Characterization of Influenza A Viruses among humans, pigs and poultry and factors associated with acute respiratory illness among pig workers at the human-animal interface in selected sites in Kenya

Abstract

Transmission of Influenza A viruses between humans and pigs is associated with occupational and environmental exposures. The main objective of the study was to identify the influenza viruses circulating among humans, pigs and poultry and determine factors associated with acute respiratory illness among pig workers at household and slaughterhouse levels. The study was conducted in four repeated cross-sectional studies among humans, pigs and poultry with the household component conducted in Kiambu county while the slaughterhouse component was done in Kiambu, Siaya and Kisumu counties. Three participants were randomly selected in each selected household, while the pigs were sampled proportionate to herd size. Nasopharyngeal (NP) and Oropharyngeal (OP) swabs were collected from participants who reported acute respiratory illness (ARI) defined as cough with/without history of fever within the previous seven days. Nasal swabs and blood samples were collected from pigs and poultry. The human and animal swab samples were tested for viral nucleic acid by RT-PCR and animal sera tested by ELISA for antibodies. Data were collected using an interviewer administered questionnaire and a logistic generalized linear mixed effect model was implemented to assess the association between pig exposure and occurrence of ARI within 30 days of sampling. All study participants gave informed consent and the study obtained ethical approval. In the household component of the study, 1,267 including 384 (30.3%) pig workers and 883 (69.7%) non-pig workers were enrolled. Of 130 human NP/OP swabs tested, four (3.1%) were positive for Influenza A virus. Seroprevalence of animal sera was 6.2% (265/4273), including 11.6% (230/1990) in pigs and 1.5% (25/2283) in poultry. In the slaughterhouse component of the study, a total of 288 participants were sampled, 91.3% of them being male. Fifteen (5.2%) participants had ARI but the nine swabs collected from them were negative for influenza A virus by PCR. Of the 1,128 pigs sampled, five (0.4%) nasal swabs tested positive for influenza A/H1N1/pdm09 by PCR whereas seroprevalence was 19.8%. The adjusted odds ratio for the association between pig workers and reporting ARI was 1.12 (95%CI [0.77 – 1.63]) at household level and 0.48 (95%CI [0.24, 0.96]) at slaughterhouse level. Having a member of the household with an episode of ARI in the previous three months (3.6 [95%CI 2.28 – 5.68]) and chronic disease (1.96 [95%CI [1.26-3.06]) were associated with reporting ARI on multivariable regression. The study reports detection of influenza virus (A/H1N1/pdm09) among pigs, a virus associated with human seasonal influenza. There is need to conduct influenza surveillance among pig workers and pigs in slaughterhouses as an important early warning system for influenza related zoonotic events.