ABSTRACT
SARS-CoV-2 variants of concern (VOC) and variants of interest (VOI) are heavily altering the COVID-19 pandemics course due to their increased transmissibility, virulence and immune escape abilities. Data on their spread in western sub-Saharan Africa is however still scarce. We therefore sequenced viral genomes from SARS-CoV-2 cases identified in central and northern Cote dIvoire between May 2020 and March 2021. We report the introduction of VOC B.1.1.7 as early as mid-January 2021, followed by detection of a single case of VOC B.1.351, as well as VOI B.1.525. Since early 2021 VOC/VOI are gradually dominating the SARS-CoV-2 virus pool in Cote dIvoire, as seen in other regions of the world. Intriguingly, we also find that another lineage, A.27, has also been on the rise over the same period. In sum, this study highlights again the extremely rapid local diffusion of VOC, VOI and possibly A.27, and the importance of further reinforcing capacities for genomic surveillance on the African continent.
ABSTRACT
The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations, predominantly from Europe, which diminished following the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1 and C.1.1. Although distorted by low sampling numbers and blind-spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a breeding ground for new variants.
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.