Zoonotic infections and genomic evolution of novel reassortant swine influenza A viruses in Spain

  1. Paloma A. Encinas
  2. Brady O’Boyle
  3. Alexander Maksaiev
  4. Martha I. Nelson
  5. Adolfo García-Sastre
  6. Gustavo del Real
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Abstract

Influenza A virus (IAV) circulates widely in European pig populations and continues to diversify through frequent introductions from humans, followed by reassortment within swine. Spain represents a particularly dynamic ecological setting due to the coexistence of intensive white⍰pig production, extensive Iberian⍰pig systems, and abundant wild boar populations. This study provides an integrated analysis of IAV evolution and genomic diversity in swine in Spain between 2019 and 2022, expanding on previous surveillance from 2016 to 2019. Sampling across 24 provinces yielded 66 new whole⍰genome sequences from Iberian and white pigs.

We identified 18 genotypes, including 11 novel reassortants not detected in our previous survey. Several genotypes, such as H1huN2 G21 and G22, H3N2 G23, and the unusual H3N1 G12, were exclusive to the country. Some genotypes were detected across white pigs, Iberian pigs, and wild boar in Toledo and Badajoz, suggesting viral flow among swine populations.

Phylogenetic analyses revealed ongoing introductions of H1N1pdm09 from humans into pigs, generating at least five reassortant genotypes (G10, G16–G19). These lineages incorporated pandemic internal cassettes and, in some cases, human⍰seasonal N2 segments, highlighting the continued role of humans as a source of viral incursions. Conversely, four zoonotic infections (H1N1v) detected in Spain between 2022 and 2026 were linked to genotypes circulating in white pigs, underscoring the bidirectional nature of IAV transmission at the human swine interface.

Overall, this study demonstrates that Spain provides ecological conditions conducive to IAV diversification, reassortment, and zoonotic risk. The findings reinforce the need for sustained One Health surveillance.

Highlights

  • Novel swine influenza virus (SIV) genotypes exclusive to Spain

  • Phylogenetic analysis of genomic segments of zoonotic variants of swine origin detected in Spain since 2022

  • Shared circulation of influenza A compatible with interbreed transmission among domestic pigs and wild boar

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  1. Version published to 10.64898/2026.05.22.724525 on bioRxiv