Diagnostics and Spread of SARS-CoV-2 in Western Africa: An Observational Laboratory-Based Study from Benin

Abstract

Background: Information on severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spread in Africa is limited by fragile surveillance systems and insufficient diagnostic capacity. Methods: We assessed the coronavirus disease-19 (COVID-19)-related diagnostic workload in Benin, Western Africa, characterized SARS-CoV-2 genomes from 12 acute cases of COVID-19, used those together with public data to estimate SARS-CoV-2 transmission dynamics in a Bayesian framework, validated a widely used diagnostic dual target RT-PCR kit donated to African countries, and conducted serological analyses in 68 sera from confirmed COVID-19 cases and from febrile patients sampled before the predicted SARS-CoV-2 introduction. Findings: We found a 15-fold increase in the monthly laboratory workload due to COVID-19. Genomic surveillance showed introductions of three distinct SARS-CoV-2 lineages. SARS-CoV-2 genome-based analyses yielded an R0 estimate of 4.4 (95% confidence interval: 2.0-7.7), suggesting intense spread of SARS-CoV-2 in Africa. RT-PCR-based tests were highly sensitive but showed variation of internal controls and between diagnostic targets. Commercially available SARS-CoV-2 ELISAs showed up to 25% false-positive results depending on antigen and antibody types, likely due to unspecific antibody responses elicited by acute malaria according to lack of SARS-CoV-2-specific neutralizing antibody responses and relatively higher parasitemia in those sera. Interpretation: We confirm an overload of the diagnostic capacity in Benin and provide baseline information on the usability of genome-based surveillance in resource-limited settings. Sero-epidemiological studies needed to assess SARS-CoV-2 spread may be put at stake by low specificity of tests in tropical settings globally. The increasing diagnostic challenges demand continuous support of national and supranational African stakeholders. Funding: This work was supported by the Deutsche Gesellschaft fur Internationale Zusammenarbeit (GIZ) GmbH. Declaration of Interests: The authors declare no conflict of interests. Ethics Approval Statement: This study was approved by the ethics committee of the Ministry of Health (Arrete 2020 No. 030/MS/DC/SGM/DNSP/CJ/SA/027SGG2020) and followed the Declaration of Helsinki. Written consent was obtained from all the patients participating in the study.