The genome sequence and aspects of epidemiology of rabies-related Duvenhage virus

Abstract

Duvenhage virus (DUVV) belongs to genotype (gt) 4 of the lyssavirus genus, in the family Rhabdoviridae, order Mononegavirales. This virus causes fatal rabies encephalitis and has only been reported from the African continent. To date there have been only five isolations of DUVV, three of which were from human fatalities and all of which were associated with insectivorous bat species. Genotype 4 lyssaviruses have not been well studied and as such little is known about them. The aim of this study was to determine the full genome sequence and investigate the epidemiology of this uniquely African lyssavirus. Standard methods of PCR and sequencing were used to determine the coding and non coding regions of various DUVV isolates. In order to determine the full genome sequence, an RNA circularization technique was used to obtain the genomic terminal sequences. Using various molecular techniques we then analyzed the sequence data, at both phylogenetic and evolutionary levels. Our analysis showed the evolutionary forces acting against DUVV, to be similar to that which has been found for its closest relative, European bat lyssavirus type 1 (EBLV1) (gt 5). Both these viruses have strong constraints against amino acid change, with no evidence of positive selection. Phylogenetic studies showed that not all Lyssavirus genes are equal for phylogenetic or lyssavirus classification analysis. High intergenotypic values at the nucleoprotein amino acid level emphasize that there is a need to reinvestigate the criteria for lyssavirus genotype classification. The strong support observed in our full genome studies suggests that full genomes may in fact be best for Lyssavirus analysis, so as to avoid the potential bias of individual gene analyses. Analysis of DUVV indicates that it is an older virus within the lyssavirus genus and as shown by the discovery of the most recent isolate, the genetic diversity and incidence of this virus is greatly underestimated. Poor surveillance of rabies-related lyssaviruses as well as the poor diagnostic capabilities through most of Africa are large contributors to our lack of information. Improved surveillance of the African rabies-related lyssaviruses will extend our knowledge on the geographic distribution, host species associations and epidemiology of these viruses.