Aguilar Nágila Rocha, Santos Beatriz Senra Alvares da Silva, Carraro Bruno Zinato, Rocha Brenda Monique Magalhães, Bernardino Jardelina de Souza Todao, Fraiha Ana Luiza Soares, Lima Alex Ranieri Jeronimo, Ribeiro Gabriela, Dias Alessandra Silva, Carvalho Renata Rezende, Ribeiro Bruna Ferreira Sampaio, Giovanetti Marta, Alcântara Luiz Carlos Júnior, Sampaio Sandra Coccuzzo, Sabbaga Maria Carolina Quartim Barbosa Elias, Nicolino Rafael Romero, Lobato Zélia Inês Portela, Guedes Maria Isabel Maldonado Coelho, Mota Filho Cesar Rossas, Viala Vincent Louis, Lopes Bruna Coelho, Costa Erica Azevedo
Laboratório de Pesquisa em Virologia Animal, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil.
Integrall Soluções em Produção Animal, Patos de Minas 38700-052, Brazil.
Pathogens. 2025 Jul 31;14(8):753. 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.
传统上，甲型猪流感病毒（swIAV）监测主要集中于呼吸道样本，然而新出现的证据表明，粪便排毒及继发性环境污染也可能促进病毒传播。在本研究中，我们收集并分析了来自巴西米纳斯吉拉斯州一个商业化农场自然感染猪的鼻腔、直肠、环境、牛奶和初乳样本。在25%的样本中检测到了IAV RNA，其中包括42%来自无症状动物的样本，鼻腔拭子的检出率（30%）高于直肠拭子（20%），不过直肠样本的Ct值始终较高，表明病毒载量较低。我们成功地从粪便和废水样本中分离出了活病毒。全基因组测序显示，地方流行性pH1N1进化枝#2（HA）和pN1进化枝#4（NA）共同传播，同时还有人源H3N2序列聚集在进化枝3C.2a1b.2a.2a.1内，以及与2001年至2002年3C之前的人类谱系相关的N2片段。系统发育和p距离分析支持了近期的反向人畜共患病和历史传播事件。从直肠拭子和处理后的废水中检测到完整的HA/NA序列，进一步强调了非呼吸道样本的监测价值。整合呼吸道和粪便/环境样本对于在猪群中实现更全面的IAV监测似乎很重要，并且可能对巴西及其他地区的“同一个健康”战略产生重大影响。
