INTRODUCTION
The exports of live pigs and pork products from Thailand have increased since the second half of 2019 due to African swine fever (ASF) outbreaks in China and the neighboring countries in Southeast Asia (SEA). The role of international trade and globalization facilitates the potential spread of many transboundary animal diseases, which later become endemic in the areas. Porcine circovirus type 2 (PCV2) emerged a few decades ago and has caused economic losses to the swine industry globally. The virus induces numerous syndromes and diseases called porcine circovirus-associated disease (PCVAD) consisting of postweaning multisystemic wasting syndrome (PMWS), multisystemic inflammation, porcine dermatitis and nephropathy syndrome (PDNS), reproductive failure, and respiratory disease (Opriessnig & Langohr, 2013; Segales, 2012). The disease manifestations caused by PCV2 vary widely in their severity, ranging from none to severe clinical signs affecting directly or indirectly the growth performance.
PCV2 is a non-enveloped single-stranded DNA virus containing a circular genome of 1766-1768 nucleotides (nt) (L. J. Guo, Lu, Wei, Huang, & Liu, 2010) containing three main open reading frames (ORFs). Replicase protein encoded by ORF1 (Rep gene) is essential for viral replication (Mankertz, Buhk, Blaess, & Mankertz, 1998). Capsid protein encoded by ORF2 (Cap gene) is a viral structural protein playing a significant role in the immunogenicity, virulence, and characteristics of the virus genotypes (Nawagitgul et al., 2000; Olvera, Cortey, & Segales, 2007). Additionally, a non-structural protein encoded by ORF3 could induce apoptosis (Olvera et al., 2007).
PCV2 rapidly evolves prompting, consequently, the emergence of new virus genotypes. To date, the virus is classified into eight distinct genotypes (PCV2a-2h) based on the nucleotide sequence of capsid gene (Franzo & Segales, 2018). The virus shows a high mutation rate (i.e., 10-3-10-4 substitution/site/year) (Franzo, Cortey, Segales, Hughes, & Drigo, 2016) and phylodynamic studies revealed two major genetic shifts: PCV2a towards PCV2b around 2003 and PCV2b towards PCV2d around 2012 (Wang et al., 2020). Recently, PCV2d has overtaken PCV2b and become the predominant genotype worldwide (Xiao, Halbur, & Opriessnig, 2015). PCV2d might derive from the solid selection pressure or vaccine-driven selection pressure by the massive vaccination worldwide and the virus might evolve to enhance its virulence compared with the previously existing PCV2a and PCV2b (L. Guo et al., 2012). Beside the point mutation, recombinant PCV2 strains has also been reported in some countries such as China, India, and South Korea (Jang, Yoo, Kim, Yang, & Lee, 2021; S et al., 2021; Wei et al., 2019). Hence, intra-genotypic or inter-genotypic recombination between the predominant PCV2d and the coexisting genotypes is possible.
In Thailand, the complete genetic data for each PCV2 genotype are limited and have not been updated since 2015 (Thangthamniyom et al., 2017). Therefore, this study aimed to investigate the current prevalence and genetic diversity of the Thai PCV2 based on the whole-genome sequences. The findings may represent the genetic variation of PCV2 not only in Thailand but also in parts of the SEA region. In addition, this study found a novel recombinant strain originating from PCV2b and PCV2d with recombination breakpoints located in the Rep and Capgenes (ORF1 and ORF2 regions). Thus, the information obtained from this study will be useful for better understand the current molecular epidemiology and genetic recombination of PCV2.