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Enhancing genomic visualisations for epidemics to inform the public health response
Thesis (MSc)--Stellenbosch University, 2024.
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| Format: | Thesis |
| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2024
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| _version_ | 1867613924436738048 |
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| access_status_str | Open Access |
| author | Sitharam, Nikita |
| author2 | De Oliveira, Tulio
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| author_browse | De Oliveira, Tulio
Sitharam, Nikita |
| author_facet | De Oliveira, Tulio
Sitharam, Nikita |
| author_sort | Sitharam, Nikita |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MSc)--Stellenbosch University, 2024. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/130298 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:43:52.525Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/130298 Enhancing genomic visualisations for epidemics to inform the public health response Sitharam, Nikita De Oliveira, Tulio Baxter, Cheryl Xavier, Joicymara Stellenbosch University. Faculty of Medicine and Health Sciences. Centre for Bioinformatics & Computational Biology. Climate Amplified Diseases and Epidemics (CLIMADE) -- Africa Epidemics -- Africa Communicable diseases -- Control Genomes -- Analysis Public health -- Data processing Arthropod-borne virus diseases Arbovirus infections UCTD Thesis (MSc)--Stellenbosch University, 2024. ENGLISH ABSTRACT: Introduction: Infectious disease prevention relies on effective disease surveillance and communication in preventing and controlling epidemics. An important tool that is utilised for communication, in public health informatics, is a computational dashboard. Public health dashboards are an effective way of presenting complex biological data in a concise and visual manner. This decreases the knowledge gap between researchers and the public, and allows for stakeholders and policy-makers to make informed decisions. Genomic surveillance of arthropod-borne viruses has increased due to the advancements in sequencing technologies. However, the African continent remains challenged in controlling the spread of these viruses and its vectors, due to constrained resources. Climate Amplified Diseases and Epidemics (CLIMADE) Africa is a consortium that aims to increase the genomic surveillance of arboviruses in Africa through the sharing of protocols, software applications, and capacity building. Purpose: The purpose of this study was to build the CLIMADE Africa dashboard to communicate genomic data for the three most medically-prevalent arboviruses on the African continent, Dengue Virus, Chikungunya Virus, and Zika Virus. Communicating this data could help guide the public health response in Africa. The SARS-CoV-2 Africa dashboard was enhanced by the addition of an interactive phylogenetic visualisation. This increased the amount of complex information provided on the dashboard, in a clear and user-friendly manner. Methodology: The CLIMADE Africa dashboard was produced by adapting the computational architecture of the SARS-CoV-2 Africa dashboard. The arboviral data presented was sourced from the Bacterial and Viral Bioinformatics Resource Center. The data was processed using Pandas in Python, and implemented into the dashboard using the Pycharm application. The Nextstrain SARS-CoV-2 phylogenetic build, for the SARS-CoV-2 Africa dashboard, was produced using Nextstrain’s ncov workflow. This was implemented into the filter panel on the dashboard. Results: The CLIMADE Africa dashboard was created as an easy-to-use tool that showcases the genomic epidemiology of the three most prevalent arboviruses (Dengue Virus, Chikungunya Virus, and Zika Virus) in Africa, in a digestible manner and in near-real time. This dashboard is open source and the code is available at this GitHub repository. The phylogenetic Nextstrain build presented on the SARS-CoV-2 Africa dashboard, presents a full picture of the genomic landscape of the pandemic on the African continent. Conclusion: The information extracted from the CLIMADE Africa dashboard highlights the difference between reported outbreaks and genomic surveillance on the African continent. This could be used to improve surveillance, which could then potentially improve the public health response to these arboviruses. Dashboards need to be maintained, updated, and enhanced in order to be effective at communicating accurate and up-to-date scientific information. Thus, introducing a Nextstrain build for the SARS-CoV-2 Africa dashboard, allows for more complex information to be presented in a digestible way. Future work for this study could include fully automating the data acquisition and curation for the CLIMADE Africa dashboard and fully embedding the Africa-specific Nextstrain phylogenetic build in the SARS- CoV-2 Africa dashboard. AFRIKAANSE OPSOMMING: Inleiding: Die voorkoming van aansteeklike siektes maak staat op doeltreffende toesig oor siektes en kommunikasie om epidemies