Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time 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 shed light on 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 re-emerging 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.

Introduction: The Republic of the Congo detected its first case of coronavirus disease 2019 (COVID-19) on March 14, 2020, and within several weeks, the country had introduced protective measures that were still in force in July 2020. Over the course of time, the progression in the number of clinical cases has appeared to be lower than expected, although reverse transcription polymerase chain reaction (RT-PCR) testing has been somewhat limited. In order to evaluate the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within the Congolese population, a seroprevalence study was conducted on healthy individuals from different districts of Brazzaville who were willing to know their COVID-19 infection status. Methods: Oropharyngeal swab and blood samples were collected from 754 healthy volunteers between April 2020 and July 2020. The samples were analyzed for SARS-CoV-2 using a qualitative RT-PCR assay, and Immunoglobulin G (IgG) and Immunoglobulin M (IgM) antibodies were detected using two different rapid tests. Results: A total of 56 participants (7.4%) tested positive for SARS-CoV-2. The remaining 698 participants (92.6%) had negative RT-PCR results; of these, 117 were found to have anti-SARS-CoV-2 antibodies using serological tests. For these RT-PCR-negative subjects, the seroprevalence of IgG and IgM was found to increase over time: from 1.7% and 2.5% in April, up to 14.2% and 17.6% in July, respectively. In April 2020, 5% of the women were found to have IgG or IgM antibodies, whereas the antibodies were not detected in any of the men. The seroprevalence in RT-PCR negative subjects was significantly higher in women within IgG (P = 0.012) and IgM (P = 0.045) over the first three months. Conclusion: The proportion of the population who seroconvert over the course of the first wave is an important data to predict the risk of future COVID-19 waves and this will facilitate the efficient use of limited resources in a low income country like the Republic of the Congo.

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.