Rotavirus genetic diversity, disease association, and temporal change in hospitalized rural Kenyan children

Abstract

Background: The effectiveness of rotavirus vaccines will be dependent on the immunity conferred against prevalent and emergent variants causing severe diarrheal disease. Longitudinal surveillance of disease-causing strains is a prerequisite to intervention.

Methods: Molecular characterization was conducted on rotavirus-positive stool samples from children admitted with diarrhea to a rural district hospital during 2002-2004. Extracted viral RNA was separated by polyacrylamide gel electrophoresis, and rotavirus VP4 (P types) and VP7 (G types) specificities were determined.

Results: Among 558 investigated cases, the predominant genotype was P[8]G1 (42%), followed by P[8]G9 (15%), P[4]G8 (7%), P[6]G8 (6%), and P[8]G8 (4%), with 10% mixed strains. Overall, there were 6 different P types and 7 G types. No association was identified between genotype and child age, sex, or severity of diarrhea. The P and G genotypes and polyacrylamide gel electropherotypes showed significant temporal variation in frequency: P[8]G1 decreased from 51% (95% confidence interval [CI], 43%-58%) in 2002 to 30% (95% CI, 24%-37%) in 2004, and P[4]G8 increased from 2% (95% CI, 0%-5%) in 2002 to 13% (95% CI, 9%-19%). Quarterly data revealed seasonally endemic and emergence and/or decay patterns.

Conclusions: Our study of rotavirus strains causing severe diarrhea in rural Kenyan children showed a predominance of P[8]G1 and confirms the importance of G8 and G9 strains in sub-Saharan Africa. Considerable genetic diversity of rotavirus strains was observed, including substantial mixed and unusual types, coupled with significant temporal strain variation and emergence. These results warn of variable vaccine efficacy and the need for long-term surveillance of circulating rotavirus genotypes.

Fig. 1

Variation by year (2002-04) in P-G genotype frequencies (with exact 95% CI) determined for 558 rotavirus positive samples from Kilifi District Hospital, Kenya 2002-04. Low frequency types include all single strain genotypes with a frequency over the 3 years of less than 15 cases.

Fig. 2

Seasonal variation in P-G genotypes determined for 558 group A rotavirus (GARV) positive samples from Kilifi District Hospital, Kenya 2002-04. The top left panel details totals for all variants by year and quarter (bars) and total cases of diarrhea (lines) from which GARV positives identified.