Genome Characterization and Sequence Analysis of Porcine Circovirus Type 2 Isolated with High Viral Load

Abstract

【Objective】The study was carried out to understand the genetic evolution of Porcine Circovirus Type 2 (PCV2) strains on a swine farm in Guangdong Province, and enrich molecular epidemiological data of PCV2, in order to provide reference for the selection and development of local PCV2 vaccine candidate strains.【Method】Samples suspected of PCV2 infection were detected by using qPCR methods. A PCV2-positive isolate with a high viral load was found, named GD222858. Genome-wide molecular cloning and genetic evolution analysis were performed with PCR methods. MegAlign software was used to compare the amino acid sequences encoded by the ORF1 and ORF2 genes of the strain with the PCV2 isotype reference strain, and the similarity of the amino acid sequences was analyzed. The DNAStar was used to predicte the Cap protein secondary structure and B-cell epitope of this strain and compare it with the Cap protein antigen index of four vaccine strains DBN-SX07-2 (HM641752), LG (HM038034), SH (HM038027) and ZJ (AY686764).【Result】Sequencing results showed that the genome length of GD222858 strain was 1 767 bp. The genetic evolution analysis indicated that the strain belonged to the PCV2d subtype. The nucleotide similarity with 82 reference strains at home and abroad ranged from 91.4% to 99.6%. It was closest to the Vietnamese strain Han8 (GenBank accession No.: JQ181600). Multiple specific mutation sites F70Y, F77L, W202R and N256S were found at the Rep protein encoded by ORF1. The Cap protein encoded by ORF2 was relatively conserved. Protean predicted that the potential B cell epitopes presented at amino acid positions 5-18, 24-25, 39-41, 48-49, 57-65, 99, 101, 112-114, 139-140, 145-150, 162-165, 175-181, 188-189, 205-211 and 227-232 of Cap proteins. The Cap protein antigen index of the GD222858 strain was different from that of the four vaccine strains, and the antigen index at the amino acids 45-57, 124-132 and 223-233 was significantly higher than that of the other four vaccine strains, and the difference with the LG vaccine strain (HM038034) was greatest.【Conclusion】The reason for the infection of GD222858 strain in pig herds may be due to specific mutations in multiple sites of the Rep protein and improper selection of vaccine strains.

Keywords

• porcine circovirus type 2 (pcv2)
• genetic evolution analysis
• orf1 gene
• orf2 gene
• b-cell epitope
• antigen index