Introduction
Outbreaks of influenza A viruses (IAV) have caused considerable harm to the animal and human health with several global socio-economic impacts (McLeod, Morgan, Prakash, & Hinrichs, 2005). Wild aquatic birds such as the Anseriformes and Charadriiformes are the major natural reservoirs of IAV, except H17 and H18 subtypes detected in bats (Munster et al., 2007; Tong et al., 2013). In addition to its natural reservoir circulation, IAV can cross the species barrier and infect a wide range of hosts including, canids, equids, humans, poultry, and swine (Joseph, Su, Vijaykrishna, & Smith, 2017).
Wild waterfowl migration has a dominant role in the global influenza virus spread (Franklin et al., 2019; Ren et al., 2016). Every year, low pathogenic avian influenza (LPAI) outbreaks among waterfowl occur during migration when contact rates among waterfowl populations are high (van Dijk et al., 2014). Indeed, migratory wild birds are associated with intra- and intercontinental dissemination of IAV as well as the geographic dispersion of IAV subtypes in wild bird species and poultry residents (Fourment, Darling, & Holmes, 2017; Humphreys et al., 2020).
The wildlife – livestock interface represents a significant source of disease in domestic flocks (Wang, Jiang, Jin, Tan, & Xu, 2013). Some production practices such as free-range farming may increase the likelihood of contact among wild and domestic populations, and represent a critical factor for persistence and transmission of IAV (Cappelle et al., 2014). Likewise, backyard systems are considered suitable areas for influenza surveillance due to the complex interactions between swine, poultry, humans, and wild animals (Hamilton-West et al., 2012; Jimenez-Bluhm et al., 2018).
Previous research has provided some insights into the dynamic of IAV at the wildlife –livestock interface (Wiethoelter, Beltrán-Alcrudo, Kock, & Mor, 2015). Phylogenetic analyses have revealed high sequence homology among IAV circulating in pigs, poultry, and wild birds (Bergervoet et al., 2019; Osbjer et al., 2016). Ecological and phylogeographical analyses have shown that migratory waterfowl, domestic ducks, free‐ranging animals, and agroecosystems are crucial in the maintenance and viral spread (Wei, Lin, & Xie, 2015). Serological and molecular studies of IAV have evidenced the viral circulation in backyard farms situated close to “el Yali”, one of the most important wetlands in South America (Bravo-Vasquez et al., 2016).
The Lerma marshes constitute a critical surveillance area where wild ducks, backyard poultry, backyard pigs, and humans co-occur in time and space. Some molecular studies in wild ducks and their environment have been conducted in this Natural Protected Area (Cuevas-Domínguez et al., 2009; Ornelas-Eusebio, Obregón-Ascencio, Chávez-Maya, & García-Espinosa, 2015; Ramírez-Martínez, Loza-Rubio, Mosqueda, González-Garay, & García-Espinosa, 2018). Nevertheless, the aims of these studies were no centered on the interrelation among diverse species, and a persistent gap in knowledge about IAV dynamics in the wildlife – livestock interface remains in the region. Therefore, this study performed molecular and phylogenetic characterization of IAV in wild ducks, backyard swine, and backyard poultry at this interface of Central Mexico.