Genomic Analysis and Surveillance of the Coronavirus Dominant in Ducks in China

The genetic diversity, evolution, distribution, and taxonomy of some coronaviruses dominant in birds other than chickens remain enigmatic. In this study we sequenced the genome of a newly identified coronavirus dominant in ducks (DdCoV), and performed a large-scale surveillance of coronaviruses in c...

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Bibliographic Details
Published in:PloS one 2015-06, Vol.10 (6), p.e0129256-e0129256
Main Authors: Zhuang, Qing-Ye, Wang, Kai-Cheng, Liu, Shuo, Hou, Guang-Yu, Jiang, Wen-Ming, Wang, Su-Chun, Li, Jin-Ping, Yu, Jian-Min, Chen, Ji-Ming
Format: Article
Language:English
Subjects:
Animal taxonomy
Animals
Aquatic birds
Biological evolution
Birds
Bronchitis
Chickens
China - epidemiology
Conserved Sequence
Coronaviridae
Coronavirus - classification
Coronavirus - genetics
Coronavirus Infections - veterinary
Coronaviruses
Deoxyribonucleic acid
DNA
Ducks
Ecological niches
Epidemiology
Evolution
Feces
Gene Order
Genetic diversity
Genome, Viral
Genomes
Genomic analysis
Genomics
Homology
Niches
Phylogenetics
Phylogeny
Polymerase chain reaction
Poultry
Poultry Diseases - epidemiology
Poultry Diseases - virology
Proteins
Public Health Surveillance
Recombination
Recombination, Genetic
Respiratory diseases
Ribonucleic acid
RNA
RNA viruses
Species classification
Surveillance
Tandem Repeat Sequences
Taxonomy
Viruses
Waterfowl
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Summary:The genetic diversity, evolution, distribution, and taxonomy of some coronaviruses dominant in birds other than chickens remain enigmatic. In this study we sequenced the genome of a newly identified coronavirus dominant in ducks (DdCoV), and performed a large-scale surveillance of coronaviruses in chickens and ducks using a conserved RT-PCR assay. The viral genome harbors a tandem repeat which is rare in vertebrate RNA viruses. The repeat is homologous to some proteins of various cellular organisms, but its origin remains unknown. Many substitutions, insertions, deletions, and some frameshifts and recombination events have occurred in the genome of the DdCoV, as compared with the coronavirus dominant in chickens (CdCoV). The distances between DdCoV and CdCoV are large enough to separate them into different species within the genus Gammacoronavirus. Our surveillance demonstrated that DdCoVs and CdCoVs belong to different lineages and occupy different ecological niches, further supporting that they should be classified into different species. Our surveillance also demonstrated that DdCoVs and CdCoVs are prevalent in live poultry markets in some regions of China. In conclusion, this study shed novel insight into the genetic diversity, evolution, distribution, and taxonomy of the coronaviruses circulating in chickens and ducks.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0129256