#17,615
When we talk about influenza A viruses in swine, we are generally talking about H1N1, H1N2, H3N2, or very rarely H3N1. The CDC lists 3 Swine viruses (1-H1N2, and 2-H3N2) as having moderate pandemic potential in their IRAT (Influenza Risk Assessment Tool) list.
Pigs, however, are famously susceptible to infection and coinfection with a wide variety of human-avian-swine influenza A viruses, which raises the possibility of reassortment events creating new hybrid viruses.
But influenza surveillance in the United States is limited, and in many countries it is non-existent. Exactly what is circulating in pigs in across large swaths of Asia, Africa, or South America is largely unknown.
We get glimpses, of course.
Hong Kong routinely tests pigs coming from the mainland, we sometimes see investigations following spillover events (to humans), and every once in a while we get a surveillance report or analysis from a university or biomedical research team.
In recent months, with the proliferation of H5N1 around the globe, we've seen increasing concerns over the potential for HPAI to infect swine herds, which could lead to increased mammalian adaptation.
While HPAI H5 has been detected occasionally over the past two decades in pigs in China and Indonesia - proving that pigs were at least partially susceptible - H5N1's recently acquired penchant for spilling over into mammals has scientists increasingly concerned.
This was also a concern voiced 6 months ago, when the ECDC/EFSA Avian Influenza Overview December 2022 – March 2023 warned:
The additional reports of transmission events to and potentially between mammals, e.g. mink, sea lion, seals, foxes and other carnivores as well as seroepidemiological evidence of transmission to wild boar and domestic pigs, associated with evolutionary processes including mammalian adaptation are of concern and need to be closely followed up.
Last May, we looked at a report out of Italy (see Seroconversion of a Swine Herd in a Free-Range Rural Multi-Species Farm against HPAI H5N1 2.3.4.4b Clade Virus), and today we have a report from Senegal on a 15-month (Sept 2018 - Dec 2019) active influenza surveillance study conducted at the lone pig slaughterhouse in Dakar.
Note: This study was completed before the emergence and global spread of our current H5N1 threat.
While no active infections with avian H5, H7, or H9 viruses were detected by PCR, > 80% of pigs tested showed serological evidence of past avian flu infection. H7N7 and H9N2 led the way, but H5N1 and H5N2 were well represented.
Due to its length, I've only included some excerpts. Follow the link to read the report in its entirety.
Influenza A Virus in Pigs in Senegal and Risk Assessment of Avian Influenza Virus (AIV) Emergence and Transmission to Human
Mamadou Malado Jallow 1,2, Mamadou Aliou Barry 3, Amary Fall 1, Ndiendé Koba Ndiaye 1, Davy Kiori 1, Sara Sy 1, Déborah Goudiaby 1, Mbayame Ndiaye Niang 1, Gamou Fall 1, Malick Fall 2,† and Ndongo Dia 1,*,†
Microorganisms 2023, 11(8), 1961; https://doi.org/10.3390/microorganisms11081961
Received: 22 May 2023 / Revised: 25 July 2023 / Accepted: 26 July 2023 / Published: 31 July 2023
Abstract
We conducted an active influenza surveillance in the single pig slaughterhouse in Dakar to investigate the epidemiology and genetic characteristics of influenza A viruses (IAVs) and to provide serologic evidence of avian influenza virus (AIV) infection in pigs at interfaces with human populations in Senegal. Nasal swab and blood samples were collected on a weekly basis from the same animal immediately after slaughter. Influenza A viruses were diagnosed using RT-qPCR and a subset of positive samples for H3 and H1 subtypes were selected for full genome amplification and NGS sequencing.
Serum samples were tested by HI assay for the detection of antibodies recognizing four AIVs, including H9N2, H5N1, H7N7 and H5N2.
Between September 2018 and December 2019, 1691 swine nasal swabs were collected and tested. Influenza A virus was detected in 30.7% (520/1691), and A/H1N1pdm09 virus was the most commonly identified subtype with 38.07% (198/520), followed by A/H1N2 (16.3%) and A/H3N2 (5.2%). Year-round influenza activity was noted in pigs, with the highest incidence between June and September. Phylogenetic analyses revealed that the IAVs were closely related to human IAV strains belonging to A/H1N1pdm09 and seasonal H3N2 lineages.
