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Evolutionary history and molecular epidemiology of rabbit haemorrhagic disease virus in the Iberian Peninsula and Western Europe.

Alda F, Gaitero T, Suárez M, Merchán T, Rocha G, Doadrio I - BMC Evol. Biol. (2010)

Bottom Line: Evolutionary relationships of RHDV revealed three main lineages with significant phylogeographic structure.The Iberian Peninsula showed evidences of genetic isolation, probably due to geographic barriers to gene flow, and was also the region with the youngest MRCA.Overall, demographic analyses showed an initial increase and stabilization of the relative genetic diversity of RHDV, and a subsequent reduction in genetic diversity after the first epidemic breakout in 1984, which is compatible with a decline in effective population size.Consequently, this relationship is suggested to condition RHDV demographic history.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dpto Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain. alda.fernando@gmail.com

ABSTRACT

Background: Rabbit haemorrhagic disease virus (RHDV) is a highly virulent calicivirus, first described in domestic rabbits in China in 1984. RHDV appears to be a mutant form of a benign virus that existed in Europe long before the first outbreak. In the Iberian Peninsula, the first epidemic in 1988 severely reduced the populations of autochthonous European wild rabbit. To examine the evolutionary history of RHDV in the Iberian Peninsula, we collected virus samples from wild rabbits and sequenced a fragment of the capsid protein gene VP60. These data together with available sequences from other Western European countries, were analyzed following Bayesian Markov chain Monte Carlo methods to infer their phylogenetic relationships, evolutionary rates and demographic history.

Results: Evolutionary relationships of RHDV revealed three main lineages with significant phylogeographic structure. All lineages seem to have emerged at a common period of time, between ~1875 and ~1976. The Iberian Peninsula showed evidences of genetic isolation, probably due to geographic barriers to gene flow, and was also the region with the youngest MRCA.Overall, demographic analyses showed an initial increase and stabilization of the relative genetic diversity of RHDV, and a subsequent reduction in genetic diversity after the first epidemic breakout in 1984, which is compatible with a decline in effective population size.

Conclusions: Results were consistent with the hypothesis that the current Iberian RHDV arose from a single infection between 1869 and 1955 (95% HPD), and rendered a temporal pattern of appearance and extinction of lineages. We propose that the rising positive selection pressure observed throughout the history of RHDV is likely mediated by the host immune system as a consequence of the genetic changes that rendered the virus virulent. Consequently, this relationship is suggested to condition RHDV demographic history.

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Phylogenetic tree obtained by Bayesian inference for all the RHDV strains analyzed. Numbers above branches indicate bootstrap values above 50 for ML analysis, and posterior probabilities above 0.80 for BI are shown below branches. Year and region of isolation is indicated for all samples. 95% HPD for the tMRCA of the main lineages found are indicated. Iberian clades within Lineage I are shown based on previous studies [24,42] and new data. Names in italics indicate avirulent RHDV strains.
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Figure 1: Phylogenetic tree obtained by Bayesian inference for all the RHDV strains analyzed. Numbers above branches indicate bootstrap values above 50 for ML analysis, and posterior probabilities above 0.80 for BI are shown below branches. Year and region of isolation is indicated for all samples. 95% HPD for the tMRCA of the main lineages found are indicated. Iberian clades within Lineage I are shown based on previous studies [24,42] and new data. Names in italics indicate avirulent RHDV strains.

Mentions: The phylogenetic methods used rendered congruent topologies (Figure 1). Both analyses indicated three main lineages (Lineage I, II and III) in which most of the RHDV samples were included. Lineage I included RHDV strains isolated in different European regions (Figure 1), some of which had been isolated in the UK before the description of the disease in 1984 and others isolated during the first outbreaks in France, Germany and Spain (AST/89 and MC-89). Also, this lineage included all the Iberian RHDV samples isolated in Spain and Portugal from 1994 to 2007 (Figure 1). Six Iberian clades were described based on previous findings (Genogroup 1 [24], IB1, IB2 and IB3 [42]) and the new isolates from this study (IB4, IB5, IB6). No clear geographic structure was observed among the Iberian samples, although most of the clades were restricted in time, with the exception of IB3 that was the most widespread clade both in time and space (Figure 1, Additional File 1). In Lineage II, we exclusively found European strains of RHDV, mainly from the UK, Germany and France. Conversely, Lineage III included strains from different continents. German strains were found at a basal position with respect to all the Chinese strains, except a sample from 1984, which seemed more related to those of Lineage I and II, but without bootstrap or posterior probability support. This lineage also contained samples from the United States, France and Reunion Island in the Indian Ocean. Conversely, several RHDV strains from different regions (France, Germany, Czech Republic, China, Mexico and New Zealand) and strains prior to 1989 were not included in any of the three main lineages identified (Figure 1).


