Fecal and Environmental Shedding of Influenza A Virus in Brazilian Swine: Genomic Evidence of Recent Human-to-Swine Transmission

Surveillance of swine influenza A virus (IAV) traditionally focuses on respiratory matrices, yet emerging evidence suggests fecal and environmental routes may play significant roles in viral dissemination. In this study, we collected and analyzed nasal, rectal, environmental, milk, and colostrum samples from naturally infected pigs in a commercial farm in Minas Gerais, Brazil. IAV RNA was detected in 28% of samples, including 42% from asymptomatic animals, with nasal swabs showing higher detection rates (31%) than rectal swabs (24%), though rectal Ct values were consistently higher, indicative of lower viral loads. We successfully isolated viable virus from feces and effluent samples. Whole-genome sequencing revealed co-circulation of enzootic pH1N1 clade #2 (HA) and pN1 clade #4 (NA), alongside human-origin H3N2 sequences clustering within clade 3C.2a1b.2a.2a.1, and N2 segments related to pre 3C human lineages from 2001–2002. Phylogenetic and p-distance analyses support both recent reverse zoonosis and historical transmission events. Detection of complete HA/NA sequences from rectal swabs and treated effluent further emphasizes the surveillance value of non respiratory matrices. The integration of respiratory and fecal/environmental sampling is essential for more comprehensive IAV monitoring in swine herds, with significant implications for One Health strategies in Brazil and beyond.