Rotavirus strain diversity in Blantyre, Malawi, from 1997 to 1999

In a 2-year study of viral gastroenteritis in children in Blantyre, Malawi, the diversity of rotavirus strains was investigated by using electropherot yping, reverse transcription-PCR amplification of the VP7 and VP4 genes (G and P genotyping), and nucleotide sequencing. Of 414 rotavirus strains char acterized, the following strain types were identified: P[8], G1 (n = 111; 2 6.8%); P[6], G8 (n = 110; 26.6%); P[8], G3 (n = 93; 22.5%); P[4], G8 (n = 3 1; 7.5%); P[8], G4 (n = 21; 5.1%); P[6], G3 (n = 12; 2.9%); P[6], G1 (n = 7 ; 1.7%); P[6], G9 (n = 3; 0.7%); P[6], G4 (It = 3; 0.7%); P[4], G3 (n = 1; 0.2%); and mixed (n = 15;3.6%). While all strains could be assigned a G typ e, seven strains (1,7%) remained P nontypeable. The majority of serotype G8 strains and all serotype G9 strains had short electropherotype profiles. A ll remaining typeable strains had long electropherotypes. Divergent serotyp e G1 rotaviruses, which contained multiple base substitutions in the 9T-1 p rimer binding site, were commonly identified in the second year of surveill ance, Serotype G2 was not identified. Overall, G8 was the most frequently i dentified VP7 serotype (n = 144; 34.8%) and P[8] was the most frequently de tected VP4 genotype (n = 227; 54.8%). Partial sequence analysis of the VP4 gene of genotype P[gl rotaviruses identified three distinct clusters, which predominantly (but not exclusively) comprised strains belonging to a disti nct VP7 serotype (G1, G3, or G4). As a result of mutations in the IT-1 prim er binding site, strains belonging to each cluster required a separate prim er for efficient typing. One cluster, represented by P[8], G4 strain OP354, was highly divergent from the established Wa and F45 VP4 P[8] lineages. As is the case for some other countries, the diversity of rotaviruses in Mala wi implies that rotavirus vaccines in development will need to protect agai nst a wider panel of serotypes than originally envisioned.