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06-07-2022 | Original Article

Molecular genotypic analysis of porcine circovirus type 2 reveals the predominance of PCV2d in Vietnam (2018–2020) and the association between PCV2h, the recombinant forms, and Vietnamese vaccines

Authors: Huong Thi Thanh Doan, Roan Thi Do, Pham Thi Phuong Thao, Xuyen Thi Kim Le, Khue Thi Nguyen, Nguyen Thi Thu Hien, Luu Minh Duc, Linh Thi Khanh Pham, Thanh Hoa Le

Published in: Archives of Virology | Issue 10/2022

Abstract

We conducted nucleotide and amino acid sequence alignment and phylogenetic analysis of porcine circovirus ORF2 (Cap protein) from 17 PCV2-positive clinical samples from nine different northern Vietnamese provinces (Mar 2018–Nov 2020), four local vaccines, and 77 reference strains. We identified one PCV2a (1/17 = 5.9%), five PCV2b (5/17 = 29.9%), and 11 PCV2d (11/17 = 64.7%) isolates, while only PCV2d was detected in 2020. Timeline analysis indicated an increasing predominance of PCV2d nationwide (2018–2020). With strong nodal support (98% for nucleotides and 74% for amino acids), the phylogenetic tree topology revealed a distinct PCV2h clade including recombinant/intermediate strains and local vaccines. The Cap protein sequences from 11 PCV2d field strains had the 2d-genotype-typical motif ⁸⁶SNPLSV⁹¹ in loop CD, the motif TGID in loop GH-HI, and the motif ²³⁰PLNPK²³⁴ in loop CT. The PCV2h isolates (and vaccines) had the ⁸⁶SNPLSV⁹¹, SAID, and ²³⁰L(N/H)PK²³⁴ motifs. Selection pressure analysis indicated positive selection at seven sites: A⁶⁸N in immunoreactive region (IRR)-A; ¹¹⁹G and ¹³⁰V in IRR-B; and ¹⁶⁷L, T¹⁹⁰(A/S), ¹⁹⁴D and ²⁰²F in IRR-C. We identified PCV2h as the genotype of the recombinant strains, which resulted from intergenotype recombination of PCV2a, PCV2b, and PCV2d. The current data provide new information about the diversity, distribution, and dominance of the PCV2 genotype in Vietnam.

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Title: Molecular genotypic analysis of porcine circovirus type 2 reveals the predominance of PCV2d in Vietnam (2018–2020) and the association between PCV2h, the recombinant forms, and Vietnamese vaccines
Authors: Huong Thi Thanh Doan
Roan Thi Do
Pham Thi Phuong Thao
Xuyen Thi Kim Le
Khue Thi Nguyen
Nguyen Thi Thu Hien
Luu Minh Duc
Linh Thi Khanh Pham
Thanh Hoa Le
Publication date: 06-07-2022
Publisher: Springer Vienna
Published in: Archives of Virology / Issue 10/2022
Print ISSN: 0304-8608
Electronic ISSN: 1432-8798
DOI: https://doi.org/10.1007/s00705-022-05517-4

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