{"doi":"10.1128/jvi.01926-07","title":"Evidence of the Recombinant Origin of a Bat Severe Acute Respiratory Syndrome (SARS)-Like Coronavirus and Its Implications on the Direct Ancestor of SARS Coronavirus","abstract":"<jats:title>ABSTRACT</jats:title><jats:p>Bats have been identified as the natural reservoir of severe acute respiratory syndrome (SARS)-like and SARS coronaviruses (SLCoV and SCoV). However, previous studies suggested that none of the currently sampled bat SLCoVs is the descendant of the direct ancestor of SCoV, based on their relatively distant phylogenetic relationship. In this study, evidence of the recombinant origin of the genome of a bat SLCoV is demonstrated. We identified a potential recombination breakpoint immediately after the consensus intergenic sequence between open reading frame 1 and the S coding region, suggesting the replication intermediates may participate in the recombination event, as previously speculated for other CoVs. Phylogenetic analysis of its parental regions suggests the presence of an uncharacterized SLCoV lineage that is phylogenetically closer to SCoVs than any of the currently sampled bat SLCoVs. Using various Bayesian molecular-clock models, interspecies transfer of this SLCoV lineage from bats to the amplifying host (e.g., civets) was estimated to have happened a median of 4.08 years before the SARS outbreak. Based on this relatively short window period, we speculate that this uncharacterized SLCoV lineage may contain the direct ancestor of SCoV. This study sheds light on the possible host bat species of the direct ancestor of SCoV, providing valuable information on the scope and focus of surveillance for the origin of SCoV.</jats:p>","journal":"Journal of Virology","year":2008,"id":44247,"datarank":10.10792214818013,"base_score":5.4638318050256105,"endowment":5.4638318050256105,"self_citation_contribution":0.8195747707538417,"citation_network_contribution":9.288347377426287,"self_endowment_contribution":0.8195747707538417,"citer_contribution":9.288347377426287,"corpus_percentile":null,"corpus_rank":null,"citation_count":235,"citer_count":200,"citers_with_citation_signal":194,"citers_with_endowment":194,"datacite_reuse_total":4,"is_dataset":false,"is_dataset_confidence":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":208630,"name":"Tsan-Yuk Lam","orcid":null,"position":1,"is_corresponding":false},{"id":17716,"name":"Zheng-Li Shi","orcid":null,"position":2,"is_corresponding":false},{"id":34990,"name":"Alexei J. Drummond","orcid":"0000-0003-4454-2576","position":3,"is_corresponding":false},{"id":208631,"name":"Chi-Wai Yip","orcid":null,"position":4,"is_corresponding":false},{"id":208632,"name":"Fanya Zeng","orcid":null,"position":5,"is_corresponding":false},{"id":208633,"name":"Pui-Yi Lam","orcid":null,"position":6,"is_corresponding":false},{"id":208634,"name":"Frederick Chi-Ching Leung","orcid":null,"position":7,"is_corresponding":false},{"id":113562,"name":"Chung-Chau Hon","orcid":"0000-0002-3741-7577","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":5.4638318050256105,"endowment":5.4638318050256105,"datacite_reuse_total":4,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"18057240","pmcid":"PMC2258724","openalex_id":"https://openalex.org/W2144073791","authors":[],"funders":[],"total_grants":0,"fwci":4.2276,"citation_percentile":0.94606262,"influential_citations":14,"citation_trend":[{"year":2012,"count":6},{"year":2013,"count":13},{"year":2014,"count":6},{"year":2015,"count":3},{"year":2016,"count":6},{"year":2017,"count":9},{"year":2018,"count":9},{"year":2019,"count":4},{"year":2020,"count":61},{"year":2021,"count":43},{"year":2022,"count":25},{"year":2023,"count":12},{"year":2024,"count":6},{"year":2025,"count":3}],"oa_status":"green","license":"https://journals.asm.org/non-commercial-tdm-license","oa_locations":[{"url":"https://zotero.org/groups/5435545/items/59G34YKR","host_type":"repository"},{"url":"https://europepmc.org/articles/pmc2258724?pdf=render","host_type":"GREEN"},{"url":"https://zotero.org/groups/5435545/items/59G34YKR","host_type":"repository"},{"url":"https://journals.asm.org/doi/pdf/10.1128/JVI.01926-07","host_type":"publisher"},{"url":"https://doi.org/10.1128/jvi.01926-07","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/18057240","host_type":"repository"},{"url":"http://hdl.handle.net/10722/89227","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2258724","host_type":"repository"}],"fields_of_study":["SARS-CoV-2 and COVID-19 Research","Viral Infections and Outbreaks Research","Bat Biology and Ecology Studies","Medicine","Biology","Environmental Science","Animals","Base Sequence","Bayes Theorem","Chiroptera","Genome, Viral","Models, Genetic","Molecular Sequence Data","Phylogeny","Recombination, Genetic","Severe acute respiratory syndrome-related coronavirus"],"mesh_terms":["Animals","Base Sequence","Bayes Theorem","Chiroptera","Models, Genetic","Molecular Sequence Data","Phylogeny","Recombination, Genetic","Genome, Viral","Severe acute respiratory syndrome-related coronavirus"],"keywords":["Biology","Coronavirus","Coronavirus disease 2019 (COVID-19)","Severe acute respiratory syndrome coronavirus","Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","2019-20 coronavirus outbreak","Virology","Betacoronavirus","Sars virus","Coronavirus Infections","Pandemic","Recombinant DNA","Severe acute respiratory syndrome","Ancestor","Outbreak","Genetics","Gene","Medicine","Infectious disease (medical specialty)","Disease"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Good health and well-being"}],"linked_datasets":[{"doi":"10.6084/m9.figshare.14253984.v1","title":"Additional file 1 of Indels in SARS-CoV-2 occur at template-switching hotspots","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.14253984","title":"Additional file 1 of Indels in SARS-CoV-2 occur at template-switching hotspots","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.15128115.v1","title":"Additional file 2 of Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.15128115","title":"Additional file 2 of Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2","publisher":"figshare","resource_type":"JournalArticle"}],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"gen"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-17T17:04:18.066496Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}