Genomic Surveillance of SARS-CoV-2 in Ghana: Leveraging an Integrated National Influenza and SARS-CoV-2 Platform

Background: Existing surveillance networks provide a possible platform to integrate SARS-CoV-2 and influenza surveillance in Africa and other settings.Methods: We utilised the Ghana Influenza Surveillance network to undertake integrated influenza and SARS-CoV-2 surveillance in Ghana. Samples from patients with influenza like illness and severe acute respiratory illness were tested for SARS-CoV-2 and influenza. Selected SARS-CoV-2 samples were were sequenced using the Oxford Nanopore platform.Results: Overall SARS-CoV-2 caused 13.4% of ILI cases and Influenza 8.4%. Conversely SARS-CoV-2 caused 12.0% of SARI compared to 19.7% of cases which were due to influenza. We detected four waves of SARS-CoV-2 in Ghana. The. B.1 and B.1.1 were the most prevalent lineages in wave one, while the B.1.1.7/Alpha variant was responsible for the second wave. The third wave was driven by Delta and Delta+ variants. We were able to detect the Omicron variant among travellers which subsequently spread to cause the 4 th wave of infections in Ghana. We identified transmission of B.1.1.318, which contains the E484K mutation shown to impact antibody recognition, and identified that this has a high cumulative prevalence rate in several neighbouring West African countries, suggesting potential regional circulation.Conclusions: We demonstrates the value of repurposing existing influenza surveillance platforms for SARS-CoV-2. We highlight continued circulation of Influenza during 2020 and 2021 and that it remained a major cause of severe acute respiratory illness, especially in younger individuals. We detected importations of SARS-CoV-2 variants into Ghana including those which did and did not lead to onward community transmission.Funding Information: This study is part of the EDCTP2 programme supported by the European (Grant Number RIA2020EF-2983-CSIGN).Declaration of Interests: The authors have no conflict of interest to declare.Ethics Approval Statement: This study was approved by the Ghana Health Service Ethics Research Committee. The sentinel sites for routine national influenza virus surveillance in Ghana were set up in collaboration with the Ghana Health Service as well as the Ghana Armed Forces as part of the Integrated Disease Surveillance and Response (IDSR) system of the Ghana Health Service. Oral consent was sought from all participants before samples were collected. All procedures were performed according to relevant guidelines and regulations. No administrative permissions were required to access this data. Data was anonymized before use and only laboratory identities were used during data analysis.