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AlKalamouni H, Abou Hassan FF, Bou Hamdan M, Page AJ, Lott M, Matthews M, Ghosn N, Rady A, Mahfouz R, Araj GF, Dbaibo G, Zaraket H, Melhem NM, Matar GM. Genomic surveillance of SARS-CoV-2 in COVID-19 vaccinated healthcare workers in Lebanon. BMC Med Genomics 2023; 16:14. [PMID: 36707851 PMCID: PMC9880935 DOI: 10.1186/s12920-023-01443-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The emergence of SARS-CoV-2 variants including the Delta and Omicron along with waning of vaccine-induced immunity over time contributed to increased rates of breakthrough infection specifically among healthcare workers (HCWs). SARS-CoV-2 genomic surveillance is an important tool for timely detection and characterization of circulating variants as well as monitoring the emergence of new strains. Our study is the first national SARS-CoV-2 genomic surveillance among HCWs in Lebanon. METHODS We collected 250 nasopharyngeal swabs from HCWs across Lebanon between December 2021 and January 2022. Data on the date of positive PCR, vaccination status, specific occupation, and hospitalization status of participants were collected. Extracted viral RNA from nasopharyngeal swabs was converted to cDNA, library prepped using the coronaHIT method, followed by whole genome sequencing on the Illumina NextSeq 500 platform. RESULTS A total of 133 (57.1%) samples belonging to the Omicron (BA.1.1) sub-lineage were identified, as well as 44 (18.9%) samples belonging to the BA.1 sub-lineage, 28 (12%) belonging to the BA.2 sub-lineage, and only 15 (6.6%) samples belonging to the Delta variant sub-lineage B.1.617.2. These results show that Lebanon followed the global trend in terms of circulating SARS-CoV-2 variants with Delta rapidly replaced by the Omicron variant. CONCLUSION This study underscores the importance of continuous genomic surveillance programs in Lebanon for the timely detection and characterization of circulating variants. The latter is critical to guide public health policy making and to timely implement public health interventions.
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Affiliation(s)
- Habib AlKalamouni
- grid.22903.3a0000 0004 1936 9801Department of Experimental Pathology, Immunology, and Microbiology, Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, 1107 2020 Lebanon ,grid.22903.3a0000 0004 1936 9801Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Farouk F. Abou Hassan
- grid.22903.3a0000 0004 1936 9801Medical Laboratory Sciences Program, Division of Health Professions, Faculty of Health Sciences, American University of Beirut, Beirut, 1107 2020 Lebanon
| | - Mirna Bou Hamdan
- grid.22903.3a0000 0004 1936 9801Medical Laboratory Sciences Program, Division of Health Professions, Faculty of Health Sciences, American University of Beirut, Beirut, 1107 2020 Lebanon
| | - Andrew J. Page
- grid.420132.6Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Martin Lott
- grid.420132.6Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Michaela Matthews
- grid.420132.6Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Nada Ghosn
- grid.490673.f0000 0004 6020 2237Epidemiological Surveillance Unit, Ministry of Public Health, Beirut, Lebanon
| | | | - Rami Mahfouz
- grid.22903.3a0000 0004 1936 9801Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon ,grid.22903.3a0000 0004 1936 9801Department of Pathology and Laboratory Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - George F. Araj
- grid.22903.3a0000 0004 1936 9801Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon ,grid.22903.3a0000 0004 1936 9801Department of Pathology and Laboratory Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ghassan Dbaibo
- grid.22903.3a0000 0004 1936 9801Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon ,grid.22903.3a0000 0004 1936 9801Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hassan Zaraket
- grid.22903.3a0000 0004 1936 9801Department of Experimental Pathology, Immunology, and Microbiology, Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, 1107 2020 Lebanon ,grid.22903.3a0000 0004 1936 9801Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Nada M. Melhem
- grid.22903.3a0000 0004 1936 9801Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon ,grid.22903.3a0000 0004 1936 9801Medical Laboratory Sciences Program, Division of Health Professions, Faculty of Health Sciences, American University of Beirut, Beirut, 1107 2020 Lebanon
| | - Ghassan M. Matar
- grid.22903.3a0000 0004 1936 9801Department of Experimental Pathology, Immunology, and Microbiology, Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, 1107 2020 Lebanon ,grid.22903.3a0000 0004 1936 9801Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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