Abstract
Porcine circovirus type 2 (PCV2) is the pivotal pathogen causing porcine circovirus-associated diseases. In this study, 62 PCV2 isolates were identified from seven farms in southern China from 2013 to 2015 and phylogenetic trees were reconstructed based on whole-genome sequences or the cap gene. In this investigation, PCV2b was the main genotype in circulation throughout these farms. Furthermore, an emerging mutant (PCV2b-1C), isolated from PCV2-vaccinated farms, was the predominant strain prevalent on these farms. In addition, we isolated a new cluster that may represent evolution of the virus through recombination of PCV2b-1A/1B and PCV2b-1C. Finally, we discuss evidence that antigenicity and surface structure variation of the capsid resulted from mutation of the C-terminal loop (Loop CT) of the PCV2b-1C Cap in silico.
Highlights
Porcine circoviruses (PCVs), the smallest, non-enveloped animal viruses of the genus Circovirus in the family Circoviridae, have a circular ssDNA genome (Cheung, 2006)
Based on PCR, 62/160 (38.8%) samples were apparently Porcine circovirus type 2 (PCV2)-positive; these 62 samples were subjected to genomic DNA amplification (Table S1, available in the online Supplementary Material) and sequence analysis
A phylogenetic tree was reconstructed using complete genomic DNA sequences of the 62 PCV2 isolates along with 27 PCV2 and one porcine circovirus type 1 (PCV1) reference strains deposited in GenBank (Fig. 1)
Summary
Porcine circoviruses (PCVs), the smallest, non-enveloped animal viruses of the genus Circovirus in the family Circoviridae, have a circular ssDNA genome (Cheung, 2006). There are two known main genotypes, porcine circovirus type 1 (PCV1) and PCV2, with high levels of nucleotide homology and a common genomic organization (Segales et al, 2013). The first isolation of PCV1 was from a porcine kidney cell line (PK15; ATCC CCL-33) as a contaminant and non-pathogenic agent in swine (Tischer et al, 1986, 1974). PCV2 has a circular genome of 1766–1768 nt (Wei et al, 2013) with three major ORFs. Whereas ORF1 encodes
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