Evolutionary history and molecular epidemiology of rabbit haemorrhagic disease virus in the Iberian Peninsula and Western Europe.

Alda F, Gaitero T, Suárez M, Merchán T, Rocha G, Doadrio I - BMC Evol. Biol. (2010)

Phylogenetic tree obtained by Bayesian inference for all the RHDV strains analyzed. Numbers above branches indicate bootstrap values above 50 for ML analysis, and posterior probabilities above 0.80 for BI are shown below branches. Year and region of isolation is indicated for all samples. 95% HPD for the tMRCA of the main lineages found are indicated. Iberian clades within Lineage I are shown based on previous studies [24,42] and new data. Names in italics indicate avirulent RHDV strains.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2992527&req=5

Figure 1: Phylogenetic tree obtained by Bayesian inference for all the RHDV strains analyzed. Numbers above branches indicate bootstrap values above 50 for ML analysis, and posterior probabilities above 0.80 for BI are shown below branches. Year and region of isolation is indicated for all samples. 95% HPD for the tMRCA of the main lineages found are indicated. Iberian clades within Lineage I are shown based on previous studies [24,42] and new data. Names in italics indicate avirulent RHDV strains.
Mentions: The phylogenetic methods used rendered congruent topologies (Figure 1). Both analyses indicated three main lineages (Lineage I, II and III) in which most of the RHDV samples were included. Lineage I included RHDV strains isolated in different European regions (Figure 1), some of which had been isolated in the UK before the description of the disease in 1984 and others isolated during the first outbreaks in France, Germany and Spain (AST/89 and MC-89). Also, this lineage included all the Iberian RHDV samples isolated in Spain and Portugal from 1994 to 2007 (Figure 1). Six Iberian clades were described based on previous findings (Genogroup 1 [24], IB1, IB2 and IB3 [42]) and the new isolates from this study (IB4, IB5, IB6). No clear geographic structure was observed among the Iberian samples, although most of the clades were restricted in time, with the exception of IB3 that was the most widespread clade both in time and space (Figure 1, Additional File 1). In Lineage II, we exclusively found European strains of RHDV, mainly from the UK, Germany and France. Conversely, Lineage III included strains from different continents. German strains were found at a basal position with respect to all the Chinese strains, except a sample from 1984, which seemed more related to those of Lineage I and II, but without bootstrap or posterior probability support. This lineage also contained samples from the United States, France and Reunion Island in the Indian Ocean. Conversely, several RHDV strains from different regions (France, Germany, Czech Republic, China, Mexico and New Zealand) and strains prior to 1989 were not included in any of the three main lineages identified (Figure 1).

Bottom Line: Evolutionary relationships of RHDV revealed three main lineages with significant phylogeographic structure.The Iberian Peninsula showed evidences of genetic isolation, probably due to geographic barriers to gene flow, and was also the region with the youngest MRCA.Overall, demographic analyses showed an initial increase and stabilization of the relative genetic diversity of RHDV, and a subsequent reduction in genetic diversity after the first epidemic breakout in 1984, which is compatible with a decline in effective population size.Consequently, this relationship is suggested to condition RHDV demographic history.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dpto Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain. alda.fernando@gmail.com

ABSTRACT

Background: Rabbit haemorrhagic disease virus (RHDV) is a highly virulent calicivirus, first described in domestic rabbits in China in 1984. RHDV appears to be a mutant form of a benign virus that existed in Europe long before the first outbreak. In the Iberian Peninsula, the first epidemic in 1988 severely reduced the populations of autochthonous European wild rabbit. To examine the evolutionary history of RHDV in the Iberian Peninsula, we collected virus samples from wild rabbits and sequenced a fragment of the capsid protein gene VP60. These data together with available sequences from other Western European countries, were analyzed following Bayesian Markov chain Monte Carlo methods to infer their phylogenetic relationships, evolutionary rates and demographic history.

Results: Evolutionary relationships of RHDV revealed three main lineages with significant phylogeographic structure. All lineages seem to have emerged at a common period of time, between ~1875 and ~1976. The Iberian Peninsula showed evidences of genetic isolation, probably due to geographic barriers to gene flow, and was also the region with the youngest MRCA.Overall, demographic analyses showed an initial increase and stabilization of the relative genetic diversity of RHDV, and a subsequent reduction in genetic diversity after the first epidemic breakout in 1984, which is compatible with a decline in effective population size.

Conclusions: Results were consistent with the hypothesis that the current Iberian RHDV arose from a single infection between 1869 and 1955 (95% HPD), and rendered a temporal pattern of appearance and extinction of lineages. We propose that the rising positive selection pressure observed throughout the history of RHDV is likely mediated by the host immune system as a consequence of the genetic changes that rendered the virus virulent. Consequently, this relationship is suggested to condition RHDV demographic history.

Show MeSH
Related in: MedlinePlus