IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-28420-7.html
   My bibliography  Save this article

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

Author

Listed:
  • Haogao Gu

    (The University of Hong Kong)

  • Ruopeng Xie

    (The University of Hong Kong
    The University of Hong Kong)

  • Dillon C. Adam

    (The University of Hong Kong)

  • Joseph L.-H. Tsui

    (The University of Hong Kong)

  • Daniel K. Chu

    (The University of Hong Kong)

  • Lydia D. J. Chang

    (The University of Hong Kong)

  • Sammi S. Y. Cheuk

    (The University of Hong Kong)

  • Shreya Gurung

    (The University of Hong Kong)

  • Pavithra Krishnan

    (The University of Hong Kong)

  • Daisy Y. M. Ng

    (The University of Hong Kong)

  • Gigi Y. Z. Liu

    (The University of Hong Kong)

  • Carrie K. C. Wan

    (The University of Hong Kong)

  • Samuel S. M. Cheng

    (The University of Hong Kong)

  • Kimberly M. Edwards

    (The University of Hong Kong
    The University of Hong Kong)

  • Kathy S. M. Leung

    (The University of Hong Kong
    Hong Kong Science and Technology Park)

  • Joseph T. Wu

    (The University of Hong Kong
    Hong Kong Science and Technology Park)

  • Dominic N. C. Tsang

    (The Government of Hong Kong Special Administrative Region)

  • Gabriel M. Leung

    (The University of Hong Kong
    Hong Kong Science and Technology Park)

  • Benjamin J. Cowling

    (The University of Hong Kong
    Hong Kong Science and Technology Park)

  • Malik Peiris

    (The University of Hong Kong
    The University of Hong Kong
    Hong Kong Science and Technology Park)

  • Tommy T. Y. Lam

    (The University of Hong Kong
    Hong Kong Science and Technology Park
    Hong Kong Science and Technology Park)

  • Vijaykrishna Dhanasekaran

    (The University of Hong Kong
    The University of Hong Kong)

  • Leo L. M. Poon

    (The University of Hong Kong
    The University of Hong Kong
    Hong Kong Science and Technology Park)

Abstract

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.

