Abstract
Swine play a key role in the ecology and transmission of influenza A viruses (IAVs) between species. However, the epidemiology and diversity of swine IAVs is not completely understood. In this cohort study, we sampled on a weekly basis 132 3-week old pigs for 15 weeks. We found two overlapping epidemic events of infection in which most pigs (98.4%) tested PCR positive for IAVs. The prevalence rate of infection ranged between 0 and 86% per week and the incidence density ranged between 0 and 71 cases per 100 pigs-week. Three distinct influenza viral groups (VGs) replicating as a “swarm” of viruses were identified (swine H1-gamma, H1-beta, and H3-cluster-IV IAVs) and co-circulated at different proportions over time suggesting differential allele fitness. Furthermore, using deep genome sequencing 13 distinct viral genome constellations were differentiated. Moreover, 78% of the pigs had recurrent infections with IAVs closely related to each other or IAVs clearly distinct. Our results demonstrated the molecular complexity of swine IAVs during natural infection of pigs in which novel strains of IAVs with zoonotic and pandemic potential can emerge. These are key findings to design better health interventions to reduce the transmission of swine IAVs and minimize the public health risk.
Highlights
influenza A viruses (IAVs) are Orthomyxoviruses that contain eight single stranded negative sense RNA gene segments namely polymerase B2 (PB2, segment 1), polymerase B1 (PB1, segment 2), polymerase A (PA, segment 3), hemagglutinin (HA, segment 4), nucleoprotein (NP, segment 5), neuraminidase (NA, segment 6), matrix (M, segment 7), and non-structural protein (NS, segment 8)
We found that three different influenza viral groups (VG) co-circulated at different proportions over time and produced two overlapping epidemic events in which the majority of the pigs had recurrent infections with IAV
A total of 2,080 individual nasal swabs were collected over 15 weeks, and 369 (17.7%) tested positive for IAV by real time reverse transcriptase polymerase chain reaction (RRT-PCR)
Summary
IAVs are Orthomyxoviruses that contain eight single stranded negative sense RNA gene segments namely polymerase B2 (PB2, segment 1), polymerase B1 (PB1, segment 2), polymerase A (PA, segment 3), hemagglutinin (HA, segment 4), nucleoprotein (NP, segment 5), neuraminidase (NA, segment 6), matrix (M, segment 7), and non-structural protein (NS, segment 8). According to the United States Department of Agriculture (USDA), National Agricultural Statistical Service (NASS), in the USA there are almost 72 million pigs and approximately 9 to 10 million are slaughtered every month[19], which illustrates the high turnover rate of swine populations The majority of these pigs are weaned at 3 weeks of age from farrow-to-wean herds and moved to growing pig production sites (i.e wean to finish farms) where they are reared until market (~24 weeks of age). We found that three different influenza viral groups (VG) co-circulated at different proportions over time and produced two overlapping epidemic events in which the majority of the pigs had recurrent infections with IAV These results are important because they unraveled a deeper layer of the epidemiology and molecular diversity of swine IAVs at the herd level and will help to design better health interventions to reduce the transmission of IAVs between pigs and from pigs to humans
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