- Title
- Recovery and molecular identification of Aichi virus 1, enteric human bocaviruses and enteric human adenoviruses in untreated sewage and mussel samples collected in the Eastern Cape Province of South Africa
- Creator
- Onosi, Oikwathaile
- ThesisAdvisor
- Knox, Caroline
- Subject
- Sewage -- Analysis -- South Africa -- Eastern Cape
- Subject
- Sewage -- Microbiology -- South Africa -- Eastern Cape
- Subject
- Viral pollution of water -- South Africa -- Eastern Cape
- Subject
- Sewage disposal in rivers, lakes, etc. -- South Africa -- Eastern Cape
- Subject
- Enteroviruses -- South Africa -- Eastern Cape
- Subject
- Picornaviruses -- South Africa -- Eastern Cape
- Subject
- Aichi virus 1
- Subject
- Parvoviruses -- South Africa -- Eastern Cape
- Subject
- Adenoviruses -- South Africa -- Eastern Cape
- Date
- 2019
- Type
- text
- Type
- Thesis
- Type
- Masters
- Type
- MSc
- Identifier
- http://hdl.handle.net/10962/69456
- Identifier
- vital:29539
- Description
- Gastroenteritis, commonly known as diarrhoeal disease, is one of the top killers responsible for substantial human morbidity and mortality especially in third world countries where most people do not have access to potable water and where hygiene levels are low. Many bacterial, viral and protozoal agents are known causes of gastroenteritis and viral gastroenteritis is responsible for over 70% of cases. Rotaviruses are the main causes of viral gastroenteritis and are responsible for most of the cases worldwide. Other viral agents associated with this disease include human noroviruses, Aichi virus 1, enteric human bocavirus, enteric human adenovirus and many other emerging viral agents such as klassivirus, Saffold virus, cosavirus and others. In 2009 the South African government introduced a rotavirus vaccine, RotaRixTM into the expanded programme on immunisation (EPI). More than a 50% decrease in diarrhoea related morbidity and mortality due to rotavirus infections was noted during surveillance studies on the efficacy of the vaccine. However, over 40% of cases of gastroenteritis are of unknown aetiology. The present study aimed to perform a preliminary study to investigate the presence of Aichi virus 1 and enteric human bocaviruses in the Eastern Cape Province by the use of molecular techniques. Furthermore, the study aimed to add to the limited molecular data about enteric adenoviruses in South Africa. Samples used in this study were swab samples collected from Belmont Valley Wastewater Treatment Plant in Grahamstown, South Africa, as well as mussel samples collected from the Swartkops River in Port Elizabeth, South Africa. Both raw sewage and shellfish give a broad idea of what microbes are circulating in the communities. In the present study, twenty swabs and twenty mussel samples were prepared by centrifugation, sonication and filtration. Samples were then subjected to transmission electron microscopy (TEM) analysis, for which the electron micrographs revealed presence of viral particles with diameters ranging from around 20 nm to just over 100 nm. Viral nucleic acids were extracted from 140 μL of the twenty swabs and twenty mussels samples using the QIAamp® Viral RNA Mini Kit, following manufacturer‟s instructions. For detection of Aichi virus 1 from the swab and mussel samples three reverse transcriptase- polymerase chain reaction (RT-PCR) assays using the Verso 1-Step RT-PCR Hot-Start Kit were developed. The first RT-PCR assay targeted amplification of the highly conserved 5′ UTR using published primers. However, despite many amplification attempts no positive results were obtained from both swab and mussel samples. It was only after the addition of DMSO (to a final concentration of 10%) that one swab sample was positive for this assay. In addition, a 2-step RT-PCR was developed using the Maxima H Minus First Strand cDNA Synthesis Kit. By using this 2-step RT-PCR assay, an additional swab sample was positive for the Aichi virus 1 5′ UTR. Using Basic Logarithm Alignment Search Tool (BLAST) analysis these two samples were 98% identical to an Aichi virus isolate from South Korea. The second one-step RT-PCR assay targeted amplification of the 266 bp partial 3CD coding region of Aichi virus 1 using published primers. By using this assay, positive results were obtained from both the swab and mussel samples, which when analysed by BLAST were all 99% identical to various Aichi virus 1 isolates in GenBank. A phylogenetic tree constructed based on this region showed that isolates from the present study clustered with Genotype B isolates in GenBank. The third assay was a semi-nested RT-PCR assay that targeted amplification of the hypervariable VP1 coding region of Aichi virus 1 using a combination of published primers and those designed in the present study. Amplicons which were 472 bp in size were produced from two swab samples. When analysed by BLAST, these two swab samples had percentage identities of 98% to an Aichi virus isolate from South Korea. A phylogenetic tree constructed based on this region showed that isolates from the present study clustered with Genotype B isolates in GenBank. This was consistent with phylogenetic results discussed above which were based on the partial 3CD region. For detection of enteric human bocaviruses from the swab and mussel samples a nested polymerase chain reaction (PCR) assay, using the Ampliqon Taq PCR kit (Ampliqon Bio Reagents and Molecular Diagnostics, Denmark) was developed based on PCR amplification of the 382 bp partial VP1/VP2 coding region using published primers. A total of six swab samples and six mussel samples were analysed for which five swabs and six mussel samples gave positive results. When analysed by BLAST, the swab samples had percentage identities of between 98% and 99% to an enteric human bocavirus 3 strain from China while the mussel samples were all 99% identical to an enteric human bocavirus 2 isolate from Australia. A phylogenetic tree constructed based on this VP1/VP2 region showed that isolates from the present study clustered with human bocavirus 2 and human bocavirus 3 isolates in GenBank for those isolated from swab samples and mussel samples respectively. Lastly, for detection of enteric human adenoviruses from the swab and mussel samples a nested PCR assay, using the Ampliqon Taq PCR kit (Ampliqon Bio Reagents and Molecular Diagnostics, Denmark) was developed. This reaction was based on PCR amplification of the 168 bp partial hexon coding region using published primers for which ten swab samples gave positive results. When analysed by BLAST, the swab samples had percentage identities of between 96% and 99% to enteric human adenoviruses in GenBank. A phylogenetic tree constructed based on the hexon coding region showed that isolates from the present study clustered with subtypes C, D and F which are associated with gastroenteritis worldwide. Despite several amplification attempts no positive results were obtained from mussel samples. The results from the present study show that Aichi virus 1, enteric bocaviruses and enteric adenoviruses are present in the Eastern Cape Province of South Africa. These viruses could possibly be responsible for enteric infections in South Africa. Although only a few samples were analysed, this study is the first to confirm the presence of Aichi virus 1 and enteric bocaviruses in South Africa and provides a platform for further investigation into prevalence and epidemiology of these viruses in the country.
- Format
- 238 pages, pdf
- Publisher
- Rhodes University, Faculty of Science, Biochemistry and Microbiology
- Language
- English
- Rights
- Onosi, Oikwathaile
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Collections
RU Department of Biochemistry and Microbiology (2015-)
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