COVID-19 in Africa: the spread and response

Loembé, Marguerite Massinga; Tshangela, Akhona; Salyer, Stephanie J.; Varma, Jay K.; Ouma, Ahmed E Ogwell; Nkengasong, John N.

doi:10.1038/s41591-020-0961-x

Cited by 192 publications

(157 citation statements)

References 8 publications

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“…Mutations in this receptor are a likely pathway to evade antibody recognition, such as described in other viruses [ 40 , 41 ]. In all the genomes analyzed, 36 non-synonymous RBD mutations were identified and all these mutations had a low frequency (<0.01) in the genomes of six continents, which is consistent with several studies that have found that mutations are extremely rare in the RBD region [ 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 42 , 43 ]. The calculated binding-free energy of mutant RBDs of spike protein complexed with human ACE2 revealed only four RBD mutant types (D364Y, N440K, N450K, S477R) displaying a much lower binding-free energy (ΔG), indicating a significantly higher affinity for the ACE2, which could influence the pathogenicity of SARS-CoV-2.…”

Section: Discussionsupporting

confidence: 88%

“…Furthermore, the dynamics of transmission showed that the least divergent African variants were grouped with Asian strains, while the most divergent were grouped with Europe and North America. This distribution points to different sources of infection [ 26 , 27 ]. South America’s genomes appear to originate from North America and Europe, showing a close clustering with Europe in low and high divergence strains, which is concordant with a previous study [ 28 ].…”

Section: Discussionmentioning

confidence: 99%

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Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the “Confined Virus”?

Alouane¹,

Laamarti²,

Essabbar³

et al. 2020

Pathogens

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The COVID-19 pandemic has been ongoing since its onset in late November 2019 in Wuhan, China. Understanding and monitoring the genetic evolution of the virus, its geographical characteristics, and its stability are particularly important for controlling the spread of the disease and especially for the development of a universal vaccine covering all circulating strains. From this perspective, we analyzed 30,983 complete SARS-CoV-2 genomes from 79 countries located in the six continents and collected from 24 December 2019, to 13 May 2020, according to the GISAID database. Our analysis revealed the presence of 3206 variant sites, with a uniform distribution of mutation types in different geographic areas. Remarkably, a low frequency of recurrent mutations has been observed; only 169 mutations (5.27%) had a prevalence greater than 1% of genomes. Nevertheless, fourteen non-synonymous hotspot mutations (>10%) have been identified at different locations along the viral genome; eight in ORF1ab polyprotein (in nsp2, nsp3, transmembrane domain, RdRp, helicase, exonuclease, and endoribonuclease), three in nucleocapsid protein, and one in each of three proteins: Spike, ORF3a, and ORF8. Moreover, 36 non-synonymous mutations were identified in the receptor-binding domain (RBD) of the spike protein with a low prevalence (<1%) across all genomes, of which only four could potentially enhance the binding of the SARS-CoV-2 spike protein to the human ACE2 receptor. These results along with intra-genomic divergence of SARS-CoV-2 could indicate that unlike the influenza virus or HIV viruses, SARS-CoV-2 has a low mutation rate which makes the development of an effective global vaccine very likely.

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Section: Discussionsupporting

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the “Confined Virus”?

Alouane¹,

Laamarti²,

Essabbar³

et al. 2020

Pathogens

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“…African governments implemented early and strong non-pharmaceutical intervention (NPI) policies that may have effectively contained disease transmission [ 5 , 19 ]. The first case of COVID-19 was reported in SSA one month later than the first cases in Europe, allowing countries to prepare and implement NPIs, particularly lockdowns, social distancing, masks, and regulated domestic travel, during the early stages of the pandemic [ 3 , 19 , 20 ]. Beginning in June, several SSA countries began relaxing lockdown NPIs in response to the economic and social costs of lockdown given the low reported case numbers.…”

Section: Introductionmentioning

confidence: 99%

Reconciling model predictions with low reported cases of COVID-19 in Sub-Saharan Africa: insights from Madagascar

