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.

Keywords: Co-circulating lineages; Dog rabies; Monitoring elimination; Resource-limited countries.

Fig. 1.

Temporal distribution of samples analyzed per quarter. Orange bars indicate the total number of samples included in the phylogenetic analyses. Green bars indicate total number of DFA positive samples confirmed at EPHI. The red border indicates total number of samples per quarter. From top to bottom we find the temporal distribution of all samples; temporal distribution of all dog samples; temporal distribution of cat samples; and temporal distribution of other species (jackals, and Ethiopian wolf).

Fig. 2.

Designation of viral lineages and their geographic/temporal distribution per quarter. (A) Bayesian tree indicating robust branches with relevant posterior probabilities highlighted in blue. Main Ethiopian’s AF1a lineages were highlighted with colored bars between branches and taxa names, indicating all taxa for each lineage included in final phylogenetic reconstruction. Wider colored lines on the right of the taxa names indicate minor and major African clades, whose coarse geographic distribution is shown in the same color on the Africa’s map on panel B. (B) Map of Ethiopia showing the geographic distribution of all five Ethiopia’s AF1a lineages displayed with same colors as shown in the Bayesian tree, panel A. Pie charts within Ethiopia’s map depict centroid locations of lineages and their relative proportion, per location. Pie’s size do not represent total number samples per lineage, only depict relative abundance. Projection from the center to the right upper side shows samples with overlapping distributions within Addis Ababa. The projection on the left shows the location of Ethiopia within the African continent as well as the distribution of major and minor lineages across the African continent. (C) Overlapping temporal distribution of all lineages per quarter. Lineage C was not depicted, since all 2010 do not have dates by day and month. Color codes for the lineages are the same displayed for the tree and map in A and B.