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Journal of Clinical Microbiology, March 2001, p. 836-843, Vol. 39, No. 3
0095-1137/01/$04.00+0   DOI: 10.1128/JCM.39.3.836-843.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Rotavirus Strain Diversity in Blantyre, Malawi, from 1997 to 1999

N. A. Cunliffe,1,2,3 J. S. Gondwe,2 S. M. Graham,2 B. D. M. Thindwa,1 W. Dove,3 R. L. Broadhead,2 M. E. Molyneux,1,4 and C. A. Hart3,*

Wellcome Trust Research Laboratories1 and Department of Paediatrics,2 College of Medicine, University of Malawi, Blantyre, Malawi, and School of Tropical Medicine4 and Department of Medical Microbiology and Genito-Urinary Medicine,3 University of Liverpool, Liverpool, United Kingdom

Received 20 July 2000/Returned for modification 13 November 2000/Accepted 21 December 2000

In a 2-year study of viral gastroenteritis in children in Blantyre, Malawi, the diversity of rotavirus strains was investigated by using electropherotyping, reverse transcription-PCR amplification of the VP7 and VP4 genes (G and P genotyping), and nucleotide sequencing. Of 414 rotavirus strains characterized, the following strain types were identified: P[8], G1 (n = 111; 26.8%); P[6], G8 (n = 110; 26.6%); P[8], G3 (n = 93; 22.5%); P[4], G8 (n = 31; 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 (n = 3; 0.7%); P[4], G3 (n = 1; 0.2%); and mixed (n = 15; 3.6%). While all strains could be assigned a G type, seven strains (1.7%) remained P nontypeable. The majority of serotype G8 strains and all serotype G9 strains had short electropherotype profiles. All remaining typeable strains had long electropherotypes. Divergent serotype G1 rotaviruses, which contained multiple base substitutions in the 9T-1 primer binding site, were commonly identified in the second year of surveillance. Serotype G2 was not identified. Overall, G8 was the most frequently identified VP7 serotype (n = 144; 34.8%) and P[8] was the most frequently detected VP4 genotype (n = 227; 54.8%). Partial sequence analysis of the VP4 gene of genotype P[8] rotaviruses identified three distinct clusters, which predominantly (but not exclusively) comprised strains belonging to a distinct VP7 serotype (G1, G3, or G4). As a result of mutations in the 1T-1 primer binding site, strains belonging to each cluster required a separate primer 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 Malawi implies that rotavirus vaccines in development will need to protect against a wider panel of serotypes than originally envisioned.

* Corresponding author. Mailing address: Department of Medical Microbiology and Genito-Urinary Medicine, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, United Kingdom. Phone: 44-151-706-4381. Fax: 44-151-706-5805. E-mail: cahmm{at}liv.ac.uk.

Journal of Clinical Microbiology, March 2001, p. 836-843, Vol. 39, No. 3
0095-1137/01/$04.00+0   DOI: 10.1128/JCM.39.3.836-843.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


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