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. 2018 May 30;18(1):246.
doi: 10.1186/s12879-018-3157-y.

Genetic and epidemiological analysis of norovirus from children with gastroenteritis in Botswana, 2013-2015

Kgomotso Makhaola  1 , Sikhulile Moyo  2   3 , Kwana Lechiile  4 , David M Goldfarb  4   5 , Lemme P Kebaabetswe  6
Affiliations

Genetic and epidemiological analysis of norovirus from children with gastroenteritis in Botswana, 2013-2015

Kgomotso Makhaola et al. BMC Infect Dis. .

Abstract

Background: Norovirus is a leading cause of viral gastroenteritis worldwide with a peak of disease seen in children. The epidemiological analysis regarding the virus strains in Africa is limited. The first report of norovirus in Botswana was in 2010 and currently, the prevalence and circulating genotypes of norovirus are unknown, as the country has no systems to report the norovirus cases. This study investigated the prevalence, patterns and molecular characteristics of norovirus infections among children ≤5 years of age admitted with acute gastroenteritis at four hospitals in Botswana.

Methods: A total of 484 faecal samples were collected from children who were admitted with acute gastroenteritis during the rotavirus vaccine impact survey between July 2013 and December 2015. Norovirus was detected using real-time RT-PCR. Positive samples were genotyped using conventional RT-PCR followed by partial sequencing of the capsid and RdRp genes. Norovirus strains were determined by nucleotide sequence analysis using the online Norovirus Genotyping Tool Version 1.0, and confirmed using maximum likelihood tree construction as implemented in MEGA 6.0.

Results: The prevalence of norovirus was 9.3% (95% CI 6.7-11.9). The genotype diversity was dominated by the GII.4 strain at 69.7%. This was followed by GII.2, GII.12 each at 9.1%, GI.9 at 6.6% and GII.6, GII.10 each at 3.0%. The most common combined RdRp/Capsid genotype was the GII.Pe/GII.4 Sydney 2012. Norovirus was detected during most part of the year; however, there was a preponderance of cases in the wet season (December to March).

Conclusion: The study showed a possible decline of norovirus infections in the last 10 years since the first report. An upward trend seen between 2013 and 2015 may be attributable to the success of rotavirus vaccine introductions in 2012. Knowledge of circulating genotypes, seasonal trends and overall prevalence is critical for prevention programming and possible future vaccine design implications.

Keywords: Botswana; GII.4 variants; GII.Pe-GII.4; Genotyping; Norovirus.

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Conflict of interest statement

Ethics approval and consent to participate

Written informed consent was obtained from all parents and guardians of the children that were enrolled in this study. Ethical approval for the study, to perform molecular analyses on the samples was obtained from Botswana’s institutional review board, the Health Research and Development Council (HRDC). Furthermore, permission to collect data, samples from patients and subsequent analysis was sought from HRDC, McMaster University and University of Pennsylvania as reported in the previous study [22]. This study was conducted according to the principles expressed in the Declaration of Helsinki.

Competing interests

The authors declare that they have no competing interests.

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Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Phylogenetic tree of noroviruses based on (a) partial capsid and (b) RdRp genes of norovirus strains detected in children with acute gastroenteritis in Botswana, 2013–2015. The study samples are in shaded triangles and reference strains (unshaded triangles) are indicated by GenBank accession numbers. The scale bar represents nucleotide substitutions per site and the number above each branch corresponds to the bootstrap value. Scale bar is proportional to genetic distance
Fig. 2
Fig. 2
Distribution of norovirus genotypes by year from Botswana, 2013–2015. a Capsid and b RNA dependent RNA polymerase
See this image and copyright information in PMC

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