Phylogenetic and evolutionary relationships among yellow fever virus isolated in Africa

Previous studies with a limited number of strains have indicated that there are two genotypes of yellow fever (YF) virus in Africa, one in west Africa and the other in east and central Africa, We have examined the prM/M and a portion of the E protein for a panel of 38 wild strains of YF virus from A frica representing different countries and times of isolation. Examination of the strains revealed a more complex genetic relationship than previously reported. Overall, nucleotide substitutions varied from 0 to 25.8% and ami no acid substitutions varied from 0 to 9.18, Phylogenetic analysis using pa rsimony and neighbor-joining algorithms identified five distinct genotypes: central/east Africa, east Africa, Angola, west Africa I, and west Africa I I. Extensive variation within genotypes was observed, Members of west Afric an genotype II and central/east African genotype differed by 2.8% or less, while west Africa genotype I varied up to 6.8% at the nucleotide level, We speculate that the former two genotypes exist in enzootic transmission cycl es, while the latter is genetically more heterogeneous due to regular human epidemics. The nucleotide sequence of the Angola genotype diverged from th e others by 15.7 to 23.0% but only 0.4 to 5.6% at the amino acid level, sug gesting that this genotype most likely diverged from a progenitor YF virus in east/central Africa many years ago, prior to the separation of the other east/central African strains analyzed in this study, and has evolved indep endently. These data demonstrate that there are multiple genotypes of YF vi rus in Africa and suggest independent evolution of YF virus in different ar eas of Africa.