The emergence and successful elimination of SARS-CoV-2 dominant strains with increasing epidemic potential in Taiwan's 2021 outbreak

Chin-Rur Yang; Sui-Yuan Chang; Yu-Nong Gong; Chung-Guei Huang; Tsung-Hua Tung; Wei Liu; Ta-Chien Chan; Kuo-Sheng Hung; Hung-Sheng Shang; Jih-Jin Tsai; Chuan-Liang Kao; Hui-Lin Wu; Li-Yu Daisy Liu; Wan-Yu Lin; Yi-Chin Fan; Chwan-Chuen King; Chia-Chi Ku

doi:10.1016/j.heliyon.2023.e22436

The emergence and successful elimination of SARS-CoV-2 dominant strains with increasing epidemic potential in Taiwan's 2021 outbreak

Heliyon. 2023 Nov 20;9(12):e22436. doi: 10.1016/j.heliyon.2023.e22436. eCollection 2023 Dec.

Authors

Chin-Rur Yang¹, Sui-Yuan Chang^{2

3}, Yu-Nong Gong^{4

5}, Chung-Guei Huang^{5

6}, Tsung-Hua Tung^{7

8}, Wei Liu⁷, Ta-Chien Chan⁹, Kuo-Sheng Hung¹⁰, Hung-Sheng Shang¹¹, Jih-Jin Tsai^{12

13

14}, Chuan-Liang Kao^{2

7}, Hui-Lin Wu^{15

16}, Li-Yu Daisy Liu¹⁷, Wan-Yu Lin⁷, Yi-Chin Fan⁷, Chwan-Chuen King⁷, Chia-Chi Ku¹

Affiliations

¹ Graduate Institute of Immunology, College of Medicine, National Taiwan University, 1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan, ROC.
² Department (Dept.) of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan, ROC.
³ Dept. of Laboratory Medicine, National Taiwan University Hospital, Taipei, 10051, Taiwan, ROC.
⁴ Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, 33302, Taiwan, ROC.
⁵ Dept. of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 33302, Taiwan, ROC.
⁶ Dept. of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, 33302, Taiwan, ROC.
⁷ Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC.
⁸ Dept. of Health, Taipei City Government, Taipei, Taiwan, ROC.
⁹ Research Center for Humanities and Social Sciences, Academia Sinica, Taipei, 11529, Taiwan, ROC.
¹⁰ Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan, ROC.
¹¹ Division of Clinical Pathology, Dept. of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan, ROC.
¹² School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC.
¹³ Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, 80756, Taiwan, ROC.
¹⁴ Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, 80756, Taiwan, ROC.
¹⁵ Hepatitis Research Center, National Taiwan University Hospital, Taipei, 10051, Taiwan, ROC.
¹⁶ Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan, ROC.
¹⁷ Division of Biometry, Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan, ROC.

Abstract

Taiwan's experience with severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003 guided its development of strategies to defend against SARS-CoV-2 in 2020, which enabled the successful control of Coronavirus disease 2019 (COVID-19) cases from 2020 through March 2021. However, in late-April 2021, the imported Alpha variant began to cause COVID-19 outbreaks at an exceptional rate in Taiwan. In this study, we aimed to determine what epidemiological conditions enabled the SARS-CoV-2 Alpha variant strains to become dominant and decline later during a surge in the outbreak. In conjunction with contact-tracing investigations, we used our bioinformatics software, CoVConvert and IniCoV, to analyze whole-genome sequences of 101 Taiwan Alpha strains. Univariate and multivariable regression analyses revealed the epidemiological factors associated with viral dominance. Univariate analysis showed the dominant Alpha strains were preferentially selected in the surge's epicenter (p = 0.0024) through intensive human-to-human contact and maintained their dominance for 1.5 months until the Zero-COVID Policy was implemented. Multivariable regression found that the epidemic periods (p = 0.007) and epicenter (p = 0.001) were two significant factors associated with the dominant virus strains spread in the community. These dominant virus strains emerged at the outbreak's epicenter with frequent human-to-human contact and low vaccination coverage. The Level 3 Restrictions and Zero-COVID policy successfully controlled the outbreak in the community without city lockdowns. Our integrated method can identify the epidemiological conditions for emerging dominant virus with increasing epidemiological potential and support decision makers in rapidly containing outbreaks using public health measures that target fast-spreading virus strains.

Keywords: Bioinformatics; Community outbreak; Epicenter; Reproduction number; SARS-CoV-2; Spatio-temporal analysis; Taiwan; Transmission; Viral variants; Whole-genome sequencing.