitrix: small helpers and tricks for epidemics analysis 2019","author":"Jombart"},{"key":"2022031506295585100_ref25","doi-asserted-by":"crossref","first-page":"5006","DOI":"10.1038\/s41467-020-18836-4","article-title":"Inference of person-to-person transmission of COVID-19 reveals hidden super-spreading events during the early outbreak phase","volume":"11","author":"Wang","year":"2020","journal-title":"Nat Commun"},{"key":"2022031506295585100_ref26","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1056\/NEJMc2107717","article-title":"Effect of vaccination on household transmission of SARS-CoV-2 in England","volume":"385","author":"Harris","year":"2021","journal-title":"N Engl J Med"},{"key":"2022031506295585100_ref27","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1056\/NEJMc2108479","article-title":"Breakthrough SARS-CoV-2 infections in prison after vaccination","volume":"385","author":"Brinkley-Rubinstein","year":"2021","journal-title":"N Engl J Med"},{"key":"2022031506295585100_ref28","doi-asserted-by":"crossref","first-page":"2212","DOI":"10.1056\/NEJMoa2105000","article-title":"Vaccine breakthrough infections with SARS-CoV-2 variants","volume":"384","author":"Hacisuleyman","year":"2021","journal-title":"N Engl J Med"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/2\/bbab594\/42805054\/bbab594.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/2\/bbab594\/42805054\/bbab594.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,15]],"date-time":"2022-03-15T02:35:26Z","timestamp":1647311726000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbab594\/6513436"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,22]]},"references-count":28,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2022,3,10]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbab594","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.06.25.21259565","asserted-by":"object"}]},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,3]]},"published":{"date-parts":[[2022,1,22]]},"article-number":"bbab594"}}