First identification of porcine parvovirus 6 in North America by viral metagenomic sequencing of serum from pigs infected with porcine reproductive and respiratory syndrome virus

Abstract

BackgroundCurrently, eight species in four genera of parvovirus have been described that infect swine. These include ungulate protoparvovirus 1 (classical porcine parvovirus, PPV), ungulate tetraparvovirus 2 (PPV3), ungulate tetraparvovirus 3 (which includes PPV2, porcine hokovirus, porcine partetravirus and porcine PARV4), ungulate copiparvovirus 2 (which includes PPV4 and PPV5), ungulate bocaparvovirus 2 (which includes porcine bocavirus 1, 2 and 6), ungulate bocaparvovirus 3 (porcine bocavirus 5), ungulate bocaparvovirus 4 (porcine bocavirus 7) and ungulate bocaparvovirus 5 (porcine bocavirus 3, 4–1 and 4–2). PPV6, the most recently described porcine parvovirus, was first identified in China in late 2014 in aborted pig fetuses. Prevalence of PPV6 in China was found to be similar in finishing age pigs from farms with and without evidence of swine reproductive failure.MethodsPorcine parvovirus 6 (PPV6) was detected by sequence-independent single primer amplification (SISPA) and confirmed by overlapping and real-time PCR in the serum of porcine reproductive and respiratory virus (PRRSv) positive samples.ResultsSeven nearly complete genomes of PPV6 were identified in PRRSv genotype 2 positive serum samples submitted to state veterinary diagnostic laboratories in 2014. Further testing using overlapping and real-time PCR determined PPV6 to be present in 13.2 % of the serums tested. Additionally, PPV6 was present in samples from all of the geographic locations sampled encompassing nine states in the United States and one state in Mexico. The presence of PPV6 in serum indicates that the PPV6 infection is disseminated and not localized to a specific tissue type. Alignments of the near full length genomes, NS1, and capsid genes identified one of the five PPV6 isolates from China (98.6–99.5 % identity with the North American strains) to be the North American strains nearest relative.ConclusionsThese results are the first to report the presence of PPV6 in North America and demonstrate that the virus is found in multiple geographic areas in the United States and in Mexico. The overall prevalence of PPV6 in PRRSv viremic animals is relatively low. Further, all of the PPV6 genomes found in North America are most closely related to a PPV6 strain first identified in 2014 in healthy pigs from the Tianjin province of China.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-015-0401-6) contains supplementary material, which is available to authorized users.

Increasing diversity of swine parvoviruses and their epidemiology in African pigs

“…In the following year, Ni et al (2014) for the first time identified another novel pig parvovirus, tentatively named as PPV6, from aborted swine foetuses which showed negative results for other swine's reproductive failure pathogens in pigs in China. Subsequently, the virus has been detected through a high throughput sequencing of PRRSV positive serum samples from swine in the USA and Mexico, with a very high similarity to the PPV6 discovered in China (Schirtzinger et al, 2015). Reports from the two investigations have unanimously proposed the classification of the novel PPV6 under the genus Copiparvovirus alongside the PPVs 4 and 5, as they all formed the same cluster in their phylogenetic analyses and as it could be seen in Fig.…”

“…More recent ones are yet to be assigned into species and genus under the subfamily. These include PPVs 5, 6 and 7 (Xiao et al, 2013a;Ni et al, 2014;Schirtzinger et al, 2015;Palinski et al, 2016;Xing et al, 2018).…”

“…Protoparvovirus) in the classification, while porcine parvovirus 2 (PPV2) and porcine parvovirus 3 (PPV3) were categorized together with human parvovirus 4 (PARV4) in the genus Tetraparvovirus due to their relatively close genomic homologies. The porcine parvovirus 4 (PPV4) belongs to the genus Copiparvovirus alongside with bovine parvovirus 2 (Cotmore et al, 2014), and the genus have been proposed to contain the novel PPVs 5 and 6 as they have constantly clustered within the group in phylogenetic analyses (Xiao et al, 2013b;Ni et al, 2014;Schirtzinger et al, 2015). In addition, eigth pig viruses and virus variants are presently grouped under the genus Bocaparvovirus to make four distinct genera of swine parvoviruses in the published classification (Cotmore et al, 2014).…”

A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections

“…Again, we detected PPV6-related sequences in pigs that were slaughtered even in 1998 (and in a period spanning 1998–2004), more than 10 years before this virus was first recognized in China from specimens collected in 2010–2013 [32] and then identified in the United States and Mexico [19]. …”

Possible risks posed by single‐stranded DNA viruses of pigs associated with xenotransplantation

“…Human parvoviruses are known to be intransigent to in vitro culture and only a few have been propagated in cell culture such as the B19V and HBoV . In pigs, eight species of the Parvoviridae family classified under four genera are described (Table ); ungulate protoparvovirus 1 [classical porcine parvovirus (PPV) or PPV1], ungulate tetraparvovirus 2 (PPV3), ungulate tetraparvovirus 3 (PPV2, also known as porcine hokovirus or porcine partetravirus or porcine PARV4), ungulate copiparvovirus 2 (PPV4, PPV5 and PPV6), ungulate bocaparvovirus 2 [porcine bocavirus (PBoV) 1, 2 and 6], ungulate bocaparvovirus 3 (PBoV 5), ungulate bocaparvovirus 4 (PBoV 7), and ungulate bocaparvovirus 5 (PBoV 3, PBoV4.1 and PBoV4.2) . PPV1 was first identified in the early 1970s in association with abortions in pigs .…”