Tracking the shifting landscape of SARS-CoV-2 variants in Lebanon among healthcare workers and hospitalized patients
Habib Alkalamouni, Mirna Bou Hamdan, Farouk Abou Hassan, Fatima Dakroub, Lama Hamadeh, Alissar Rady, Moubadda Assi, Nada Ghosn, Rami Mahfouz, Carine Sakr, Nada Kara Zahreddine, Hassan Zaraket, Ghassan Dbaibo, Nada M. Melhem, Ghassan M. MatarABSTRACT
Genomic surveillance of SARS-CoV-2 is critical for tracking viral evolution and informing public health responses. This study characterized variants circulating among healthcare workers (HCWs) and hospitalized patients in Lebanon between January 2022 and September 2024. A total of 530 SARS-CoV-2-positive nasopharyngeal swabs were collected from five Lebanese governorates and subjected to whole-genome sequencing. Correlations between variant circulation and a number of demographic and clinical variables were assessed. Most HCWs were female (64%), young adults (20–30 years, 39%), and had no comorbidities (97%). In contrast, hospitalized patients were mostly older adults (>60 years, 55.6%) with underlying conditions (77%). Early 2022 was marked by BA.1- and BA.2-like Omicron variants, followed by the predominance of BA.5-like lineages. In 2023, recombinant XBB sublineages became widespread. By 2024, these were largely replaced by next-generation variants, including JN.1 and KP.3.1.1. Despite differences in demographics and exposure risk, both groups showed parallel variant evolution. These findings reflect global and regional patterns and highlight the dynamic nature of SARS-CoV-2 circulation in Lebanon.
IMPORTANCE
This study provides a comprehensive snapshot of SARS-CoV-2 variant evolution in Lebanon between 2022 and 2024, focusing on healthcare workers and hospitalized patients. By combining genomic and clinical data, it reveals how successive Omicron subvariants emerged and spread within key population groups. The detection of diverse and evolving lineages, including XBB recombinants and next-generation variants such as JN.1, underscores the ongoing antigenic drift of SARS-CoV-2. These insights reinforce the value of continued genomic surveillance for pandemic preparedness, especially in regions where data remain limited. Understanding local variant dynamics can guide targeted vaccination strategies and health policy decisions.