PhD (Microbiology) / Department of Microbiology / Globally, one in ten child deaths before the age of 5 years is due to diarrheal disease,
causing almost 800,000 mortalities worldwide, which mostly occur in Sub-Saharan
Africa and South Asia. Eighty-eight percent (88%) of diarrheal deaths worldwide are
attributable to unsafe water, inadequate sanitation and poor hygiene. Unsanitary
environments and poor hygiene practices allow diarrhea causing pathogens including
viruses, bacteria and parasites to spread more easily.
Norovirus (NoV) are now considered the most common cause of outbreaks of
nonbacterial gastroenteritis. However, the factors which control the genetic diversity, the
sources of sporadic NoV infections, the transmission and persistence of infection are
poorly understood. Limited data are available for NoVs strains in South Africa,
especially in rural and peri-urban areas. Despite the excessive burden of diarrhea
disease in developing countries, NoVs outbreaks have been to date mostly reported in
developed countries. Given that the contribution of the various pathogens to diarrhea
may differ substantially between regions depending on local meteorological,
geographic, and socio-economic conditions, there is a need to investigate intensively
the role of viral agents associated with diarrhea in different settings in Africa continent.
How would poor living conditions in rural setting impact the prevalence and genetic
characteristics of Norovirus strains circulating Limpopo province is the research
question of this study.
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To determine the prevalence and genetic diversity of NoVs strains circulating in the rural
communities in the Limpopo Province, South Africa and investigate the genetic
relationship between NoVs strains, a cross-sectional study was performed on human
stools collected from rural communities. We used qualitative variables of poor living
environmental conditions including type of water used at the household of child’s parent
or guardian, use of toilet seat, presence of livestock at the household and parent
employment status to assess possible environmental risk factors of NoV infection within
the study area.
Prior to this prospective study, we conducted a systematic review of the PubMed and
EMBASE databases for published articles of Human NoVs in Africa between 1990 and
2013 in order to assess the contribution of Human NoVs to diarrhoeal diseases in
Africa. This review provides a picture of Human NoVs studies in Africa and reveals that
unreported sporadic gastroenteritis cases of Human NoVs are common in Africa. Most
are community-associated infections reported from urban settings. Possible
environmental transmission routes have been documented. Combined environmental
and clinical studies are required for targeted actions to control transmission of Human
NoVs in Africa.
Between July 2014 and April 2015, outpatient children under 5 years of age from rural
communities of Vhembe district, South Africa, were enrolled for the study. A total of 303
stool specimens were collected from those with diarrhea (n=253) and without (n=50)
diarrhea. NoVs were identified using real-time one-step RT-PCR. Nucleotide
sequencing methods were performed to genotype the strains. Phylogenetic analyses
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were performed to compare identified NoVs genotypes to the worldwide circulating
strains. One hundred and four (41.1%) NoVs were detected. NoV detection rates in
symptomatic and asymptomatic children (OR = 1.24; 95% CI 0.66 – 2.33) were not
significantly different. Comparison of the median CT values for NoV in symptomatic and
asymptomatic children revealed significant statistical difference of estimated GII viral
load from both groups, with a much higher viral burden in symptomatic children to our
knowledge this is the first study reporting on the differences in estimated viral load of GII
and GI NoV positive cases and controls. The study findings may have implications for
the diagnosis of NoV disease and future vaccine development, which may only need to
consider GII as the genogroup associated with diarrhea in the South African population.
Sequence analyses demonstrated multiple NoV genotypes identified in rural
communities of Vhembe district. The most prevalent NoV genotypes were GII.4 Sydney
2012 variants (n=7) among the capsid genotypes, GII.Pe (n=9) among the polymerase
genotypes and GII.Pe/GII.4 Sydney 2012 (n=8) putative recombinants among the
RdRp/Capsid genotypes. Two unassigned GII.4 variants and an unusual RdRp
genotype GII.P15 were found. With note, the rare GII.P15 identified in this study, has a
common ancestor with GII.P15 strain from Japan previously reported as GII /
untypeable recombinant strain implicated in a gastroenteritis outbreak. To our
knowledge this is the first report of this unusual genotype in the African continent.
Though not proven predictive of diarrhea disease in this study, the high detection rate of
NoV reflects the substantial exposure of children from rural communities to enteric
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pathogens possibly. However in this study no risk factor has been found between NoV
positive and qualitative environmental variables of poor living conditions in rural setting.
The results also suggest that the difference between asymptomatic and symptomatic
children with NoV may be at the level of the viral load of NoV genogroups involved.
The findings highlighted NoV genetic diversity and revealed continuous pandemic
spread and predominance of GII.Pe/GII.4 Sydney 2012, indicative of increased NoV
activity. An unusual RdRp genotype GII.P15 and two unassigned GII.4 variants were
also identified from rural settings of the Vhembe district/South Africa. NoV surveillance / NRF
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:univen/oai:univendspace.univen.ac.za:11602/1163 |
| Date | 21 September 2018 |
| Creators | Kabue Ngandu, Jean - Pierre |
| Contributors | Potgieter, Natasha, Hunter, Paul, Emma, Meader |
| Source Sets | South African National ETD Portal |
| Language | English |
| Detected Language | English |
| Type | Thesis |
| Format | 1 online resource (xviii, 187 leaves : color illustrations, color maps) |
| Rights | University of Venda |
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