OmniVira

Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins.

Tommy Tsan-Yuk Lam1,2 Na Jia3 Ya-Wei Zhang3 Marcus Ho-Hin Shum2 Jia-Fu Jiang3 Hua-Chen Zhu1,2 Yi-Gang Tong4 Yong-Xia Shi5 Xue-Bing Ni2 Yun-Shi Liao2 Wen-Juan Li4 Bao-Gui Jiang3 Wei Wei6 Ting-Ting Yuan3 Kui Zheng5 Xiao-Ming Cui3 Jie Li3 Guang-Qian Pei3 Xin Qiang3 William Yiu-Man Cheung2 Lian-Feng Li7 Fang-Fang Sun5 Si Qin3 Ji-Cheng Huang5 Gabriel M Leung2 Edward C Holmes8 Yan-Ling Hu9,10 Yi Guan11,12 Wu-Chun Cao13
Affiliations 13 institutions
  1. Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China.
  2. State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China.
  3. State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.
  4. Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China.
  5. Guangzhou Customs Technology Center, Guangzhou, P. R. China.
  6. Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China.
  7. School of Information and Management, Guangxi Medical University, Nanning, P. R. China.
  8. Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia.
  9. Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China. [email protected].
  10. Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, P. R. China. [email protected].
  11. Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China. [email protected].
  12. State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China. [email protected].
  13. State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China. [email protected].
PMID32218527 DOI10.1038/s41586-020-2169-0 Year2020 Journal Nature Languageeng Statusppublish

Abstract

The ongoing outbreak of viral pneumonia in China and across the world is associated with a new coronavirus, SARS-CoV-21. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection2. Although bats are probable reservoir hosts for SARS-CoV-2, the identity of any intermediate host that may have facilitated transfer to humans is unknown. Here we report the identification of SARS-CoV-2-related coronaviruses in Malayan pangolins (Manis javanica) seized in anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin-associated coronaviruses that belong to two sub-lineages of SARS-CoV-2-related coronaviruses, including one that exhibits strong similarity in the receptor-binding domain to SARS-CoV-2. The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of new coronaviruses and should be removed from wet markets to prevent zoonotic transmission.

Supporting text Virus Host Location
Evolution, Molecular 176 Sequence Homology, Nucleic Acid 9 Amino Acid Sequence 128 Animals 1948 Betacoronavirus 78 China 229 Chiroptera 371 Coronavirus Infections 171 COVID-19 425 Disease Reservoirs 149 Eutheria 9 Genome, Viral 317 Genomics 32 Humans 1440 Malaysia 13 Pandemics 108 Phylogeny 805 Pneumonia, Viral 42 Recombination, Genetic 59 SARS-CoV-2 453 Sequence Alignment 51 Spike Glycoprotein, Coronavirus 274 Zoonoses 397

Evidence records

2 total
Zoonotic Surveillance
2 records · 2 evidence types
Evidence type Viral Detection
1 records
OVE3697 Viral Detection
Key finding

SARS-CoV-2-related coronaviruses were detected in Malayan pangolins (Manis javanica) from southern China using metagenomic sequencing.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
Malayan pangolin Manis javanica Natural host
Location
China
Supporting text

Here we report the identification of SARS-CoV-2-related coronaviruses in Malayan pangolins (Manis javanica) seized in anti-smuggling operations in southern China.

Method
metagenomic sequencing
Sample type
pangolin-associated samples
Geographic raw
southern China
Country inferred
CHN
Evidence type Reservoir Ecology
1 records
OVE3699 Reservoir Ecology
Key finding

Malayan pangolins seized in southern China carried multiple lineages of pangolin coronaviruses closely related to SARS-CoV-2, suggesting pangolins may act as possible hosts in coronavirus emergence.

Virus
SARS-related coronavirus Severe acute respiratory syndrome coronavirus 2
Host
pangolins Manidae Natural host Malayan pangolin Manis javanica Natural host
Location
China
Supporting text

Here we report the identification of SARS-CoV-2-related coronaviruses in Malayan pangolins (Manis javanica) seized in anti-smuggling operations in southern China. The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of new coronaviruses and should be removed from wet markets to prevent zoonotic transmission.

Method
metagenomic sequencing
Sample type
pangolin tissue
Geographic raw
southern China
Country inferred
CHN