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Phylogeography and evolutionary dynamics analysis of porcine delta-coronavirus with host expansion to humans
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  • Gen Li,
  • Shao-Lun Zhai,
  • Xia Zhou,
  • Tianbao Chen,
  • Jiawei Niu,
  • YS Xie,
  • Guangbin Si,
  • Feng Cong,
  • Ruiai Chen,
  • Dongsheng He
Gen Li
South China Agricultural University College of Veterinary Medicine
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Shao-Lun Zhai
Institute of Animal Health Guangdong Academy of Agricultural Sciences Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province Ministry of Agriculture of Rural Affairs and Key Laboratory of Animal Disease Prevention of Guangdong Province Guangzhou 510640 China
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Xia Zhou
South China Agricultural University College of Veterinary Medicine
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Tianbao Chen
South China Agricultural University College of Veterinary Medicine
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Jiawei Niu
South China Agricultural University College of Veterinary Medicine
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YS Xie
South China Agricultural University College of Veterinary Medicine
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Guangbin Si
South China Agricultural University College of Veterinary Medicine
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Feng Cong
Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals Guangzhou 510633 China
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Ruiai Chen
South China Agricultural University College of Veterinary Medicine
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Dongsheng He
South China Agricultural University College of Veterinary Medicine
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Abstract

From 2003 onwards, three pandemics have been caused by coronaviruses: severe acute respiratory syndrome coronavirus (SARS-CoV); middle east respiratory syndrome coronavirus (MERS-CoV); and, most recently, SARS-CoV-2. Notably, all three were transmitted from animals to humans. This would suggest that animals are potential sources of epidemics for humans. The emerging porcine delta-coronavirus was reported to infect children. This is a red flag that marks the ability of PDCoV to break barriers of cross-species transmission to humans. Therefore, we conducted molecular genetic analysis of global clade PDCoV to characterize spatio-temporal patterns of viral diffusion and genetic diversity. PDCoV was classified into three major lineages, according to distribution and phylogenetic analysis of PDCoV. It can be determined that PDCoV originated in Asia—most likely in Southeast Asia—through inference of migration rate and transmission routes. We also selected six special spike amino acid sequences to align and analyze to find seven significant mutation sites. The accumulation of these mutations may enhance dynamic movements, accelerating spike protein membrane fusion events and transmission. Altogether, our study offers a novel insight into the diversification, evolution, and interspecies transmission and origin of PDCoV and emphasizes the need to study the zoonotic potential of the PDCoV and comprehensive surveillance and enhanced biosecurity precautions for PDCoV.
17 Sep 2021Submitted to Transboundary and Emerging Diseases
17 Sep 2021Submission Checks Completed
17 Sep 2021Assigned to Editor
19 Sep 2021Reviewer(s) Assigned
20 Oct 2021Review(s) Completed, Editorial Evaluation Pending
23 Oct 2021Editorial Decision: Revise Major
10 Nov 20211st Revision Received
10 Nov 2021Submission Checks Completed
10 Nov 2021Assigned to Editor
12 Nov 2021Reviewer(s) Assigned
15 Dec 2021Review(s) Completed, Editorial Evaluation Pending
16 Dec 2021Editorial Decision: Revise Major
31 Jan 20222nd Revision Received
03 Feb 2022Submission Checks Completed
03 Feb 2022Assigned to Editor
04 Feb 2022Reviewer(s) Assigned
14 Feb 2022Review(s) Completed, Editorial Evaluation Pending
14 Feb 2022Editorial Decision: Revise Minor
17 Feb 20223rd Revision Received
17 Feb 2022Assigned to Editor
17 Feb 2022Submission Checks Completed
20 Feb 2022Reviewer(s) Assigned
21 Feb 2022Review(s) Completed, Editorial Evaluation Pending
22 Feb 2022Editorial Decision: Accept
19 Mar 2022Published in Transboundary and Emerging Diseases. 10.1111/tbed.14503