Genetic diversity of circulating rotavirus strains in Tanzania prior to the introduction of vaccination - PubMed (original) (raw)

Clinical Trial

Genetic diversity of circulating rotavirus strains in Tanzania prior to the introduction of vaccination

Sabrina J Moyo et al. PLoS One. 2014.

Abstract

Background: Tanzania currently rolls out vaccination against rotavirus-diarrhea, a major cause of child illness and death. As the vaccine covers a limited number of rotavirus variants, this study describes the molecular epidemiology of rotavirus among children under two years in Dar es Salaam, Tanzania, prior to implementation of vaccination.

Methods: Stool specimens, demographic and clinical information, were collected from 690 children admitted to hospital due to diarrhea (cases) and 545 children without diarrhea (controls) during one year. Controls were inpatient or children attending child health clinics. Rotavirus antigen was detected using ELISA and positive samples were typed by multiplex semi-nested PCR and sequencing.

Results: The prevalence of rotavirus was higher in cases (32.5%) than in controls (7.7%, P<0.001). The most common G genotypes were G1 followed by G8, G12, and G4 in cases and G1, G12 and G8 in controls. The Tanzanian G1 variants displayed 94% similarity with the Rotarix vaccine G1 variant. The commonest P genotypes were P[8], P[4] and P[6], and the commonest G/P combination G1 P[8] (n = 123), G8 P[4] and G12 P[6]. Overall, rotavirus prevalence was higher in cool (23.9%) than hot months (17.1%) of the year (P = 0.012). We also observed significant seasonal variation of G genotypes. Rotavirus was most frequently found in the age group of four to six months. The prevalence of rotavirus in cases was lower in stunted children (28.9%) than in non-stunted children (40.1%, P = 0.003) and lower in HIV-infected (15.4%, 4/26) than in HIV-uninfected children (55.3%, 42/76, P<0.001).

Conclusion: This pre-vaccination study shows predominance of genotype G1 in Tanzania, which is phylogenetically distantly related to the vaccine strains. We confirm the emergence of genotype G8 and G12. Rotavirus infection and circulating genotypes showed seasonal variation. This study also suggests that rotavirus may not be an opportunistic pathogen in children infected with HIV.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. A and B. Phylogenetic trees of the rotavirus nucleotide sequence of the partial VP7 and VP4 genes.

The phylogenetic tree: Phylogenetic trees based on the nucleotide sequence of the partial VP7 gene (figure 1A) and VP4 gene (figure 1B) of rotaviruses from Tanzania with known rotavirus reference strains from GenBank database and rotavirus vaccine strains i.e Rotateq and Rotarix. Reference strains, vaccine strains and strains from this study are indicated by accession numbers. The Genius software package was used to build the tree with the UPGMA method and bootstrapped with 1,000 repetitions; The Kimura-2 substitution model was used. The bar indicates nucleotide substitutions per site.

Figure 2

Figure 2. Seasonal variation of rotavirus infection and G genotypes among children admitted with diarrhea.

The graph shows the total number of rotavirus infected children admitted due to diarrhea (cases) per month with G genotypes.

Figure 3

Figure 3. Prevalence of rotavirus infection in different age groups.

The graph shows the prevalence of rotavirus from ELISA results per age group in cases and controls.

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