Genomic surveillance of SARS-CoV-2 in Ghana: Leveraging a national influenza platform

ABSTRACT

Introduction/ Background: Genomic surveillance of SARS-CoV-2 is crucial for monitoring the spread of the disease and guiding public health decisions but the capacity for SARSCoV- 2 sequencing in Africa remains low. This research aims to increase the genomic contribution from the Africa and gain insights of the SARS-CoV-2 infections in Ghana and Africa. Methods: We utilised samples from two sources;firstly, community surveillance undertaken using the Ghana Influenza Surveillance Network and secondly imported cases of SARS-CoV-2 detected in travellers. A total of 457 patients from Ghana, collected from 1st April 2020 to 31st August 2021, were sequenced using Oxford Nanopore Technology sequencing and the ARTIC tiled amplicon method. The sequence lineages were typed using Pangolin and the phylogenetic analysis was carried out using IQtree and TreeTime. Results: We detected three waves of SARS-CoV-2 infections in Ghana. The first wave of infection was mainly contained in the Greater Accra, later spreading to other regions in the second and third wave. B.1 and B.1.1. were the most prevalent lineages in wave one, while the B.1.1.7/alpha variant is responsible for the second wave. An investigation into the lineages detected in Ghana led us to discover that B.1.1.318 (which contains the E484K mutation shown to impact antibody recognition) has a high cumulative prevalence rate in a number of neighbouring West African countries, suggesting that there might be a regional circulation. Impact The high-quality sequences produced from this study were submitted to the largest open-access SARSCoV- 2 sequence database, increasing the genomic contribution from Africa. By sequencing both community samples and imported cases in Ghana, the study revealed an insight into the SARS-CoV-2 epidemiology in Ghana and West Africa. Conclusion: This study not only informed us of the epidemiological characteristics of the SARS-CoV-2 outbreaks in Ghana, but also shed light on the epidemiological trends of neighbouring countries that may have less sequencing capacity, highlighting the important role of pathogen genomic sequencing in cross-border and regional disease surveillance.