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Pathogens
. 2025 Jul 31;14(8):753.
doi: 10.3390/pathogens14080753. Fecal and Environmental Shedding of Influenza A Virus in Brazilian Swine: Genomic Evidence of Recent Human-to-Swine Transmission
Nágila Rocha Aguilar 1 , Beatriz Senra Alvares da Silva Santos 1 , Bruno Zinato Carraro 2 , Brenda Monique Magalhães Rocha 1 , Jardelina de Souza Todao Bernardino 3 , Ana Luiza Soares Fraiha 1 , Alex Ranieri Jeronimo Lima 3 , Gabriela Ribeiro 3 , Alessandra Silva Dias 4 , Renata Rezende Carvalho 1 , Bruna Ferreira Sampaio Ribeiro 1 , Marta Giovanetti 5 6 7 , Luiz Carlos Júnior Alcântara 5 6 , Sandra Coccuzzo Sampaio 3 , Maria Carolina Quartim Barbosa Elias Sabbaga 3 , Rafael Romero Nicolino 8 , Zélia Inês Portela Lobato 1 , Maria Isabel Maldonado Coelho Guedes 1 , Cesar Rossas Mota Filho 9 , Vincent Louis Viala 3 10 , Bruna Coelho Lopes 9 , Erica Azevedo Costa 1
Affiliations
Surveillance of swine influenza A virus (swIAV) traditionally focuses on respiratory matrices, yet emerging evidence suggests that fecal shedding and secondary environmental contamination may also contribute to 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 25% of samples, including 42% from asymptomatic animals, with nasal swabs showing higher detection rates (30%) than rectal swabs (20%), though rectal Ct values were consistently higher, indicative of lower viral loads. We successfully isolated viable viruses 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 to 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 appears important to achieve more comprehensive IAV monitoring in swine herds and may have significant implications for One Health strategies in Brazil and beyond.
Keywords: H3N2; environmental surveillance; fecal shedding; influenza A virus; pH1N1; phylogenetics; reverse zoonosis; swine.
. 2025 Jul 31;14(8):753.
doi: 10.3390/pathogens14080753. Fecal and Environmental Shedding of Influenza A Virus in Brazilian Swine: Genomic Evidence of Recent Human-to-Swine Transmission
Nágila Rocha Aguilar 1 , Beatriz Senra Alvares da Silva Santos 1 , Bruno Zinato Carraro 2 , Brenda Monique Magalhães Rocha 1 , Jardelina de Souza Todao Bernardino 3 , Ana Luiza Soares Fraiha 1 , Alex Ranieri Jeronimo Lima 3 , Gabriela Ribeiro 3 , Alessandra Silva Dias 4 , Renata Rezende Carvalho 1 , Bruna Ferreira Sampaio Ribeiro 1 , Marta Giovanetti 5 6 7 , Luiz Carlos Júnior Alcântara 5 6 , Sandra Coccuzzo Sampaio 3 , Maria Carolina Quartim Barbosa Elias Sabbaga 3 , Rafael Romero Nicolino 8 , Zélia Inês Portela Lobato 1 , Maria Isabel Maldonado Coelho Guedes 1 , Cesar Rossas Mota Filho 9 , Vincent Louis Viala 3 10 , Bruna Coelho Lopes 9 , Erica Azevedo Costa 1
Affiliations
- PMID: 40872267
- PMCID: PMC12388998
- DOI: 10.3390/pathogens14080753
Surveillance of swine influenza A virus (swIAV) traditionally focuses on respiratory matrices, yet emerging evidence suggests that fecal shedding and secondary environmental contamination may also contribute to 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 25% of samples, including 42% from asymptomatic animals, with nasal swabs showing higher detection rates (30%) than rectal swabs (20%), though rectal Ct values were consistently higher, indicative of lower viral loads. We successfully isolated viable viruses 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 to 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 appears important to achieve more comprehensive IAV monitoring in swine herds and may have significant implications for One Health strategies in Brazil and beyond.
Keywords: H3N2; environmental surveillance; fecal shedding; influenza A virus; pH1N1; phylogenetics; reverse zoonosis; swine.