Homologous recombination in pestiviruses: Identification of three putative novel events between different subtypes/genogroups

Abstract

Viruses from the genus Pestivirus of the family Flaviviridae have a non-segmented, single-stranded RNA genome and can cause diseases in animals from the order Artiodactyla. Homologous recombination is rarely reported in this virus family. To detect possible recombination events, all complete pestivirus genomes that are available in GenBank were screened using distinct algorithms to detect genetic conversions and incongruent phylogenies. Three putative recombinant viruses derived from recombination from different pestivirus subtypes/genogroups were detected: Bovine viral diarrhea virus 1 (BVDV-1) strain 3156, BVDV-2 strain JZ05-1 and Classical swine fever virus (CSFV) strain IND/UK/LAL-290. The present study demonstrated that the pestivirus classification cannot be based only on the analysis of one fragment of the genome because genetic conversions can lead to errors. The designation of the recombinant forms (RF) provides a more informative structure for the nomenclature of the genetic variant. The present work reinforces that homologous recombination occurs in pestivirus populations under natural replication and describes the first evidence of recombination in BVDV-2.

Demonstration of homologous recombination events in the evolution of bovine viral diarrhoea virus by in silico investigations

“…The programmes confirmed the results of Weber et al (2015) by revealing a possible double cross-recombinant (JN704144), which strain was demonstrated in China from a field case ( Fig. 2A) (Weber et al, 2015). The major parent is the Av69 Vedevac strain also sequenced in China, the minor parent is a field strain (SD1).…”

“…At the same time, this finding proves the robustness of the applied test methods. The programmes confirmed the results of Weber et al (2015) by revealing a possible double cross-recombinant (JN704144), which strain was demonstrated in China from a field case ( Fig. 2A) (Weber et al, 2015).…”

“…Another recombination event described previously by other authors (GQ888686, Weber et al, 2015) was not confirmed by our results.…”

“…2C); the P values were not as strong as in the case of the other chimaeras, what is more, Table 1 The most prominent BVDV recombination events detected after complete sequence alignment of all BVDV sequences. Some of the events were identified earlier by others [ a (Weber et al, 2015), Table 2 GenBank data of recombinant strains, major and minor parents one of the tests did not reveal recombination in this case, the P value was below the threshold for the 3Seq method. We decided to introduce this event to prove that the results of the tests must be treated with consideration; comparison of the results of the different methods and visual re-evaluation of the graphs are always necessary, as it was suggested previously (Leal et al, 2012).…”

“…a (Weber et al, 2015), b (Jones and Weber, 2004) Acta Veterinaria Hungarica 64, 2016 The RDP graphs demonstrating the approximate size and localisation of the recombinations found by the RDP 4.46 BETA software are shown in Fig. 2A-E, while the exact localisation of the changed genomic parts is listed in Table 1.…”