Amplification of Sars-Cov2 Viral Markers in Côte d’Ivoire

Abstract

The COVID-19 pandemic is causing millions of deaths worldwide. In West Africa, particularly in Côte d’Ivoire, many cases of illness and death have also been reported. The country has applied the diagnostic method recommended by the World Health Organization based on the detection of the genetic material of the SARS-CoV2 virus using RT-qPCR, which requires native or recombinant positive controls to validate the diagnostics. Recombinant plasmids are used for in vitro amplification in E. coli strains. This study aims to propose a bank of recombinant viral genomes for the diagnosis of SARS-CoV-2. A total of fifty (50) positive nasopharyngeal samples have been collected during the pandemic from 2020 to 2022. ARN viral extraction was applied, and the viral targets of Envelope, Membrane, Nucleoprotein, and Glycoprotein Spike were amplified using RT-qPCR methods. The PCR products were cloned to obtain recombinant plasmids. Our results show positive amplification of the three genes E, M, and N detected with positive rates of 50%, 40%, and 36%. A partial 995 bp fragment of the S gene was amplified at a low rate.  Recombinant plasmids of SARS-CoV-2 were obtained, 50, 40, and 13 for the E gene, M gene, and N gene respectively. The recombinant plasmids were detected positive by conventional PCR and real-time PCR of SARSCoV-2. The nucleotide sequence of recombinant plasmids shows sequences homologies of 95% to 100% with the Wuhan reference strain for all three genes. This study has provided reliable recombinant plasmids for the diagnosis of SARS-CoV-2 in Côte d’Ivoire and offers the way for future studies to diagnostics tools.