RESUMO
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.
RESUMO
Many high-income countries have met the SARS-CoV-2 pandemic with overwhelming sequencing resources and have identified numerous distinct lineages, including some with notably altered biology. Over a year into the pandemic following unprecedented reductions in worldwide human mobility, distinct introduced lineages of SARS-CoV-2 without sequenced antecedents are increasingly discovered in high-income countries as a result of ongoing SARS-CoV-2 genomic surveillance initiatives. We here describe one such SARS-CoV-2 lineage, carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69{Delta}, Y144{Delta}, and LLA241/243{Delta}. This lineage - designated B.1.620 - is known to circulate in Lithuania and has now been found in several European states, but also in increasing numbers in central Africa owing to important recent increases in genome sequencing efforts on the continent. We provide evidence of likely ongoing local transmission of B.1.620 in Lithuania, France, Germany, Spain, Belgium and the Central African Republic. We describe the suite of mutations this lineage carries, its potential to be resistant to neutralising antibodies, travel histories for a subset of the European cases, and evidence of local B.1.620 transmission in Europe. We make a case for the likely Central African origin of this lineage by providing travel records as well as the outcomes of carefully crafted phylogenetic and phylogeographic inference methodologies, the latter of which is able to exploit individual travel histories recorded for infected travellers having entered different European countries.
RESUMO
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.