Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong

• Published in: Nature communications Vol. 13; no. 1; pp. 736 - 10
• Main Authors: Gu, Haogao, Xie, Ruopeng, Adam, Dillon C., Tsui, Joseph L.-H., Chu, Daniel K., Chang, Lydia D. J., Cheuk, Sammi S. Y., Gurung, Shreya, Krishnan, Pavithra, Ng, Daisy Y. M., Liu, Gigi Y. Z., Wan, Carrie K. C., Cheng, Samuel S. M., Edwards, Kimberly M., Leung, Kathy S. M., Wu, Joseph T., Tsang, Dominic N. C., Leung, Gabriel M., Cowling, Benjamin J., Peiris, Malik, Lam, Tommy T. Y., Dhanasekaran, Vijaykrishna, Poon, Leo L. M.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 08.02.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 45/23; 45/77; 45/90; 631/181/757; 631/326/596/2562; 631/326/596/2563; 631/326/596/4130; 692/700/478/174; Border stations; COVID-19; COVID-19 - epidemiology; COVID-19 - transmission; COVID-19 - virology; Epidemiology; Gene sequencing; Genomics; Hong Kong - epidemiology; Humanities and Social Sciences; Humans; multidisciplinary; Nucleotides; Outbreaks; Public Health; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; SARS-CoV-2 - physiology; Science; Science (multidisciplinary); Severe acute respiratory syndrome coronavirus 2; Travel; Hong Kong; Hong Kong China; China
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-28420-7

Hong Kong employed a strategy of intermittent public health and social measures alongside increasingly stringent travel regulations to eliminate domestic SARS-CoV-2 transmission. By analyzing 1899 genome sequences (>18% of confirmed cases) from 23-January-2020 to 26-January-2021, we reveal the effects of fluctuating control measures on the evolution and epidemiology of SARS-CoV-2 lineages in Hong Kong. Despite numerous importations, only three introductions were responsible for 90% of locally-acquired cases. Community outbreaks were caused by novel introductions rather than a resurgence of circulating strains. Thus, local outbreak prevention requires strong border control and community surveillance, especially during periods of less stringent social restriction. Non-adherence to prolonged preventative measures may explain sustained local transmission observed during wave four in late 2020 and early 2021. We also found that, due to a tight transmission bottleneck, transmission of low-frequency single nucleotide variants between hosts is rare. Hong Kong has used an elimination strategy to control SARS-CoV-2 with stringent measures including traveller quarantine. Here, the authors show that the majority of community-acquired cases until January 2021 resulted from three importations, and that increased transmission followed prolonged periods of restrictions, likely due to adherence fatigue.