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Literature detail

Pangolin HKU4-related coronaviruses found in greater bamboo bats from southern China.

Min Guo1 Kai Zhao2 Xingwen Peng1 Xiangyang He1 Jin Deng1 Bo Wang3 Xinglou Yang4,5 Libiao Zhang6
Affiliations 6 institutions
  1. Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China.
  2. Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650023, China.
  3. Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24060, USA.
  4. Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650023, China
  5. Hubei Jiangxia Lab, Wuhan, 430071, China. Electronic address: [email protected].
  6. Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China. Electronic address: [email protected].
PMID 37967719 2023 Virol Sin eng ppublish
PubMed DOI Browse context

Article

Publication summary

Coronavirus (CoV) spillover originating from game animals, particularly pangolins, is currently a significant concern. Meanwhile, vigilance is urgently needed for coronaviruses carried by bats, which are known as natural reservoirs of many coronaviruses. In this study, we collected 729 anal swabs of 20 different bat species from nine locations in Yunnan and Guangdong provinces, southern China, in 2016 and 2017, and described the molecular characteristics and genetic diversity of alphacoronaviruses (αCoVs) and betacoronaviruses (βCoVs) found in these bats. Using RT-PCR, we identified 58 (8.0%) bat CoVs in nine bat species from six locations. Furthermore, using the Illumina platform, we obtained two representative full-length genomes of the bat CoVs, namely TyRo-CoV-162275 and TyRo-CoV-162269. Sequence analysis showed that TyRo-CoV-162275 shared the highest identity with Malayan pangolin (Manis javanica) HKU4-related coronaviruses (MjHKU4r-CoVs) from Guangxi Province, whereas TyRo-CoV-162269 was closely related to HKU33-CoV discovered in a greater bamboo bat (Tylonycteris robustula) from Guizhou Province. Notably, TyRo-CoV-162275 has a putative furin protease cleavage site in its S protein and is likely to utilize human dipeptidyl peptidase-4 (hDPP4) as a cell-entry receptor, similar to MERS-CoV. To the best of our knowledge, this is the first report of a bat HKU4r-CoV strain containing a furin protease cleavage site. These findings expand our understanding of coronavirus geographic and host distributions.

Bat HKU4r-CoV Coronavirus Pangolin HKU4r-CoV Spillover risk Tylonycteris robustula Chiroptera Coronavirus Infections Middle East Respiratory Syndrome Coronavirus Animals China Furin Humans Pangolins Phylogeny

Structured evidence records

Evidence records

5 total
Genomic Evolution 2 records
Genomic Evolution Extraction confidence 0.92
Key finding

A full-length genome of TyRo-CoV-162275 from greater bamboo bats was closely related to Malayan pangolin HKU4-related coronaviruses, demonstrating cross-species genomic similarity and evolutionary linkage.

Virus
Merbecovirus
Location
Not specified
Supporting text

Using the Illumina platform, we obtained two representative full-length genomes of the bat CoVs, namely TyRo-CoV-162275 and TyRo-CoV-162269. Sequence analysis showed that TyRo-CoV-162275 shared the highest identity with Malayan pangolin (Manis javanica) HKU4-related coronaviruses (MjHKU4r-CoVs) from Guangxi Province.

Genes or proteins
S protein
Analysis methods
sequence analysis; phylogenetic analysis
Genomic Evolution Extraction confidence 0.90
Key finding

A full-length genome of TyRo-CoV-162269 from bats clustered with the HKU33-CoV lineage, revealing phylogenetic relatedness within bat coronaviruses.

Virus
Merbecovirus
Location
Not specified
Supporting text

Sequence analysis showed that TyRo-CoV-162269 was closely related to HKU33-CoV discovered in a greater bamboo bat (Tylonycteris robustula) from Guizhou Province.

Analysis methods
sequence analysis; phylogenetic analysis
Molecular Adaptation 1 records
Molecular Adaptation Extraction confidence 0.90
Key finding

The bat coronavirus TyRo-CoV-162275 contains a furin protease cleavage site in its spike protein and likely uses the human DPP4 receptor, suggesting molecular adaptation for cell entry similar to MERS-CoV.

Virus
Merbecovirus
Host
Not specified
Location
Not specified
Supporting text

Notably, TyRo-CoV-162275 has a putative furin protease cleavage site in its S protein and is likely to utilize human dipeptidyl peptidase-4 (hDPP4) as a cell-entry receptor, similar to MERS-CoV.

Genes or proteins
S protein
Receptors
human dipeptidyl peptidase-4 (hDPP4)
Mechanism types
receptor_binding; cell_entry; pathogenicity
Receptor Usage 1 records
Receptor Usage Extraction confidence 0.80
Key finding

The bat coronavirus TyRo-CoV-162275 is predicted to use human DPP4 as its cell-entry receptor, analogous to MERS-CoV, and contains a furin cleavage site in the spike protein.

Virus
Merbecovirus
Location
Not specified
Supporting text

TyRo-CoV-162275 has a putative furin protease cleavage site in its S protein and is likely to utilize human dipeptidyl peptidase-4 (hDPP4) as a cell-entry receptor, similar to MERS-CoV.

Method
sequence analysis
Receptors
human dipeptidyl peptidase-4 (hDPP4)
Host factors
furin
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.95
Key finding

Coronavirus surveillance of bats in southern China identified alphacoronaviruses and betacoronaviruses, including HKU4-related strains in greater bamboo bats.

Host
Chiroptera
Location
China China
Supporting text

In this study, we collected 729 anal swabs of 20 different bat species from nine locations in Yunnan and Guangdong provinces, southern China, in 2016 and 2017, and described the molecular characteristics and genetic diversity of alphacoronaviruses (αCoVs) and betacoronaviruses (βCoVs) found in these bats.

Method
RT-PCR; Illumina sequencing
Sample type
anal swab
Geographic raw
Yunnan and Guangdong provinces, southern China
Country inferred
China