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The article discusses a study conducted by Shah and colleagues on the genetic characteristics and phylogeographic dynamics of lagoviruses. The study aimed to provide an update on the evolutionary history of lagoviruses and their emergence and re-emergence. However, the authors of this response argue that the methodologies used in the analysis were inappropriate and led to incorrect and misleading inferences. They highlight the importance of considering recombination in phylogenetic analysis and criticize the conclusions drawn by Shah et al. They also point out errors in the classification system proposed by Shah et al. and suggest that their analysis will only generate confusion in the already complex classification of lagoviruses. [Extracted from the article]

Simple Summary: Rabbit Haemorrhagic Disease is caused by a virus that affects the liver, the spleen and the lungs of rabbits, causing hepatitis, splenomegaly and haemorrhages. A new genotype of the virus was first reported in France in 2010 and has spread globally since then, replacing most of the circulating former viruses in many countries. The detection of the virus and the differentiation of both genotypes is of crucial importance for disease surveillance. In this article, a rapid test for antigen detection is described and evaluated, providing the first description of a quick and easy-to-use test that allows for the simultaneous detection and differentiation of the genotypes. A total of 136 samples, rabbit liver samples and liver exudates (liquid collected after freeze–thawing) classified as infected and non-infected, were analysed, with good results. These data confirm that the developed rapid test can be used as a reliable diagnostic test for disease surveillance, especially in farms and the field. Rabbit Haemorrhagic Disease Virus 2 (RHDV2, recently named Lagovirus europaeus/GI.2) was first reported in France in 2010 and has spread globally since then, replacing most of the circulating former RHDV (genotype GI.1) in many countries. The detection and differentiation of both genotypes is of crucial importance for the surveillance of the disease. In this article, a duplex lateral flow assay (LFA) for antigen detection is described and evaluated, providing the first description of a quick and easy-to-use test that allows for the simultaneous detection and differentiation of RHDV genotypes GI.1 and GI.2. A panel of GI.1- or GI.2-infected and non-infected rabbit liver samples and liver exudates (136 samples) was analysed, obtaining a total sensitivity of 94.4% and specificity of 100%. These data confirm that the developed duplex LFA can be used as a reliable diagnostic test for RHD surveillance, especially in farms and the field. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]