Phylogenetic analysis of rabbit haemorrhagic disease virus (RHDV) strains isolated in Poland

Fitzner, A.; Niedbalski, W.

doi:10.1007/s00705-017-3476-0

Cited by 14 publications

(21 citation statements)

References 23 publications

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“…The first outbreaks of the disease were reported in 1984 in China [ 7 ], and later in several countries worldwide (reviewed in Reference [ 8 ]). These first strains correspond to variant GI.1c (see nomenclature in Reference [ 9 ]), and other variants were later recognized: GI.1a, found mainly in domestic rabbits [ 10 , 11 ]; GI.1b, which was almost entirely restricted to the Iberian Peninsula [ 12 , 13 ]; and GI.1d, occurring in several European countries [ 14 , 15 ]. Less-pathogenic (MRCV) [ 16 ] and nonpathogenic strains (GI.3 and GI.4) [ 17 , 18 , 19 ] have also been recovered.…”

Section: Introductionmentioning

confidence: 99%

Retrospective Analysis Shows That Most RHDV GI.1 Strains Circulating Since the Late 1990s in France and Sweden Were Recombinant GI.3P–GI.1d Strains

Abrantes

Lopes

Lemaitre

et al. 2020

Genes

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Recombination is one of the major sources of genetic variation in viruses. RNA viruses, such as rabbit hemorrhagic disease virus (RHDV), are among the viruses with the highest recombination rates. Several recombination events have been described for RHDV, mostly as a consequence of their genomic architecture. Here, we undertook phylogenetic and recombination analyses of French and Swedish RHDV strains from 1994 to 2016 and uncovered a new intergenotypic recombination event. This event occurred in the late 1990s/early 2000s and involved nonpathogenic GI.3 strains as donors for the nonstructural part of the genome of these recombinants, while pathogenic GI.1d strains contributed to the structural part. These GI.3P–GI.1d recombinant strains did not entirely replace GI.1d (nonrecombinant) strains, but became the dominant strains in France and Sweden, likely due to a fitness advantage associated with this genomic architecture. GI.3P–GI.1d (P stands for polymerase) strains persisted until 2013 and 2016 in Sweden and France, respectively, and cocirculated with the new genotype GI.2 in France. Since strains from the first GI.2 outbreaks were GI.3P–GI.2, we hypothesize that GI.3P–GI.1d could be the parental strain. Our results confirm the outstanding recombination ability of RHDV and its importance in the evolution of lagoviruses, which was only revealed by studying complete genomic sequences.

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Section: Introductionmentioning

confidence: 99%

Retrospective Analysis Shows That Most RHDV GI.1 Strains Circulating Since the Late 1990s in France and Sweden Were Recombinant GI.3P–GI.1d Strains

Abrantes

Lopes

Lemaitre

et al. 2020

Genes

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“…In the following years, the disease spread rapidly among breeding rabbits, mainly on the small-scale farms. The new native RHDV isolates identified between 1994 and 2004 showed a genetic profile corresponding to European strains from G3-G5 groups (Fitzner & Niedbalski, 2017). In the middle of the first decade of 21 st century, the RHDV strains exhibiting antigenic and genetic features like RHDVa variant were isolated in RHD outbreaks in Poland (Chrobocińska & Mizak, 2007;Fitzner, 2009).…”

Section: Introductionmentioning

confidence: 99%

“…In the middle of the first decade of 21 st century, the RHDV strains exhibiting antigenic and genetic features like RHDVa variant were isolated in RHD outbreaks in Poland (Chrobocińska & Mizak, 2007;Fitzner, 2009). RHDVa (G6) was the only representative of pathogenic RHDV continuously detected in Poland from 2004 to 2017 (Fitzner et al, 2012;Fitzner et al, 2017). The first Polish strains of RHDV2 were identified in 2016-2017 (Fitzner & Niedbalski, 2018), and subsequent infections were confirmed in 2018.…”

Section: Introductionmentioning

confidence: 99%

Evidence of independent introductions of RHDV2 strains in Poland based on the genome analysis of viral isolates from 2016–2018

