Complete Genome Characteristics of Porcine circovirus Type 2 (PCV2) Isolates from Papuan Pigs, Indonesia

Abstract

Porcine circovirus type 2 (PCV2) has been recognised as an important pathogen in the pig industry world-wide. The virus was recently identified in Papuan pigs, yet information about the characteristics of Papuan PCV2 isolates is limited. The aim of the present study was to characterise the complete genome of Papuan PCV2 isolates. Viral DNA was isolated from 13 blood samples of village pigs from the Jayawijaya region. Four of the PCR positive samples were selected for full genome sequencing. Neighbour Joining phylogeny with P-distance model showed that the four Papuan PCV2 isolates belong to genotype PCV2-IM3. Sequence identity analysis of the Papuan PCV2 genomes further showed 99.5% to 99.6% similarity with a Chinese PCV2-IM3 reference strain. The current study revealed that genotyping based on the ORF2 sequence resulted in a substantially different characterisation of PCV2 genotypes compared to classification based on the complete genome sequences. Furthermore, the study showed that the topology of the PCV2 phylogeny based on the ORF2 sequence was different from the topology based on capsid proteins. Genotyping using the complete genome, ORF2 region or capsid protein sequences resulted in substantial variance in the classification of the PCV2 isolates. The clinical consequence of these different genotyping methods needs further study.