Poultry trading behaviours in Vietnamese live bird markets as risk factors for avian influenza infection in chickens

Sealy, Joshua E.; Fournie, Guillaume; Trang, Pham Hong; Dang, Nguyen Hoang; Sadeyen, Jean-Remy; Thanh, To Long; van Doorn, H. Rogier; Bryant, Juliet E.; Iqbal, Munir

All variables with p < .05 from univariable analysis had VIF < 5 so were kept for subsequent stepwise variable selection. A final model of explanatory variables with LBMs as random effects was used in multivariable analysis. Final selection of explanatory variables was conducted by backward stepwise variable selection in R. Mantel tests were conducted in the R package, "ecodist", where virus isolates with whole-genome sequencing data were included (Mantel, 1967) . For each of the virus isolates, the ORF of each gene segment was concatenated and a dissimilarity matrix, or genetic distance matrix, was constructed from the pairwise nucleotide differences in MEGA (Kumar et al., 2016) . Additional dissimilarity matrices were also constructed from the explanatory variables of same dimension as the genetic distance matrix, and related to the characteristics of the poultry from which the viruses were isolated. We refer to them as sample characteristic matrices M. For any of those matrices, an element m ij = 1 if strains i and j are from samples with the same characteristic (e.g. poultry sold in the same market, poultry originating from the same type of premise, farm or market, and poultry originating from the same province), if not, mij = 0 (e.g. poultry sold in different markets, poultry originating from different types of premises and from different provinces).