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. 2018 Feb 7;14(1):43.
doi: 10.1186/s12917-018-1345-z.

Genetic variation analysis of PCV1 strains isolated from Guangxi Province of China in 2015

Liang Cao  1   2 , Wenchao Sun  2 , Huijun Lu  2 , Mingyao Tian  2 , Changzhan Xie  1   2 , Guanyu Zhao  2   3 , Jicheng Han  2 , Wei Wang  2 , Min Zheng  4 , Rui Du  5 , Ningyi Jin  6   7 , Aidong Qian  8
Affiliations

Genetic variation analysis of PCV1 strains isolated from Guangxi Province of China in 2015

Liang Cao et al. BMC Vet Res. .

Abstract

Background: Porcine circovirus type 1 (PCV1) was discovered in 1974 as a contaminant of a porcine kidney (PK-15) cell line and was generally accepted to be nonpathogenic. But recently it was shown to cause lesions in experimentally infected pig fetuses. Serological evidence and genetic studies suggested that PCV1 was widespread in domestic pigs. Thus, the molecular epidemiology and genetic variation of PCV1 are still necessary to understand.

Results: Here 247 tissue samples were collected from piglets in Guangxi Province, China and performed whole-genome sequencing of the PCV1 genome. Thirteen PCV1 strains were sequenced from the samples. Similarity analysis showed that there were 97.8% to 99.6% nucleotide similarity to each other and 97.1% to 99.8% nucleotide similarity to the 40 reference strains. Besides, based on sequence analysis, we found one putative recombinant virus named GXdx84 strain contained the open-reading frame 1 (ORF1) of PCV1 and the ORF2 of PCV2d-2, which was consistent with the results of phylogenetic analysis that compared PCV1 and PCV2 strains. Variation analysis of the amino acids of the capsid protein revealed that the GXyl224 strain, which encoded 235 amino acids, had two amino acids more than other strains. This is the first study to report that a cap gene mutation resulted in lengthening of in the gene sequence.

Conclusions: These data contribute to the understanding of PCV1 evolution and molecular epidemiology that will facilitate programs for its control and prevention.

Keywords: Genetic variation; Phylogenetic study; Porcine circovirus 1; Putative recombinant virus.

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Conflict of interest statement

Ethics approval and consent to participate

Experimental protocols for obtaining pigs clinical samples used in this study were obtained from Guangxi Center for Animal Disease Control and Prevention and carried out in strict accordance with the Animal Ethics Procedures and Guidelines of the People's Republic of China. All pigs were euthanized by an anesthetic overdose with the pentobarbital before collected the samples and all pig owners agree the samples’ usage before participation in the study.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Alignment of the nucleotide sequence and deduced amino acid for the cap gene, and Cap protein of partial strains analyzed in this study. Conserver residues are indicated by dashed lines. PCV1 is used as the majority sequence for this alignment (AY193712). a The cap gene of GXyl224 inside the red box is one wherein the stop codon mutation led to an increase in the number of nucleotides. b The major nucleotide mutation sites of Cap protein are presented within the red box
Fig. 2
Fig. 2
Phylogenetic tree analysis based on the nucleotide sequences of the complete genome (a), cap gene (b), and rep gene (c), performed using the ML method. Numbers along the branches indicate the percentage of confidence in the ML analysis. Only bootstrap support values of >50% are indicated. PCV1 strains isolated in this study are denoted by triangle (▲)
Fig. 3
Fig. 3
Simplot analysis the recombination events. One recombination event might be occurred in GXdx84 strain with the PCV1G strain (JN398656) and PCV2b strain (AF112862) as two parent groups. The Y–axis refers to the percentage of similarity. The X–axis refers to the nucleotide position in alignment. The crossed point might be the potential location of recombination event
Fig. 4
Fig. 4
Plot for the difference between non-synonymous and synonymous rates (dN–dS) and amino acid entropy rate for the rep (a) and cap (b) genes
See this image and copyright information in PMC

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