Beta- and Novel Delta-Coronaviruses Are Identified from Wild Animals in the Qinghai-Tibetan Plateau, China.

Wentao Zhu¹ Jing Yang^1,2,3 Shan Lu^1,2,3 Ruiting Lan⁴ Dong Jin^1,2,3 Xue-Lian Luo¹ Ji Pu¹ Shusheng Wu⁵ Jianguo Xu^6,7,8,9

Affiliations 9 institutions

State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China.
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
Yushu Prefecture Center for Disease Control and Prevention, Yushu, 815000, China.
State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China. [email protected].
Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China. [email protected].
Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China. [email protected].
Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, China. [email protected].

PMID33259031 DOI10.1007/s12250-020-00325-z Year2021 Journal Virologica Sinica Virol Sin Languageeng Statusppublish

Abstract

Outbreaks of severe virus infections with the potential to cause global pandemics are increasingly concerning. One type of those commonly emerging and re-emerging pathogens are coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2). Wild animals are hosts of different coronaviruses with the potential risk of cross-species transmission. However, little is known about the reservoir and host of coronaviruses in wild animals in Qinghai Province, where has the greatest biodiversity among the world's high-altitude regions. Here, from the next-generation sequencing data, we obtained a known beta-coronavirus (beta-CoV) genome and a novel delta-coronavirus (delta-CoV) genome from faecal samples of 29 marmots, 50 rats and 25 birds in Yushu Tibetan Autonomous Prefecture, Qinghai Province, China in July 2019. According to the phylogenetic analysis, the beta-CoV shared high nucleotide identity with Coronavirus HKU24. Although the novel delta-CoV (MtCoV) was closely related to Sparrow deltacoronavirus ISU42824, the protein spike of the novel delta-CoV showed highest amino acid identity to Sparrow coronavirus HKU17 (73.1%). Interestingly, our results identified a novel host (Montifringilla taczanowskii) for the novel delta-CoV and the potential cross-species transmission. The most recent common ancestor (tMRCA) of MtCoVs along with other closest members of the species of Coronavirus HKU15 was estimated to be 289 years ago. Thus, this study increases our understanding of the genetic diversity of beta-CoVs and delta-CoVs, and also provides a new perspective of the coronavirus hosts.

Supporting text Virus Host Location

Coronavirus 195 Marmot 2 Montifringilla taczanowskii 1 Qinghai-Tibetan plateau 1 Rat 5 Phylogeny 805 Animals 1948 Animals, Wild 187 Birds 212 China 229 Coronavirus 92 Marmota 4 Rats 73 Tibet 5

Evidence records

6 total

Zoonotic Surveillance

4 records · 2 evidence types

Evidence type Viral Detection

3 records

OVE4323 Viral Detection

Key finding

A known beta-coronavirus genome was detected in faecal samples from wild marmots, rats, and birds collected in Qinghai Province, China.

Virus

Host

Marmota Natural host

rats Rattus Natural host

birds Aves Natural host

Location

Supporting text

From the next-generation sequencing data, we obtained a known beta-coronavirus (beta-CoV) genome from faecal samples of 29 marmots, 50 rats and 25 birds in Yushu Tibetan Autonomous Prefecture, Qinghai Province, China in July 2019.

Method: next-generation sequencing
Sample type: faecal samples
Geographic raw: Yushu Tibetan Autonomous Prefecture, Qinghai Province, China
Country inferred: CHN

OVE4324 Viral Detection

Key finding

A novel delta-coronavirus genome was detected in faecal samples from wild marmots, rats, and birds collected in Qinghai Province, China.

Virus

Host

Marmota Natural host

rats Rattus Natural host

birds Aves Natural host

Location

Supporting text

From the next-generation sequencing data, we obtained a novel delta-coronavirus (delta-CoV) genome from faecal samples of 29 marmots, 50 rats and 25 birds in Yushu Tibetan Autonomous Prefecture, Qinghai Province, China in July 2019.

Method: next-generation sequencing
Sample type: faecal samples
Geographic raw: Yushu Tibetan Autonomous Prefecture, Qinghai Province, China
Country inferred: CHN

OVE4326 Viral Detection

Key finding

Detection of a novel delta-coronavirus (MtCoV) in Montifringilla taczanowskii indicates potential cross-species transmission among wild birds and other wild animals in Qinghai Province, China.

Virus

Host

Location

Supporting text

Here, from the next-generation sequencing data, we obtained a known beta-coronavirus (beta-CoV) genome and a novel delta-coronavirus (delta-CoV) genome from faecal samples of 29 marmots, 50 rats and 25 birds in Yushu Tibetan Autonomous Prefecture, Qinghai Province, China in July 2019. Interestingly, our results identified a novel host (Montifringilla taczanowskii) for the novel delta-CoV and the potential cross-species transmission.

Method: next-generation sequencing | phylogenetic analysis
Geographic raw: Qinghai Province, China

Evidence type Reservoir Ecology

1 records

OVE4325 Reservoir Ecology

Key finding

Montifringilla taczanowskii was identified as a novel host species for the novel deltacoronavirus MtCoV collected in Qinghai Province, China, suggesting an ecological reservoir relationship.

Virus

Host

Location

Supporting text

Method: next-generation sequencing | phylogenetic analysis
Sample type: faecal samples
Geographic raw: Qinghai Province | Yushu Tibetan Autonomous Prefecture, China
Country inferred: CHN

Genomic Evolution

2 records · 1 evidence types

Evidence type Phylogenetic Evolution

2 records

OVE4328 Phylogenetic Evolution

Key finding

Phylogenetic analysis placed the novel delta-CoV (MtCoV) close to Sparrow deltacoronavirus ISU42824, and the spike protein showed highest amino acid identity to Sparrow coronavirus HKU17, indicating evolutionary similarity among avian deltacoronaviruses.

Virus

Host

Location

Supporting text

Although the novel delta-CoV (MtCoV) was closely related to Sparrow deltacoronavirus ISU42824, the protein spike of the novel delta-CoV showed highest amino acid identity to Sparrow coronavirus HKU17 (73.1%).

Genes or proteins: spike protein
Analysis methods: phylogenetic analysis | amino acid identity comparison

OVE4327 Phylogenetic Evolution

Key finding

Phylogenetic analysis showed that the beta-CoV recovered from wild animals in Qinghai shared high nucleotide identity with Coronavirus HKU24, indicating close evolutionary relatedness.

Virus

Host

Location

Supporting text

According to the phylogenetic analysis, the beta-CoV shared high nucleotide identity with Coronavirus HKU24.

Analysis methods: phylogenetic analysis

References

38 references

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