Genome plasticity of triple-reassortant H1N1 influenza A virus during infection of vaccinated pigs

Abstract

To gain insight into the evolution of influenza A viruses (IAVs) during infection of vaccinated pigs, we experimentally infected a 3-week-old naive pig with a triple-reassortant H1N1 IAV and placed the seeder pig in direct contact with a group of age-matched vaccinated pigs (n510). We indexed the genetic diversity and evolution of the virus at an intra-host level by deep sequencing the entire genome directly from nasal swabs collected at two separate samplings during infection. We obtained 13 IAV metagenomes from 13 samples, which included the virus inoculum and two samples from each of the six pigs that tested positive for IAV during the study. The infection produced a population of heterogeneous alleles (sequence variants) that was dynamic over time. Overall, 794 polymorphisms were identified amongst all samples, which yielded 327 alleles, 214 of which were unique sequences. A total of 43 distinct haemagglutinin proteins were translated, two of which were observed in multiple pigs, whereas the neuraminidase (NA) was conserved and only one dominant NA was found throughout the study. The genetic diversity of IAVs changed dynamically within and between pigs. However, most of the substitutions observed in the internal gene segments were synonymous. Our results demonstrated remarkable IAV diversity, and the complex, rapid and dynamic evolution of IAV during infection of vaccinated pigs that can only be appreciated with repeated sampling of individual animals and deep sequence analysis.

Genetic variability of influenza A virus in pigs at weaning in Midwestern United States swine farms

“…Results reported in this study widen the landscape of IAV diversity in US swine. Co-circulation of different IAVs and their variants in piglets is known to occur prior to weaning at both the population and individual level (Diaz, Enomoto, et al, 2015;Diaz, Marthaler, Corzo, et al, The detection of multiple subtypes and genotypes in piglets and farms at a given time was frequently observed in our study. New IAVs were clearly identified both at the piglet and at the farm levels.…”

“…Piglets play a crucial role in generating, maintaining and disseminating IAV infections within farms (Diaz, Enomoto, et al, 2015; Munoz, 2002; Pitzer et al, 2016; Reynolds, Torremorell, & Craft, 2014). Though piglets are not infected with IAV at birth, they can acquire these viruses during the suckling period (Diaz, Enomoto, et al, 2015) and sustain the infections without manifesting clinical signs, despite the presence of maternal immunity (Allerson, Deen, et al, 2013). Such piglets act as silent carriers of IAV and may spread the virus to other destinations or farms (Allerson, Cardona, & Torremorell, 2013; Allerson, Deen, et al, 2013; Diaz, Marthaler, Corzo, et al, 2017).…”

Complete Genome Sequencing of Influenza A Viruses within Swine Farrow-to-Wean Farms Reveals the Emergence, Persistence, and Subsidence of Diverse Viral Genotypes

“…IAVs are transmitted with a collection of HA alleles (sequence variants) that can emerge or disappear during infection of humans and pigs ( 47 – 49 ). This dynamic transmission of different IAV alleles during infection of vaccinated pigs involves the entire genome of the virus, not only HA ( 49 ), and suggests that the emergence, maintenance, and subsidence of diverse IAV genotypes on farrow-to-wean farms may be due to the combination of different alleles present at the individual level. Moreover, the cocirculation of two or more IAVs contributes to genetic reassortment and the emergence of novel IAVs ( 50 , 51 ).…”

Neutral Theory and Rapidly Evolving Viral Pathogens

“…2015 ). The same is not said to be true in pigs, however, as diversity within even partially immune swine is significant and highly dynamic over the course of infection ( Diaz et al. 2015 ), underscoring the role played by within-host evolution in antigenic shift and the need for further NGS studies of genetic plasticity in intermediate hosts.…”