Phylogenetic analysis of porcine circovirus type 3 and porcine circovirus type 2 in China detected by duplex nanoparticle-assisted PCR.

Porcine circovirus 2 causes different clinical syndromes resulting in a significant economic loss in the pork industry and PCV3 infection was mainly distributed in the pig herds exhibiting PDNS and reproductive failure symptoms and was widely prevalent in the swine population in several states of the USA. Subsequently, PCV3 was also detected in the Chinese pig herds in Hubei and Shandong Provinces, etc. In a screening of 265 clinical samples from Beijing, Zhejiang, Guangdong and Hebei in China for PCV2, PCV3 and co-infection of PCV2 and PCV3, 14.2%, 16.6% and 6.8% of the samples tested positive, respectively. Under novel and optimized nano-dPCR reaction conditions, two specific fragments of 528 bp (PCV2) and 251 bp (PCV3) were amplified, respectively. No fragments were amplified when other porcine viruses were used as template. In this study, three PCV2 and three PCV3 isolates were evaluated by phylogenetic and alignment analysis and the results revealed that the PCV2 and PCV3 isolates appear new nucleotide substitutions and PCV3 isolates from China still included branch of porcine circovirus in USA. [ABSTRACT FROM AUTHOR]