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

Thesis (MSc)--Stellenbosch University, 2023.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.Master

Insights into SARS-CoV-2 in Angola during the COVID-19 peak: molecular epidemiology and genome surveillance

Background: In Angola, COVID-19 cases have been reported in all provinces, resulting in >105,000 cases and >1900 deaths. However, no detailed genomic surveillance into the introduction and spread of the SARS-CoV-2 virus has been conducted in Angola. We aimed to investigate the emergence and epidemic progression during the peak of the COVID-19 pandemic in Angola. Methods: We generated 1210 whole-genome SARS-CoV-2 sequences, contributing West African data to the global context, that were phylogenetically compared against global strains. Virus movement events were inferred using ancestral state reconstruction. Results: The epidemic in Angola was marked by four distinct waves of infection, dominated by 12 virus lineages, including VOCs, VOIs, and the VUM C.16, which was unique to South-Western Africa and circulated for an extended period within the region. Virus exchanges occurred between Angola and its neighboring countries, and strong links with Brazil and Portugal reflected the historical and cultural ties shared between these countries. The first case likely originated from southern Africa. Conclusion: A lack of a robust genome surveillance network and strong dependence on out-of-country sequencing limit real-time data generation to achieve timely disease outbreak responses, which remains of the utmost importance to mitigate future disease outbreaks in Angola

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Epidemiology and antibiotic resistance of staphylococci on commercial pig farms in Cape Town, South Africa

Abstract Staphylococci are responsible for a wide range of infections in animals. The most common species infecting animals include Staphylococcus aureus, Staphylococcus epidermidis and Staphylococcus intermedius. Recent increases in antibiotic use and antibiotic resistance in animals highlight the need to understand the potential role of commercial livestock as a reservoir of staphylococci and antibiotic resistance genes. Nasal swabs were collected from 143 apparently healthy pigs and 21 pig farm workers, and 45 environmental swabs of feed and water troughs, from two commercial pig farms in the Western Cape, South Africa. Staphylococci were isolated, identified using mass-spectrometry, and antimicrobial susceptibility testing and Illumina whole genome sequencing were performed. One hundred and eighty-five (185) Staphylococcus spp. isolates were obtained, with Mammalicoccus sciuri (n = 57; 31%) being the most common, followed by S. hyicus (n = 40; 22%) and S. aureus (n = 29; 16%). S. epidermidis was predominantly identified in the farm workers (n = 18; 86%). Tetracycline resistance was observed across all species, with rates ranging from 67 to 100%. Majority of M. sciuri isolates (n = 40; 70%) were methicillin resistant, with 78% (n = 31) harbouring mecA. M. sciuri isolates had genes/elements which were associated with SCCmec_type_III (3A) and SCCmec_type_VIII(4A) and were mostly observed in ST61 strains. ST239 strains were associated with SCCmec_type_III(3A). High rates of tetracycline resistance were identified among staphylococci in the pig farms in Western Cape, South Africa. This highlights the need for policy makers to regulate the use of this antibiotic in pig farming

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020-2022

AbstractEthiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, &gt;499 000 cases, and ∼7 500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the introduction and spread of SARS-CoV-2 in Ethiopia. In this study, we reconstructed and elucidated the COVID-19 epidemic dynamics. Specifically, we investigated the introduction, local transmission, ongoing evolution, and spread of SARS-CoV-2 during the first four infection waves using 353 high-quality near-whole genomes sampled in Ethiopia. Our results show that whereas viral introductions seeded the first wave, subsequent waves were seeded by local transmission. The B.1.480 lineage emerged in the first wave and notably remained in circulation even after the emergence of the Alpha variant. The B.1.480 was out-competed by the Delta variant. Notably, Ethiopia’s lack of local sequencing capacity was further limited by sporadic, uneven, and insufficient sampling that limited the incorporation of genomic epidemiology in the epidemic public health response in Ethiopia. These results highlight Ethiopia’s role in SARS-CoV-2 dissemination and the urgent need for balanced, near-real-time genomic sequencing.</jats:p

Genomic Characterization of Circulating Dengue Virus, Ethiopia, 2022–2023

In Ethiopia, dengue virus (DENV) infections have been reported in several regions; however, little is known about the genetic diversity of circulating viruses. We conducted clinical surveillance of DENV during the 2023 nationwide outbreak in Ethiopia. We enrolled patients at 3 sentinel hospital sites. Using reverse transcription PCR, we screened serum samples for 3 arboviruses and then serotyped and whole-genome sequenced DENV-positive samples. We detected DENV-1 and DENV-3 serotypes. Phylogenetic analysis identified 1 transmission cluster for DENV-1 (genotype III major lineage A) and 2 clusters for DENV-3 (genotype III major lineage B). The first DENV-3 cluster was closely related to an isolate from a 2023 dengue outbreak in Italy; the second cluster was related to isolates from India. Co-circulation of DENV-1 and DENV-3 in Ethiopia highlights the potential for severe dengue. Intensified surveillance and coordinated public health responses are needed to address the threat of severe dengue outbreaks

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020&ndash;2022

Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, &gt;499,000 cases, and ~7500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the introduction and spread of SARS-CoV-2 in Ethiopia. In this study, we reconstructed and elucidated the COVID-19 epidemic dynamics. Specifically, we investigated the introduction, local transmission, ongoing evolution, and spread of SARS-CoV-2 during the first four infection waves using 353 high-quality near-whole genomes sampled in Ethiopia. Our results show that whereas viral introductions seeded the first wave, subsequent waves were seeded by local transmission. The B.1.480 lineage emerged in the first wave and notably remained in circulation even after the emergence of the Alpha variant. The B.1.480 was outcompeted by the Delta variant. Notably, Ethiopia&rsquo;s lack of local sequencing capacity was further limited by sporadic, uneven, and insufficient sampling that limited the incorporation of genomic epidemiology in the epidemic public health response in Ethiopia. These results highlight Ethiopia&rsquo;s role in SARS-CoV-2 dissemination and the urgent need for balanced, near-real-time genomic sequencing

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022

Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, &gt;499,000 cases, and ~7500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the introduction and spread of SARS-CoV-2 in Ethiopia. In this study, we reconstructed and elucidated the COVID-19 epidemic dynamics. Specifically, we investigated the introduction, local transmission, ongoing evolution, and spread of SARS-CoV-2 during the first four infection waves using 353 high-quality near-whole genomes sampled in Ethiopia. Our results show that whereas viral introductions seeded the first wave, subsequent waves were seeded by local transmission. The B.1.480 lineage emerged in the first wave and notably remained in circulation even after the emergence of the Alpha variant. The B.1.480 was outcompeted by the Delta variant. Notably, Ethiopia’s lack of local sequencing capacity was further limited by sporadic, uneven, and insufficient sampling that limited the incorporation of genomic epidemiology in the epidemic public health response in Ethiopia. These results highlight Ethiopia’s role in SARS-CoV-2 dissemination and the urgent need for balanced, near-real-time genomic sequencing.</jats:p