COVID-19 outbreak during investigation of acute respiratory syndrome among pilgrims in Senegal: An Integrated real time surveillance approach

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.