Genetic diversity of SARS-CoV-2 infections in Ghana from 2020-2021

Abstract

The COVID-19 pandemic is one of the fastest evolving pandemics in recent history. As such, the SARS-CoV-2 viral evolution needs to be continuously tracked. This study sequenced 1123 SARS-CoV-2 genomes from patient isolates (121 from arriving travellers and 1002 from communities) to track the molecular evolution and spatio-temporal dynamics of the SARS-CoV-2 variants in Ghana. The data show that initial local transmission was dominated by B.1.1 lineage, but the second wave was overwhelmingly driven by the Alpha variant. Subsequently, an unheralded variant under monitoring, B.1.1.318, dominated transmission from April to June 2021 before being displaced by Delta variants, which were introduced into community transmission in May 2021. Mutational analysis indicated that variants that took hold in Ghana harboured transmission enhancing and immune escape spike substitutions. The observed rapid viral evolution demonstrates the potential for emergence of novel variants with greater mutational fitness as observed in other parts of the world.

Fig. 1. Overall genomic epidemiology of the circulating variants across various regions in Ghana (N = 1123).

a Map showing the ten sampled regions (n = 1002) and travellers arriving in the country (121) at the Kotoka International Airport in the Greater Accra Region. The colour scheme shows the population density per hectare in each region, while the numbers are samples sequenced per region. b Overall SARS-CoV-2 lineages in Ghana for both local participants and travellers (n = 1123); the lineages are represented by different colours, while the percentages represent the proportion of cases with that particular lineage out of 1123 participants. Lineages with <6 participants are represented as “Other Variants”. c Out of the 1002 samples sequenced from community samples, 200 samples were sequenced in 2020 and 802 samples sequenced in 2021. The stacked plot shows the percentage distribution of lineages in six regions in 2020. Lineages are represented in unique colours as indicated on the plots. d The stacked plot shows the percentage distribution of lineages in 2021 from ten regions across Ghana (n = 802).

Fig. 2. Trends in the variant epidemiology in Ghana.

a Trends of COVD-19 in the World, Africa and Ghana, which indicates the date reported against the number of new cases. This shows the number of confirmed COVID-19 cases recorded daily in the World, Africa, and Ghana from January 2020 to October 2021. The data were obtained from World Health Organisation (https://covid19.who.int/WHO-COVID-19-global-data.csv). b Trends in prevalence of major variants circulating in Ghana from March 2020 to September 2021. The Y-axis shows the percentage distribution (n = 1002/1123) of various variants including VOCs across the various months (X-axis) while the lineages are represented by different colours. c Impact of emergence of variants of concern (VOCs) on dynamics of viral lineages dominating community transmission in Ghana in 2021 (802/1002).

Fig. 3. Genetic diversity and molecular evolutionary relationships of variants identified in Ghana.

a The spread/range and magnitude of mutation per lineage (n = 1002). Each filled circle represents a sample, and the circle’s width is proportional to the number of mutations present in a particular sample. b Maximum likelihood phylogenetic tree with ancestral state reconstruction in a backdrop of reference sequences from Wuhan and evolutionary relationship of the Ghanaian variants over time (n = 1002). Colours show the VOC; Delta lineages, Alpha, B.1.1.318, and Beta, based on Nextstrain’s emerging lineages designations. c Root-to-tip divergence as a function of sampling time. The Y-axis denoted divergence (the number of mutations in the genome relative to the root), and the X-axis shows the sampling date of each genome. d Annotated mutational fitness of all the B.1.1.318 lineage in Ghana; the samples with the highest fitness are coloured red.

Fig. 4. Analysis of amino acid substitutions in variants circulating in Ghana.

a Frequencies of amino acid substitutions across all the SARS-CoV-2 proteins in all genomes that were sequenced. The mutations are sorted and coloured per gene. b Spike glycoprotein amino acid substitutions present/absent in major SARS-CoV-2 variants circulating in Ghana. Purple shading indicates substitutions within the lineages, whereas white indicates the absence of the substitution in a particular variant in all the samples. The bottom panel plot shows the frequencies of individual substitutions across all the samples.