Molecular identification and phylogenetic characterization of influenza A virus at a wildlife–livestock interface in Mexico

Abstract

Influenza A virus (IAV) outbreaks constitute a constant threat to public health and pose a remarkable impact on socio-economic systems worldwide. Interactions between wild and domestic birds, humans and swine can lead to spillover events. Backyard livestock systems in proximity to wetlands represent high-risk areas for viral spread. However, some gaps remain in our knowledge of IAV transmission at the wildlife-livestock interface in Mexico. Hence, the study aimed at molecular identification and phylogenetic characterization of IAV in the wild duck-backyard livestock interface at a wetland of Mexico. A total of 875 animals were tested by real-time RT-PCR (qRT-PCR). We detected IAV in 3.68% of the wild ducks sampled during the winter season 2016-2017. Nonetheless, the samples obtained from backyard poultry and swine tested negative. The highest IAV frequency (11.10%) was found in the Mexican duck (Anas diazi). Subtypes H1N1, H3N2 and H5N2 were detected.Phylogenetic analyses revealed that IAV detected in wild birds from the Lerma wetlands was mostly related to swine and poultry IAV strains previously isolated in the United States and Mexico. Except, the UIFMVZ377/H5N2 related to North American waterbirds. In conclusion, the co-circulation of three IAV subtypes in wild ducks close to backyard farms in Mexico, as well as the local identification of influenza viruses genetically related to Mexican and North American IAV strains, highlights the importance of the Lerma marshes for influenza surveillance given the close interaction among wild birds, poultry, pigs and humans.

A systematic review of influenza A virus prevalence and transmission dynamics in backyard swine populations globally

“…The study's objective was to determine IAV circulation at this interface and identify and characterize the IAV subtypes. While none of the swine nasal swabs tested IAV positive, which ruled out active IAV infection in the backyard swine, three IAV subtypes, including H1N1, H3N2, and H5N2, were detected in the Mexican duck ( Anas diazi ), which emphasized the significance of active IAV surveillance in the region to monitor the possible future spillover [ 44 ].…”

“…While a few studies (n = 13; 38.24%) reported that swine were the only household animals in the backyards [ 19 , 21 , 22 , 41 , 43 , 45 ], most of the studies reported either the presence of swine and poultry (n = 19; 55.88%) [ 20 , 24 , 44 , 47 – 49 ] or swine, poultry, and cattle (n = 2; 5.88%) [ 42 , 46 ] (Fig. 10 a).…”

“…10 a). Interestingly, 13 (38.24%) studies reported that swine and poultry regularly interacted in the backyards [ 12 , 20 , 23 , 27 , 28 , 33 , 35 , 37 , 39 , 40 , 47 – 49 ], while seven (20.58%) studies reported interactions among the wild birds, swine, and poultry [ 24 – 26 , 30 , 32 , 36 , 44 ]. Two (5.88%) studies reported interactions among the swine, poultry, and cattle [ 42 , 46 ], while the other remaining studies (n = 12; 35.29%) did not mention any interactions between backyard swine and other animal species [ 18 , 21 , 22 , 29 , 31 , 34 , 38 , 41 , 45 ] (Fig.…”

“…The molecular investigations that utilized real-time RT-PCR and Sanger sequencing for detection and characterization of IAV reported that pandemic A(H1N1)pdm09 virus clade 1A.3.3.2 was the more frequently present IAV subtype (n = 6; 27.27%) [ 19 , 21 , 24 , 26 , 27 , 50 ] in backyard swine populations compared to H1N2 (n = 2; 9.09%) [ 20 , 48 ], H3N2 (n = 2; 9.09%) [ 19 , 32 ], and H5N1 (n = 2; 9.09%) [ 12 , 36 ] subtypes. Several molecular investigations (n = 9; 40.91%) could not detect IAV in backyard swine swab or tissue samples under investigation [ 23 , 25 , 28 , 34 , 35 , 43 , 44 , 47 ], which resulted in a negative IAV prevalence, suggesting the absence of IAV active infection at the time of the investigation (Fig. 10 e).…”