The epidemiology and phylogenetic trends of Omicron subvariants from BA.5 to XBB.1 in Taiwan
Background: Omicron, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, entered Taiwan at the end of 2021. The Taiwanese government ended its ''zero-COVID'' policy in March 2022. Multiple coronavirus disease 2019 (COVID-19) outbreaks began in April 2022. We m...
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Elsevier
2024-11-01
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| Series: | Journal of Infection and Public Health |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1876034124002909 |
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| author | Jih-Jin Tsai Shyh-Shin Chiou Po-Chih Chen Chun-Hong Chen Ping-Chang Lin Ching-Yi Tsai Wan-Long Chuang Shang-Jyh Hwang Inn-Wen Chong Li-Teh Liu |
| author_facet | Jih-Jin Tsai Shyh-Shin Chiou Po-Chih Chen Chun-Hong Chen Ping-Chang Lin Ching-Yi Tsai Wan-Long Chuang Shang-Jyh Hwang Inn-Wen Chong Li-Teh Liu |
| author_sort | Jih-Jin Tsai |
| collection | DOAJ |
| description | Background: Omicron, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, entered Taiwan at the end of 2021. The Taiwanese government ended its ''zero-COVID'' policy in March 2022. Multiple coronavirus disease 2019 (COVID-19) outbreaks began in April 2022. We monitored the replacement of Omicron subvariants after BA.1/BA.2 and analyzed their correlation with COVID-19 outbreaks. Methods: We collected SARS-CoV-2 real-time qRTPCR-positive nasopharyngeal swabs from Kaohsiung Medical University Hospital (KMUH), Kaohsiung City, Taiwan, and performed sequencing for specimens exhibiting a cytopathic effect in Vero E6 cells to determine their clades and lineages. We analyzed the medical records of COVID-19 patients and identified hospitalization risk factor(s). We retrieved SARS-CoV-2 sequences identified in Taiwan from GISAID and analyzed their correlation with COVID-19 data from the Taiwan Centers for Disease Control. Results: We analyzed the phylogenesis of KMUH-47 to KMUH-104 (SARS-CoV-2 isolates identified herein) and all of the Omicron subvariants from BA.5 to XBB.1 (n = 1930). Age and comorbidities were hospitalization risk factors. Men generally exhibited a greater fatality rate than women. COVID-19-related deaths predominantly occurred in individuals over 70 years old. The COVID-19-related case fatality rate increased as nucleotide (NT) and amino acid (AA) substitutions increased. The number of COVID-19-related cases and deaths progressively decreased with each outbreak between August 2022 and October 2023. Conclusion: Hospitalization was associated with age and the presence of comorbidities. COVID-19-related fatality was linked to sex, age, and the accumulation of NT and AA substitutions in emerging Omicron subvariants. |
| format | Article |
| id | doaj-art-bef98a2f87504ff4bf911e1599392fa5 |
| institution | OA Journals |
| issn | 1876-0341 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Infection and Public Health |
| spelling | doaj-art-bef98a2f87504ff4bf911e1599392fa52025-08-20T02:11:37ZengElsevierJournal of Infection and Public Health1876-03412024-11-01171110255610.1016/j.jiph.2024.102556The epidemiology and phylogenetic trends of Omicron subvariants from BA.5 to XBB.1 in TaiwanJih-Jin Tsai0Shyh-Shin Chiou1Po-Chih Chen2Chun-Hong Chen3Ping-Chang Lin4Ching-Yi Tsai5Wan-Long Chuang6Shang-Jyh Hwang7Inn-Wen Chong8Li-Teh Liu9Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, TaiwanGraduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Pediatric Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, TaiwanDepartment of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, TaiwanNational 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, TaiwanTropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, TaiwanTropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, TaiwanSchool of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, TaiwanSchool of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, TaiwanDepartment of Internal Medicine and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Pulmonary Medicine, Kaohsiung Medical University Hospital, Kaohsiung, TaiwanDepartment of Medical Laboratory Science and Biotechnology, College of Medical Technology, Chung Hwa University of Medical Technology, Tainan, Taiwan; Correspondence to: Department of Medical Laboratory Science and Biotechnology, College of Medical Technology, Chung Hwa University of Medical Technology, No. 89, Wenhua 1st St., Rende Dist., Tainan 717302, Taiwan.Background: Omicron, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, entered Taiwan at the end of 2021. The Taiwanese government ended its ''zero-COVID'' policy in March 2022. Multiple coronavirus disease 2019 (COVID-19) outbreaks began in April 2022. We monitored the replacement of Omicron subvariants after BA.1/BA.2 and analyzed their correlation with COVID-19 outbreaks. Methods: We collected SARS-CoV-2 real-time qRTPCR-positive nasopharyngeal swabs from Kaohsiung Medical University Hospital (KMUH), Kaohsiung City, Taiwan, and performed sequencing for specimens exhibiting a cytopathic effect in Vero E6 cells to determine their clades and lineages. We analyzed the medical records of COVID-19 patients and identified hospitalization risk factor(s). We retrieved SARS-CoV-2 sequences identified in Taiwan from GISAID and analyzed their correlation with COVID-19 data from the Taiwan Centers for Disease Control. Results: We analyzed the phylogenesis of KMUH-47 to KMUH-104 (SARS-CoV-2 isolates identified herein) and all of the Omicron subvariants from BA.5 to XBB.1 (n = 1930). Age and comorbidities were hospitalization risk factors. Men generally exhibited a greater fatality rate than women. COVID-19-related deaths predominantly occurred in individuals over 70 years old. The COVID-19-related case fatality rate increased as nucleotide (NT) and amino acid (AA) substitutions increased. The number of COVID-19-related cases and deaths progressively decreased with each outbreak between August 2022 and October 2023. Conclusion: Hospitalization was associated with age and the presence of comorbidities. COVID-19-related fatality was linked to sex, age, and the accumulation of NT and AA substitutions in emerging Omicron subvariants.http://www.sciencedirect.com/science/article/pii/S1876034124002909COVID-19Omicron subvariantAgeSexFatalityVaccination |
| spellingShingle | Jih-Jin Tsai Shyh-Shin Chiou Po-Chih Chen Chun-Hong Chen Ping-Chang Lin Ching-Yi Tsai Wan-Long Chuang Shang-Jyh Hwang Inn-Wen Chong Li-Teh Liu The epidemiology and phylogenetic trends of Omicron subvariants from BA.5 to XBB.1 in Taiwan Journal of Infection and Public Health COVID-19 Omicron subvariant Age Sex Fatality Vaccination |
| title | The epidemiology and phylogenetic trends of Omicron subvariants from BA.5 to XBB.1 in Taiwan |
| title_full | The epidemiology and phylogenetic trends of Omicron subvariants from BA.5 to XBB.1 in Taiwan |
| title_fullStr | The epidemiology and phylogenetic trends of Omicron subvariants from BA.5 to XBB.1 in Taiwan |
| title_full_unstemmed | The epidemiology and phylogenetic trends of Omicron subvariants from BA.5 to XBB.1 in Taiwan |
| title_short | The epidemiology and phylogenetic trends of Omicron subvariants from BA.5 to XBB.1 in Taiwan |
| title_sort | epidemiology and phylogenetic trends of omicron subvariants from ba 5 to xbb 1 in taiwan |
| topic | COVID-19 Omicron subvariant Age Sex Fatality Vaccination |
| url | http://www.sciencedirect.com/science/article/pii/S1876034124002909 |
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