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Molecular epidemiology, evolution and phylogeny of SARS coronavirus.
Infect Genet Evol. 2019 07; 71:21-30.IG

Abstract

Shortly after its emergence in southern China in 2002/2003, Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) was confirmed to be the cause of SARS. Subsequently, SARS-related CoVs (SARSr-CoVs) were found in palm civets from live animal markets in Guangdong and in various horseshoe bat species, which were believed to be the ultimate reservoir of SARSr-CoV. Till November 2018, 339 SARSr-CoV genomes have been sequenced, including 274 from human, 18 from civets and 47 from bats [mostly from Chinese horseshoe bats (Rhinolophus sinicus), n = 30; and greater horseshoe bats (Rhinolophus ferrumequinum), n = 9]. The human SARS-CoVs and civet SARSr-CoVs were collected in 2003/2004, while bat SARSr-CoVs were continuously isolated in the past 13 years even after the cessation of the SARS epidemic. SARSr-CoVs belong to the subgenus Sarbecovirus (previously lineage B) of genus Betacoronavirus and occupy a unique phylogenetic position. Overall, it is observed that the SARSr-CoV genomes from bats in Yunnan province of China possess the highest nucleotide identity to those from civets. It is evident from both multiple alignment and phylogenetic analyses that some genes of a particular SARSr-CoV from bats may possess higher while other genes possess much lower nucleotide identity to the corresponding genes of SARSr-CoV from human/civets, resulting in the shift of phylogenetic position in different phylogenetic trees. Our current model on the origin of SARS is that the human SARS-CoV that caused the epidemic in 2002/2003 was probably a result of multiple recombination events from a number of SARSr-CoV ancestors in different horseshoe bat species.

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Authors+Show Affiliations

Luk HKH
Department of Microbiology, The University of Hong Kong, Hong Kong, China.
Li X
Department of Microbiology, The University of Hong Kong, Hong Kong, China.
Fung J
Department of Microbiology, The University of Hong Kong, Hong Kong, China.
Lau SKP
Department of Microbiology, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310006, China. Electronic address: skplau@hku.hk.
Woo PCY
Department of Microbiology, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310006, China. Electronic address: pcywoo@hku.hk.

MeSH

AnimalsChinaChiropteraDisease ReservoirsEvolution, MolecularGenome, ViralHumansMolecular EpidemiologyPhylogenyRecombination, GeneticSARS VirusSevere Acute Respiratory SyndromeViverridaeZoonoses

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Review

Language

eng

PubMed ID

30844511

Citation

Luk, Hayes K H., et al. "Molecular Epidemiology, Evolution and Phylogeny of SARS Coronavirus." Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, vol. 71, 2019, pp. 21-30.
Luk HKH, Li X, Fung J, et al. Molecular epidemiology, evolution and phylogeny of SARS coronavirus. Infect Genet Evol. 2019;71:21-30.
Luk, H. K. H., Li, X., Fung, J., Lau, S. K. P., & Woo, P. C. Y. (2019). Molecular epidemiology, evolution and phylogeny of SARS coronavirus. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 71, 21-30. https://doi.org/10.1016/j.meegid.2019.03.001
Luk HKH, et al. Molecular Epidemiology, Evolution and Phylogeny of SARS Coronavirus. Infect Genet Evol. 2019;71:21-30. PubMed PMID: 30844511.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Molecular epidemiology, evolution and phylogeny of SARS coronavirus. AU - Luk,Hayes K H, AU - Li,Xin, AU - Fung,Joshua, AU - Lau,Susanna K P, AU - Woo,Patrick C Y, Y1 - 2019/03/04/ PY - 2018/12/11/received PY - 2019/02/27/revised PY - 2019/03/01/accepted PY - 2019/3/8/pubmed PY - 2020/2/11/medline PY - 2019/3/8/entrez KW - Evolution KW - Molecular epidemiology KW - Phylogeny KW - SARS coronavirus SP - 21 EP - 30 JF - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JO - Infect Genet Evol VL - 71 N2 - Shortly after its emergence in southern China in 2002/2003, Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) was confirmed to be the cause of SARS. Subsequently, SARS-related CoVs (SARSr-CoVs) were found in palm civets from live animal markets in Guangdong and in various horseshoe bat species, which were believed to be the ultimate reservoir of SARSr-CoV. Till November 2018, 339 SARSr-CoV genomes have been sequenced, including 274 from human, 18 from civets and 47 from bats [mostly from Chinese horseshoe bats (Rhinolophus sinicus), n = 30; and greater horseshoe bats (Rhinolophus ferrumequinum), n = 9]. The human SARS-CoVs and civet SARSr-CoVs were collected in 2003/2004, while bat SARSr-CoVs were continuously isolated in the past 13 years even after the cessation of the SARS epidemic. SARSr-CoVs belong to the subgenus Sarbecovirus (previously lineage B) of genus Betacoronavirus and occupy a unique phylogenetic position. Overall, it is observed that the SARSr-CoV genomes from bats in Yunnan province of China possess the highest nucleotide identity to those from civets. It is evident from both multiple alignment and phylogenetic analyses that some genes of a particular SARSr-CoV from bats may possess higher while other genes possess much lower nucleotide identity to the corresponding genes of SARSr-CoV from human/civets, resulting in the shift of phylogenetic position in different phylogenetic trees. Our current model on the origin of SARS is that the human SARS-CoV that caused the epidemic in 2002/2003 was probably a result of multiple recombination events from a number of SARSr-CoV ancestors in different horseshoe bat species. SN - 1567-7257 UR - https://www.unboundmedicine.com/medline/citation/30844511/Molecular_epidemiology_evolution_and_phylogeny_of_SARS_coronavirus_ DB - PRIME DP - Unbound Medicine ER -