Vaccination against swine flu causes different patterns of evolution – Abstracts

Influenza A viruses can infect a wide variety of bird and mammal species. Its genome is characterized by 8 segments of single-stranded RNA. The low corrective activity of their polymerases and genomic rearrangements between different subtypes of influenza A virus allow them to continuously evolve, which poses a constant threat to human and animal health. The 2009 influenza A virus pandemic highlighted the importance of the pig host in the adaptation of these viruses between humans and birds. The number of pigs and the incidence of swine influenza A virus are constantly growing. In previous studies, despite vaccination, the growth and evolution of influenza A virus was confirmed in vaccinated and challenged pigs. However, how vaccination may influence the evolutionary dynamics of swine influenza A virus following co-infection with the two subtypes has not been well studied. In the present study, vaccinated and unvaccinated pigs were challenged by direct contact with pigs inoculated with swine influenza A viruses independent of H1N1 and H3N2. Nasal swab samples were collected daily, and on the day of necropsy, bronchoalveolar lavage fluid was also collected from each pig for swine influenza A virus detection and whole genome sequencing. A total of 39 complete genome sequences of swine influenza A virus were obtained by next-generation sequencing from samples collected from both experimental groups. Subsequently, genomic and evolutionary analyzes were performed to detect both genomic rearrangements and single-nucleotide variants.

Regarding the segments detected in the sample, the co-occurrence of segments of both subtypes was much lower in vaccinated animals, indicating that the vaccine reduces the likelihood of genomic rearrangement events. Regarding intrahost diversity of swine influenza A virus, a total of 239 and 74 single nucleotide variants were detected in the H1N1 and H3N2 subtypes, respectively. Different proportions of synonymous and non-synonymous substitutions were found, indicating that the vaccine may influence the underlying mechanism shaping the evolution of swine influenza A virus, exhibiting natural, neutral and purifying selection in the different scenarios analyzed. The genome of swine influenza A virus has identified single nucleotide variants with important nonsynonymous substitutions in polymerases, surface glycoproteins, and nonstructural proteins that may affect viral replication, immune evasion, and viral virulence. respectively.

The present study also highlights the enormous evolutionary capacity of swine influenza A virus in natural infection and vaccine pressure scenarios.

Lopez-Valinhas A, Valle M, Wang M, Dargie A, Cantero G, Chiapponi S, Segales J, Gang L, Nunez HI. Vaccination of pigs against swine flu causes different evolutionary patterns during experimental infection with the swine flu virus and reduces the likelihood of genome recombination. Frontiers in cellular and infectious microbiology. 2023; 13. https://www.frontiersin.org/articles/10.3389/fcimb.2023.1111143.