Diarrhoeal disease is considered the second most common cause of morbidity and fourth
most common cause of mortality, worldwide. Low-income countries such as those in Africa
and Asia bear the greatest burden of gastroenteritis. Diarrhoeal disease affects individuals of
all ages, however, children <5 years of age, the immunocompromised and the elderly
population ≥65 years of age are most severely affected. The elderly population, particularly
immunocompromised patients residing in long-term care facilities represent high-risk groups
for gastroenteritis and surveillance of these individuals in South Africa is under-represented.
It has been observed that an individual’s fucosyltransferase 2 (FUT2) secretor status has been
associated with different degrees of infection by rotaviruses and noroviruses.
A total of 1 012 stool specimens from elderly patients were collected over an 18-month
surveillance period, of which 340 specimens met the inclusion criteria and were tested. Virus
screening was performed using a lyophilised real-time multiplex RT-PCR/PCR screening
iv
assay testing for norovirus GI and GII, rotavirus, human adenovirus, human astrovirus and
sapovirus. Careful analysis of the real-time (RT)-PCR amplification plots and export data
identified 50 viruses in 40 patient specimens.
Seven norovirus GI/GII dual-infections were observed and three co-infections were
identified, each with an astrovirus accompanying infection by a rotavirus, sapovirus and
human adenovirus. FUT2 genotyping was performed to acquire the secretor status for all the
rotavirus- and norovirus-positive individuals.
The real-time TaqMan® SNP Genotyping Assay was inconsistent in amplifying the SNP in
the FUT2 gene from stool-extracted DNA of elderly patients, and therefore an alternative,
conventional genotyping PCR approach was performed. This approach was successful in
acquiring the secretor status of 14/21 patient specimens. A total of 10 homozygous secretors,
three heterozygous secretors and one homozygous non-secretor were identified.
Virus-positive specimens identified in this study were genotyped and subjected to
phylogenetic analysis. Overall, 14 norovirus- GI, 12 norovirus- GII, 10 sapovirus-, six human
adenovirus-, six human astrovirus- and two rotavirus-positives were identified. From the 14
norovirus GI positives, three polymerase regions and two capsid regions were successfully
genotyped. The polymerase strains all belonged to genotype GI.P1 and the capsid sequences
were all GI.1 genotypes. Only one virus was successfully dual-genotyped as GI.1[P1]. For
norovirus GII, a total of nine polymerase and nine capsid strains were genotyped
successfully. All the polymerase sequences belonged to the GII.P31 genotype and eight
capsid sequences identified as GII.4 Sydney 2012 strains, with a single GII.6 genotype
identified. Three of the six adenovirus positives were genotyped, of which one strain grouped
into species C and two strains grouped into species D, and shared a clade with a type 17
reference strain. Human astrovirus dual-genotyping was successful for three strains, which
identified as type 2 for both the serine protease and capsid types. A single rotavirus strain was
genotyped for VP4 and VP7 and identified as G9P[6]. Only two sapovirus-positives were
successfully genotyped as GI.2 and GIV.1, respectively. This study highlights the
epidemiological importance of clinical surveillance in the geriatric population, acting as a
cornerstone for future studies in South Africa. / Dissertation (MSc (Medical Virology))--University of Pretoria, 2019. / The dissertation is under embargo until September 2022. / National Research Foundation / Poliomyelitis Research Foundation / Medical Virology / MSc (Medical Virology) / Restricted
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:up/oai:repository.up.ac.za:2263/73858 |
| Date | January 2019 |
| Creators | Kuča, Adam |
| Contributors | Mans, Janet, Adamkuca01@gmail.com, Van Zyl, Walda B. |
| Publisher | University of Pretoria |
| Source Sets | South African National ETD Portal |
| Language | English |
| Detected Language | English |
| Type | Dissertation |
| Rights | © 2019 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. |
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