Virological Diagnosis of SARS-CoV-2 in a Tunisian Orthopedic Institute

Abstract

Background: The objective of this study was to investigate the epidemiological profile of the virological diagnosis of COVID 19 at Mohamed Kassab Institute of Orthopedics. Methods: The virological diagnosis was performed by RT-PCR from november 2020 to september 2021 on 33505 nasopharyngeal swabs which different reagent kits were used: Allplex® 2019 nCoV Assay, WANTAI® SARS-CoV-2 RT-PCR, WONDFO® 2019- nCoV Real-Time RT-PCR Assay, GENESIG® Real time PCR coronavirus (COVID-19), GENESIG® COVID-19 2G . The duration from onset to laboratory test in COVID-19 suspected cases and contact individuals ranged from 0 to 14 days with a median of 3 days. The present study provides some genetic information on the lineages of SARS-CoV-2 that circulated in Tunisia over 6 months from april to september 2021. Lineages were assigned for 13 samples using whole-genome sequencing, partial S gene sequencing. Results: A total of 33505 PCR tests were performed from five governorates including Manouba which represented 88.2% (29560). The positive samples were 35% (11695) and 57% (19223) were negative. The sex ratio of confirmed cases was 0.9 (5540/6155). The age group 20-65 years was the most represented with 65.9%. For sequencing her we describe the third wave was marked by the predominance of the Alpha VOC, and the fourth wave was characterized by the predominance of the Delta VOC. This study adds new genomic data to the global context of COVID-19, particularly from the North African region, and highlights the importance of the timely molecular characterization of circulating strains. Conclusion: This study adds new genomic data to the global context of COVID-19, particularly from the North African region, and highlights the importance of the timely molecular characterization of circulating strains.