OmniVira

Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses.

Hong Zhou1 Jingkai Ji1 Xing Chen2 Yuhai Bi3 Juan Li1 Qihui Wang3 Tao Hu1 Hao Song4 Runchu Zhao5,6 Yanhua Chen2 Mingxue Cui1 Yanyan Zhang1 Alice C Hughes7,8 Edward C Holmes9 Weifeng Shi10,11
Affiliations 11 institutions
  1. Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, China.
  2. Landscape Ecology Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China.
  3. CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China.
  4. Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
  5. CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
  6. Institute of Physical Science and Information, Anhui University, Hefei 230039, China.
  7. Landscape Ecology Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
  8. Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China. Electronic address: [email protected].
  9. Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia. Electronic address: [email protected].
  10. Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, China
  11. School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, China. Electronic address: [email protected].
PMID34147139 DOI10.1016/j.cell.2021.06.008 Year2021 Journal Cell Languageeng Publication statusOther Editorial Notice
Other Editorial Notice Last checked 2026-09-29 03:30:37 Source: NCBI PubMed Searching for relatives of SARS-CoV-2 in bats. (2021-08-01) Virus hunters: Discovering the evolutionary origins of SARS-CoV-2. (2021-07-14)

Abstract

Despite the discovery of animal coronaviruses related to SARS-CoV-2, the evolutionary origins of this virus are elusive. We describe a meta-transcriptomic study of 411 bat samples collected from a small geographical region in Yunnan province, China, between May 2019 and November 2020. We identified 24 full-length coronavirus genomes, including four novel SARS-CoV-2-related and three SARS-CoV-related viruses. Rhinolophus pusillus virus RpYN06 was the closest relative of SARS-CoV-2 in most of the genome, although it possessed a more divergent spike gene. The other three SARS-CoV-2-related coronaviruses carried a genetically distinct spike gene that could weakly bind to the hACE2 receptor in vitro. Ecological modeling predicted the co-existence of up to 23 Rhinolophus bat species, with the largest contiguous hotspots extending from South Laos and Vietnam to southern China. Our study highlights the remarkable diversity of bat coronaviruses at the local scale, including close relatives of both SARS-CoV-2 and SARS-CoV.

Supporting text Virus Host Location
bats 47 coronavirus 198 COVID-19 470 evolution 65 phylogeny 834 porcine epidemic diarrhea virus 3 SARS-CoV-2 556 spike protein 32 swine acute diarrhea syndrome 1 Evolution, Molecular 178 Amino Acid Sequence 128 Angiotensin-Converting Enzyme 2 178 Animals 1981 Asia, Southeastern 10 China 234 Chiroptera 376 Coronavirus 93 COVID-19 427 Ecological and Environmental Phenomena 1 Genome, Viral 324 Humans 1455 Models, Molecular 99 Phylogeny 826 SARS-CoV-2 456

Evidence records

4 total
Zoonotic Surveillance
2 records · 1 evidence types
Evidence type Viral Detection
2 records
OVE11597 Viral Detection
Key finding

Coronavirus RNA genomes related to SARS-CoV-2 were detected in bat samples from Yunnan province, China.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
bats Chiroptera Natural host
Location
China
Supporting text

We describe a meta-transcriptomic study of 411 bat samples collected from a small geographical region in Yunnan province, China, between May 2019 and November 2020. We identified 24 full-length coronavirus genomes, including four novel SARS-CoV-2-related and three SARS-CoV-related viruses.

Method
meta-transcriptomic sequencing
Sample type
bat samples
Geographic raw
Yunnan province, China
Country inferred
CHN
OVE11598 Viral Detection
Key finding

Coronavirus RNA genomes related to SARS-CoV were detected in bat samples from Yunnan province, China.

Virus
Severe Acute Respiratory Syndrome Coronavirus
Host
bats Chiroptera Natural host
Location
China
Supporting text

We describe a meta-transcriptomic study of 411 bat samples collected from a small geographical region in Yunnan province, China, between May 2019 and November 2020. We identified 24 full-length coronavirus genomes, including four novel SARS-CoV-2-related and three SARS-CoV-related viruses.

Method
meta-transcriptomic sequencing
Sample type
bat samples
Geographic raw
Yunnan province, China
Country inferred
CHN
Functional Mechanism
1 records · 1 evidence types
Evidence type Receptor Usage
1 records
OVE11600 Receptor Usage
Key finding

Spike genes of the three SARS-CoV-2-related bat coronaviruses were shown to weakly bind to the human ACE2 receptor in vitro.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
human Homo sapiens Experimental system bats Chiroptera Experimental system
Location
Not specified
Supporting text

We describe a meta-transcriptomic study of 411 bat samples collected from a small geographical region in Yunnan province, China, between May 2019 and November 2020. The other three SARS-CoV-2-related coronaviruses carried a genetically distinct spike gene that could weakly bind to the hACE2 receptor in vitro.

Method
in vitro receptor-binding assay
Receptors
hACE2
Genomic Evolution
1 records · 1 evidence types
Evidence type Phylogenetic Evolution
1 records
OVE11599 Phylogenetic Evolution
Key finding

Phylogenetic analysis identified Rhinolophus pusillus virus RpYN06 as the closest relative of SARS-CoV-2 across most of the genome, with a more divergent spike gene.

Virus
Rhinolophus pusillus virus RpYN06 Severe acute respiratory syndrome coronavirus 2
Host
least horseshoe bat Rhinolophus pusillus Natural host
Location
Not specified
Supporting text

Rhinolophus pusillus virus RpYN06 was the closest relative of SARS-CoV-2 in most of the genome, although it possessed a more divergent spike gene.

Genes or proteins
spike gene | genome
Analysis methods
phylogenetic analysis | comparative genomic analysis