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.

Fig 1. Epidemiological characteristics of COVID-19 in Africa.

Cumulative cases of COVID-19 in Africa. Countries indicated on the map represent those with highest number of cases in each five regions (West, East, Central, Southern and North Africa) as of June 15, 2020. Highlighted countries represent countries with highest number of cases in the five regions at the early phase of COVID-19 in Africa. The figure contains information from OpenStreetMap and OpenStreetMap Foundation, which is made available under the Open Database License.

Fig 2. Correlation analysis of COVID-19 cases and mutant variants with fatality rate.

Correlation analysis of cumulative cases with number of deaths (a); variant frequencies of SARS-CoV-2’ S 614G with fatality rates of COVID-19 among the five regions of Africa (b); ORF1ab P4715L with fatality rates of COVID-19 among the five regions of Africa (c); ORF1ab/RdRp with fatality rates of COVID-19 among the five regions of Africa (d). Pearson’s correlation coefficients (r) and p values were calculated.

Fig 3. Phylogeny analysis of SARS-CoV-2 in Africa.

Phylogeny analysis SARS-CoV-2 using 224 genome sequences form GISAID and NC_045512 reference genome from NCBI. Phylogenetic tree is divided into clades, and all clades are further divided into sub-groups. There were three clades formed: one from the highlighted NC 045512 Wuhan-Hu-1 isolate to Mali-2, another from Fuyang-1 (an isolate from China) to Iran-3, and the last from Nanchang -1 (from China) to Japan-2. Labels in blue represent African countries.