Genetic divergence of poliovirus strains isolated in the Karachi region of Pakistan.

Seventy-seven wild poliovirus strains isolated from poliomyelitis cases in the Civil Hospital of Karachi in Pakistan in 1989-1993 were selected for partial sequence analysis covering the VP1/2A junction region of the viral genome to study the genetic relationships and epidemiological links between strains. Viral RNA was partially amplified by RT-PCR and sequenced by a solid phase method. Computer analysis revealed genetic divergence of the strains within each serotype. Most of the nucleotide differences between strains were silent: only a few specific amino acid substitutions were seen in the sequenced region. Three genotypes of poliovirus type 1 and two of poliovirus type 3 were co-circulating, while type 2 strains were represented by a single genotype. Representatives of all the genotypes present have been found among previously or concurrently characterized stains isolated elsewhere, but direct epidemiological links were found only in the case of serotype 1. Many of the epidemics caused by poliovirus type 1 in other countries were genetically linked to Pakistan. This study clearly shows the endemic circulation and wide variation of all three poliovirus serotypes in southern Pakistan and indicates the need for more effective vaccination programmes to prevent the further spread of these wild viruses.