Molecular Diversity and Risk Factors of Avian Paramyxovirus in Domestic poultry in Kenya

Abstract

Avian paramyxoviruses (APMV) circulating in domestic poultry in Kenya were evaluated for their genetic characteristics and identification of risk factors. Through a cross-sectional study of 225 poultry farms and 21 live bird markets in five regions in Kenya. The study used the large polymerase protein (L) and Fusion (F) gene fragments as well as the whole genome to characterize the genetic diversity of APMV and multivariate regression to analyze the association between APMV occurrence and. management/trade factors. Based on this evaluation, the virus was significantly higher in poultry farms which introduced ‘new’ birds from markets or neighbors, kept mixed poultry species or those with chicken flock size (>30). Live bird markets located in cities or major towns and traders who purchased their stock from multiple sources also had significantly higher APMV infection. The average mean haplotype diversity L and F gene was 0.759 (±0.02) and 0.906 (±0.03) respectively. The average mean nucleotide diversity L and F gene was 0.018 (±0.001) and 0.021 (±0.001) respectively Phylogenetically, Kenyan APMV-1 together with Ugandan strains were classified in a novel sub-genotype of genotype V, Clade II. The genome of Kenyan strains was 18% (±1.7%) distant from that of commonly used vaccine strain Lasota. Unique signatures were identified in APMV-1 strains circulating in Kenya. The study also detected signature of selection on different lineages and amino acid sites of APMV-1 genes. Selective pressure was highest on the fusion protein gene (dN/dS=0.289) and phosphoprotein gene (dN/dS=0.272). Three amino acid codons of fusion gene and one codon of the nucleoprotein gene under positive selection. In conclusion, the study showed that management and trade factors are associated with APMV occurrence in domestic poultry in Kenya and revealed presence of virulent closely related genetic variants of APMV-1 strains of a novel sub-genotype. Further, the study showed that natural selection affects the variation and diversity of lineages and proteins of global APMV-1 strains.