Porcine circovirus type 2 (PCV2) genomic diversity in Canadian swine diagnostic samples collected from 2021 to 2023: Highlighting PCV2d and PCV2e genotypes.

OBJECTIVE

In light of growing concerns regarding potential increases in porcine circovirus type 2 (PCV2)-associated diseases in Quebec between 2021 and 2022, the objective was to characterize PCV2 genotype diversity in Canada.

SAMPLES AND PROCEDURE

A total of 54 analyzed samples (2021 to 2023) either were submitted by veterinarians to the Molecular Diagnostic Laboratory (MDL) of the Centre de Diagnostic Vétérinaire de l'Université de Montréal (CDVUM) or were collected from pigs necropsied at the Quebec Ministry of Agriculture, Fishery and Food (MAPAQ) laboratories. The sick pigs from which samples were collected had various clinical signs, including those of PCV2-associated diseases. Whole-genome sequencing for PCV2 was done either by Sanger sequencing from 2 PCR amplicons covering the entire viral genome or by high-throughput sequencing.

RESULTS

The main PCV2 subtype identified as circulating in Canada was PCV2d (48.1%). Only 1 strain clustered into the PCV2e subtype (1.9%). In previous reports, PCV2b was the main subtype present in the field. However, only 5 PCV2b sequences (9.3%) were identified in 2022 and 2023.

CONCLUSION AND CLINICAL RELEVANCE

This is apparently the first official identification of PCV2d and 2e genotypes in diseased Canadian pigs. Results also provided an overview of PCV2 strains now circulating in Canada compared to reports from 2007 to 2008.