Phylogenetic analysis of canine distemper virus in South African wildlife

Canine distemper virus (CDV) causes a severe contagious disease in a broad range of hosts. This is the first study to genetically characterise CDV strains from four different wildlife species in South Africa. The phylogenetic diversity of CDV is examined, using the haemagglutinin gene. The South African wildlife CDV isolates showed a high degree of similarity to CDV in South African domestic dogs. Phylogenetic analyses confirmed the presence of 12 geographical lineages with CDV strains from South African wildlife falling within the Southern African lineage. The study reveals two possible co-circulating sub-genotypes corresponding to the northern and southern regions of South Africa respectively. CDV strains from the non-canid species were distinct, but similar to CDV isolates from domestic dog and wild canids. Residues at amino acid sites of the SLAM binding region support the notion that CDV strains encoding 519I / 549H are better adapted to non-canid species than canid species. The amino acids present at site 530 are conserved regardless of host species. Strains from South African wild carnivores showed no difference between host species with all strains presenting 530N. All non-canid strains in this study presented the combination 519I/549H. No evidence of host adaptation or lineage grouping was observed for the Nectin-4 binding region. Further studies should include CDV strains isolated from various hosts from a wider geographical range in South Africa.S1 Table. H gene sequence isolates used in determining the phylogenetic relationship of canine distemper virus. The accession number, host species, year and country of origin (when available) are indicated for each strain. South African strains isolated for this study indicated with asterisk ( ).S2 Table. Residues at amino acid sites of the SLAM and nectin-4 cell binding regions on the canine distemper virus H-protein, arranged in geographical lineages and host species (domestic dog, wild canid and non-canid). The accession number, host species, year and country of origin are indicated for each strain. South African strains isolated for this study indicated with asterisk ( ). Identical amino acids are indicated with a dash (-), varying amino acids are indicated by single letter amino acid codes.http://www.plosone.orgam2019Veterinary Tropical Disease