Use of partial N-gene sequences as a tool to monitor progress on rabies control and elimination efforts in Ethiopia

Abstract

Ethiopia is one of the African countries most affected by rabies. A coarse catalog of rabies viruses (RABV) was created as a benchmark to assess the impact of control and elimination activities. We evaluated a 726 bp amplicon at the end of the N-gene to infer viral lineages in circulation using maximum likelihood and Bayesian methods for phylogenetic reconstruction. We sequenced 228 brain samples from wild and domestic animals collected in five Ethiopian regions during 2010–2017. Results identified co-circulating RABV lineages that are causing recurrent spillover infections into wildlife and domestic animals. We found no evidence of importation of RABVs from other African countries or vaccine-induced cases in the area studied. A divergent RABV lineage might be involved in an independent rabies cycle in jackals. This investigation provides a feasible approach to assess rabies control and elimination efforts in resource-limited countries.

The Importance of Accurate Host Species Identification in the Framework of Rabies Surveillance, Control and Elimination

“…Similarly, we detected four individuals closely related (but not fully resolved) as side-striped jackals ( C. adustus ) among a group of samples originally identified as fox ( n = 1) or simply referred as “jackals” ( n = 3). A similar pattern of misidentification in jackals originally identified as foxes or domestic dogs has been notified in Sub-Saharan Africa [ 23 ]. Our findings stress how poorly investigated the animal biodiversity, from the genetic point of view, in the African continent is, as well as the limitations for the correct taxonomic identification of animals in highly biodiverse underserved regions where human encroachment is dramatically increasing, favoring crossbreeding of domestic with wild species and giving rise to previously unseen hybrid species.…”

“…Despite the importance of appropriate host species’ identification, very few lyssavirus surveillance efforts have coupled virological and host identification approaches, thereby jeopardizing the early detection and accurate identification of putative new host species for both RABV and non-RABV lyssaviruses [ 18 , 19 , 20 , 21 , 22 , 23 ].…”

“…Similarly, in large ecological studies samples can be misidentified or mislabeled leading to the exportation of tissues potentially containing select agents or endangered species that may require special permits. Whatever the case, these involuntary mistakes may compromise large investigations leading to the destruction and elimination of tissues compromising the robustness of large scale eco-epidemiological studies [ 23 ]. Thus, herein we urge the prioritization of the implementation of classic taxonomic identification tools, by trained and experienced personnel, to identify suspected rabid animals to family level whenever possible.…”

“…On the other hand, a recent modelling study indicated that in South-East Tanzania a third of the inferred rabies transmission events might involve wildlife-to-wildlife transmission, with sustained transmission chains within jackal populations [ 39 ], although in this particular case species identification was defined on an interview basis. Similarly, the recurrent identification of a specific rabies sub lineage in Ethiopian side-striped jackals over two years potentially indicates a rabies cycle diverging into wildlife [ 23 ]. In this specific case, a genetic characterization of partial Cytb was attempted by Binkley et al [ 23 ], in the absence of a host full resolution.…”

“…Similarly, the recurrent identification of a specific rabies sub lineage in Ethiopian side-striped jackals over two years potentially indicates a rabies cycle diverging into wildlife [ 23 ]. In this specific case, a genetic characterization of partial Cytb was attempted by Binkley et al [ 23 ], in the absence of a host full resolution. However, we predict that is not possible to determine the role of wild canids without genetically identifying the hosts included in modelling analyses.…”