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Background: The implementation genomic-based surveillance on emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in low-income countries, which have inadequate molecular and sequencing capabilities and limited vaccine storage, represents a challenge for public health. To date, there is little evidence on molecular investigations of SARS-CoV-2 variants in areas where they might emerge. We report the findings of an experimental SARS-CoV-2 molecular surveillance programme for migrants, refugees, and asylum seekers arriving to Europe via Italy through the Mediterranean Sea., Methods: We descriptively analysed data on migrants collected at entry points in Sicily from February 2021 to May 2022. These entry points are integrated with a network of laboratories fully equipped for molecular analyses, which performed next-generation sequencing and used Nextclade and the Pangolin coronavirus disease 2019 (COVID-19) tools for clade/lineage assignment., Results: We obtained 472 full-length SARS-CoV-2 sequences and identified 12 unique clades belonging to 31 different lineages. The delta variant accounted for 43.6% of all genomes, followed by clades 21D (Eta) and 20A (25.4% and 11.4%, respectively). Notably, some of the identified lineages (A.23.1, A.27, and A.29) predicted their introduction into the migration area. The mutation analysis allowed us to identify 617 different amino acid substitutions, 156 amino acid deletions, 7 stop codons, and 6 amino acid insertions. Lastly, we highlighted the geographical distribution patterns of some mutational profiles occurring in the migrants' countries of origin., Conclusions: Genome-based molecular surveillance dedicated to migrant populations from low-resource areas may be useful for forecasting new epidemiological scenarios related to SARS-CoV-2 variants or other emerging pathogens, as well as for informing the updating of vaccination strategies., Competing Interests: Disclosure of interest: The authors completed the ICMJE Disclosure of Interest Form (available upon request from the corresponding author) and disclose no relevant interests., (Copyright © 2024 by the Journal of Global Health. All rights reserved.)

Refugees and migrants remain one of the most vulnerable people and the COVID-19 pandemic has posed additional challenges both in terms of increased risk of infection and death experienced, highlighting existing inequities in access to and utilization of health services, as underlined by World Health Organization in 2020 in the Health and Migration Programme. In the context of the Programme 'Epidemiological surveillance and control of COVID-19 in metropolitan urban areas and for the containment of the circulation of SARS-CoV-2 in the migrant population in Italy', coordinated by the Italian Centre for Disease Control and Prevention (CCM) and funded by the Italian Ministry of Health, an experimental epidemiological, virological, and molecular SARS-CoV-2 surveillance system addressed to migrant populations in Sicily through Mediterranean routes was implemented. To this end, a multidisciplinary network supported by a hub&spoke system of laboratories was established in Sicily Region (Southern Italy), using molecular and Next Generation Sequencing (NGS) techniques to identify different SARS-CoV-2 strains in relation to migration flows. Herein, the lesson learnt through this integrated surveillance model, that was in place from February 2021 till the end of the COVID-19 emergency in Italy, are reported. Overall, the data emphasized the need for enhancing molecular surveillance in the areas of the globe where testing and sequencing resources are limited. The epidemiological, virological, and molecular SARS-CoV-2 monitoring, targeted to the migrant population, may also provide a valuable experimental model.