OmniVira

Literature detail

Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human.

Huai-Dong Song1 Chang-Chun Tu Guo-Wei Zhang Sheng-Yue Wang Kui Zheng Lian-Cheng Lei Qiu-Xia Chen Yu-Wei Gao Hui-Qiong Zhou Hua Xiang Hua-Jun Zheng Shur-Wern Wang Chern Feng Cheng Chun-Ming Pan Hua Xuan Sai-Juan Chen Hui-Ming Luo Duan-Hua Zhou Yu-Fei Liu Jian-Feng He Peng-Zhe Qin Ling-Hui Li Yu-Qi Ren Wen-Jia Liang Ye-Dong Yu Larry Anderson Ming Wang Rui-Heng Xu Xin-Wei Wu Huan-Ying Zheng Jin-Ding Chen Guodong Liang Yang Gao Ming Liao Ling Fang Li-Yun Jiang Hui Li Fang Chen Biao Di Li-Juan He Jin-Yan Lin Suxiang Tong Xiangang Kong Lin Du Pei Hao Hua Tang Andrea Bernini Xiao-Jing Yu Ottavia Spiga Zong-Ming Guo Hai-Yan Pan Wei-Zhong He Jean-Claude Manuguerra Arnaud Fontanet Antoine Danchin Neri Niccolai Yi-Xue Li Chung-I Wu Guo-Ping Zhao
Affiliations 1 institutions
  1. State Key Laboratory for Medical Genomics/Pôle Sino-Français de Recherche en Sciences du Vivant et Génomique, Ruijin Hospital Affiliated to Shanghai Second Medical University, 197 Rui Jin Road II, Shanghai 200025, China.
PMID 15695582 2005 Proc Natl Acad Sci U S A eng ppublish
PubMed DOI Browse context

Article

Publication summary

The genomic sequences of severe acute respiratory syndrome coronaviruses from human and palm civet of the 2003/2004 outbreak in the city of Guangzhou, China, were nearly identical. Phylogenetic analysis suggested an independent viral invasion from animal to human in this new episode. Combining all existing data but excluding singletons, we identified 202 single-nucleotide variations. Among them, 17 are polymorphic in palm civets only. The ratio of nonsynonymous/synonymous nucleotide substitution in palm civets collected 1 yr apart from different geographic locations is very high, suggesting a rapid evolving process of viral proteins in civet as well, much like their adaptation in the human host in the early 2002-2003 epidemic. Major genetic variations in some critical genes, particularly the Spike gene, seemed essential for the transition from animal-to-human transmission to human-to-human transmission, which eventually caused the first severe acute respiratory syndrome outbreak of 2002/2003.

Evolution, Molecular Amino Acid Substitution Animals China Disease Outbreaks Genes, Viral Humans Membrane Glycoproteins Phylogeny Polymorphism, Single Nucleotide Severe Acute Respiratory Syndrome Severe acute respiratory syndrome-related coronavirus Species Specificity Spike Glycoprotein, Coronavirus Viral Envelope Proteins Viverridae Zoonoses

Structured evidence records

Evidence records

4 total
Genomic Evolution 2 records
Genomic Evolution Extraction confidence 0.95
Key finding

Phylogenetic and genomic analyses of SARS-CoV isolates from humans and palm civets revealed strong sequence similarity and key variations in the Spike gene linked to cross-species transmission and adaptation.

Virus
SARS-CoV
Location
Not specified
Supporting text

The genomic sequences of severe acute respiratory syndrome coronaviruses from human and palm civet of the 2003/2004 outbreak in the city of Guangzhou, China, were nearly identical. Phylogenetic analysis suggested an independent viral invasion from animal to human in this new episode. ... Major genetic variations in some critical genes, particularly the Spike gene, seemed essential for the transition from animal-to-human transmission to human-to-human transmission.

Genes or proteins
Spike gene
Analysis methods
genomic sequencing; phylogenetic analysis
Genomic Evolution Extraction confidence 0.95
Key finding

Sequence substitution analysis indicated rapid molecular evolution of SARS-CoV in palm civets consistent with adaptive processes similar to those in human isolates during the early epidemic.

Virus
SARS-CoV
Location
Not specified
Supporting text

The ratio of nonsynonymous/synonymous nucleotide substitution in palm civets collected 1 yr apart from different geographic locations is very high, suggesting a rapid evolving process of viral proteins in civet as well, much like their adaptation in the human host in the early 2002-2003 epidemic.

Analysis methods
nonsynonymous/synonymous substitution analysis
Molecular Adaptation 1 records
Molecular Adaptation Extraction confidence 0.90
Key finding

Spike gene variations in SARS coronavirus were associated with adaptation from palm civet to human and enabling human-to-human transmission.

Virus
SARS-CoV
Host
Not specified
Location
Not specified
Supporting text

Major genetic variations in some critical genes, particularly the Spike gene, seemed essential for the transition from animal-to-human transmission to human-to-human transmission, which eventually caused the first severe acute respiratory syndrome outbreak of 2002/2003.

Genes or proteins
Spike gene
Mechanism types
receptor_binding; host_range_expansion; transmission_fitness
Spillover Event 1 records
Spillover Event Extraction confidence 0.95
Key finding

Severe acute respiratory syndrome coronavirus was transmitted from palm civets to humans during the 2003/2004 outbreak in Guangzhou, China.

Virus
SARS-CoV
Location
China China
Supporting text

Phylogenetic analysis suggested an independent viral invasion from animal to human in this new episode.

Method
sequencing; phylogenetic analysis
Study design
phylogenetic analysis
Transmission direction
animal-to-human
Geographic raw
Guangzhou, China
Country inferred
China