te voorkom en te beheer. ʼn Rekenaarpaneelbord is ʼn belangrike instrument wat vir kommunikasie in openbaregesondheidsinformatika aangewend word. Openbaregesondheidspaneelborde is ʼn doeltreffende manier om ingewikkelde biologiese data bondig en visueel aan te bied. Dit maak die kennisgaping tussen navorsers en die publiek kleiner en stel belanghebbers en beleidvormers in staat om ingeligte besluite te neem. Die genomiese toesig oor virusse wat deur geleedpotiges oorgedra word, het weens die vooruitgang in volgordebepalingstegnologie toegeneem. Die beheer van die verspreiding van hierdie virusse en die vektore daarvan bly egter steeds, weens beperkte hulpbronne, ʼn uitdaging vir Afrika. Climate Amplified Diseases and Epidemics (CLIMADE) Africa is ʼn konsortium wat beoog om die genomiese toesig oor arbovirusse in Afrika uit te brei deur die uitruil van protokolle, programmatuurtoepassings en kapasiteitsbou. Doelwit: Die studie het beoog om ʼn paneelbord vir CLIMADE Africa te bou om genomiese data vir die drie arbovirusse wat medies die algemeenste in Afrika voorkom (denguevirus, chikungunya-virus en zikavirus) te kommunikeer. Die kommunikasie van hierdie data kan help om die openbaregesondheidsrespons in Afrika te rig. Die paneelbord vir SARS-CoV-2 in Afrika is verbeter deur die byvoeg van ʼn interaktiewe filogenetiese visualisering. Dit het die hoeveelheid komplekse inligting wat op die paneelbord aangedui word, op duidelike en gebruikersvriendelike wyse vergroot. Metodologie: Die CLIMADE Africa-paneelbord is gebou deur die rekenaarargitektuur van die SARS-CoV-2 Africa-paneelbord aan te pas. Die ingevoerde arbovirusdata is van die Bacterial and Viral Bioinformatics Resource Center (Bakteriese en Virale Bioinformatika- hulpbronsentrum) ontvang. Die data is met behulp van pandas in Python verwerk, en met behulp van die PyCharm-toepassing in die paneelbord geïmplementeer. Die opstel van die Nextstrain- filogenetiese boom vir die SARS-CoV-2 Africa-paneelbord is met behulp van Nextstrain se ncov-werkvloei gedoen. Dit is in die filterpaneel op die paneelbord geïmplementeer. Resultate: Die CLIMADE Africa-paneelbord is geskep as ʼn maklik bruikbare instrument om die genomiese epidemiologie van die drie algemeenste arbovirusse (denguevirus, chikungunya- virus en zikavirus) in Afrika op verteerbare wyse en feitlik intyds ten toon te stel. Hierdie paneelbord is ʼn oop bron en is in hierdie GitHub-bewaarplek beskikbaar. Die Nextstrain- filogenetiese boom wat op die SARS-CoV-2 Africa-paneelbord aangebied word, gee ʼn volledige prentjie van die genomiese landskap van die pandemie in Afrika. Gevolgtrekking: Die inligting wat uit die CLIMADE Africa-paneelbord onttrek is, lig die verskil tussen uitbrake wat aangemeld is en genomiese toesig in Afrika uit. Dit kan gebruik word om toesig te verbeter, wat dan moontlik die openbaregesondheidsrespons op hierdie arbovirusse kan verbeter. Paneelborde moet in stand gehou, bygewerk en versterk word om doeltreffend met die kommunikasie van die jongste akkurate wetenskaplike inligting te wees. Die invoeg van ʼn Nextstrain-boom vir die SARS-CoV-2 Africa-paneelbord maak dit moontlik om meer komplekse inligting op verteerbare wyse aan te bied. In die toekoms kan hierdie studie ook lei tot werk aan die volledige outomatisering van die dataverkryging en -kuratorskap vir die CLIMADE Africa-paneelbord en die volledige vaslegging van die Afrika-spesifieke Nextstrain- filogenetiese boom in die SARS-CoV-2 Africa-paneelbord. Masters 2024-02-22T08:40:24Z 2024-04-26T12:31:07Z 2024-02-22T08:40:24Z 2024-04-26T12:31:07Z 2024-03 Thesis https://scholar.sun.ac.za/handle/10019.1/130298 en_ZA Stellenbosch University xvi, 97 pages : illustrations (some color), maps application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Climate Amplified Diseases and Epidemics (CLIMADE) -- Africa Epidemics -- Africa Communicable diseases -- Control Genomes -- Analysis Public health -- Data processing Arthropod-borne virus diseases Arbovirus infections UCTD Sitharam, Nikita Enhancing genomic visualisations for epidemics to inform the public health response |
| title | Enhancing genomic visualisations for epidemics to inform the public health response |
| title_full | Enhancing genomic visualisations for epidemics to inform the public health response |
| title_fullStr | Enhancing genomic visualisations for epidemics to inform the public health response |
| title_full_unstemmed | Enhancing genomic visualisations for epidemics to inform the public health response |
| title_short | Enhancing genomic visualisations for epidemics to inform the public health response |
| title_sort | enhancing genomic visualisations for epidemics to inform the public health response |
| topic | Climate Amplified Diseases and Epidemics (CLIMADE) -- Africa Epidemics -- Africa Communicable diseases -- Control Genomes -- Analysis Public health -- Data processing Arthropod-borne virus diseases Arbovirus infections UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/130298 |
| work_keys_str_mv | AT sitharamnikita enhancinggenomicvisualisationsforepidemicstoinformthepublichealthresponse |