Diagnosis and genomic characterization of SARSCOV- 2 in a Senegalese laboratory of public sector

ABSTRACT

Introduction/ Background: In Senegal, several labs are involved in COVID-19 diagnosis but only a few have the capacity of genomic sequencing, especially in the public sector. The aim of this study was to describe the contribution of a public health laboratory in COVID-19 diagnosis and molecular epidemiology of SARS-COV-2 in Senegal. Methods: From nasopharyngeal swabs collected from COVID- 19 patients, viral RNA was extracted and an RT-PCR was carried out to detect SARS-COV-2 genes using different kits targeting ORF1ab and N genes using Dan-An Gene Co (LTD of Sun-Yat-Sen University) and Sansure Bio Tech Inc or RdRp and N gene with Abbot Real-Time RT-PCR kit. Genomic characterization of SARS-COV-2 strains were carried out on a subset of positive samples collected from the 3 waves by sequenced using MinIon Oxford Nanopore technology. Results: From July 2020 to Sept 2021, 7988 COVID-19 suspected patients or travelers were tested at Laboratoire de Bacteriologie- Virologie (LBV) of Aristide Le Dantec hospital, an University Teaching Hospital. Among them, 964 patients were positive to SARS-COV-2 giving a positivity rate of 12%. Thereafter, 115 (11.9%) were sequenced including 32, 40, and 43 from the first, second, and third waves, respectively. The most detected variants of the first wave were B.1.1.420 (23%). For the second wave, B.1.1.420 (27.5%) and B.1.1.7 (35%) were the most detected. For the third wave, 42 sequences were Delta variant (B.1.617), and one from 19A clade. Impact The results of this study highlight the need to enlarge the sequencing capacity to laboratories from the public sector in Senegal, especially university teaching hospitals as they may contribute efficiently to COVID -19 response. Conclusion: Despite the low number of positive samples, the LBV through this experience has proven its capacity to contribute to the national response of the COVID-19 pandemic and in genomic characterization of SARSCOV- 2 in the country. It was also a very good opportunity for a technology transfer from IRESSEF and MCR-Gambia.