Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020-2022 (preprint)

Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, >499 000 cases, and ~7 500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the introduction and spread of SARS-CoV-2 in Ethiopia. In this study, we reconstructed and elucidated the COVID-19 epidemic dynamics. Specifically, we investigated the introduction, local transmission, ongoing evolution, and spread of SARS-CoV-2 during the first four infection waves using 353 high-quality near-whole genomes sampled in Ethiopia. Our results show that whereas viral introductions seeded the first wave, subsequent waves were seeded by local transmission. The B.1.480 lineage emerged in the first wave and notably remained in circulation even after the emergence of the Alpha variant. The B.1.480 was out-competed by the Delta variant. Notably, Ethiopia lack of local sequencing capacity was further limited by sporadic, uneven, and insufficient sampling that limited the incorporation of genomic epidemiology in the epidemic public health response in Ethiopia. These results highlight Ethiopia role in SARS-CoV-2 dissemination and the urgent need for balanced, near-real-time genomic sequencing.

A novel variant of interest of SARS-CoV-2 with multiple spike mutations is identified from travel surveillance in Africa (preprint)

At the end of 2020, the Network for Genomic Surveillance in South Africa (NGS-SA) detected a SARS-CoV-2 variant of concern (VOC) in South Africa (501Y.V2 or PANGO lineage B.1.351)1. 501Y.V2 is associated with increased transmissibility and resistance to neutralizing antibodies elicited by natural infection and vaccination2,3. 501Y.V2 has since spread to over 50 countries around the world and has contributed to a significant resurgence of the epidemic in southern Africa. In order to rapidly characterize the spread of this and other emerging VOCs and variants of interest (VOIs), NGS-SA partnered with the Africa Centres for Disease Control and Prevention and the African Society of Laboratory Medicine through the Africa Pathogen Genomics Initiative to strengthen SARS-CoV-2 genomic surveillance across the region. Here, we report the first genomic surveillance results from Angola, which has had 21 500 reported cases and around 500 deaths from COVID-19 up to March 2021 (Supplemental Fig S1). On 15 January 2021, in response to the international spread of VOCs, the government instituted compulsory rapid antigen testing of all passengers arriving at the main international airport, in addition to the existing requirement to present a negative PCR test taken within 72 hours of travel. All individuals with a positive antigen test are isolated in a government facility for a minimum of 14 days and require two negative RT-PCR tests at least 48 hours apart for de-isolation, whilst all travelers with a negative test on arrival proceed to mandatory self-quarantine for 10 days followed by a repeat test. In March 2021, we received 118 nasopharyngeal swab samples collected between June 2020 and February 2021, a number of which were from incoming air travelers (Supplemental Fig S1). From these, we produced 73 high quality genomes (>80% coverage), 14 of which were known VOCs/VOIs (seven 501Y.V2/B.1.351, six B.1.1.7, one B.1.525), 44 of which were C.16 (a common lineage circulating in Portugal), and twelve of which were other lineages (Supplemental Fig S2). In addition, we detected a new VOI in three incoming travelers from Tanzania who were tested together at the airport in mid-February. The three genomes from these passengers were almost identical and presented highly divergent sequences within the A lineage (Figure 1A & 1B). The GISAID database contains nine other sequences reported to be sampled from cases involving travel from Tanzania, two of which are basal to the three sampled in Angola (Figure 1A, Supplemental Table S1). This new VOI, temporarily designated A.VOI.V2, has 31 amino acid substitutions (11 in spike) and three deletions (all in spike) (Figure 1C & 1D). The spike mutations include three substitutions in the receptor-binding domain (R346K, T478R and E484K); five substitutions and three deletions in the N-terminal domain, some of which are within the antigenic supersite (Y144{Delta}, R246M, SYL247-249{Delta} and W258L)4; and two substitutions adjacent to the S1/S2 cleavage site (H655Y and P681H). Several of these mutations are present in other VOCs/VOIs and are evolving under positive selection.