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Evaluation of swab pooling and transport medium to improve the identification of avian influenza viruses in farmed ostriches in South Africa
Mini Dissertation (MSc (Tropical Animal Health))--University of Pretoria, 2019.
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| Format: | Thesis |
| Language: | English |
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University of Pretoria
2020
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| _version_ | 1867613518892630016 |
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| access_status_str | Open Access |
| author2 | Abolnik, Celia |
| author_browse | Abolnik, Celia |
| author_facet | Abolnik, Celia |
| collection | Thesis |
| dc_rights_str_mv | © 2020 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 | Mini Dissertation (MSc (Tropical Animal Health))--University of Pretoria, 2019. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/76761 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:37:25.898Z |
| 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:2263/76761 Evaluation of swab pooling and transport medium to improve the identification of avian influenza viruses in farmed ostriches in South Africa Abolnik, Celia u18379941@tuks.co.za Pieterse, Renee UCTD Mini Dissertation (MSc (Tropical Animal Health))--University of Pretoria, 2019. Avian influenza (AI) control in farmed ostriches relies on rapid and accurate diagnostic testing to detect the presence and spread of disease in avian populations, as flocks are in unavoidable contact with wild bird reservoirs, increasing the possibility of infection. Increasing swab pools from five to ten would significantly decrease the cost of testing by reducing the number of tests performed; however detection of highly pathogenic avian influenza (HPAI) at low virus titres by RT-qPCR and virus isolation is critical to ensure that the disease is detected and accurately characterised. The present study found that pooling a single HPAI positive ostrich swab with four or nine AI negative ostrich tracheal swabs did not significantly affect the detection of influenza A virus by RT-qPCR (p < 0.05) over the dilution range. RT-qPCR had a high sensitivity detecting up to 102.5 EID50/ ml (~ RT-qPCR Ct value = 35) virus titre compared to virus isolation, that detected only up 104.8 EID50/ml (~ RT-qPCR Ct value = 29) virus titre, confirming that weak positive swab pools with a low virus titre detected by RT-qPCR (Ct value ≥ 35) may not be detected by standard virus isolation techniques. Both virus transport media evaluated (10% v/v glycerol in brain heart infusion (BHI) broth supplemented with antibiotics (VTM) and 50% v/v glycerol PBS transport medium (pH 7.2)) facilitated the isolation of influenza A virus at ~ 104.5 EID50/ml (RT-qPCR Ct value ~ 27); however VTM improved the efficiency of the method, potentially reducing the reporting time. Sampling costs can be reduced by increasing swabs pools to ten and efficacy of virus isolation can be improved by using antibiotic supplemented VTM, without compromising the detection of influenza A virus by RT-qPCR. It is recommended that costs and efforts are focused at isolating virus from pooled swab samples, with a virus titre of ≥ 104 EID50/ ml (RT-qPCR Ct value ≤ 29), followed by full molecular sequencing and characterisation of the viral isolate. Samples with a low virus titre < 104 EID50/ ml (RT-qPCR Ct value > 29) should be characterised by direct sequencing of PCR amplicons or type-specific RT-qPCR assays. Veterinary Tropical Diseases MSc (Tropical Animal Health) Unrestricted 2020-11-04T15:09:48Z 2020-11-04T15:09:48Z 2020/04/22 2019 Mini Dissertation Pieterse, R 2019, Evaluation of swab pooling and transport medium to improve the identification of avian influenza viruses in farmed ostriches in South Africa, MSc (Tropical Animal Health) Mini Dissertation, University of Pretoria, Pretoria, viewed yymmdd <http://hdl.handle.net/2263/76761> A2020 http://hdl.handle.net/2263/76761 en © 2020 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 Evaluation of swab pooling and transport medium to improve the identification of avian influenza viruses in farmed ostriches in South Africa |
| title | Evaluation of swab pooling and transport medium to improve the identification of avian influenza viruses in farmed ostriches in South Africa |
| title_full | Evaluation of swab pooling and transport medium to improve the identification of avian influenza viruses in farmed ostriches in South Africa |
| title_fullStr | Evaluation of swab pooling and transport medium to improve the identification of avian influenza viruses in farmed ostriches in South Africa |
| title_full_unstemmed | Evaluation of swab pooling and transport medium to improve the identification of avian influenza viruses in farmed ostriches in South Africa |
| title_short | Evaluation of swab pooling and transport medium to improve the identification of avian influenza viruses in farmed ostriches in South Africa |
| title_sort | evaluation of swab pooling and transport medium to improve the identification of avian influenza viruses in farmed ostriches in south africa |
| topic | UCTD |
| url | http://hdl.handle.net/2263/76761 |