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

We assessed whether the genetic distance between viral isolates was associated with their sampling location and the origin of chickens (i.e. the LBM that chickens were sampled in, the LBM/ farm type that poultry originated from or the province that poultry originated from). To do this, we utilized the 12 Vietnamese H9N2 viruses which we had full-genome sequence data for and concatenated their open reading frames. The genetic distance between any two of the 12 fully sequenced H9N2 isolates decreased if these two isolates originated from the same LBM (Mantel test, r = −.41, p = .004), or sampled chickens were sourced in the same province (r = −.37, p = .031) (see Table S1 for genotype distribution between sampled LBM and province source). In the light of this, we were able to classify viruses into seven different sub-genotypes using a > 98% nucleotide difference cut-off for each gene segment (for viruses where full-genome sequencing data were available) ( Figure 2 ). From this, we could see that several strains which originated from the same LBM were also grouped into the same genotype; genotype VN4 contained three viruses from LBM Pho Hien, and genotype VN5 contained three viruses from LBM Do. HA and NP genes had the greatest maximum nucleotide pairwise distance with 6.7% and 6.9%, respectively, followed by NS with 5.7%, NA with 5%, PB1 with 4%, PB2 with 3.9%, M with 1.6% and PA with 1.5%.