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Molecular characterisation of human adenoviruses from environmental samples in Tshwane, Gauteng
Dissertation (MSc (Medical Virology))--University of Pretoria, 2020.
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2021
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| access_status_str | Open Access |
| author2 | Van Zyl, Walda B. |
| author_browse | Van Zyl, Walda B. |
| author_facet | Van Zyl, Walda 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 | Dissertation (MSc (Medical Virology))--University of Pretoria, 2020. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/78754 |
| institution | University of Pretoria (South Africa) |
| last_indexed | 2026-06-10T12:39:38.583Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| 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:2263/78754 Molecular characterisation of human adenoviruses from environmental samples in Tshwane, Gauteng Van Zyl, Walda B. u14105447@tuks.co.za Mans, Janet Davids, Michaela UCTD Human adenoviruses (HAdV) Non-enveloped viruses Icosahedral capsid Double-stranded DNA genome Adenoviridae Mastadenovirus HAdV species (A-G) Genotypes Acute gastroenteritis HAdV-F40 Respiratory droplets Contaminated environments Wastewater treatment plant (WWTP) Molecular characterisation Health sciences theses SDG-03 SDG-03: Good health and well-being Health sciences theses SDG-06 SDG-06: Clean water and sanitation Health sciences theses SDG-09 SDG-09: Industry, innovation and infrastructure Health sciences theses SDG-14 SDG-14: Life below water Dissertation (MSc (Medical Virology))--University of Pretoria, 2020. Human adenoviruses (HAdV) are non-enveloped viruses with an icosahedral capsid and a linear double-stranded DNA genome. These viruses belong to the family Adenoviridae and genus Mastadenovirus. An important property of the HAdV is that it is non-enveloped making it highly resistant to detergents and harsh environmental conditions. This virus is grouped in seven species (A-G) with more than 88 genotypes. These seven species are associated with several diseases, such as, respiratory infections, keratoconjunctivitis, urinary infections, hepatitis and gastrointestinal infections. The HAdV is one of the etiological causes of acute gastroenteritis, mainly caused by HAdV-F40 and HAdV-F41. The virus can be transmitted via the faecal-oral route, inhalation of respiratory droplets and direct contact with contaminated environments. The virus is known to be ubiquitous in environments where human contamination is likely to occur such as wastewater treatment plants. These human contaminations could occur through contaminated secretion and excretions within aqueous environments. There is currently a limited amount of information on the HAdV in water Molecular characterisation of human adenoviruses from environmental environments, particularly in Tshwane, Gauteng. Therefore, the aim of the study was to investigate the presence and genotypes of human adenovirus in environmental samples namely raw sewage and treated effluent, using molecular methods. For genotypic characterisation, Sanger sequencing was used on amplicons from 12 HAdV positive samples and next generation sequencing were used on all the amplicons from HAdV positive samples. A total of 150 environmental samples (75 raw sewage and 75 effluent) were collected from two wastewater treatment plants in Tshwane over the study period of 18 months. These environmental samples comprised of 1 L raw sewage and 10 L treated effluent samples. The primary viral recovery for the 1 L raw sewage and 10 L treated effluent samples were performed using skimmed milk flocculation procedure and glass wool adsorption elution technique, respectively. For secondary viral recovery, both environmental samples were subjected to polyethylene glycol/sodium chloride precipitation. Manual extraction was used to extract the nucleic acids from the virus concentrate with mengovirus (MV) used as an extraction control. For the quantification of HAdV, standard curves prepared from known dilutions of HAdV and MV were used. Human adenovirus was detected in 140/150 (93%) of the environmental samples comprising of 69/75 (92%) being raw sewage and 71/75 (95%) being effluent samples. The HAdV concentrations detected in wastewater treatment plant 1 (WWTP 1) ranged from 1.38x105 gc/L to 4.50 x 109 gc/L for raw sewage and 5.08x103 gc/l to 4.30x108 gc/L for effluent. The HAdV concentrations detected in WWTP 2 ranged from 6.84x104 gc/L to 1.69x1012 gc/L for raw sewage and 5.27x103 gc/L to 1.16x108 gc/L for effluent. The HAdV hexon amplification success rate from the nucleic acids was 43/140 (31%). Eighteen HAdV genotypes were successfully characterised using Sanger sequencing. The HAdV-D was the most predominant species in both WWTPs, follow by HAdV-B and HAdV-F. The HAdV-A and HAdV-E species were the least identified. Next generation sequencing identified four times as many genotypes as Sanger sequencing (77 different genotypes). The HAdV-D (types 8, 9, 13, 17, 19, 20, 23, 24, 28, 29, 32, 33, 36, 42, 44, 47, 49, 51, 56, 60, 62, 64, 67 and 81) and HAdV-B (types 2, 3, 7, 11 and 66) were the most predominant species followed by HAdV-F (types 40 and 41), HAdV-A (types 12 and 76), HAdV-E ( type 4) and HAdV-C (type 1). Testing wastewater treatment plants is advantageous as it allows for the detection and identification of HAdV types circulating in the surrounding communities. Due to the large number of species identified using NGS, it is the superior typing method and should be used for future studies. These include strains causing symptomatic and asymptomatic infections. Human adenovirus was detected at comparable frequencies in raw sewage and treated effluent wastewater, with slightly higher detection in effluent samples. However, the viability of these viruses is unknown and should be investigated in further studies. The detection of viruses in wastewater treatment plants are a public health concern as the treated effluent is discharged into rivers, which may be used by communities for domestic and recreational purposes. NRF, PRF em2025 Medical Virology MSc (Medical Virology) Restricted SDG-03: Good health and well-being SDG-06: Clean water and sanitation SDG-09: Industry, innovation and infrastructure SDG-14: Life below water 2021-02-18T11:48:21Z 2021-02-18T11:48:21Z 2019-04 2020 Dissertation Davids, M 2020, Molecular characterisation of human adenoviruses from environmental samples in Tshwane, Gauteng, MSc (Medical Virology) Dissertation, University of Pretoria, Pretoria, viewed yymmdd <http://hdl.handle.net/2263/78754> A2021 http://hdl.handle.net/2263/78754 © 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 Human adenoviruses (HAdV) Non-enveloped viruses Icosahedral capsid Double-stranded DNA genome Adenoviridae Mastadenovirus HAdV species (A-G) Genotypes Acute gastroenteritis HAdV-F40 Respiratory droplets Contaminated environments Wastewater treatment plant (WWTP) Molecular characterisation Health sciences theses SDG-03 SDG-03: Good health and well-being Health sciences theses SDG-06 SDG-06: Clean water and sanitation Health sciences theses SDG-09 SDG-09: Industry, innovation and infrastructure Health sciences theses SDG-14 SDG-14: Life below water Molecular characterisation of human adenoviruses from environmental samples in Tshwane, Gauteng |
| title | Molecular characterisation of human adenoviruses from environmental samples in Tshwane, Gauteng |
| title_full | Molecular characterisation of human adenoviruses from environmental samples in Tshwane, Gauteng |
| title_fullStr | Molecular characterisation of human adenoviruses from environmental samples in Tshwane, Gauteng |
| title_full_unstemmed | Molecular characterisation of human adenoviruses from environmental samples in Tshwane, Gauteng |
| title_short | Molecular characterisation of human adenoviruses from environmental samples in Tshwane, Gauteng |
| title_sort | molecular characterisation of human adenoviruses from environmental samples in tshwane gauteng |
| topic | UCTD Human adenoviruses (HAdV) Non-enveloped viruses Icosahedral capsid Double-stranded DNA genome Adenoviridae Mastadenovirus HAdV species (A-G) Genotypes Acute gastroenteritis HAdV-F40 Respiratory droplets Contaminated environments Wastewater treatment plant (WWTP) Molecular characterisation Health sciences theses SDG-03 SDG-03: Good health and well-being Health sciences theses SDG-06 SDG-06: Clean water and sanitation Health sciences theses SDG-09 SDG-09: Industry, innovation and infrastructure Health sciences theses SDG-14 SDG-14: Life below water |
| url | http://hdl.handle.net/2263/78754 |