Molecular epidemiological studies of porcine circovirus 3, a novel virus identified in domestic pig and wild boar

Resumen

Porcine circovirus 3 (PCV-3) is a recently discovered circovirus species found in domestic pigs and wild boar. The virus was found in 2016, through metagenomic sequencing approach, in animals affected by reproductive failure, cardiac and multisystemic inflammation. Since then, the virus has been described in pigs with different clinical/pathological presentations as well as in healthy ones, with a widespread circulation. Therefore, the main objective of this Thesis was to gain insights into the molecular epidemiology of PCV-3 in samples from domestic pigs and wild boar from Spain. In the first study, the presence of PCV-3 in the Spanish pig population was retrospectively evaluated from 1996 to 2017 in sera from animals of different production phases and clinical/pathological conditions. The detection of PCV-3 genome in such samples was attempted by PCR and partial genome sequences were obtained from selected PCV-3 positive samples from different years. Compiled data confirmed that PCV-3 has been circulating in the Spanish pig population since 1996. The overall frequency of PCV-3 PCR positive samples in the study period was 11.47% (75 out of 654). Phylogenetic analysis of the PCV-3 obtained sequences showed high identity with the already known PCV-3 sequences, with low variations among years. Although the available information was limited, PCV-3 did not appear to be linked to any specific pathological condition or pig age-group. The second study of this Thesis aimed to assess the dynamics of PCV-3 infection by means of PCR in serum. A total of 152 pigs from 4 different healthy farms, which were sampled longitudinally five or six times from 2-4 weeks of age until the end of the fattening period, were analyzed. PCV-3 genome was found in pigs from all tested ages and farms; few animals had an apparent long-term infection during a period ranging from 4 to 23 weeks. Phylogenetic analysis showed high similarity among the obtained sequences and with available PCV-3 genomes from different countries. Results confirmed that PCV-3 circulated in all studied farms from Spain, suggesting that infection is probably widespread in the country. Most pigs got infection during their life, although PCV-3 did not appear to circulate mostly at any specific age. In the third study, the frequency of PCV-3 infection was retrospectively assessed in Spanish wild boar from 2004 to 2018, as well as in captured and re-captured animals (at least two times in a time period of 1 month to 1 year). Obtained results confirmed the susceptibility of wild boar to the virus, showing high frequency of PCV-3 detection (221 out of 518, 42.66%) and demonstrating circulation at least since 2004. Compiled data suggests that PCV-3 is apparently able to cause persistent infection, since 5 out of 10 PCV-3 PCR positive captured/re-captured boars showed positivity in samplings separated for more than 5 months. The frequency of PCV-3 genome was also investigated for the first time in different tissue samples and feces, where all tested tissue types’ harbored PCV-3 genome. The highest percentage of PCR positivity was found in submandibular lymph node, tonsil, lung, liver, spleen and kidney. The amount of DNA in all tested PCV-3 PCR positive samples was moderate to low. All partial and complete PCV-3 sequences obtained from wild boar displayed high nucleotide similarity (>98%). In conclusion, the obtained results of this Thesis provide relevant data on the epidemiology of this novel virus, PCV-3, in both domestic pig and wild boar, which appear to be widespread. Moreover, the phylogenetic information suggests low genetic variability of PCV-3, in contrast with other single stranded-DNA viruses.