tetano
Editor, Senior Moderator
Kaohsiung J Med Sci
. 2023 Mar 23.
doi: 10.1002/kjm2.12665. Online ahead of print.
The identification and phylogenetic analysis of SARS-CoV-2 delta variants in Taiwan
Li-Teh Liu[SUP] 1 [/SUP], Jih-Jin Tsai[SUP] 2 3 4 [/SUP], Justin Jang Hann Chu[SUP] 5 6 7 8 [/SUP], Chun-Hong Chen[SUP] 9 10 [/SUP], Liang-Jen Chen[SUP] 11 [/SUP], Ping-Chang Lin[SUP] 2 [/SUP], Ching-Yi Tsai[SUP] 2 [/SUP], Miao-Chen Hsu[SUP] 2 [/SUP], Wan-Long Chuang[SUP] 3 12 [/SUP], Shang-Jyh Hwang[SUP] 3 13 [/SUP], Inn-Wen Chong[SUP] 14 15 [/SUP]
Affiliations
Abstract
In Taiwan, coronavirus disease 2019 (COVID-19) involving the delta variant occurred after that involving the alpha variant in 2021. In this study, we aimed to analyze the Delta variant. A total of 318 patients in Taiwan infected with delta variants were identified. The case fatality rate (CFR) of patients infected with delta variants was 0.94% in Taiwan compared with that of those infected with alpha variants (5.95%). The possible reasons for the low CFR might be hybrid immunity due to infection and rapid promotion of the COVID-19 vaccination program during the alpha variant outbreak. We identified three 21J delta variants. Two long gene deletions were detected in these severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) isolates: ORF7aΔ91 in KMUH-8 and SpikeΔ30 in KMUH-9. Protein structure prediction indicates that ORF7aΔ91 results in malfunction of NS7a as an interferon antagonist and that SpikeΔ30 results in a truncated spike protein (N679-A688del), resulting in a lower infection rate compared with the delta variant without these deletions. The impact of these two deletions on SARS-CoV-2-associated pathogenesis deserves further investigation. Delta variants still exist in many regions in the omicron era, and the backbone of the delta variant genome possibly spread worldwide in the form of delta-omicron hybrids (deltacron; e.g., XBC.1 and XAY.2), which casts a potential threat to public health. Our study further highlighted the importance of more understanding of the delta variants.
Keywords: COVID-19; SARS-CoV-2; delta variant; phylogenetic analysis; whole-genome sequencing.
. 2023 Mar 23.
doi: 10.1002/kjm2.12665. Online ahead of print.
The identification and phylogenetic analysis of SARS-CoV-2 delta variants in Taiwan
Li-Teh Liu[SUP] 1 [/SUP], Jih-Jin Tsai[SUP] 2 3 4 [/SUP], Justin Jang Hann Chu[SUP] 5 6 7 8 [/SUP], Chun-Hong Chen[SUP] 9 10 [/SUP], Liang-Jen Chen[SUP] 11 [/SUP], Ping-Chang Lin[SUP] 2 [/SUP], Ching-Yi Tsai[SUP] 2 [/SUP], Miao-Chen Hsu[SUP] 2 [/SUP], Wan-Long Chuang[SUP] 3 12 [/SUP], Shang-Jyh Hwang[SUP] 3 13 [/SUP], Inn-Wen Chong[SUP] 14 15 [/SUP]
Affiliations
- PMID: 36951529
- DOI: 10.1002/kjm2.12665
Abstract
In Taiwan, coronavirus disease 2019 (COVID-19) involving the delta variant occurred after that involving the alpha variant in 2021. In this study, we aimed to analyze the Delta variant. A total of 318 patients in Taiwan infected with delta variants were identified. The case fatality rate (CFR) of patients infected with delta variants was 0.94% in Taiwan compared with that of those infected with alpha variants (5.95%). The possible reasons for the low CFR might be hybrid immunity due to infection and rapid promotion of the COVID-19 vaccination program during the alpha variant outbreak. We identified three 21J delta variants. Two long gene deletions were detected in these severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) isolates: ORF7aΔ91 in KMUH-8 and SpikeΔ30 in KMUH-9. Protein structure prediction indicates that ORF7aΔ91 results in malfunction of NS7a as an interferon antagonist and that SpikeΔ30 results in a truncated spike protein (N679-A688del), resulting in a lower infection rate compared with the delta variant without these deletions. The impact of these two deletions on SARS-CoV-2-associated pathogenesis deserves further investigation. Delta variants still exist in many regions in the omicron era, and the backbone of the delta variant genome possibly spread worldwide in the form of delta-omicron hybrids (deltacron; e.g., XBC.1 and XAY.2), which casts a potential threat to public health. Our study further highlighted the importance of more understanding of the delta variants.
Keywords: COVID-19; SARS-CoV-2; delta variant; phylogenetic analysis; whole-genome sequencing.