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SARS-CoV-2 Genome Set Reveals Evolution, Spread in Africa

NEW YORK – By digging into the first 100,000 SARS-CoV-2 genomes from Africa, an international research team has retraced the spread of SARS-CoV-2 variants and their contributions to disease surges on the continent, while offering a look at enhanced genomic sequencing capacity in Africa.

"Scaling up sequencing in Africa has provided a wealth of information on how the pandemic unfolded on the continent," co-corresponding authors Eduan Wilkinson and Tulio de Oliveira and their colleagues wrote in Science on Thursday.

Wilkinson is affiliated with Stellenbosch University and the University of KwaZulu-Natal, while de Oliveira is affiliated with those same universities, as well as the Centre for the AIDS Programme of Research in South Africa and the University of Washington.

The Beta and Omicron variant of concern (VOC) lineages were found first in Africa, the team explained, and the Alpha and Delta VOCs are also known to have contributed to African SARS-CoV-2 infection waves. In contrast, past analyses suggested the Gamma VOC lineage, believed to have arisen in Brazil, contributed relatively little to COVID-19 cases in Africa.

To get a more refined look at evolution and spread of the coronavirus on the continent, the researchers analyzed 10,000 SARS-CoV-2 genomes generated in 2020, along with a further 90,000 genomes produced through expanded sequencing efforts from the spring of 2021 to March 2022. The precise patterns varied within countries and regions, they found, with variants of interest often surging briefly before being replaced by better-known VOCs.

"Scaling up sequencing in Africa has provided a wealth of information on how the pandemic unfolded on the continent," the authors wrote. "The epidemic has largely been spatially heterogeneous across Africa, but most countries have experienced multiple waves of infection, with significant local and regional diversity in the first and, to a lesser extent, the second waves, followed by successive sweeps of the continent with Delta and Omicron."

In North Africa, for example, the investigators described B.1 viral lineage replacement by the Alpha VOC during the transition from the first to second wave, followed by a surge in Delta infections and an Omicron-related fourth wave.

In contrast, Beta SARS-CoV-2 isolates appeared to contribute most markedly to the second wave of infections in southern Africa, where a variant of interest lineage with potential immune escape and mutation profiles was also tracked over time before being outpaced by the Delta VOC.

The team's Central Africa findings highlighted the importance of B.1.620 lineage infections from early 2021 to June of that year, while second wave infections in Uganda and other parts of East Africa were marked by a SARS-CoV-2 lineage known as A.23.1.

The team brought in phylogenetics and phylogeographic analyses to better understand relationships among SARS-CoV-2 lineages arising and spreading at these sites and beyond, including international infection patterns.

The uptick in viral sequencing and dip in turnaround time was achieved with the help of local sequencing facilities, regional sequencing hubs, centralized sites, and collaborations with investigators outside of Africa, the researchers explained, noting that nearly half of the SARS-CoV-2 sequences were generated with the help of Oxford Nanopore technology.

Even so, the authors argued that "Africa needs to continue expanding genomic sequencing technologies on the continent in conjunction with diagnostics capabilities. … Beyond the current pandemic, continued investment in diagnostic and sequencing capacity for [emerging or re-emerging pathogens] could serve the public health of the continent well into the 21st century."