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ORIGINAL RESEARCH article

Front. Microbiol.
Sec. Virology
Volume 15 - 2024 | doi: 10.3389/fmicb.2024.1423367

Genetic characterization of the first Deltacoronavirus from wild birds around Qinghai Lake

Provisionally accepted
Ye Tian Ye Tian 1Tianqi Yu Tianqi Yu 1*Jun Wang Jun Wang 2*Haoxiang Zhang Haoxiang Zhang 1Yingna Jian Yingna Jian 3*Xiuping Li Xiuping Li 3*Geping Wang Geping Wang 3*Guanghua Wang Guanghua Wang 3*Yong Hu Yong Hu 3*Chenhe Lu Chenhe Lu 1*Jiyong Zhou Jiyong Zhou 1*Liqing Ma Liqing Ma 3*Min Liao Min Liao 1*
  • 1 Key Laboratory of Animal Virology, Ministry of Agriculture, College of Animal Science, Zhejiang University, Hangzhou, Jiangsu Province, China
  • 2 Animal Husbandry and Veterinary Workstation of the Third Division of Xinjiang Production and Construction Corps, Tumushuke, China
  • 3 Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Xining, China

The final, formatted version of the article will be published soon.

    Deltacoronavirus, widely distributed among pigs and wild birds, pose a significant risk of crossspecies transmission, including potential human epidemics. Metagenomic analysis of bird samples from Qinghai Lake, China in 2021 reported the presence of Deltacoronavirus. A specific gene fragment of Deltacoronavirus was detected in fecal samples from wild birds at a positive rate of 5.94% (6/101). Next-generation Sequencing identified a novel Deltacoronavirus strain, which was closely related to isolates from the United Arab Emirates (2018), China (2022), and Poland (2023).Subsequently the strain was named A/black-headed gull/Qinghai/2021(BHG-QH-2021) upon confirmation of the Cytochrome b gene of black-headed gull in the sample. All available genome sequences of avian Deltacoronavirus, including the newly identified BHG-QH-2021 and 5 representative strains of porcine Deltacoronavirus (PDCoV), were classified according to ICTV criteria. In contrast to Coronavirus HKU15, which infects both mammals and birds and shows the possibility of cross-species transmission from bird to mammal host, our analysis revealed that BHG-QH-2021 is classified as Putative species 4. Putative species 4 has been reported to infect 5 species of birds but not mammals, suggesting that cross-species transmission of Putative species 4 is more prevalent among birds. Recombination analysis traced BHG-QH-2021 origin to dut148cor1 and MW01_1o strains, with MW01_1o contributing the S gene. Surprisingly, SwissModle prediction showed that the optimal template for receptor-binding domain(RBD) of BHG-QH-2021 is derived from the human coronavirus 229E, a member of the Alphacoronavirus, rather than the anticipated RBD structure of PDCoV of Deltacoronavirus. Further molecular docking analysis revealed that substituting the loop 1-2 segments of HCoV-229E significantly enhanced the binding capability of BHG-QH-2021 with human Aminopeptidase N (hAPN), surpassing its native receptor-binding domain (RBD). Most importantly, this finding was further confirmed by co-immunoprecipitation experiment that loop 1-2 segments of HCoV-229E enable BHG-QH-2021 RBD binding to hAPN, indicating that the loop 1-2 segment of the RBD in Putative species 4 is a probable key determinant for the virus ability to spill over into humans. Our results summarize the phylogenetic relationships among known Deltacoronavirus, reveal an independent putative avian Deltacoronavirus species with inter-continental and inter-species transmission potential, and underscore the importance of continuous surveillance of wildlife Deltacoronavirus.

    Keywords: Wildbirds, Qinghai Lake, deltacoronavirus, Black-headed Gull, receptor-binding

    Received: 25 Apr 2024; Accepted: 15 May 2024.

    Copyright: © 2024 Tian, Yu, Wang, Zhang, Jian, Li, Wang, Wang, Hu, Lu, Zhou, Ma and Liao. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Tianqi Yu, Key Laboratory of Animal Virology, Ministry of Agriculture, College of Animal Science, Zhejiang University, Hangzhou, 310027, Jiangsu Province, China
    Jun Wang, Animal Husbandry and Veterinary Workstation of the Third Division of Xinjiang Production and Construction Corps, Tumushuke, China
    Yingna Jian, Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Xining, China
    Xiuping Li, Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Xining, China
    Geping Wang, Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Xining, China
    Guanghua Wang, Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Xining, China
    Yong Hu, Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Xining, China
    Chenhe Lu, Key Laboratory of Animal Virology, Ministry of Agriculture, College of Animal Science, Zhejiang University, Hangzhou, 310027, Jiangsu Province, China
    Jiyong Zhou, Key Laboratory of Animal Virology, Ministry of Agriculture, College of Animal Science, Zhejiang University, Hangzhou, 310027, Jiangsu Province, China
    Liqing Ma, Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Xining, China
    Min Liao, Key Laboratory of Animal Virology, Ministry of Agriculture, College of Animal Science, Zhejiang University, Hangzhou, 310027, Jiangsu Province, China

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