Suggested Citation

  • Haogao Gu & Ruopeng Xie & Dillon C. Adam & Joseph L.-H. Tsui & Daniel K. Chu & Lydia D. J. Chang & Sammi S. Y. Cheuk & Shreya Gurung & Pavithra Krishnan & Daisy Y. M. Ng & Gigi Y. Z. Liu & Carrie K. C, 2022. "Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28420-7
    DOI: 10.1038/s41467-022-28420-7
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-28420-7
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-28420-7?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Thomas Hale & Noam Angrist & Rafael Goldszmidt & Beatriz Kira & Anna Petherick & Toby Phillips & Samuel Webster & Emily Cameron-Blake & Laura Hallas & Saptarshi Majumdar & Helen Tatlow, 2021. "A global panel database of pandemic policies (Oxford COVID-19 Government Response Tracker)," Nature Human Behaviour, Nature, vol. 5(4), pages 529-538, April.
    2. Katelyn M Gostic & Lauren McGough & Edward B Baskerville & Sam Abbott & Keya Joshi & Christine Tedijanto & Rebecca Kahn & Rene Niehus & James A Hay & Pablo M De Salazar & Joel Hellewell & Sophie Meaki, 2020. "Practical considerations for measuring the effective reproductive number, Rt," PLOS Computational Biology, Public Library of Science, vol. 16(12), pages 1-21, December.
    3. Claudia Alteri & Valeria Cento & Antonio Piralla & Valentino Costabile & Monica Tallarita & Luna Colagrossi & Silvia Renica & Federica Giardina & Federica Novazzi & Stefano Gaiarsa & Elisa Matarazzo &, 2021. "Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    4. Alexei J Drummond & Simon Y W Ho & Matthew J Phillips & Andrew Rambaut, 2006. "Relaxed Phylogenetics and Dating with Confidence," PLOS Biology, Public Library of Science, vol. 4(5), pages 1-1, March.
    5. Fan Wu & Su Zhao & Bin Yu & Yan-Mei Chen & Wen Wang & Zhi-Gang Song & Yi Hu & Zhao-Wu Tao & Jun-Hua Tian & Yuan-Yuan Pei & Ming-Li Yuan & Yu-Ling Zhang & Fa-Hui Dai & Yi Liu & Qi-Min Wang & Jiao-Jiao , 2020. "A new coronavirus associated with human respiratory disease in China," Nature, Nature, vol. 579(7798), pages 265-269, March.
    6. Jemma L. Geoghegan & Xiaoyun Ren & Matthew Storey & James Hadfield & Lauren Jelley & Sarah Jefferies & Jill Sherwood & Shevaun Paine & Sue Huang & Jordan Douglas & Fábio K. Mendes & Andrew Sporle & Mi, 2020. "Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand," Nature Communications, Nature, vol. 11(1), pages 1-7, December.
    7. Fan Wu & Su Zhao & Bin Yu & Yan-Mei Chen & Wen Wang & Zhi-Gang Song & Yi Hu & Zhao-Wu Tao & Jun-Hua Tian & Yuan-Yuan Pei & Ming-Li Yuan & Yu-Ling Zhang & Fa-Hui Dai & Yi Liu & Qi-Min Wang & Jiao-Jiao , 2020. "Author Correction: A new coronavirus associated with human respiratory disease in China," Nature, Nature, vol. 580(7803), pages 7-7, April.
    8. Emma B. Hodcroft & Moira Zuber & Sarah Nadeau & Timothy G. Vaughan & Katharine H. D. Crawford & Christian L. Althaus & Martina L. Reichmuth & John E. Bowen & Alexandra C. Walls & Davide Corti & Jesse , 2021. "Spread of a SARS-CoV-2 variant through Europe in the summer of 2020," Nature, Nature, vol. 595(7869), pages 707-712, July.
    9. Andrey B. Komissarov & Ksenia R. Safina & Sofya K. Garushyants & Artem V. Fadeev & Mariia V. Sergeeva & Anna A. Ivanova & Daria M. Danilenko & Dmitry Lioznov & Olga V. Shneider & Nikita Shvyrev & Vadi, 2021. "Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    10. Steven A. Kemp & Dami A. Collier & Rawlings P. Datir & Isabella A. T. M. Ferreira & Salma Gayed & Aminu Jahun & Myra Hosmillo & Chloe Rees-Spear & Petra Mlcochova & Ines Ushiro Lumb & David J. Roberts, 2021. "SARS-CoV-2 evolution during treatment of chronic infection," Nature, Nature, vol. 592(7853), pages 277-282, April.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Haogao Gu & Ahmed Abdul Quadeer & Pavithra Krishnan & Daisy Y. M. Ng & Lydia D. J. Chang & Gigi Y. Z. Liu & Samuel M. S. Cheng & Tommy T. Y. Lam & Malik Peiris & Matthew R. McKay & Leo L. M. Poon, 2023. "Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Ruopeng Xie & Kimberly M. Edwards & Dillon C. Adam & Kathy S. M. Leung & Tim K. Tsang & Shreya Gurung & Weijia Xiong & Xiaoman Wei & Daisy Y. M. Ng & Gigi Y. Z. Liu & Pavithra Krishnan & Lydia D. J. C, 2023. "Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Prakash Kumar Paudel & Rabin Bastola & Sanford D. Eigenbrode & Amaël Borzée & Santosh Thapa & Dana Rad & Jayaraj Vijaya Kumaran & Suganthi Appalasamy & Mohammad Mosharraf Hossain & Anirban Ash & Raju , 2022. "Perspectives of scholars on the origin, spread and consequences of COVID-19 are diverse but not polarized," Palgrave Communications, Palgrave Macmillan, vol. 9(1), pages 1-11, December.
