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

Abstract

Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks.One-Sentence SummaryExpanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.

SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs

“…Expanding genomic sequencing capabilities, especially in LMICs, is a global priority 26 and current investments in sequencing must continue. 27,28 Simultaneously, sustained investments in public health systems are required to expand access to, and availability of, diagnostic testing to underpin SARS-CoV-2 surveillance programs. Here, we primarily focused on LMICs but our findings on the impact of testing rates and representativeness on genomic surveillance programs are equally important for HICs as they consider dismantling parts of their testing and surveillance infrastructure in the post-crisis phase of the pandemic.…”

Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria

“…We also found that the Eta variant (B.1.525) emerged in Nigeria in late July, with high levels of export to Europe reflected in the genomic and estimated export index. The true extent of bidirectional transmission with other African nations will be severely underestimated in phylogeographic reconstructions, as Africa remains disproportionately undersampled despite heroic efforts 28 . Our findings should be interpreted in the light of our own sampling fraction, which was 0.026%.…”

Leveraging South African HIV research to define SARS‐CoV‐2 immunity triggered by sequential variants of concern

“…In the space of 2 years and under the extremely heavy constraints of the pandemic, the Africa CDC PGI 38 has expanded next‐generation sequencing capacity in Africa from just 7 countries in November 2019 to 31 countries in January 2022. 39 …”

“…The newly formed Network for Genomic Surveillance in South Africa (NGS-SA) 37 In the space of 2 years and under the extremely heavy constraints of the pandemic, the Africa CDC PGI 38 has expanded next-generation sequencing capacity in Africa from just 7 countries in November 2019 to 31 countries in January 2022. 39 South African laboratories have also been heavily involved in…”

“…Later, this partnership systematically expanded the reach of next‐generation sequencing across Africa through virtual and in‐person training conducted by NGS‐SA. In the space of 2 years and under the extremely heavy constraints of the pandemic, the Africa CDC PGI 38 has expanded next‐generation sequencing capacity in Africa from just 7 countries in November 2019 to 31 countries in January 2022 39 …”