Molecular epidemiology, evolution and phylogeny of SARS coronavirus

Autor: Patrick C. Y. Woo, Joshua Fung, Susanna K. P. Lau, Xin Li, Hayes K.H. Luk
Rok vydání: 2019
Předmět:
0301 basic medicine
Microbiology (medical)
China
SARS coronavirus
Evolution
viruses
Lineage (evolution)
030106 microbiology
Genome
Viral
Severe Acute Respiratory Syndrome
Horseshoe bat
Microbiology
Article
Evolution
Molecular
03 medical and health sciences
Viverridae
Phylogenetics
Chiroptera
Zoonoses
Genetics
Animals
Humans
Molecular Biology
Phylogeny
Ecology
Evolution
Behavior and Systematics
Rhinolophus sinicus
Disease Reservoirs
Recombination
Genetic
Molecular Epidemiology
biology
Molecular epidemiology
Phylogenetic tree
Rhinolophus ferrumequinum
virus diseases
respiratory system
biochemical phenomena
metabolism
and nutrition
biology.organism_classification
respiratory tract diseases
030104 developmental biology
Infectious Diseases
Severe acute respiratory syndrome-related coronavirus
Evolutionary biology
Civet
Zdroj: Infection, Genetics and Evolution
ISSN: 1567-1348
Popis: 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.
Highlights • 313 SARSr-CoV genomes have been sequenced (274 from human, 18 civets and 47 bats). • SARSr-CoV genomes of bats in Yunnan possess highest nt identity to those from civets. • The origin of human SARS-CoV was probably a result of multiple recombination events. • Recombination from a number of SARSr-CoV ancestors in different horseshoe bat species.
Databáze: OpenAIRE
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