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

Abstract

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.

Rabbit haemorrhagic disease virus Lagovirus europaeus/GI.1d strain: genome sequencing, in vivo virus replication kinetics, and viral dose effect

“…The 00-21 strain belongs to the GI.1d variant group according to the proposal for a unified classification system for lagoviruses [9]. Complete or almost complete GI.1d genome sequences (without complete UTR sequences) from Bahrain in 2001 and from European countries collected until 2004 have been already obtained [11,18,19], but not from France where this variant has circulated since 1990 [10,12]. The present study characterised the complete genome sequence of a GI.1d strain collected in France in 2000.…”

“…In Europe, except in the Iberian Peninsula where GI.1b persisted, these two variants were replaced by a new variant GI.1d [10,11]. After the emergence of GI.2, GI.1d strains became a minority but continued to be occasionally identified in France [12]. GII contains pathogenic (EBHSV) and non-pathogenic viruses (hare calicivirus (HaCV)) related to EBHSV [9].…”

Viral Disease in Lagomorphs: A Molecular Perspective

“…Genetic diversity among pathogenic RHDV isolates has been the subject of intense study with the capsid protein (partial or complete) being the main target. Recent advances in sequencing techniques has allowed full genome analysis in Viral Disease in Lagomorphs: A Molecular Perspective DOI: http://dx.doi.org/10.5772/intechopen.98272 retrospective studies and demonstrate the importance of analysing complete genomes [187,188].…”

Report on simultaneous infection of rabbit haemorrhagic disease virus type 1 and type 2 in kits in China

“…In 2017, Nanbu/China/2011 isolates were found in China with a recombination event between the G2 and G6 strains (BoHu et al, 2016). The study reported that phylogenetic and recombination analyses of French and Swedish RHDV strains from 1994 to 2016 revealed that most of the prevalent RHDV G .1 strains were recombinant G .3P-G .1d strains (JoanaAbrantes et al, 2020). Researchers reveal recombination between RHDV (G .2) and EBHSV (G .1) in response to whole-genome sequencing of German rabbit haemorrhagic disease virus (JoanaAbrantes et al, 2020).…”

“…The study reported that phylogenetic and recombination analyses of French and Swedish RHDV strains from 1994 to 2016 revealed that most of the prevalent RHDV G .1 strains were recombinant G .3P-G .1d strains (JoanaAbrantes et al, 2020). Researchers reveal recombination between RHDV (G .2) and EBHSV (G .1) in response to whole-genome sequencing of German rabbit haemorrhagic disease virus (JoanaAbrantes et al, 2020). Research has found that, Spillover events of RHDV2 (recombinant G .4P-G .2) from Lagomorpha to Eurasian badger (Abade dos Santos et al, 2021).…”