Delays in the arrival of the waves of COVID-19: a comparison between Gabon and the African continent
Authors: Haruka Abe, Yuri Ushijima, Rodrigue Bikangui, Georgelin Nguema Ondo, Bertrand Lell, Ayola A Adegnika, Jiro Yasuda
Journal: The Lancet Microbe (2022)

2 years since COVID-19 was declared a pandemic by WHO, genomic surveillance of SARS-CoV-2 has become active in Africa, both in surveillance-leading countries such as South Africa and in other surveillance-developing countries. Sequence data from Africa identified the omicron (B.1.1.529) variant, which showed rapid expansion worldwide.1Viana R Moyo S Amoako DG et al.Rapid epidemic expansion of the SARS-CoV-2 omicron variant in southern Africa.Nature. 2022; 603: 679-686Crossref PubMed Scopus (202) Google Scholar, 2Wolter N Jassat W Walaza S et al.Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study.Lancet. 2022; 399: 437-446Summary Full Text Full Text PDF PubMed Scopus (155) Google Scholar Despite the availability of free vaccination programmes, waves of the delta (B.1.617.2) and omicron variants were observed in most African countries. A great effort by the government has promoted whole-genome sequencing of SARS-CoV-2 in Gabon; as a result, in the early period of 2021, we identified imported cases of variants of concern in Gabon, demonstrating the importance of tracking travellers with COVID-19.3Zoa-Assoumou S Ndeboko B Manouana GP et al.SARS-CoV-2 emerging variants in Africa: view from Gabon.Lancet Microbe. 2021; 2: e349Summary Full Text Full Text PDF PubMed Scopus (5) Google Scholar We have also conducted continuous genomic surveillance since the beginning of the COVID-19 pandemic, covering the first three waves of COVID-19 that occurred in Gabon. Our data clearly showed that Gabon experienced three major waves of COVID-19 before December 2021, similar to the entire African continent. However, the peak of COVID-19 cases occurred approximately 1 or 2 months later in Gabon than the African continent, except for the first wave when the diagnostic strategies were largely unestablished, and the number of cases was expected to be underestimated. Although the main lineages of SARS-CoV-2 prevalent in each wave in Gabon were similar to those in the African continent, a large proportion of infections in the second wave in Gabon were occupied by B.1.1.318 (30·6%), which has mostly been detected in the USA and basin countries of the Gulf of Guinea, whereas it was minuscule in the corresponding wave in the African continent (0·34%). The main policies implemented by the government seemed to have few clear correlations with the delay in the infection waves. There were approximately 1-month or 2-month delays in the infection peaks of COVID-19 in Gabon compared with the African continent, potentially providing a brief preparation period to develop countermeasures against an upcoming infection wave expected from the African continent. The spread of B.1.1.318 indicated frequent cross-border overland transfers between Gabon and countries surrounding the Gulf of Guinea, whereas no delays in the arrival of the waves of COVID-19 were observed in countries such as Nigeria and Ghana. There is an urgent need to clarify why the delay of the infection peak was generated, to seek more effective countermeasures to block COVID-19, and for urgent studies on the development of novel vaccines and antiviral drugs. For more on nextstrain see https://nextstrain.org/ncov/gisaid/africa For more on nextstrain see https://nextstrain.org/ncov/gisaid/africa We declare no competing interests. This study was supported by the Science and Technology Research Partnership for Sustainable Development, Japan International Cooperation Agency, and Japan Agency for Medical Research and Development (grant number JP20jm0110013 and JP20wm0225003); and a Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science, grant number JP19K24679. We thank the COVID-19 diagnosis team at the Centre de Recherches Médicales de Lambaréné for daily sampling and RT-qPCR tests. Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage studyOur early analyses suggest a significantly reduced odds of hospitalisation among individuals with SGTF versus non-SGTF infections diagnosed during the same time period. SGTF-infected individuals had a significantly reduced odds of severe disease compared with individuals infected earlier with the delta variant. Some of this reduced severity is probably a result of previous immunity. Full-Text PDF Open AccessSARS-CoV-2 emerging variants in Africa: view from GabonSince SARS-CoV-2 appeared in late 2019 in Wuhan, China, variants have emerged around the world. The general concern is that these variants appear to cause more severe disease, spread more easily between humans, and might change the effectiveness of current treatment and vaccines.1–5 Travel-related dissemination of SARS-CoV-2 fuels the global pandemic and the spread of variants. Therefore, SARS-CoV-2 genomic surveillance would help trace the emergence and spread of variants to better understand and anticipate their impact on public health. Full-Text PDF Open Access