OmniVira

A Bat-Derived Putative Cross-Family Recombinant Coronavirus with a Reovirus Gene.

Canping Huang1 William J Liu1,2 Wen Xu3 Tao Jin4 Yingze Zhao1 Jingdong Song1 Yi Shi5 Wei Ji1 Hao Jia1,2 Yongming Zhou3 Honghua Wen6 Honglan Zhao1 Huaxing Liu6 Hong Li3 Qihui Wang7 Ying Wu5 Liang Wang5 Di Liu5,8 Guang Liu4 Hongjie Yu9 Edward C Holmes10 Lin Lu3 George F Gao1,2,5,11,12,13
Affiliations 13 institutions
  1. National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.
  2. College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
  3. Yunnan Provincial Center for Disease Control and Prevention, Kunming Yunnan, China.
  4. China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China.
  5. CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
  6. Center for Disease Control and Prevention of Mengla County, Mengla Yunnan, China.
  7. CAS Key Laboratory of Microbial and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
  8. Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
  9. Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, China.
  10. Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.
  11. Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
  12. Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
  13. Office of Director-General, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.
PMID27676249 DOI10.1371/journal.ppat.1005883 Year2016 Journal PLoS pathogens PLoS Pathog Languageeng Statusepublish

Abstract

The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002 and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 has generated enormous interest in the biodiversity, genomics and cross-species transmission potential of coronaviruses, especially those from bats, the second most speciose order of mammals. Herein, we identified a novel coronavirus, provisionally designated Rousettus bat coronavirus GCCDC1 (Ro-BatCoV GCCDC1), in the rectal swab samples of Rousettus leschenaulti bats by using pan-coronavirus RT-PCR and next-generation sequencing. Although the virus is similar to Rousettus bat coronavirus HKU9 (Ro-BatCoV HKU9) in genome characteristics, it is sufficiently distinct to be classified as a new species according to the criteria defined by the International Committee of Taxonomy of Viruses (ICTV). More striking was that Ro-BatCoV GCCDC1 contained a unique gene integrated into the 3'-end of the genome that has no homologs in any known coronavirus, but which sequence and phylogeny analyses indicated most likely originated from the p10 gene of a bat orthoreovirus. Subgenomic mRNA and cellular-level observations demonstrated that the p10 gene is functional and induces the formation of cell syncytia. Therefore, here we report a putative heterologous inter-family recombination event between a single-stranded, positive-sense RNA virus and a double-stranded segmented RNA virus, providing insights into the fundamental mechanisms of viral evolution.

Supporting text Virus Host Location

Evidence records

2 total
Zoonotic Surveillance
1 records · 1 evidence types
Evidence type Viral Detection
1 records
OVE2429 Viral Detection
Key finding

Rousettus bat coronavirus GCCDC1 (Ro-BatCoV GCCDC1) genetic material was detected in rectal swab samples from Rousettus leschenaulti bats using pan-coronavirus RT-PCR and next-generation sequencing.

Virus
Coronaviridae
Host
Leschenault's rousette Rousettus leschenaultii Natural host
Location
Not specified
Supporting text

Herein, we identified a novel coronavirus, provisionally designated Rousettus bat coronavirus GCCDC1 (Ro-BatCoV GCCDC1), in the rectal swab samples of Rousettus leschenaulti bats by using pan-coronavirus RT-PCR and next-generation sequencing.

Method
pan-coronavirus RT-PCR | next-generation sequencing
Sample type
rectal swab samples
Genomic Evolution
1 records · 1 evidence types
Evidence type Recombination or Reassortment
1 records
OVE2430 Recombination or Reassortment
Key finding

Ro-BatCoV GCCDC1 has acquired a gene at the 3′ end of its genome derived from the p10 gene of a bat orthoreovirus, representing a heterologous inter-family recombination event.

Virus
Rousettus bat coronavirus Orthoreovirus
Host
Not specified
Location
Not specified
Supporting text

Ro-BatCoV GCCDC1 contained a unique gene integrated into the 3'-end of the genome that has no homologs in any known coronavirus, but which sequence and phylogeny analyses indicated most likely originated from the p10 gene of a bat orthoreovirus.

Event type
recombination
Genes or segments
p10 gene | 3'-end of genome