Diagnostic Surveillance, Molecular Epidemiology and Phylogenetic Analyses of Rabies Virus Strains in Mali

Rabies is a highly infectious and vaccine preventable disease of humans and animals which is transmitted by dogs. There has been a breadth of emphasis regarding rabies elimination strategies in Asia and Africa due to highly endemic status of rabies in these states. Diagnostic surveillance system is operated by Central Veterinary Laboratory (CVL) only in the capital city of Mali, and hence other cities are at high risk of rabies due to lack of diagnostic labs and reporting mechanism. Therefore, present study has been designed to evaluate the suitability of diagnostic methods of rabies for characterization of circulating rabies virus (RABV) isolates in Mali. Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR), Rapid Immunochromatographic Diagnostic Test (RIDT) and Fluorescent antibody test (FAT) were performed on these 18 brain samples which were previous submitted to the CVL in 2017. Out of these 18 samples, only 16 (88%) were positive for RABV through FAT. These 16 positive samples were processed through RT-PCR and RIDT tests, and both tests further confirmed 15 (93.75%) and 7 (43.75%) samples positive for RABV. Positive samples generated from RT-PCR were sequenced using Sanger sequencing method at Inqaba Biotec and further subjected to phylogenetic analysis. All the sequences analysed by Blastn shared at least 93.5% nucleotide identity to the rabies nucleoprotein gene thereby confirming RABV infection of dogs in Mali. Phylogenetic analysis revealed that all the sequences belonged to the Africa 2 lineage of which 5 were connected to the sub-lineage H, 4 to the sub-lineage F and 2 to the sub-lineage G. The sensitivity of RIDT was low as compared to FAT, while the genetic characterization of the RABV confirmed previous findings of the circulation of the sub-lineages H, F and G belonging to the Africa 2 lineage in Mali. In conclusion, RT-PCR could be used together with FAT for the detection and genetic characterization of RABV in Mali. Further studies using large number of samples are required to validate the suitability of the new RIDT for the diagnosis of rabies in Mali.