Molecular epidemiology of dog rabies in Nigeria : phylogeny based on N and G gene sequences

The domestic dog is the principal reservoir of rabies in Nigeria and the source of infection for over 99% of human cases that have been documented. The first recorded cases of human and dog rabies were in 1912 and 1928 respectively. The disease has been continually diagnosed in the domestic dog until to date. One of the control measures practiced in this West African country includes the vaccination of domestic dogs with readily available rabies vaccines. However, trend analyses show that dog rabies is increasing probably indicating that the vaccination programmes are inadequate. Rabies is a member of the Lyssavirus genus and currently comprises of seven genotypes (GT 1-7) namely the classical rabies virus (RABV) GT1, Lagos bat virus (LBV) GT2, Mokola virus (MOKV) GT3, Duvenhage (DUVV) GT4, European bat lyssavirus type-1 (EBLV-1) GT5, European bat lyssavirus type-2 (EBLV-2) GT6 and Australian bat lyssavirus (ABL) GT7. Three of these have been identified in Nigeria (classical rabies (RABV) (GT 1), Lagos bat virus (LBV) (GT 2) and Mokola virus (MOKV) (GT 3). The domestic dog is the major maintenance and vector species of rabies in this country and the West Africa sub-region. This study was therefore undertaken to further elucidate the epidemiology of dog rabies in Nigeria. Secondly, it was the aim of this study to determine the phylogenetic relationships of dog rabies viruses and the distribution of the respective rabies variants. Finally, to assess the phylogenetic relationships of the viruses in the study sample with those of the neighbouring countries (Chad, Cameroon, Benin and Niger). A panel of 100 viruses recovered primarily from the domestic dog was included in the study. Partial regions of the nucleoprotein gene (n=100) and the cytoplasmic domain of the glycoprotein and the G-L intergenic region (n=80) were successfully amplified, sequenced and phylogenetically analysed. Nucleotide sequences of representative rabies viruses of the partial N gene of the neighbouring countries and elsewhere in Africa available in the GenBank were also included in the phylogenetic analysis. The phylogenetic analysis demonstrated that the rabies viruses from the study sample were closely related with a 99% sequence homology for both the N and G regions but despite the close homogeneity the viruses segregated into two major clusters. Within the major cluster 1, three sub-clades were identified comprising of rabies isolates from the northern part of Nigeria whereas cluster 2 was made of viruses from the southern part of the country together with an isolate from a stray dog. Further analysis of representative viruses from the study sample with viruses from the GenBank revealed an evolutionary link with the viruses from Chad, Benin, Cameroon and Niger with a ≥96% sequence homology. The demonstration of the evolutionary link of rabies viruses in the study sample and those from neighbouring countries indicates the transboundary nature of rabies and the existence of an active rabies cycle in the region. The study data revealed that a single major virus variant is circulating in domestic dogs in Nigeria belonging to the Africa 2 dog lineage. These data suggest that control strategies including mass vaccination with effective coverage of ≥70% and the control of stray dogs will contribute to the breaking of the rabies cycle. This will dramatically reduce the demand for post-exposure prophylaxis which is costly and not readily available in most states of the country. There is also a need to enforce strict movement of animals across international borders so as to diminish the spread of the infection from one area to another, as rabies still inflicts a considerable public health burden in the region and many parts of Africa.