Vaccines against porcine circovirus 2 (PCV2) are now widely used to control the diseases caused by the virus. Although the vaccines protect pigs against the disease, they do not lead to sterilizing immunity and therefore infections with PCV2 continue in farms. It is expected that, due to its high evolutionary rate, PCV2 can adapt quickly to environmental pressures such as vaccination. The goal of this study was to elucidate the molecular variation of PCV2 in relation to vaccination. PCV2 variability was investigated from samples of infected pigs from five farms where vaccination had never been applied and two farms where pigs had been vaccinated for at least 2 years. For the genetic analysis, full PCV2 genomes were amplified and subsequently pooled by vaccination status from serum of eight vaccinated, infected pigs and 16 non-vaccinated, infected pigs. Variability of viral populations was quantified using next-generation sequencing and subsequent bioinformatics analysis. The number of segregating sites was similar in the non-vaccinated (n5109) and vaccinated pools (n596), but the distribution of these sites in the genome differed. Most notably, in the capsid gene, the number of segregating sites was observed only in the nonvaccinated population. Based on the structural analysis, it is expected that some low-frequency amino acids result in biologically low-fit viruses. On the contrary, D294 in replicase represents a novel amino acid which was dominant and unique in the vaccinated pool. This work showed that variable PCV2 populations were circulating in commercial farms, and that this variability was different in samples obtained from vaccinating and non-vaccinating farms.
14Torque teno virus (TTV) is a non-enveloped, single stranded DNA (ssDNA) 15 virus infecting human and non-primate species. Two genogroups of TTV (TTV1 and 16 TTV2) have been described in swine so far. In the present study, TTV1 and TTV2 17 prevalences in serum, and nasal as well as rectal swabs of 55 randomly selected piglets 18 from seven Spanish multi-site farms, were monitored from 1 to 15 weeks of age. Also, 19 blood from their dams (n=41) were taken at 1 week post-farrowing. Samples were 20 tested by means of two TTV genogroup specific PCRs. Although prevalence of TTV1 21 and TTV2 in sows was relatively high (54% and 32%, respectively), it was not directly 22 associated to their prevalence in the offspring. Percentage of viremic pigs for both TTV 23 genogroups followed similar dynamics, increasing progressively over time, with the 24 highest rate of detection at 11 weeks of age for TTV1 and at 15 weeks for TTV2. Forty-25 two (76%) and 33 (60%) of the 55 studied pigs were TTV1 and TTV2 PCR positive in 26 serum, respectively, in more than one sampling time. TTV1 and TTV2 viremia lasted in 27 a number of animals up to 15 and 8 weeks, respectively. Co-infection with both TTV 28 genogroups in serum was detected at all sampling points, but at 1 week of age. On the 29 contrary, there were animals PCR negative to both genogroups in serum at all sampling 30 times but at 15 weeks of age. During the study period, TTV1 and TTV2 nasal shedding 31 increased also over time and faecal excretion was intermittent and of low percentage 32 (<20%). In conclusion, the present study describes for the first time the infection 33 dynamics of TTV1 and TTV2 as well as the nasal and faecal excretion throughout the 34 life of in pigs from conventional, multi-site farms. Moreover, results indicate that both 35 swine TTV genogroups are able to establish persistent infections in a number of pigs. 36
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