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Genetic assessment of infectious hepatitis A virus strains detected in selected water sources in Gauteng, South Africa
Thesis (PhD (Medical Virology))--University of Pretoria, 2019.
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University of Pretoria
2020
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| _version_ | 1867613536260194304 |
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| access_status_str | Open Access |
| author2 | Taylor, Maureen B. |
| author_browse | Taylor, Maureen B. |
| author_facet | Taylor, Maureen B. |
| collection | Thesis |
| dc_rights_str_mv | © 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. |
| description | Thesis (PhD (Medical Virology))--University of Pretoria, 2019. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/77336 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:37:42.457Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | University of Pretoria |
| publisherStr | University of Pretoria |
| record_format | dspace |
| source_str | UPSpace — University of Pretoria Institutional Repository |
| spelling | oai:repository.up.ac.za:2263/77336 Genetic assessment of infectious hepatitis A virus strains detected in selected water sources in Gauteng, South Africa Taylor, Maureen B. achidasaid@gmail.com Rachida, Said UCTD Medical Virology Genetic assessment Hepatitis A virus Water sources SDG-03: Good health and well-being Thesis (PhD (Medical Virology))--University of Pretoria, 2019. Hepatitis A is a vaccine preventable liver inflammation caused by the hepatitis A virus (HAV). Hepatitis A virus is the most common cause of acute viral hepatitis worldwide that is transmitted via the faecal-oral route with waterborne transmission recognised as a major public health concern. Hepatitis A virus is classified in the genus Hepatovirus of the family Picornaviridae. The stability of HAV regarding pH, temperature and different treatment systems contributes to the virus’ persistence in the environment. The virion of HAV has a 7.5 kb positive-sense single-stranded RNA genome. Nucleotide sequence analysis of the VP1 region has identified six geographically distinct genotypes infecting humans (genotypes I, II and III) and non-human primates (genotypes IV, V and VI). In South Africa (SA), unique HAV IB strains have been detected in surface and wastewater samples, as well as on fresh produce at the point of retail. However, as the viruses were detected by molecular-based assays it is unknown whether the detected strains were still infectious. Although hepatitis A is a notifiable disease in SA there is gross underreporting, no routine surveillance system and a paucity of epidemiological data on HAV strains in circulation. Recently, the pretreatment of water and food samples with intercalating dyes prior to nucleic acid extraction was successfully applied for the quantification of potentially infectious HAV using molecular assays. Given that analysing sewage, wastewater and surface waters would provide a more accurate estimation of the HAV strains circulating in the country, the present study aimed to detect and characterise infectious HAV strains from selected South African water sources. From April 2015 to March 2016, 118 samples consisting of sewage, treated wastewater discharge and a downstream dam water were collected monthly from five wastewater treatment plants (WWTP 1, 2, 3, 4, 5). High titres of HAV were detected in the sewage (1.34 x e5 and 3.70 x e10 genome copies [gc]/litre [L]) and treated discharge (4.74 x e3 to 3.39 x e7 gc/L) samples. None of the dam water samples tested positive for HAV. Genetic characterisation of the detected strains by Sanger sequencing revealed the circulation of HAV IB strains that carried the R298K amino acid change over the VP1 region or the R63K and R71S change over the VP1/P2B junction or the C70S and M104I change over the VP1/P2B junction. The quasispecies dynamic of HAV has been detected in sewage samples. Hepatitis A virus strains carrying amino acid mutation at the immunodominant and neutralisation epitopes were characterised in both the sewage and treated discharge samples. The virus concentrates of HAV-positive sewage and treated discharge samples were treated with a combination of PMA-water (50 μM) and Tween®20 (0.5%) and the quantification of HAV from the samples was repeated. Potentially infectious HAV was quantified from the wastewater samples, with titres ranging up to e6 and e4 gc/L of sewage and treated discharge samples, respectively. Characterisation of these potentially infectious strains by Sanger sequencing confirmed the circulation of HAV strains carrying the R298K amino acid change over the VP1 region or the R63K and R71S change over the VP1/P2B junction or the C70S and M104I change over the VP1/P2B junction. The complete coding sequence, obtained from sewage and treated discharge samples by NGS, confirmed the circulation of HAV strains carrying the R63K and R71S changes but not the C70S and M104I changes over the VP1/P2B junction. The present study provides a methodology for the quantification and genetic characterisation of potentially infectious HAV from wastewaters. Rand Water Chair in Public Health; Poliomyelitis Research Foundation for co-funding this project (Research Grant no: 17/19) and for postgraduate bursary (Grant no: 16/69); University of Pretoria for a postgraduate bursary; National Research Foundation (NRF) of South Africa for a DST-NRF Innovation Doctoral Scholarship (UID 107574): The financial assistance of the NRF towards this research is hereby acknowledged. Opinions and conclusions arrived at, are those of the author and are not necessarily to be attributed to the NRF. em2026 Medical Virology PhD (Medical Virology) Unrestricted SDG-03: Good health and well-being 2020-12-10T10:56:22Z 2020-12-10T10:56:22Z 2020-04 2019-12 Thesis Rachida, S 2019, Genetic assessment of infectious hepatitis A virus strains detected in selected water sources in Gauteng, South Africa, PhD thesis, University of Pretoria, Pretoria, http://hdl.handle.net/2263/77336 A2020 http://hdl.handle.net/2263/77336 en © 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. application/pdf University of Pretoria |
| spellingShingle | UCTD Medical Virology Genetic assessment Hepatitis A virus Water sources SDG-03: Good health and well-being Genetic assessment of infectious hepatitis A virus strains detected in selected water sources in Gauteng, South Africa |
| title | Genetic assessment of infectious hepatitis A virus strains detected in selected water sources in Gauteng, South Africa |
| title_full | Genetic assessment of infectious hepatitis A virus strains detected in selected water sources in Gauteng, South Africa |
| title_fullStr | Genetic assessment of infectious hepatitis A virus strains detected in selected water sources in Gauteng, South Africa |
| title_full_unstemmed | Genetic assessment of infectious hepatitis A virus strains detected in selected water sources in Gauteng, South Africa |
| title_short | Genetic assessment of infectious hepatitis A virus strains detected in selected water sources in Gauteng, South Africa |
| title_sort | genetic assessment of infectious hepatitis a virus strains detected in selected water sources in gauteng south africa |
| topic | UCTD Medical Virology Genetic assessment Hepatitis A virus Water sources SDG-03: Good health and well-being |
| url | http://hdl.handle.net/2263/77336 |