Rotavirus strains circulating in Africa during 1996-1999: emergence of G9 strains and P[6] strains.

Rotavirus infection is associated with 150000-200000 deaths annually in Africa. Although the withdrawal of the RotaShield vaccine has been a major setback in rotavirus vaccine development, new vaccine candidates are under development and approaching phase II and III trials. Before these trials could be conducted in Africa, a comprehensive survey of the circulating VP7 serotypes and VP4 genotypes is required. During the past 3 years, over 3000 rotavirus-positive specimens from several African countries have been analysed. RT-PCR techniques for the VP7 and VP4 genotypes and by monoclonal antibodies to the VP6 subgroup and VP7 serotype have been performed. Almost 75% of the strains were typed by the VP7 monoclonal antibodies or RT-PCR. VP4 genotyping was done in approximately half of these strains. The predominant strains circulating across Africa during 1996-1999 were P[6]G1 and P[6]G3 strains. Geographic differences were noted and West Africa displayed the most diverse strains with G3/8 and G1/3 "mosaic" viruses occurring commonly. G9 strains were identified in several countries indicating that the strain is emerging in Africa too. G9 was the predominant strain in certain countries during 1999. The circulating types observed will have implications for the new rotavirus vaccine candidates.