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Kodsi IA, Rayes DE, Koweyes J, Khoury CA, Rahy K, Thoumi S, Chamoun M, Haddad H, Mokhbat J, Tokajian S. Tracking SARS-CoV-2 variants during the 2023 flu season and beyond in Lebanon. Virus Res 2024; 339:199289. [PMID: 38036064 PMCID: PMC10704499 DOI: 10.1016/j.virusres.2023.199289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/12/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Early SARS-CoV-2 variant detection relies on testing and genomic surveillance. The Omicron variant (B.1.1.529) has quickly become the dominant type among the previous circulating variants worldwide. Several subvariants have emerged exhibiting greater infectivity and immune evasion. In this study we aimed at studying the prevalence of the Omicron subvariants during the flu season and beyond in Lebanon through genomic screening and at determining the overall standing and trajectory of the pandemic in the country. METHODS A total of 155 SARS-CoV-2 RNA samples were sequenced, using Nanopore sequencing technology. RESULTS Nanopore sequencing of 155 genomes revealed their distribution over 39 Omicron variants. XBB.1.5 (23.29 %) was the most common, followed by XBB.1.9.1 (10.96 %) and XBB.1.42 (7.5 %). The first batch collected between September and November 2022, included the BA.2.75.2, BA.5.2, BA.5.2.20, BA.5.2.25 and BQ.1.1.5 lineages. Between December 2022 and January 2023, those lineages were replaced by BA.2.75.5, BN.1, BN.1.4, BQ.1, BQ.1.1, BQ.1.1.23, CH.1.1, CM.4 and XBK. Starting February 2023, we observed a gradual emergence and dominance of the recombinant XBB and its sub-lineages (XBB.1, XBB.1.5, XBB.1.5.2, XBB.1.5.3, XBB.1.9, XBB.1.9.1, XBB.1.9.2, XBB.1.16, XBB.1.22 and XBB.1.42). CONCLUSIONS The timely detection and characterization of SARS-CoV-2 variants is important to reduce transmission through established disease control measures and to avoid introductions into animal populations that could lead to serious public health implications.
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Affiliation(s)
- Ibrahim Al Kodsi
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Douaa El Rayes
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Charbel Al Khoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Kelven Rahy
- School of Medicine, Lebanese American University, Lebanon
| | - Sergio Thoumi
- Department of Computer Science and Mathematics, School of Arts and Sciences, Lebanese American University, Lebanon
| | | | - Hoda Haddad
- Clinical Microbiology laboratory, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Jacques Mokhbat
- Clinical Microbiology laboratory, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon.
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Liu LT, Chiou SS, Chen PC, Chen CH, Lin PC, Tsai CY, Chuang WL, Hwang SJ, Chong IW, Tsai JJ. Epidemiology and analysis of SARS-CoV-2 Omicron subvariants BA.1 and 2 in Taiwan. Sci Rep 2023; 13:16583. [PMID: 37789031 PMCID: PMC10547678 DOI: 10.1038/s41598-023-43357-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/22/2023] [Indexed: 10/05/2023] Open
Abstract
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first detected in October 2021, possessed many mutations compared to previous variants. We aimed to identify and analyze SARS-CoV-2 Omicron subvariants among coronavirus disease 2019 (COVID-19) patients between January 2022 and September 2022 in Taiwan. The results revealed that BA.2.3.7, featuring K97E and G1251V in the spike protein compared with BA.2, emerged in March 2022 and persistently dominated between April 2022 and August 2022, resulting in the largest COVID-19 outbreak since 2020. The accumulation of amino acid (AA) variations, mainly AA substitution, in the spike protein was accompanied by increasing severity in Omicron-related COVID-19 between April 2022 and January 2023. Older patients were more likely to have severe COVID-19, and comorbidity was a risk factor for COVID-19-related mortality. The accumulated case fatality rate (CFR) dropped drastically after Omicron variants, mainly BA.2.3.7, entered Taiwan after April 2022, and the CFR was 0.16% in Taiwan, which was lower than that worldwide (0.31%) between April 2021 and January 2023. The relatively low CFR in Omicron-related COVID-19 patients can be attributed to adjustments to public health policies, promotion of vaccination programs, effective antiviral drugs, and the lower severity of the Omicron variant.
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Affiliation(s)
- Li-Teh Liu
- Department of Medical Laboratory Science and Biotechnology, College of Medical Technology, Chung Hwa University of Medical Technology, Tainan City, Taiwan
| | - Shyh-Shin Chiou
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Po-Chih Chen
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung City, Taiwan
| | - Chun-Hong Chen
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Ping-Chang Lin
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Ching-Yi Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Wan-Long Chuang
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Shang-Jyh Hwang
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Inn-Wen Chong
- Department of Internal Medicine and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
- Department of Pulmonary Medicine, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan
| | - Jih-Jin Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan.
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan.
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, No. 100, Tzyou 1st Road, Kaohsiung City, 80756, Taiwan.
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