Infection of pigs with influenza A virus H3.2010.1 clade in Ontario

Davor Ojkic, Tim Pasma, Kevin Vilaca, Meegan Larsen, Yohannes Berhane.

Animal Health Laboratory, University of Guelph, Guelph, ON (Ojkic, Pasma, Larsen); South West Veterinarians, Stratford, ON (Vilaca); National Center for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB (Berhane)

AHL Newsletter 2023;27(3):12.

In April 2023, samples from four 7-week old piglets were submitted to the University of Guelph Animal Health Laboratory (AHL).  The herd had a history of respiratory distress and an increase in mortality. Samples included formalin-fixed tissues for histologic examination as well as 4 nasal swabs for PRRSV and influenza A virus PCR tests.  Histologic examination found lung lesions consistent with influenza infection (Fig. 1), and influenza A virus antigen was detected in bronchial and bronchiolar epithelial cells in affected areas using immunohistochemistry (Fig. 2). A diagnosis of influenza was also supported by strong positive PCR test results for influenza A virus (Ct=22.21-28.6) on all four swabs.  One swab was also weakly positive for PRRSV (Ct=35.54); however, microscopic lesions suggestive of PRRSV infection were not seen in lungs.

Figure 1.  Porcine lung with lesions of suppurative bronchointerstitial pneumonia.  Bronchioles and adjacent alveoli contain large numbers of neutrophils, and there is patchy attenuation and loss of bronchiolar epithelium (black arrows).  (H&E stain)

Figure 2.  Porcine lung with positive (brown) cytoplasmic staining of bronchiolar epithelial cells lining affected bronchioles.  (Influenza A immunohistochemical stain)

Hemagglutinin gene sequencing of one positive sample revealed the virus belonged to influenza A virus subtype H3N2 clade 2010.1 (H3.2010.1).  This clade was identified in Ontario swine previously in 2017, when four cases from the same owner were detected, but that outbreak did not spread to other farms.  No other detection of H3.2010.1 clade was documented until 2023.  Interestingly, in 2022 H1N1/H1N2 subtype viruses were the most frequently detected influenza A subtype in Ontario samples: 61% of genotyped viruses were H1N1/H1N2 subtype and 39% were H3N2 subtype (Table 1).

Table 1.  Genotyping results for influenza A viruses from pigs in Ontario (January 1, 2022-December 31, 2022).

However, since April 2023, the prevalence of H3N2 viruses has increased markedly: 78.6% have been genotyped as H3N2 and only 21.4% were H1N1/H1N2.  The H3.2010.1 clade has become the dominant H3N2 strain in Ontario, and since its initial detection in April 2023, H3.2010.1 represents 84% of H3N2 influenza A viruses from pigs (Table 2).  The whole genome sequences were obtained for 5 recent cases, and they all showed a remarkably high identity among themselves, and a very high level of identity to the US viruses. 

First detected in humans during the 2010-11 flu season, genetically-related swine H3.2010.1 viruses have become established in swine populations in the US, and have been the most common clade detected in several US states.  Ontario pig herds appear to be going through a rapid transmission cycle, but it is not yet known if the virus has appeared in other Canadian provinces.  AHL

Table 2. Genotyping results for influenza A viruses from pigs in Ontario (April 15, 2023-July 26, 2023).

References

1. Rajão DS, et al.  Novel reassortant human-like H3N2 and H3N1 influenza A viruses detected in pigs are virulent and antigenically distinct from swine viruses endemic to the United States.  J Virol 2015;89(22):11213-22.

2. Powell JD, et al.  Characterization of contemporary 2010.1 H3N2 swine influenza A viruses circulating in United States pigs. Virology 2021;553:94-101.