Background

The 2009 pH1N1 influenza pandemic resulted in at least 18,500 deaths worldwide. While pH1N1 is now considered to be in a post-pandemic stage in humans it has nevertheless spilled back into swine in at least 20 countries. Understanding the factors that increase the risk of spillover events between swine and humans is essential to predicting and preventing future outbreaks. We assessed risk factors that may have led to spillover of pH1N1 from humans to swine in Cameroon, Central Africa. We sampled swine, domestic poultry and wild birds for influenza A virus at twelve sites in Cameroon from December 2009 while the pandemic was ongoing, to August 2012. At the same time we conducted point-count surveys to assess the abundance of domestic livestock and wild birds and assess interspecific contact rates. Random forest models were used to assess which variables were the best predictors of influenza in swine.

Results

We found swine with either active pH1N1 infections or positive for influenza A at four of our 12 sites. Only one swine tested positive by competitive ELISA in 2011-2012. To date we have found pH1N1 only in the North and Extreme North regions of Cameroon (regions in Cameroon are administrative units similar to provinces), though half of our sites are in the Central and Western regions. Swine husbandry practices differ between the North and Extreme North regions where it is common practice in to let swine roam freely, and the Central and Western regions where swine are typically confined to pens. Random forest analyses revealed that the three best predictors of the presence of pH1N1 in swine were contact rates between free-ranging swine and domestic ducks, contact rates between free-ranging swine and wild Columbiformes, and contact rates between humans and ducks. Sites in which swine were allowed to range freely had closer contact with other species than did sites in which swine were kept penned.

Conclusions

Results suggest that the practice of allowing swine to roam freely is a significant risk factor for spillover of influenza from humans into swine populations.

The northern Andes, with their steep elevational and climate gradients, are home to an exceptional diversity of flora and fauna, particularly rich in avian species that have adapted to divergent ecological conditions. With this diversity comes the opportunity for parasites to exploit a wide breadth of avian hosts. However, little research has focused on examining the patterns of prevalence and lineage diversity of avian parasites in the Andes. Here, we screened a total of 428 birds from 19 species (representing nine families) and identified 133 infections of avian haemosporidia (31%), including lineages of Plasmodium, Haemoproteus, and Leucocytozoon. We document a higher prevalence of haemosporidia at higher elevations and lower temperatures, as well as an overall high diversity of lineages in the northern Andes, including the first sequences of haemosporidians reported in hummingbirds (31 sequences found in 11 species within the family Trochilidae). Double infections were distinguished using PHASE, which enables the separation of distinct parasite lineages. Results suggest that the ecological heterogeneity of the northern Andes that has given rise to a rich diversity of avian hosts may also be particularly conducive to parasite diversification and specialization.

Highly pathogenic influenza A virus subtype H5N1 causes significant poultry mortality in the six countries where it is endemic and can also infect humans. Egypt has reported the third highest number of poultry outbreaks (n=1084) globally. The objective of this cross-sectional study was to identify putative risk factors for H5N1 infections in backyard poultry in 16 villages in Damietta, El Gharbia, Fayoum, and Menofia governorates from 2010-2012. Cloacal and tracheal swabs and serum samples from domestic (n=1242) and wild birds (n=807) were tested for H5N1 via RT-PCR and hemagglutination inhibition, respectively. We measured poultry rearing practices with questionnaires (n=306 households) and contact rates among domestic and wild bird species with scan sampling. Domestic birds (chickens, ducks, and geese, n=51) in three governorates tested positive for H5N1 by PCR or serology. A regression model identified a significant correlation between H5N1 in poultry and the practice of disposing of dead poultry and poultry feces in the garbage (F=15.7, p<0.0001). In addition, contact between domestic and wild birds was more frequent in villages where we detected H5N1 in backyard flocks (F=29.5, p<0.0001).