3.6.5. Chile
The backyard productive systems (BPS) for raising swine, cattle, and poultry are popular in Chile. A molecular investigation reported a negative active IAV infection across 113 BPS units within ten counties in Chile during 2012–2014 but the serological investigation detected IAV antibodies in swine at two BPS units which suggested a past exposure of swine to the IAV [332]. Interestingly, the HA gene sequence of an H12 virus was obtained from a domestic Muscovy duck at one of the BPS which appeared to have originated from a wild bird. This suggested a spillover of the IAV from wild reservoir to the domestic poultry [332].
Another study reported the prevalence of H1N2 virus in swine reared at 40 different BPS having poultry and swine in El Yali wetland during 2013–2014 [333]. One more study identified four swine sera samples (4/64; 6.3%) that were found positive for IAV antibodies collected from different BPS in Central Chile. One pool of swine nasal swab samples (1/39; 2.6%) was also detected IAV positive with real-time RT-PCR. Interestingly, 7.9% chicken, 4.3% ducks and 11.1% geese samples collected from 329 BPS in Central Chile also had active IAV infections. The breeding practice of poultry and swine in the BPS was determined to be a major risk factor for IAV transmission [334].
Briefly, the IAV strains of H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses have been reported from the swine in Argentina and Brazil while A(H1N1)pdm09 virus was reported in swine in Colombia and Peru. Swine in Chile were found infected with H1N2 virus (Figure 4F).
In summary, total 281 research articles were identified which reported several influenza viruses in swine populations globally. The highest number of studies were reported from Asia (n = 107), followed by North America (n = 76), Europe (n = 55), South America (n = 21), Africa (n = 18) and Australia (n = 4). The highest number of reports per country were documented in United States (n = 40) followed by China (n = 39) and Canada (n = 24). Until February 2020, influenza viruses have been reported from 53 countries worldwide. Four subtypes of IAV including H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses were most frequently detected in swine populations (Table 1).
Most of the large-scale studies used serological investigations including ELISA, hemagglutinin inhibition (HI), neuraminidase inhibition (NI), virus neutralization (VN), or microneutralization (MN) assays for the determination of the seroprevalence and subtyping of the influenza viruses in swine. Several investigations used virus isolation for the confirmation and subtyping of IAV. Most of the virological investigations used one-step real-time RT-PCR and/or reverse-transcription PCR for influenza virus detection and subtyping. Sanger sequencing or next-generation sequencing using MiSeq or Ion Torrent sequencing successfully generated the influenza virus sequences from the swine samples for epidemiological interpretations. Histological examinations including immunohistochemistry or immunofluorescence were used to examine the swine lung or other internal organ tissue samples for the influenza virus diagnostics (Table 2).