Duck hepatitis a virus: Full-length genome-based phylogenetic and phylogeographic view during 1986–2020

Fig. 1. Phylogenetic and phylogeographic analyses. (A) The phylogenetic tree based on the full-length genome sequences of DHAV, 1986–2020. The unrooted ML phylogenetic tree of 141 full-length DHAVs genome classifying all the strains into two major clades (DHAV-1 and DHAV-3). DHAV-1 can be further classified into seven sub-clades (1a-1 g) and DHAV-3 into five sub-clades (3a-e). The major clades and sub-clades of the DHAV are indicated. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are indicated at each node. The evolutionary distances were computed using the best-fit substitution model (GTR+F + I + G4) in the IQ-TREE multicore version 1.6.12. The red color clades represent the viruses identified in China (n = 122) and black color represents viruses identified in South Korea (n = 10), Egypt (n = 5), and Vietnam (n = 4). The tree was visualized and modified using FigTree v1.4. The detailed information about each virus is seen in Supplementary Fig. S1, where the viruses were identified using their GenBank ID, virus name, country, and year of isolation, e.g., ID-virus name-country-year. (B) Phylogeographic network…

Fig. 2. Amino acids variability landscape of DHAV polyprotein, 1986–2020. The plot represents amino acids variations in polyprotein at aa 1–1120 (A) and 1121–2254 (B). The ORF nucleotide sequences were used to acquire their consensus amino acids sequence and the Wu-Kabat variability coefficient was determined by PVS (Garcia-Boronat et al., 2008). The Wu-Kabat variability coefficient represents the susceptibility of an amino acid position to the mutations and is calculated using the following equation: variability coefficient = N*k/n (N is the number of sequences in the alignment, k is the number of kinds of amino acids at a given position and n is the frequency of the most common amino acid at that position. Y axes represents the Wu-Kabat variability coefficient values, where the estimation limit is 1. Above the limit 1 represents variations. X axes represents the amino acids positions.