Molecular epidemiology of SARS-CoV-2 in Malawi: a comparative investigation of the COVID-19 pandemic mitigation and progression

Date
2023-11
Journal Title
Journal ISSN
Volume Title
Publisher
Stellenbosch : Stellenbosch University
Abstract
ENGLISH ABSTRACT: Nations in Eastern and Southern Africa collectively reported >23 million cases of COVID-19 from 2020 until 2023. The case numbers are, however, likely to be widely underreported. Nevertheless, these African regions have endured high caseloads, placing severe strain on already burdened healthcare systems. Genome surveillance has proven invaluable for detecting harmful variants of the SARS-CoV-2 virus in the past, allowing for informed public health responses. As Variants of Interest (VOI) and Variants of Concern (VOC) commonly emerge from these regions, effective genome surveillance remains globally important. Nearly 20 million people live in Malawi, a landlocked country in South-Eastern Africa. It has been affected by five COVID-19 pandemic waves (2020-2022), comparable to other nations in the region. Despite the strain the epidemic has placed on Malawi's health services, the impact of the genomic surveillance system during the pandemic has not yet been thoroughly examined. To allow for data-driven and informed pandemic mitigation strategies to navigate the ongoing COVID-19 pandemic and to address concerns of future pandemics, a comparative investigation of the COVID-19 pandemic progression in Southern and Eastern African regions was conducted. This epidemiological information was complemented with genome surveillance data generated for Southern and Eastern African countries. This was done to gain an in-depth understanding of the data generated and circulating variants and to determine the way SARS CoV-2 variants fuelled national and international pandemic infectious waves. Therefore, this study aimed to place the South- and East-African pandemic progression and current genome surveillance initiatives into a global context. In this study, we hypothesised that investment in the laboratory and bioinformatic expertise improved the overall pathogen surveillance capacity within these regions, and most of the SARS-CoV-2 introductions into Malawi came from South Africa. However, the data generated with the surveillance networks established within Southern African regions outcompetes those in the East African regions with enhanced capacity for so-called "in country" sequencing, allowing for reduced turnaround times. Therefore, the Southern African regions, including countries such as South Africa and Botswana, served as a model for Eastern African countries such as Malawi, Tanzania, and Kenya. Moreover, import and export virus introduction events, determined using phylogenetic inferences, indicated that more introductions occurred from Southern African regions into Malawi than from East African regions. This may reflect higher sampling and subsequent genome sequencing from Southern African regions and the economic importance of these regions that largely constitute economic and travel hubs of the African continent. This comparative investigation on COVID-19 across nations highlighted areas requiring improvement in genomic surveillance to assist nations in being better prepared for future pandemics.
AFRIKAANSE OPSOMMING: Lande in Oos- en Suider-Afrika het van 2020 tot 2023 gesamentlik meer as 23 miljoen gevalle van COVID-19 aangemeld, alhoewel die werklike syfer is waarskynlik heelwat meer. Dít het erge druk op hierdie Afrikastreke se reeds oorlaaide gesondheidsorgstelsels geplaas. Genoomwaarneming was van onskatbare waarde vir die opsporing van skadelike variante van die SARS-CoV-2-virus en het ’n ingeligte openbare gesondheidsreaksie moontlik gemaak. Aangesien belangwekkende én kommerwekkende variante van die virus dikwels in dié streke opgemerk word, is doeltreffende genoomwaarneming steeds van wêreldbelang. Malawi, ’n ingeslote land in die suidooste van Afrika, met bykans 20 miljoen mense. Soos ander nasies in die streek, is Malawi deur vyf vlae van die COVID-19-pandemie getref (2020- 2022). Ondanks die druk wat die pandemie op die land se gesondheidsdienste geplaas het, is die impak van die genomiese waarnemingstelsel in dié tyd nog nie tenvolle ondersoek nie. Om vir datagedrewe en ‘n ingeligte strategieë vir die verdere hantering van COVID-19 en ander moontlike toekomstige pandemies voorsiening te maak, is ’n vergelykende ondersoek van die progressie van die pandemie in Suider- en Oos-Afrika onderneem. Hierdie epidemiologiese inligting is aangevul met genoomwaarnemingsdata van ander Suider- en Oos-Afrika lande. Die doel was om ’n diepgaande begrip te ontwikkel van die data én van variante in omloop, en om te bepaal hoe die SARS-CoV-2-variante nasionale en internasionale vlae van die pandemie gevuur het. Die studie wou dus die progressie van die pandemie in Suider- en Oos-Afrika sowel as huidige genoomwaarnemingsinisiatiewe in ’n wêreldkonteks te plaas. Die hipotese van die studie was dat belegging in laboratoriumkundigheid en bio-informatika die algehele patogeenwaarnemingsvermoë in hierdie streke verbeter het, en dat die SARS-CoV 2-variante wat Malawi bereik het hoofsaaklik uit Suid-Afrika, of Suider-Afrika, na vore gekom het. Die beskikbare data sowel as die waarnemingsnetwerke wat in Suider-Afrika geskep is, oortref egter dié van Oos-Afrika. Lande in Suider-Afrika is beter toegerus vir sogenaamde ‘binnelandse’ volgordebepaling, wat op sy beurt korter omkeertye moontlik maak. Daarom dien Suider-Afrika, waaronder lande soos Suid-Afrika en Botswana, as ’n model vir Oos-Afrika, wat nasies soos Malawi, Tanzanië, en Kenia insluit. Daarbenewens dui gevalle van inwaartse (ingevooerde) en uitwaartse (uitgevoerde) virusoordrag, wat met behulp van filogenetiese analise ondersoek is, daarop dat oordrag na Malawi meer dikwels uit Suider-Afrika as Oos Afrika ontaard het. Hierdie bevinding is moontlik die gevolg van groter steekproewe en dus meer genoomvolgordebepaling uit Suider-Afrika. Terselfdertyd onderstreep dit die belang van hierdie streke as ekonomiese en reissentrums op die Afrikavasteland. Hierdie vergelykende ondersoek na COVID-19 in verskillende lande vestig die aandag op gebiede waar genoomwaarneming verbeter moet word sodat nasies beter voorbereid kan wees op moontlike toekomstige pandemies.
Description
Thesis (MSc)--Stellenbosch University, 2023.
Keywords
Citation