Evans

Garchitorena

Rakotonanahary

et al. 2020

Global Health Action

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COVID-19 has wreaked havoc globally with particular concerns for sub-Saharan Africa (SSA), where models suggest that the majority of the population will become infected. Conventional wisdom suggests that the continent will bear a higher burden of COVID-19 for the same reasons it suffers from other infectious diseases: ecology, socio-economic conditions, lack of water and sanitation infrastructure, and weak health systems. However, so far SSA has reported lower incidence and fatalities compared to the predictions of standard models and the experience of other regions of the world. There are three leading explanations, each with different implications for the final epidemic burden: (1) low case detection, (2) differences in epidemiology (e.g. low R 0 ), and (3) policy interventions. The low number of cases have led some SSA governments to relaxing these policy interventions. Will this result in a resurgence of cases? To understand how to interpret the lower-than-expected COVID-19 case data in Madagascar, we use a simple age-structured model to explore each of these explanations and predict the epidemic impact associated with them. We show that the incidence of COVID-19 cases as of July 2020 can be explained by any combination of the late introduction of first imported cases, early implementation of non-pharmaceutical interventions (NPIs), and low case detection rates. We then re-evaluate these findings in the context of the COVID-19 epidemic in Madagascar through August 2020. This analysis reinforces that Madagascar, along with other countries in SSA, remains at risk of a growing health crisis. If NPIs remain enforced, up to 50,000 lives may be saved. Even with NPIs, without vaccines and new therapies, COVID-19 could infect up to 30% of the population, making it the largest public health threat in Madagascar for the coming year, hence the importance of clinical trials and continually improving access to healthcare.

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“…According to the volume of air travel between China and Africa, a modeling study about African countries imported COVID-19 cases demonstrates that countries with the highest importation risk are Egypt, Algeria, and South Africa [26]. However, data from the African CDC indicate that the origin of imported cases in Africa is mainly from Europe (i.e., France, Italy, and United Kingdom), although COVID-19 is first reported in China [6,27]. In addition, among these 105 patients reported as of March 10, 80 (76.19%) were distributed in Northern Africa, and most of them were imported from Europe.…”

Section: Discussionmentioning

confidence: 99%

“…After closing borders and mitigated measures, including restrictions on movement, public gatherings, and schools, some countries have seen a reduction in the average daily case growth, whereas it will undoubtedly depress economics in Africa [27]. Whether lockdown is suitable for Africa remains unknown.…”

Section: Discussionmentioning

confidence: 99%

Epidemic Characteristics of COVID-19 in Africa

et al. 2020

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The aim of this study was to investigate coronavirus disease 2019 (COVID-19) epidemic characteristics in Africa and provide some references to prevent pandemic. Methods: We collect information of the laboratory-confirmed case of COVID-19 that has been reported since April 28, 2020 in Africa, describe the epidemic characteristics in different regions of Africa, and predict the spread trend. Results: (1) There are 35,309 COVID-19 cases and 1,522 deaths in 54 African countries. Both case amount and death toll in Northern Africa are higher than those in other African regions, whereas the case fatality rate (CFR) in Africa is lower than that of the world. (2) Among the 54 countries in Africa, 39 of them (72.22%) report confirmed cases between 1 and 499. (3) In total, 596,146 tests have been conducted in 35 countries, and 28,271 patients have been confirmed, with a positive rate of 4.74%. However, there are only 335 tests (interquartile range: 145.5-874) for every 1 million people in Africa. (4) The number of infection cases will increase to around 150,000 at the end of May according to our model. Conclusion: In Africa, COVID-19 spreads faster while with a relatively lower CFR, and it may be related to higher young people ratio. In addition, test intensity of COVID-19 is obviously insufficient in Africa.

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COVID-19 in Africa: the spread and response

Cited by 192 publications

References 8 publications

Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the “Confined Virus”?

Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the “Confined Virus”?

Reconciling model predictions with low reported cases of COVID-19 in Sub-Saharan Africa: insights from Madagascar

Epidemic Characteristics of COVID-19 in Africa

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