The evolutionary history of Rift Valley fever virus (RVFV) is complex and has been greatly influenced by dramatic environmental changes throughout Africa in the past few decades. Over this time period, RVFV gene flow has been impacted on various levels such as geographic dispersal and reassortment events. Overall, there are 15 lineages, designated from A to O. In many cases, viruses from these lineages have been detected outside enzootic regions through probable movement of infected animals and/or mosquitoes. This has led to large outbreaks in countries where the disease had not been previously reported. Genomic surveillance of the virus diversity is crucial in developing intervention strategies. Therefore, we have developed a user-friendly computational tool for rapidly classifying and assigning lineages of partial or whole genome sequences of the virus using the glycoprotein Gn gene within the M-segment. The computational method is presented both as a command line tool and a web application hosted at https://www.genomedetective.com/app/typingtool/rvfv/. Validation of the tool has been performed on a large dataset comprising of partial and whole genome sequences of the M segment collected from the GenBank database. The Rift Valley Virus typing tool was able to correctly classify all 129 RVFV sequences at species level with 100% specificity, sensitivity and accuracy. All the sequences in lineages A (n = 13), B (n = 1), C(n = 44), D(n = 1), E(n = 7), F(n = 1), I(n = 2), J(n = 1), M(n = 2), N(n = 13) and O(n = 2) were correctly classified at phylogenetic level. We further tested our tool using genomic data that we generated through sequencing of samples collected following RVF outbreaks in Kenya. The tool is useful in tracing the origin of outbreaks and supporting surveillance efforts.
Availability: https://github.com/ajodeh-juma/rvfvtyping