Analysis of genetic variability and phylogenetic analysis of selected Czech and French strains of rabbit haemorrhagic disease virus (RHDV)

Abstract

The objective of this study was to analyse the genetic variability and phylogenetic analysis of six strains of rabbit haemorrhagic disease virus (RHDV), including four Czech strains (CAMPV-351, CAMPV-561, CAMPV-562, CAMPV-558) and two French strains (Fr-1, Fr-2), on the basis of a fragment of the VP60 capsid structural protein-coding gene N-terminal region. The results of our own studies were compared to 26 RHDV strains obtained from GenBank. The analysis of the genetic variability of six RHDV strains indicated that the CAMPV-561 strain is the most genetically variable. Less variable were the Fr-1 and Fr-2 strains, while the least variable was CAMPV-351. In turn, the genetic distance among the six analysed strains and 26 strains obtained from GenBank was the greatest for CAMPV-351 and Whn/China [11.3 % according to the observed divergence (OD) method and 12.2 % according to the maximum likelihood (ML) method], while it was the lowest for CAMPV-351 and FRG (0.8 % in both the OD and ML methods). In turn, the scale of the genetic distances among the six analysed strains and five RHDVa strains (99-05, NY-01, Whn/China, Triptis, Iowa2000) ranged from 9.3–10.3 % in the OD method to 10.3–13.7 % in the ML method. The image of phylogenetic dependencies generated for the strains analysed and those obtained from GenBank revealed their distribution to be in five genetic groups (G1–G5), whereas the analysed strains were included in genetic groups 2 and 3.

Evaluation of the usefulness of laboratory diagnostic methods in RHD outbreak

“…The study showed the lack of amplification of STR 2012 genetic material with P1 primer (5182-5201) from the C-terminus of the RHDV RdRp polymerase gene. The primer set P1/P2, originally proposed by Guittré et al (21), has been used for many years in many laboratories for routine amplification of classic RHDV strains, including HA-negative phenotypic variants (23,26). Similar difficulties were encountered in the amplification of cDNAs of the samples L1-L6 with the pair of primers N3-N4 encoding the N-terminal part of the VP60 gene.…”

Arrival of rabbit haemorrhagic disease virus 2 to northern Europe: Emergence and outbreaks in wild and domestic rabbits (Oryctolagus cuniculus) in Sweden

“…A sequence from European brown hare syndrome virus was used as an out‐group to root the tree. The best‐fitting evolutionary model was determined based on our previous knowledge and available information (Esteves et al., ; Hukowska‐Szematowicz, Tokarz‐Deptula, & Deptula, ) on genome dynamics and evolution of rabbit haemorrhagic disease viruses such as the pattern of nucleotide substitution and the variability of substitution rates among sites in RHDV genome. By performing an initial phylogenetic analysis using the neighbour‐joining method in combination with variation of models, the Tamura–Nei model was selected for the final analysis.…”

Mutational and phylogenetic status of west siberian strains of BLV

“…3) is of considerable interest, since this feature is not typical for most viruses. For example, rabbit hemorrhagic disease virus (RHDV) strains tend to cluster geographically [27], which was not observed in this case. These results, as well as others from a number of previous studies [13], in fact highlight the circulation of several strains in the same geographical location.…”