14The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic offers a 15 unique opportunity to study the introduction and evolution of a pathogen into a 16 completely naïve human population. We identified and analysed the amino acid 17 mutations that gained prominence worldwide in the early months of the pandemic. 18 Eight mutations have been identified along the viral genome, mostly located in 19 conserved segments of the structural proteins and showing low variability among 20 coronavirus, which indicated that they might have a functional impact. At the moment 21 of writing this paper, these mutations present a varied success in the SARS-CoV-2 virus 22 population; ranging from a change in the spike protein that becomes absolutely 23 prevalent, two mutations in the nucleocapsid protein showing frequencies around 25%, 24 to a mutation in the matrix protein that nearly fades out after reaching a frequency of 25 20%. 26
The present study was aimed at describing the infection dynamics, transmission, and evolution of porcine reproductive and respiratory syndrome virus (PRRSV) after an outbreak in a 300-sow farrow-to-wean farm that was implementing a vaccination program. Three subsequent batches of piglets (9–11 litters/batch) were followed 1.5 (Batch 1), 8 (Batch 2), and 12 months after (Batch 3) from birth to 9 weeks of age. The RT-qPCR analysis showed that shortly after the outbreak (Batch 1), one third of sows were delivering infected piglets and the cumulative incidence reached 80% by 9 weeks of age. In contrast, in Batch 2, only 10% animals in total got infected in the same period. In Batch 3, 60% litters had born-infected animals and cumulative incidence rose to 78%. Higher viral genetic diversity was observed in Batch 1, with 4 viral clades circulating, of which 3 could be traced to vertical transmission events, suggesting the existence of founder viral variants. In Batch 3 though only one variant was found, distinguishable from those circulating previously, suggesting that a selection process had occurred. ELISA antibodies at 2 weeks of age were significantly higher in Batch 1 and 3 compared to Batch 2, while low levels of neutralizing antibodies were detected in either piglets or sows in all batches. In addition, some sows present in Batch 1 and 3 delivered infected piglets twice, and the offspring were devoid of neutralizing antibodies at 2 weeks of age. These results suggest that a high viral diversity was featured at the initial outbreak followed by a phase of limited circulation, but subsequently an escape variant emerged in the population causing a rebound of vertical transmission. The presence of unresponsive sows that had vertical transmission events could have contributed to the transmission. Moreover, the records of contacts between animals and the phylogenetic analyses allowed to trace back 87 and 47% of the transmission chains in Batch 1 and 3, respectively. Most animals transmitted the infection to 1–3 pen-mates, but super-spreaders were also identified. One animal that was born-viremic and persisted as viremic for the whole study period did not contribute to transmission.
Background
Vertical transmission is key for the maintenance of porcine reproductive and respiratory syndrome virus (PRRSV) infection in endemic farms. In most cases, neutralizing antibodies (NAb) more effectively neutralize the homologous strain, but some reports indicate the existence of broadly NAb (bNAb). In vaccinated farms, where all breeders have some levels of immunity, vertical transmission can still occur. The present study correlates the age of sows and the amplitude of NAb with PRRSV-1 vertical transmission (VT) through sampling two vaccinated farms.
Results
The proportion of VT events in the two examined farms ranged from 18.9–23.0%. Young sows (parity 1–2) were 1.7 times more likely to have VT than older sows (p < 0.05). Despite higher ELISA S/P antibody ratios in younger sows (p < 0.05), NAb against the resident farm strain were at a similar level between sows delivering infected and healthy piglets although mostly with low titres (2–3 log2). The titres of NAb against the vaccine virus were also low, and no correlations with VT were observed. When a panel of another 4 strains (1 isolated in the 1990s, and 3 contemporary strains) were used for the neutralization test, most sows were not capable of neutralizing the contemporary strains.
Conclusions
Titres of NAb could not be correlated with the occurrence of PRRSV VT. The amplitude of NAb present in most vaccinated sows is limited with a considerable proportion unresponsive regarding NAb production.
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