Continual genomic surveillance in Africa provides insights into evolving SARS-CoV-2 pandemic

By Neha MathurApr 22 2022Reviewed by Danielle Ellis, B.Sc.

In a recent study posted to the medRxiv* preprint server, researchers described how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequencing efforts in Africa helped identify two of the five SARS-CoV-2 variants of concerns (VOCs), and their early analysis.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources

Background

Africa accounts for the lowest number of reported coronavirus disease 2019 (COVID-19) cases and deaths globally, with only 2,45,000 reported deaths as of February 2022. However, the continent has played an important role in shaping the global public health response to the COVID-19 pandemic with the implementation of genomic surveillance.

It is noteworthy that the sequencing effort for SARS-CoV-2 is the fastest for any human pathogen in the history of Africa and globally. Although the human immunodeficiency virus (HIV) has plagued Africa for years, only ~3,100 whole-genome HIV sequences have been shared publicly. However, the genomic surveillance for SARS-CoV-2 in Africa fetched 10,000 sequences in 2020 and an additional 90,000 sequences in the past year.

For use in devising a public health strategy, sampling for genomic surveillance needs to cover both spatial and temporal factors, which required extending the geographic coverage of sequencing capacity to capture the genomic epidemiology in almost all the locations in Africa.

In the present study, researchers directly compared the officially recorded cases in Africa with the ongoing SARS-CoV-2 genomic surveillance. To this end, they accessed the global initiative on sharing the avian influenza data (GISAID) database until February 15, 2022, for a rough estimation of the contribution of different SARS-CoV-2 variants to cases.

Study findings

Scaling up sequencing efforts in Africa helped unfold multiple waves of SARS-CoV-2 infection across the continent. In North Africa, SARS-CoV-2 B.1 lineages and Alpha dominated the first and second pandemic waves; conversely, in West Africa, the B.1.525 sub-lineage caused a large proportion of infections in the second and third pandemic waves. In Central Africa, the B.1.620 sub-lineage caused most of the infections between January and June 2021 before being replaced by Delta and later by Omicron. SARS-CoV-2 A.23.1 sub-lineage dominated the second wave of infections in Uganda and the majority of East Africa.

The Delta variant caused the highest impact on Africa between May and October 2021, causing ~38.5% of overall SARS-CoV-2 infections. The Beta variant stood second, causing an epidemic wave at the end of 2020, causing 15.7% of overall infections. Notably, Alpha accounted for barely 4.7% of total SARS-CoV-2 infections in Africa.

Phylogenetic clustering identified Alpha in 43 countries in Africa, including Ghana, Gabon, Nigeria, Kenya, and Angola, with significant community transmission. The discrete state maximum likelihood reconstruction revealed around 155 introductions into Africa, with >97% of imports attributed to the United Kingdom (UK).

Conversely, over 66% of imports into any particular African country were attributed to another African nation, suggesting substantial dispersal of the Alpha variant within the continent, ~71% of which originated in West African countries.

In 2020, the majority of sequenced genomes in Africa belonged to SARS-CoV-2 B.1 or B.1.1 lineages; however, towards the year-end, more SARS-CoV-2 lineages, such as B.1.525, B.1.1.318, B.1.1.418, and A.23.1 started to appear in Africa.

At the same time, the Alpha, Beta, Delta, and Omicron VOCs demonstrated similarities and differences in community transmission within the African continent. While Alpha and Beta were epidemiologically important only in some regions, Delta and Omicron sequentially dominated the majority of infections in the entire continent.

State-wise phylogeographic inferences revealed 2,151 viral introductions of non-VOC lineages into African countries throughout the pandemic. Although initial viral introductions were from Europe, later, 62% (1319/1347) of the overall viral introductions were from another African country. The UK accounted for 38% of total foreign viral introductions in Africa; contrastingly, Africa imported SARS-CoV-2 to Europe, North America, and Asia.

Sampling and molecular clock analyses suggested that the Beta variant originated around September 2020 in South Africa. Of the 900 introductions of Beta into African countries, only 108 were attributed to countries outside the continent, while ~50% were from South Africa. Beyond Southern Africa, most of the introductions back into the African continent were from France and other European countries.

Following introductions from Asia in the middle of 2021, Delta rapidly replaced the other circulating variants in Africa. Accordingly, by June-2021, Delta was circulating at >90% frequencies in Africa.

Similar to Beta, viral dissemination of Omicron within the continent mostly originated from Southern Africa. Foreign introductions of the Omicron back into Africa were dominated by the UK, United States of America, Australia, and New Zealand, at the rates of 47%, 33%, and 9%, respectively. Notably, Omicron reintroductions back into Africa occurred in countries outside the Southern African region.

Africa also successfully optimized the overall proportion and frequency of genomic sampling. Therefore, while South Africa and Nigeria sequenced ~1% of aggregate COVID-19 cases, their genomic surveillance programs were considered successful because their representative temporally representative sampling enabled the timely detection of Beta, Eta, and Omicron variants.

Most importantly, to maintain sequencing quality, the researchers examined genomes to determine aspects of the sequencing that needed improvisation in the future. For instance, they updated primer sets used in the sequencing to keep pace with SARS-CoV-2 evolution.

Conclusions

The local sequencing capacity in Africa was initially limited; however, it expanded after the emergence of SARS-CoV-2 VOCs. They used low-cost Oxford Nanopore Technology (ONT) for over 50% of all SARS-CoV-2 sequencing in Africa.

Accordingly, 52 out of 55 countries in Africa deposited SARS-CoV-2 genomes in the GISAID database. Yet, 16 countries had no local sequencing capacity, and many more had limited capacity for sequencing.

During subsequent SARS-CoV-2 pandemic waves, regional sequencing networks, resource sharing within the African countries, and collaborations with foreign academic collaborators helped close surveillance blind spots.

To summarize, the study demonstrated repeated dissemination of SARS-CoV-2 variants within Africa. Thus, there is an urgent need for more investment in SARS-CoV-2 genomic surveillance in Africa to remain prepared and respond on time to future infectious viral outbreaks.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources