Abstract:
Members of the genus Alphavirus, family Togaviridae are a diverse group of principally mosquito-borne RNA
viruses that produce a variety of diseases worldwide. Being RNA viruses, they are prone to genetic transformation
like other RNA viruses. The aim of this study was to investigate the genetic diversity and relatedness of ndumu
virus isolates from Garissa, Ijara, Busia and Baringo districts in Kenya. It also aimed at determining the phylogenetic
relatedness of the ndumu virus isolates to other known alphaviruses. This was achieved by culturing eight virus
isolates, two from each district in Vero cells. The isolates induced cytopathic effects (CPE) on cell culture on day 1
post inoculation. The infected cells were harvested and the cell culture supernatant used to isolate total RNA.
Some of the RNA was amplified by Reverse transcriptase polymerase chain reaction using primers specific for the
ndumu envelope gene (E1) to confirm the identity of the virus. Complete genome sequencing of the isolates using
454 pyro-sequencer was done to get the sequences. A mapping assembly of the sequence reads from the 454
sequencer was done using GS runmapper with reference to the longest ndumu virus sequence available in the
genbank. Nucleotide and amino acid sequence alignment was done using muscle v 3.7 and clustaX softwares
respectively. Phylogenetic analysis was done using MEGA v4.0. The ndumu virus isolates from Baringo, Busia and
Garissa districts exhibited minimal genetic diversity despite the geographic distance separating them. One isolate
from Ijara District was distinct. This study has facilitated the identification of single nucleotide polymorphisms
(SNPs) within ndumu virus genome. Such SNPs may change the protein coding sequence and affect the virus’
virulence and/or host susceptibility over time. When compared with other known alphaviruses, the ndumu virus
isolates were not closely related to any other alphavirus.
