Dog rabies in southern Africa: regional surveillance and phylogeographical analyses are an important component of control and elimination strategies

Abstract

In the resource-poor settings where dog rabies remains endemic, the demonstration of a need to divert scarce funds towards exhaustive surveillance activities is no easy task. Here, we investigate a recent case of human rabies in South Africa, which generated much public interest and wide media coverage. One of the factors contributing to the hype was an uncertainty about the geographical origin of the infection. This provided an opportunity to highlight the importance of increased regional surveillance and basic phylogeographical analyses in rabies control and elimination strategies. Our aim was to elucidate the origins of the virus responsible for this case, as the patient was from a well-vaccinated area that had been free from dog rabies cases for many years. The phylogeographical techniques that we applied would also be most useful in any end-stage infectious disease control programme, specifically in verifying the source of novel cases in order to rapidly respond towards maintaining the integrity of disease-free areas. The most likely origin of our case was shown to be from outside the disease-free area and indeed from outside the country of South Africa. We conclude that phylogeographical techniques can provide rapid and statistically rigorous answers to epidemiologically pertinent questions that impact on disease control strategies and resource allocation, but this will require coordinated regional surveillance practices.

Molecular characterization and phylogenetic relatedness of dog-derived Rabies Viruses circulating in Cameroon between 2010 and 2016

“…Although it is tempting to explain away failure to efficiently amplify some RABV isolates by low RABV load in 17 studied rabies-positive specimens, the presence of potentially divergent Lyssaviruses among domestic dogs cannot be wiped out. Remarkably, none of the studied isolates displayed close phylogenetic relationships either with the divergent shrew-derived Mokola Lyssavirus strain 86100CAM (GenBank N° EU293117) from Cameroon, or with the Africa-4 and Africa-3 clades which are specific to northern [ 34 ] and southern [ 32 , 43 , 52 ] Africa, respectively. One explanation for the failure to efficiently amplify potential divergent variants of the RABV in this study may be that they were so divergent from the more prevalent variants that they could be refractory to amplification with generic primers used in this study.…”

“…It is predominant in northern and eastern Africa [ 38 – 40 ] and has also been previously reported in Cameroon, Gabon, Equatorial Guinea, Ghana and Madagascar [ 38 , 41 , 42 ]. Africa-1b lineage circulates mainly in eastern and southern Africa [ 38 , 39 , 43 , 44 ].…”

Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting

“…The spatial distribution and size of subpopulations can cause spatial hierarchies of metapopulation dynamics or travelling waves of infection [ 32 ]. It is therefore essential to identify sub-populations important in source-sink dynamics or bottleneck areas, each requiring tailored management plans [ 27 , 30 ]. More generally, our data demonstrate the need to understand hierarchical ('core-satellite') epidemic dynamics for the control of established and re-emerging diseases [ 23 , 33 ].…”

Towards the elimination of dog-mediated rabies: development and application of an evidence-based management tool

“…Sequencing of viruses can resolve key questions about viral circulation, discriminating wildlife variants from dog variants [ 37 ], including the potential for host shifts [ 47 ], and providing insights about the persistent lineages in remaining foci [ 48 ], which would be useful now in Chiapas state, Mexico and in Guatemala. In a previously rabies-free area, sequencing could identify the source(s) of incursions [ 49 ], and confirm that the new virus lineage differed from those historically circulating (i.e. undetected endemic circulation) [ 30 , 50 ].…”