Porcine circovirus 2 (PCV2) population study in experimentally infected pigs developing PCV2-systemic disease or a subclinical infection

Abstract

Porcine circovirus 2 (PCV2) is a single stranded DNA virus with one of the highest mutation rates among DNA viruses. This ability allows it to generate a cloud of mutants constantly providing new opportunities to adapt and evade the immune system. This pig pathogen is associated to many diseases, globally called porcine circovirus diseases (PCVD) and has been a threat to pig industry since its discovery in the early 90’s. Although 11 ORFs have been predicted from its genome, only two main proteins have been deeply characterized, i.e. Rep and Cap. The structural Cap protein possesses the majority of the epitopic determinants of this non-enveloped virus. The evolution of PCV2 is affected by both natural and vaccine-induced immune responses, which enhances the genetic variability, especially in the most immunogenic Cap region. Intra-host variability has been also demonstrated in infected animals where long-lasting infections can take place. However, the association between this intra-host variability and pathogenesis has never been studied for this virus. Here, the within-host PCV2 variability was monitored over time by next generation sequencing during an experimental infection, demonstrating the presence of large heterogeneity. Remarkably, the level of quasispecies diversity, affecting particularly the Cap coding region, was statistically different depending on viremia levels and clinical signs detected after infection. Moreover, we proved the existence of hyper mutant subjects harboring a remarkably higher number of genetic variants. Altogether, these results suggest an interaction between genetic diversity, host immune system and disease severity.

The Isolated in Utero Environment Is Conducive to the Emergence of RNA and DNA Virus Variants

“…In contrast, six passages in cell lines did not increase PCV2 mutant spectrum complexity. As per our findings in fetuses, PCV2 genomic diversity and the association of clinical signs with virus diversity have been described in young pigs [35]. Interestingly, all iSNVs that emerged in fetuses in our study were previously reported in young or adult pigs on farms (Table S6), suggesting that in utero-emerging PCV2 variants may reach susceptible populations outside the maternal body, potentially contributing to the heterogeneity of circulating viruses and outbreaks.…”

Computational based design and tracking of synthetic variants of Porcine circovirus reveal relations between silent genomic information and viral fitness

“…According to some studies, in-host viral quasispecies represent a single selection unit, where selection is not performed based on the individual variant's fitness, but according to the population's mutant distribution 66 , 67 . A recent study tested this hypothesis on PCV2 by monitoring PCV2 variability over time during an experimental infection suggesting an interaction between genetic heterogeneity, immune system response and disease severity 35 . Our research tested a synthetic version of the quasispecies hypothesis using PCV2 for several passages within cells, without the linkage to an immune system of a host.…”

“…Furthermore, there are previous studies that aimed to estimate the fitness and dynamics of PCV2 strains in the host (see, for example 35 ). Currently it is very challenging to compare our approach to such studies as our synthetic viruses are completely different to naturally circulating strains that were shaped by evolution in pigs.…”

“…Sequence variations are mostly found in the capsid gene 33 . There are multiple lines of evidence of in-vivo recombination and co-infection that include several PCV2 genotypes—a within-host diversity of PCV2 quasispecies, demonstrating the role of the host's immune response in PCV2 evolution 34 , 35 .…”

One Dose of a Novel Vaccine Containing Two Genotypes of Porcine Circovirus (PCV2a and PCV2b) and Mycoplasma hyopneumoniae Conferred a Duration of Immunity of 23 Weeks

“…Due to their single stranded DNA nature and small genomic size, PCV2 viruses have a very high evolutionary rate. In fact, PCV2 viruses have a mutation frequency of around 10 3 –10 4 substitutions/site/year, which is one of the highest rates among DNA viruses and it is at the level of the variation seen in RNA viruses [ 4 ]. This high mutation rate, together with the high rate of recombination (second to PCV2′s propensity for multi-strain or multi-genotype co-infections and infection persistence), immune pressure lead to the genesis of novel and divergent PCV2 variants.…”