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Molecular based detection, genetic characterization and phylogenetic analysis of porcine circovirus 4 from Korean domestic swine farms
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  • Giap Nguyen,
  • Hai-Quynh Do,
  • Le Huynh,
  • Yong Ho Park,
  • Bong Kyun Park,
  • Heechun Chung
Giap Nguyen
Vietnam National University of Agriculture
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Hai-Quynh Do
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Le Huynh
Vietnam National University of Agriculture
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Yong Ho Park
Seoul National University
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Bong Kyun Park
Seoul National University
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Heechun Chung
Seoul Nationational University
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Abstract

Porcine circovirus 4 (PCV4), a novel and unclassified member of the genus Circovirus, was first reported in China in 2019. Aimed at providing more evidence about the active circulation of PCV4, this study screened 335 pooled internal organs and detected the virus (i) at the rates of 3.28%, (ii) from both clinical healthy and clinical sick pigs of various age groups, and (iii) in six out of nice provinces of Korea. The complete genomic sequence of a Korean PCV4 strain (E115) was 1,770 nucleotides in length and had 98.5% to 98.9% identity to three PCV4 strains available at GenBank up to date. Utilizing a set of bioinformatic programs, it was revealed that the Korean PCV4 strain contained several genomic features of (i) a palindrome stem-loop structure with conserved nonanucleotide, (ii) packed overlapping ORFs oriented in different directions, and (iii) two intergenic regions in between genes encoding putative replication- associated protein (Rep) and capsid (Cap) proteins. This study also predicted the presence of essential elements known so far for the replication of circoviruses, for example, the origin of DNA replication, endonuclease and helicase domains of Rep, the nuclear localization signal on the putative Cap protein. Finally, based on the phylogeny inferred from sequences of the putative Rep protein, it was suggested that PCV4 belong to genus Circovirus of family Circoviridae and losely related to three previous known porcine circoviruses of PCV1, PCV2 and PCV3.

Peer review status:ACCEPTED

03 Oct 2020Submitted to Transboundary and Emerging Diseases
03 Oct 2020Submission Checks Completed
03 Oct 2020Assigned to Editor
14 Oct 2020Reviewer(s) Assigned
27 Nov 2020Review(s) Completed, Editorial Evaluation Pending
29 Nov 2020Editorial Decision: Revise Major
14 Jan 20211st Revision Received
15 Jan 2021Assigned to Editor
15 Jan 2021Submission Checks Completed
16 Jan 2021Reviewer(s) Assigned
25 Jan 2021Review(s) Completed, Editorial Evaluation Pending
26 Jan 2021Editorial Decision: Revise Minor
26 Jan 20212nd Revision Received
26 Jan 2021Submission Checks Completed
26 Jan 2021Assigned to Editor
27 Jan 2021Reviewer(s) Assigned
30 Jan 2021Review(s) Completed, Editorial Evaluation Pending
31 Jan 2021Editorial Decision: Accept