The oldest porcine circovirus type 2 (PCV2) sequence dates back to 1962 and is among several hundreds of publicly available PCV2 sequences. Despite this resource, few studies have investigated the global genetic diversity of PCV2. To evaluate the phylogenetic relationship of PCV2 strains, 1680 PCV2 open reading frame 2 (ORF2) sequences were compared and analysed by methods of neighbour-joining, maximum-likelihood, Bayesian inference and network analysis. Four distinct clades were consistently identified and included PCV2a, PCV2b, PCV2c and PCV2d; the p-distance between PCV2d and PCV2b was 0.055±0.008, larger than the PCV2 genotype-definition cut-off of 0.035, supporting PCV2d as an independent genotype. Among the 1680 sequences, 278–285 (16.5–17 %) were classified as PCV2a, 1007–1058 (59.9–63 %) as PCV2b, three (0.2 %) as PCV2c and 322–323 (19.2 %) as PCV2d, with the remaining 12–78 sequences (0.7–4.6 %) classified as intermediate clades or strains by the various methods. Classification of strains to genotypes differed based on the number of sequences used for the analysis, indicating that sample size is important when determining classification and assessing PCV2 trends and shifts. PCV2d was initially identified in 1999 in samples collected in Switzerland, now appears to be widespread in China and has been present in North America since 2012. During 2012–2013, 37 % of all investigated PCV2 sequences from US pigs were classified as PCV2d and overall data analysis suggests an ongoing genotype shift from PCV2b towards PCV2d. The present analyses indicate that PCV2d emerged approximately 20 years ago.

Global molecular genetic analysis of porcine circovirus type 2 (PCV2) sequences confirms the presence of four main PCV2 genotypes and reveals a rapid increase of PCV2d

Porcine circoviruses: current status, knowledge gaps and challenges.

Currently, porcine circovirus type 2 (PCV2) is considered the major pathogen of porcine circovirus associated-diseases (PCVAD) that causes large economic losses for the swine industry in the world annually, including China. Since the first report of PCV2 in 1998, it has been drawing tremendous attention for the government, farming enterprises, farmers, and veterinary practitioners. Chinese researchers have conducted a number of molecular epidemiological work on PCV2 by molecular approaches in the past several years, which has resulted in the identification of novel PCV2 genotypes and PCV2-like agents as well as the description of new prevalence patterns. Since late 2009, commercial PCV2 vaccines, including the subunit vaccines and inactivated vaccines, have already been used in Chinese swine farms. The aim of this review is to update the insights into the prevalence and control of PCV2 in China, which would contribute to understanding the epidemiology, control measures and design of novel vaccines for PCV2.

/pdf/porcine-circovirus-type-2-in-china-an-update-on-and-insights-1b2iafn18h.pdf

Porcine circovirus type 2 in China: an update on and insights to its prevalence and control

In 2009 to 2010, there was a marked increase in the number of infections with highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) in China. Through phylogenetic analysis, we show that viruses from this outbreak originated from a single recombination event, illustrating the potential importance of this process for disease emergence.

Recombination Is Associated with an Outbreak of Novel Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Viruses in China

PCV2 has emerged as one of the most devastating viral infections of swine farming, causing a relevant economic impact due to direct losses and control strategies expenses. Epidemiological and experimental studies have evidenced that genetic diversity is potentially affecting the virulence of PVC2. The growing number of PCV2 complete genomes and partial sequences available at GenBank questioned the accepted PCV2 classification. Nine hundred seventy five PCV2 complete genomes and 1,270 ORF2 sequences available from GenBank were subjected to recombination, PASC and phylogenetic analyses and results were used for comparison with previous classification scheme. The outcome of these analyses favors the recognition of four genotypes on the basis of ORF2 sequences, namely PCV2a, PCV2b, PCV2c and PCV2d-mPCV2b. To deal with the difficulty of founding an unambiguous classification and accounting the impossibility to define a p-distance cut-off, a set of reference sequences that could be used in further phylogenetic studies for PCV2 genotyping was established. Being aware that extensive phylogenetic analyses are time-consuming and often impracticable during routine diagnostic activity, ORF2 nucleotide positions adequately conserved in the reference sequences were identified and reported to allow a quick genotype differentiation. Globally, the present work provides an updated scenario of PCV2 genotypes distribution and, based on the limits of the previous classification criteria, proposes new rapid and effective schemes for differentiating the four defined PCV2 genotypes.

/pdf/revisiting-the-taxonomical-classification-of-porcine-3ve77z5drr.pdf

Revisiting the taxonomical classification of Porcine Circovirus type 2 (PCV2): still a real challenge

The epidemic status and genetic diversity of 14 highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) isolates from China in 2009.

The invention discloses a nucleotide primer, a probe sequence and a method for carrying out real-time fluorescent RT (Reverse Transcription)-PCR (Polymerase Chain Reaction) detection on porcine reproductive and respiratory syndrome virus as well as an application of the method in clinically detecting the porcine reproductive and respiratory syndrome virus. The method has the characteristics of rapidity and convenience, strong specificity, high sensitivity and good reliability, and is suitable for rapidly detecting the porcine reproductive and respiratory syndrome virus.

General real-time fluorescent RT (Reverse Transcription)-PCR (Polymerase Chain Reaction) method and kit for detecting porcine reproductive and respiratory syndrome virus

The invention discloses nucleotide primer and probe sequences and a method for real-time fluorescence reverse transcription-polymerase chain reaction (RT-PCR) detection of a highly pathogenic porcine reproductive and respiratory syndrome vaccine, live (JXA1-R strain), and application of the method in detecting the highly pathogenic porcine reproductive and respiratory syndrome vaccine, live (JXA1-R strain). The method overcomes the defects of the traditional detection technology, has the characteristics of quickness, simplicity, convenience, strong specificity, high sensitivity and high reliability, and is suitable for quickly detecting the highly pathogenic porcine reproductive and respiratory syndrome vaccine, live (JXA1-R strain) and monitoring quality in vaccine production.

Real-time fluorescence reverse transcription-polymerase chain reaction (RT-PCR) detection method and kit for highly pathogenic porcine reproductive and respiratory syndrome vaccine, live

Kit for detecting porcine pseudorabies virus (PRV) and porcine parvovirus (PPV)

Identification of an emerging recombinant cluster in porcine circovirus type 2

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