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. 2015 Jul 25:11:164.
doi: 10.1186/s12917-015-0491-9.

Phylodynamic analysis of the canine distemper virus hemagglutinin gene

Guan-Ming Ke  1 , Chin-Hsiang Ho  2 , Meng-Jung Chiang  3   4 , Bintou Sanno-Duanda  5   6 , Cheng-Shu Chung  7 , Maw-Yeong Lin  8 , Yong-Ying Shi  9 , Ming-Hui Yang  10   11 , Yu-Chang Tyan  12   13 , Pao-Chi Liao  14 , Pei-Yu Chu  15   16
Affiliations

Phylodynamic analysis of the canine distemper virus hemagglutinin gene

Guan-Ming Ke et al. BMC Vet Res. .

Abstract

Background: Canine distemper (CD) is one of the most contagious and lethal viral diseases in dogs. Despite the widespread use of vaccines, the prevalence of the CD virus (CDV) has increased at an alarming rate in recent years. In this phylodynamic study, we investigated the spatiotemporal modes of dispersal, viral demographic trends, and effectiveness of vaccines for CDV. A total of 188 full-length CDV hemagglutinin (H) gene sequences dataset were subjected to recombination analysis, including seven from modified live vaccine (MLV) strains and 12 from Taiwan specimens. After excluding the MLV strains and potential recombinant strains, alignments of 176 of 188 previous CDV strains were further used to analyze phylodynamic characteristics, and evidence of selection, and co-evolution.

Results: The CDV genotype consisted of MLV-associated genotypes such as America-1 and Rockborn-like strains, which were characterized by long terminal branches and no distinct geographical patterns among lineages. In contrast, wild-type isolates clustered into lineages with a spatiotemporal structure and short terminal branches. Co-circulation and extensive diversification were simultaneously observed. The sequence variation signature was shaped by both geographic diversity and host tropism. Codon 506 was identified as a multi-epistatic interacting in the H protein.

Conclusions: The topological signature revealed in this study suggests different epidemic scenarios. For example, a ladder-like backbone is a hallmark of directional selection, and cladogenesis at long terminal branches indicates the emergence of a surviving lineage. The stable effective viral population of CDV indicate the effectiveness of vaccines currently used to control the virus.

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Figures

Fig. 1
Fig. 1
Recombination map of the canine distemper virus (CDV) H gene in strains of the 188-sequence data set. For each recombination event, the left side of the figure shows (a) the BOOTSCAN plot, and the second panel shows (b) the similarity plot. The y-axis shows (a) the percentage of permutation trees and (b) the pairwise identity of each pair in the sequence. The x-axis is the alignment position. The analysis was performed with a sliding window of 200 nt with a 20-nt step. The comparison was performed using 50 % consensus sequences with 1000 bootstrap replicates. Each curve in the figure compares the query and reference sequences. Both plots were generated with the Simplot program. Potential recombination breakpoints are identified where sudden alterations in bootstrap values or in similarity values occurred or where crossover occurred. Potential recombination breakpoints are identified where sudden alterations in bootstrap or similarity values occurred or where a crossover occurred. The third panel (c) shows a schematic diagram of potential recombinant regions and breakpoint locations identified by Recombination Detection Program v3.44 (RDP). Phylogenetic trees were compared by neighbor sequence fragment alignments flanking the breakpoint. (d). The potential recombinant strains, major parent strains, minor parent strains, and non-parent strains are indicated in red, blue, green, and purple, respectively
Fig. 2
Fig. 2
Maximum clade credibility tree based on 188 canine distemper virus H gene sequences. For each branch, the colour and thickness indicate the most probable location and most probable state, respectively. For key nodes, the size of the node cycle represents the posterior probability (PP), and support values are labeled above the nodes as either bootstrap (BS) or PP according to BS-NJ/PP-BEAST. Numbers in parentheses are the PP values of each location. The scale bar at the bottom shows the time in years. Strains are designated by accession number-year isolated (last two digits)-country abbreviation-strain name-host and are colored according to the host animal species. For each genotype, the geographic distribution and duration of isolation are also shown on the right. The modified live virus vaccine strains are shaded grey, potential recombinant strains are shaded yellow, and strains isolated in this study are shaded green. The tree was constructed using BEAST program
Fig. 3
Fig. 3
Maximum clad credibility tree based on 176 canine distemper virus H gene sequences. For each branch, the colour and thickness indicate the most probable location and probability of the state, respectively. For key nodes, the size of the node cycle represents the posterior probability (PP), and support values are labeled the nodes as either bootstrap (BS) or PP in BS-NJ/PP-BEAST. Numbers in parentheses are the PP values of each location. The scale bar on the bottom shows the time in years. The strain names are colored according to their host animal species. Genotypes and nucleotide/amino acid sequence similarities (%) appear on the right. Strains isolated in this study are shaded green
Fig. 4
Fig. 4
Bayesian skyline plot (BSP) of (a) 176-sequence dataset and (b) Taiwan strains isolated during 2003–2008 The x-axis is the time scale in years, and the y-axis is a logarithmic scale of Neτ (where Ne is the effective population size and τ is the generation time). The thick solid line indicates the median estimates, and the shaded area indicates the 95 % HPD
Fig. 5
Fig. 5
Site-specific variation among global canine distemper virus H sequences. a Detection of site-specific selection. Normalized dN-dS values were plotted for each codon site by using the SLAC method on the DataMonkey website. b Secondary structure guide for Measles virus (MeV) H protein (PDB ID codes 2ZP8). c Epistatic interactions among CDV H protein residues. Each square node represents the position of a residue in a CDV H amino acid sequence identified in at least one interaction. The analysis detected edges with marginal posterior probabilities (PPs) exceeding a default cutoff value of 0.5. Data are shown as PP(→)/PP(↔)/PP(←). The arrows indicate the directions of interactions. d The multiple epistatic sites detected in this study are labeled in the simplified secondary structure. Each amino acid residue and its coordinate structure are also denoted
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