Overview of genomic surveillance related to Severe Acute Respiratory Syndrom Coronavirus 2 (SARS- CoV-2)

Hanane Bahouq,Madiha Bahouq,Abdelmajid Soulaymani,S Bourekkadi,K Slimani,A Mokhtari,A Soulaymani,H Hami

doi:10.1051/e3sconf/202131901043

Abstract

Since the start of the Severe Acute Respiratory Syndrom Coronavirus 2 (SARS-CoV-2) pandemic, several thousand of variants circulated and others are emerging. Therefore, genomic surveillance is crucial, which aims to detect the emergence of new variants, in particular Variants of Concern (VOC) and to assess the impact of priority mutations on the transmissibility and lethality of the virus, the performance of viral diagnostic methods and vaccine efficiency. An overview of available papers was performed to understand conduct, tools and utility of genomic sequencing and surveillance related to Covid-19 disease. We also report the experience of Morocco in this filed through available data. A national SARS-Cov-2 genomic consortium has been established in order to continuously inform the health authorities of the genetic evolution of circulating strains in Morocco. Genomic sequencing shows that Moroccan genomes spread did not show a predominant SARS-CoV-2 lineage. Genomes are dispersed across the evolutionary tree of SARS-CoV-2 and held between 4 and 16 mutations. As the pandemic ongoing, continuous genomic surveillance and regular sequencing are fundamental to understand the spread of SARS-CoV-2, to rapidly identify potential global transmission networks and to consolidate response strategies especially targeted Covid-19 vaccination.

Highlights

Several coronavirus are already known to be able to infect humans
Severe Acute Respiratory Syndrom Coronavirus 2 (SARS- CoV-2), a lineage-b betacoronavirus belonging to the coronaviridae family is the seventh coronavirus pathogenic to humans responsible for the COronaVIrus Disease 2019 (Covid-19)
As 26 May 2021, 1,732,197 SARSCoV-2 genomic sequences have been shared via the Global Initiative on Sharing All Influenza Data (GISAID) database [4, 5]

Summary

Introduction

Several coronavirus are already known to be able to infect humans. Severe Acute Respiratory Syndrom Coronavirus 2 (SARS- CoV-2), a lineage-b betacoronavirus belonging to the coronaviridae family is the seventh coronavirus pathogenic to humans responsible for the COronaVIrus Disease 2019 (Covid-19). As 26 May 2021, 1,732,197 SARSCoV-2 genomic sequences have been shared via the Global Initiative on Sharing All Influenza Data (GISAID) database [4, 5] In this global health crisis, to understand viral transmission and evolution and to inform public health responses and vaccine development, national and international consortiums were established. In February 2021, the Moroccan health ministry has get up a consortium of laboratories with sequencing platform as a part of its strategy for genomic monitoring of the disease This consortium is composed of the Reference Laboratory for Influenza and respiratory Viruses of the National Institute of hygiene, the Medical Biotechnology Laboratory of Faculty of Medicine and Pharmacy and the Functional Genomic Platform of the National Scientific Research as well as to the Institute Pasteur in Casablanca. We report the available data of the Moroccan experience in this field

Phylogenetic network analysis

Conclusion

The Phylogenetic Assignment of Named Global

11. Updated Nextstain SARS-CoV-2 Clade Naming

19. Brief report