Genetic analysis revealed that Senegalese strains possessed several key amino acid changes, including D204 and N241D in the receptor binding site, S31N in the M2 gene and P560S in the PA protein.
Serological analyses revealed that 83.5% (95%CI = 81.6–85.3) of the 1636 sera tested were positive for the presence of antibodies against either H9N2, H5N1, H7N7 or H5N2. Influenza H7N7 (54.3%) and H9N2 (53.6%) were the dominant avian subtypes detected in Senegalese pigs. Given the co-circulation of multiple subtypes of influenza viruses among Senegalese pigs, the potential exists for the emergence of new hybrid viruses of unpredictable zoonotic and pandemic potential in the future.
3.6. Serological Evidence of AIV Infection in Pigs
To investigate avian influenza virus (AIV) infection in pigs from Senegal, HI activity was tested from serum samples collected during the surveillance period by using four different AIVs as antigens, namely A/H9N2, A/H5N1, A/H7N7 and A/H5N2. The seroprevalence rates of each virus are summarized in Table 3.
Of the 1636 serum samples analyzed with the HI test, 1367 (83.5%; 95%CI = 81.6–85.3) were positive for the presence of antibodies against either A/H9N2, A/H5N1, A/H7N7 or A/H5N2. In serum samples collected in 2018, AIV was detected in 92.4% (364/394), whereas in 2019, HI antibody was detected in 80.4% (1003/1248).
Overall, influenza A/H7N7 and A/H9N2 were the dominant avian subtypes detected, with seropositivity rates of 54.3% (889/1636) and 53.6% (877/1636), respectively. Antibodies against A/H5N1 and A/H5N2 were detected at similar rates, with 31% (506/1636) and 30.7% (502/1636), respectively (Figure 4).
Among the tested serum samples, we found that some pigs had antibodies against different serotypes simultaneously, with 549 being positive for both A/H9N2 and A/H7N7 (40.2%). A total of 387 samples were copositive for A/H9N2 and A/H5N1 (28.3%), whereas 335 specimens were copositive for A/H7N7 and A/H5N1 (24.5%). Antibodies against all four AIVs targeted in this study were detected simultaneously in 181 individual pigs (13.2%).
5. Conclusions
In summary, the present study provides an overview of the epidemiology and genetic characteristics of influenza viruses circulating in the Senegalese pigs population, as well as serological evidence of avian influenza infection in this swine population. Globally, results of this active surveillance have shown a relatively high prevalence of influenza viruses in Senegalese pig herds, with a year-round circulation (peak of infection during the rainy season between June and September) of at least three influenza strains, including A/H1pdm09, A/H1N2 and A/H3N2.
Molecular studies revealed multiple introductions of H1N1pdm09-like sublineage and human-like lineages that resembled pandemic A/H1N1pdm09 and seasonal A/H3N2 strains in human in Senegal, respectively. The occurrence of frequent amino acid mutations in both influenza A/H1N1pdm09 and A/H3N2 viruses support the need for whole genome sequencing, as well as analyzing virus evolution and gene mutations in a timely manner.
Our study also revealed serological evidence of infection by at least four AIVs in pigs in Senegal, including A/H9N2, A/H5N1, A/H7N7 and A/H5N2, with a high seroprevalence rates.
Given the co-circulation of multiple subtypes of influenza viruses among Senegalese pigs, the potential exists for the emergence of new hybrid viruses of unpredictable zoonotic and pandemic potential in the future. Therefore, regular monitoring and frequent surveillance of influenza viruses in pigs and in markets that contain wild birds and live poultry are essential as part of an overall approach to the prevention and pandemic preparedness of animal and human influenza.
While there is obviously some comfort to be taken from the fact that avian viruses have been spilling over into swine for years - and no pandemic-ready reassortment has emerged - past performance is no guarantee of future results.
