COVID-19 outbreak during investigation of acute respiratory syndrome among pilgrims in Senegal: An Integrated real time surveillance approach
Year: 2024
Type: preprint
Study design: Observational Study
Abstract: Background: Since the COVID-19 outbreak, global efforts have focused on controlling the disease. However, intense cross border movements pose a risk for the emergence of new SARS-CoV-2 strains. Recent example is the detection of cases among the 2024 Senegalese pilgrims returning from Mecca, Saudi Arabia, to monitor the emergence of high-threat strains. This study aims investigate new SARS-CoV-2 emerging lineages isolated from returning Senegalese Pilgrims. Methods: Whole Genome Sequencing, using midnight protocol on Oxford Nanopore Technology (ONT) platform, has been used to characterize SARS-CoV-2 strains isolated from 66 pilgrims tested Covid-19 positive. An integrated approach, involving strong collaboration with the Ministry of Health (MoH), was utilized for data sharing with patients and healthcare authorities. Results: Among 66 positive samples sequenced with coverage ≥ 80%, we detected the presence of the JN.1 sub-lineage (12.71%) and the emergence of the JN.1.18 variant (4.24%). In addition, JN.1.18.3 (14.41%) elicited more mutations than JN.1. Furthermore, we also identified variants, LF.1.1.1 (4.24%), JN.1.26 (1.69%), KP.1.1.1 (5.08%), KP.1.1.3 (1.69%), LP.2 (2.54%), JN.1.50.1 (0.85%), LB.1 (0.85%), and KS.1.1 (0.85%) which have never been identified in Africa in our knowledge. New lineages LS.1 (2.54%) and JN.1.18.5 (2.54%) were identified in real time during this intervention. Conclusion: It is important to monitor the emergence of new variants among pilgrims and the general population, as well as the clinical course of patients, to determine the virulence of these variants.
Source: Research Square
Authors: Abdou Padane, Aminata Mboup, Seyni Ndiaye, Mariema Sarr, Marilyne Aza-Gnandji, Mamadou NDAO, Abdoulaye S. Diallo, Ousmane Diop, Bacary Dembo DIATTA, Ousmane DIOUF, Abdoulaye Leye SARR, Ndèye Astou Dabo, Seynabou Selbé DIOUF, Aissatou Nogaye DIENG, Etienne Moussa SARR, Mame Matar Diop, Abdoulaye Souare, Ndèye Dieynaba Diouf, Nafissatou Leye, Astou GUEYE, Aminata DIA, Mame Sokhna GUEYE, Djibril WADE, Cyille Kouligueul Diedhiou, Ambroise Ahouidi, Papa Alassane Diaw, Badara Cisse, Moustapha MBOW, Boly DIOP, Raghavendra G. Amachawadi, Yacine A Dia, Souleymane Mboup
Language: English
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W4402895701