| Summary: | East Coast fever (ECF) is an acute fatal tick-borne disease of cattle caused by <i>Theileria</i><i> parva</i>. It causes major losses in exotic and crossbreed cattle, but this could be prevented by a vaccine of <i>T. parva</i> if the vaccine is selected properly based on information from molecular epidemiology studies. The Muguga cocktail (MC) vaccine (Muguga, Kiambu 5 and Serengeti-transformed strains) has been used on exotic and crossbreed cattle. A total of 254 <i>T. parva</i> samples from vaccinated and unvaccinated cattle were used to understand the genetic diversity of <i>T. parva</i> in Malawi using partial sequences of the Tp1 and Tp2 genes encoding <i>T. parva</i> CD8<sup>+</sup> antigens, known to be immunodominant and current candidate antigens for a subunit vaccine. Single nucleotide polymorphisms were observed at 14 positions (3.65%) in Tp1 and 156 positions (33.12%) in Tp2, plus short deletions in Tp1, resulting in 6 and 10 amino acid variants in the Tp1 and Tp2 genes, respectively. Most sequences were either identical or similar to <i>T. parva</i> Muguga and Kiambu 5 strains. This may suggest the possible expansion of vaccine components into unvaccinated cattle, or that a very similar genotype already existed in Malawi. This study provides information that support the use of MC to control ECF in Malawi.
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