et al. 2021

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The aim of this study was the molecular epidemiology of independently introduced RHDV2 strains in Poland. The nucleotide sequences of RHDV2 diagnosed in domestic rabbits in 2018 in the voivodeships of Swietokrzyskie (strain PIN), Malopolskie (strain LIB) and Mazowieckie (strain WAK), and RHDVa from 2015 (strain F77-3) recognized in wild rabbits in Kujawsko-Pomorskie voivodeship were compared to the genome sequences of the first native RHDV2 strains from 2016–2017. The reference sequences available in public databases, the representative for a classical RHDV (G1-G5 genogroups), RHDVa (G6), non-pathogenic caliciviruses (RCV, GI.3 and GI.4) as well as original and recombinant RHDV2 isolates were included for this analysis. Nucleotide sequence similarity among the most distanced RHDV2 strains isolated in Poland in 2018 was from 92.3% to 98.2% in the genome sequence encoding ORF1, ORF2 and 3’UTR, between 94.8–98.7% in the VP60 gene and between 91.3-98.1% in non-structural proteins (NSP) region. The diversity between three RHDV2 and RHDVa from 2015 was up to 16.3% in the VP60 region. Similarities are shown for the VP60 tree within the RHDV2 group, however, the nucleotide analysis of NSP region revealed the differences between older and new native RHDV2 strains. The Polish RHDV2 isolates from 2016-2017 clustered together with RHDV G1/RHDV2 recombinants, first identified in the Iberian Peninsula in 2012, while all strains from 2018 are close to the original RHDV2. The F77-3 strain clustered to well supported RHDVa (G6) genetic group, together with other Polish and European RHDVa isolates. Based on the results of phylogenetic characterization of RHDV2 strains detected in Poland between 2016–2018 and the chronology of their emergence it can be concluded that RHDV2 strains of 2018 and RHDV2 strains of 2016–2017 were introduced independently thus confirming their different origin and simultaneous pathway of spreading.

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“…The RHDV strains isolated in the earliest period of RHDV occurrence in Europe (1987Europe ( -1989 were characterised with high homology and low genetic variability among one another, and are referred to as the reference strains, and include the Czech V351 strain from 1987, as well as strains from 1989: German FRG, Spanish AST89, French SD, and Italian BS89. In 1996, the first case of RHDV was recorded (Capucci et al, 1998), which was different from classic RHDV in the aspect of antigenicity, genetic variability and phylogenetic analysis of the gene encoding structural protein VP60, referred to as RHDVa (Capucci et al, 1998;Kerr et al, 2009;Kinnear & Linde, 2010;Fitzner & Niedbalski, 2017). It was also evidenced that RHDVa strains are characterised with higher virulence and mortality rates in rabbits (Capucci et al, 1998).…”

Section: Introductionmentioning

confidence: 99%

Genetic variability and phylogenetic analysis of Lagovirus europaeus strains GI.1 (RHDV) and GI.2 (RHDV2) based on the RNA-dependent RNA polymerase (RdRp) coding gene

Hukowska-Szematowicz

2020

Acta Biochim Pol

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Lagovirus europaeus GI.1 (RHDV-rabbit haemorrhagic disease virus) and GI.2 (RHDV2-rabbit haemorrhagic disease virus 2), family Caliciviridae, genus Lagovirus, are etiological factors of the rabbit haemorrhagic disease (RHD). This small RNA virus is a great model for tracking the variability and evolution of RNA viruses, because it uses an RNA-dependent RNA polymerase (RdRp) to replicate its own genetic material. This polymerase determines the fidelity and the rates of replication and mutation of the virus, conditioning its adaptation to the environment and even to a new host, and thus influencing evolution of the virus. The aim of this study was to determine the genetic variability and phylogenetic relationships of 105 Lagovirus europaeus strains with different genotypes based on the RdRp gene. The strains came from around the world in the years of 1987–2017. The aforementioned group of 105 strains included 14 strains whose RdRp sequences were obtained and analysed in this study, and the rest were retrieved from GenBank: 74 strains classified as genotype GI.1 (RHDV), 14 as GI.2 (RHDV2), 2 strains of Lagovirus europaeus not assigned to any genotype, and a MRCV strain, the sequences of which were collected from GenBank. Among the 14 strains whose RdRp sequences were obtained in this study, the highest variability was presented in the Austrian 237 strain from 2004. The genetic distance between the Austrian 237 strain and the remaining thirteen analysed strains ranged from 0.117 to 0.123 (from 11.7% to 12.3% nucleotide substitutions). The lowest variability, however, was recorded for Hungarian, Czech and Austrian strains. On the phylogenetic tree, the 14 analysed strains were allocated into GI.1c (G2), GI.1d (G3-G5) and GI.1a (RHDVa). Analysis of the genetic variability of the 105 strains of Lagovirus europaeus indicated a growing genetic distance between the strains, both in time and location. Phylogenetic analysis showed a division of the strains into seven groups, dictated by the chronology, geographical location and evolutionary events in the history of the virus, such as mutations and recombinations.

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Phylogenetic analysis of rabbit haemorrhagic disease virus (RHDV) strains isolated in Poland

Cited by 14 publications

References 23 publications

Retrospective Analysis Shows That Most RHDV GI.1 Strains Circulating Since the Late 1990s in France and Sweden Were Recombinant GI.3P–GI.1d Strains

Retrospective Analysis Shows That Most RHDV GI.1 Strains Circulating Since the Late 1990s in France and Sweden Were Recombinant GI.3P–GI.1d Strains

Evidence of independent introductions of RHDV2 strains in Poland based on the genome analysis of viral isolates from 2016–2018

Genetic variability and phylogenetic analysis of Lagovirus europaeus strains GI.1 (RHDV) and GI.2 (RHDV2) based on the RNA-dependent RNA polymerase (RdRp) coding gene

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