tetano
Editor, Senior Moderator
J Infect Public Health
. 2024 Sep 29;17(11):102556.
doi: 10.1016/j.jiph.2024.102556. Online ahead of print. The epidemiology and phylogenetic trends of Omicron subvariants from BA.5 to XBB.1 in Taiwan
Jih-Jin Tsai[SUP] 1 [/SUP], Shyh-Shin Chiou[SUP] 2 [/SUP], Po-Chih Chen[SUP] 3 [/SUP], Chun-Hong Chen[SUP] 4 [/SUP], Ping-Chang Lin[SUP] 5 [/SUP], Ching-Yi Tsai[SUP] 5 [/SUP], Wan-Long Chuang[SUP] 6 [/SUP], Shang-Jyh Hwang[SUP] 7 [/SUP], Inn-Wen Chong[SUP] 8 [/SUP], Li-Teh Liu[SUP] 9 [/SUP]
Affiliations
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.
Keywords: Age; COVID-19; Fatality; Omicron subvariant; Sex; Vaccination.
. 2024 Sep 29;17(11):102556.
doi: 10.1016/j.jiph.2024.102556. Online ahead of print. The epidemiology and phylogenetic trends of Omicron subvariants from BA.5 to XBB.1 in Taiwan
Jih-Jin Tsai[SUP] 1 [/SUP], Shyh-Shin Chiou[SUP] 2 [/SUP], Po-Chih Chen[SUP] 3 [/SUP], Chun-Hong Chen[SUP] 4 [/SUP], Ping-Chang Lin[SUP] 5 [/SUP], Ching-Yi Tsai[SUP] 5 [/SUP], Wan-Long Chuang[SUP] 6 [/SUP], Shang-Jyh Hwang[SUP] 7 [/SUP], Inn-Wen Chong[SUP] 8 [/SUP], Li-Teh Liu[SUP] 9 [/SUP]
Affiliations
- PMID: 39388868
- DOI: 10.1016/j.jiph.2024.102556
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.
Keywords: Age; COVID-19; Fatality; Omicron subvariant; Sex; Vaccination.