Genomic and epidemiological characteristics of SARS-CoV-2 in Africa

Abstract

Since late 2019, the coronavirus disease 2019 (COVID-19) outbreak, caused by SARS-CoV-2, has rapidly evolved to become a global pandemic. Each country was affected but with a varying number of infected cases and mortality rates. Africa was hit late by the pandemic but the number of cases rose sharply. In this study, we investigated 224 SARS-CoV-2 genome sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) in the early part of the outbreak, of which 69 were from Africa. We analyzed a total of 550 mutations by comparing them with the reference SARS-CoV-2 sequence from Wuhan. We classified the mutations observed based on country and region, and afterwards analyzed common and unique mutations on the African continent as a whole. Correlation analyses showed that the duo variants ORF1ab/RdRp 4715L and S protein 614G variants, which are strongly linked to fatality rate, were not significantly and positively correlated with fatality rates (r = -0.03757, P = 0.5331 and r = -0.2876, P = 0.6389, respectively), although increased number of cases correlated with number of deaths (r = 0.997, P = 0.0002). Furthermore, most cases in Africa were mainly imported from American and European countries, except one isolate with no mutation and was similar to the original isolate from Wuhan. Moreover, unique mutations specific to countries were identified in the early phase of the outbreak but these mutations were not regional-specific. There were common mutations in all isolates across the continent as well as similar isolate-specific mutations in different regions. Our findings suggest that mutation is rapid in SARS-CoV-2 in Africa and although these mutations spread across the continent, the duo variants could not possibly be the sole cause of COVID-19 deaths in Africa in the early phase of the outbreak.

Retracted: Predictors of COVID-19 vaccine hesitancy in Germany: a cross-sectional, population-based study

“…In addition, the recurrent mutations of the virus renters the management of the disease, both in terms of prevention and treatment, more and more challenging. SARSCoV-2 is a highly transmissible virus, and in order for the chain of transmission to be broken, the vast majority of the population needs to be vaccinated 3–5. There is, however, a growing body of evidence that vaccination rates are low in many parts of the world and vaccine hesitancy is emerging as a major barrier to tackling the recurrent waves of the pandemic 2 5–7.…”

Genomic characterization of SARS-CoV-2 and its association with clinical outcomes: a 1-year longitudinal study of the pandemic in Colombia

“…These variants have become predominant and exhibit higher transmissibility and/or a significant impact on immunity and disease severity (Tracking SARS-CoV-2 Variants, 2021). Few studies have intended to longitudinally study the possible associations between the mentioned lineages, clades, or other classification systems, and clinical outcomes (Hamed et al, 2021;Lamptey et al, 2021;Nakamichi et al, 2021;Young et al, 2021).…”

Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India

“…The observation that the P681R was the second most prevalent mutation reveals the recent high dominance of the Delta variant in the region. Additionally, spike D614G was accompanied by high occurrence of the nsp12 P4715L mutation, and this duo variant which is linked to pathogenicity was observed to be not linked positively to fatality rates in Africa ( Lamptey et al, 2021 ). Such duo variants need further attention to assess host-based region-specific response.…”