Molecular epidemiology of type 1 polioviruses from Africa

The genetic relationships between type 1 polioviruses circulating in sub-Saharan Africa during the past decade have been investigated by partial genomic sequencing across the VP1/2A region of the polioviral genome. Sequencing templates were generated by single-step reverse transcription PCR amplification of the viral RNA using poliovirus-specific primers. Seven poliovirus genotypes, circulating in different geographical regions during different periods, were identified. Considerable genetic variation was exhibited by strains within several of these genotypes, indicative of sustained endemic transmission within individual countries. Two genotypes appear to be circulating in Africa at present; one major genotype, which has been in circulation since at least 1980, covers a wide geographical region and includes countries in western, central and southern Africa. Within this genotype are several smaller clusters, possibly representing strains in the process of evolving into new genotypes. The second genotype presently in circulation has been found only in Tanzania and Zambia to date, associated with a relatively small number of cases. Imported genotypes, introduced from the Middle East and the Indian subcontinent, have also recently been in circulation in eastern and central Africa. In South Africa, three genotypes, one unique to the country and the others imported from west Africa and the Middle East, co-circulated endemically between 1980 and 1985. A fourth genotype, introduced from countries to the north, displaced the endemic strains and continued to circulate until 1989. This study has generated a meaningful overview of the endemic circulation and regional transmission of type 1 polioviruses throughout sub-Saharan Africa.