    2. Giulia Orilisi & Marco Mascitti & Lucrezia Togni & Riccardo Monterubbianesi & Vincenzo Tosco & Flavia Vitiello & Andrea Santarelli & Angelo Putignano & Giovanna Orsini, 2021. "Oral Manifestations of COVID-19 in Hospitalized Patients: A Systematic Review," IJERPH, MDPI, vol. 18(23), pages 1-19, November.
    3. David Gomez-Zepeda & Danielle Arnold-Schild & Julian Beyrle & Arthur Declercq & Ralf Gabriels & Elena Kumm & Annica Preikschat & Mateusz Krzysztof Łącki & Aurélie Hirschler & Jeewan Babu Rijal & Chris, 2024. "Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    4. Alessandro Germani & Livia Buratta & Elisa Delvecchio & Claudia Mazzeschi, 2020. "Emerging Adults and COVID-19: The Role of Individualism-Collectivism on Perceived Risks and Psychological Maladjustment," IJERPH, MDPI, vol. 17(10), pages 1-15, May.
    5. Gabriela Dias Noske & Yun Song & Rafaela Sachetto Fernandes & Rod Chalk & Haitem Elmassoudi & Lizbé Koekemoer & C. David Owen & Tarick J. El-Baba & Carol V. Robinson & Glaucius Oliva & Andre Schutzer , 2023. "An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    6. Eugene Song & Jae-Eun Lee & Seola Kwon, 2021. "Effect of Public Empathy with Infection-Control Guidelines on Infection-Prevention Attitudes and Behaviors: Based on the Case of COVID-19," IJERPH, MDPI, vol. 18(24), pages 1-18, December.
    7. Kow-Tong Chen, 2022. "Emerging Infectious Diseases and One Health: Implication for Public Health," IJERPH, MDPI, vol. 19(15), pages 1-4, July.
    8. Shujuan Li & Lingli Zhu & Lidan Zhang & Guoyan Zhang & Hongyan Ren & Liang Lu, 2023. "Urbanization-Related Environmental Factors and Hemorrhagic Fever with Renal Syndrome: A Review Based on Studies Taken in China," IJERPH, MDPI, vol. 20(4), pages 1-20, February.
    9. Umit Cirakli & Ibrahim Dogan & Mehmet Gozlu, 2022. "The Relationship Between COVID-19 Cases and COVID-19 Testing: a Panel Data Analysis on OECD Countries," Journal of the Knowledge Economy, Springer;Portland International Center for Management of Engineering and Technology (PICMET), vol. 13(3), pages 1737-1750, September.
    10. Neeltje van Doremalen & Jonathan E. Schulz & Danielle R. Adney & Taylor A. Saturday & Robert J. Fischer & Claude Kwe Yinda & Nazia Thakur & Joseph Newman & Marta Ulaszewska & Sandra Belij-Rammerstorfe, 2022. "ChAdOx1 nCoV-19 (AZD1222) or nCoV-19-Beta (AZD2816) protect Syrian hamsters against Beta Delta and Omicron variants," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    11. Jaeyong Lee & Calem Kenward & Liam J. Worrall & Marija Vuckovic & Francesco Gentile & Anh-Tien Ton & Myles Ng & Artem Cherkasov & Natalie C. J. Strynadka & Mark Paetzel, 2022. "X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    12. Seán R. O’Connor & Charlene Treanor & Elizabeth Ward & Robin A. Wickens & Abby O’Connell & Lucy A. Culliford & Chris A. Rogers & Eleanor A. Gidman & Tunde Peto & Paul C. Knox & Benjamin J. L. Burton &, 2022. "The COVID-19 Pandemic and Ophthalmic Care: A Qualitative Study of Patients with Neovascular Age-Related Macular Degeneration (nAMD)," IJERPH, MDPI, vol. 19(15), pages 1-10, August.
    13. Maria de Lourdes Aguiar-Oliveira & Aline Campos & Aline R. Matos & Caroline Rigotto & Adriana Sotero-Martins & Paulo F. P. Teixeira & Marilda M. Siqueira, 2020. "Wastewater-Based Epidemiology (WBE) and Viral Detection in Polluted Surface Water: A Valuable Tool for COVID-19 Surveillance—A Brief Review," IJERPH, MDPI, vol. 17(24), pages 1-19, December.
    14. Wasim Ahmed & Josep Vidal-Alaball & Francesc Lopez Segui & Pedro A. Moreno-Sánchez, 2020. "A Social Network Analysis of Tweets Related to Masks during the COVID-19 Pandemic," IJERPH, MDPI, vol. 17(21), pages 1-9, November.
    15. Ben Zhang & Chenxu Ming, 2023. "Digital Transformation and Open Innovation Planning of Response to COVID-19 Outbreak: A Systematic Literature Review and Future Research Agenda," IJERPH, MDPI, vol. 20(3), pages 1-26, February.
    16. Yongin Choi & James Slghee Kim & Heejin Choi & Hyojung Lee & Chang Hyeong Lee, 2020. "Assessment of Social Distancing for Controlling COVID-19 in Korea: An Age-Structured Modeling Approach," IJERPH, MDPI, vol. 17(20), pages 1-16, October.
    17. Shankar Shambhu & Deepika Koundal & Prasenjit Das & Chetan Sharma, 2021. "Binary Classification of COVID-19 CT Images Using CNN: COVID Diagnosis Using CT," International Journal of E-Health and Medical Communications (IJEHMC), IGI Global, vol. 13(2), pages 1-13, July.
    18. Mengyue Yuan & Tong Liu & Chao Yang, 2022. "Exploring the Relationship among Human Activities, COVID-19 Morbidity, and At-Risk Areas Using Location-Based Social Media Data: Knowledge about the Early Pandemic Stage in Wuhan," IJERPH, MDPI, vol. 19(11), pages 1-22, May.
    19. Peter Radvak & Hyung-Joon Kwon & Martina Kosikova & Uriel Ortega-Rodriguez & Ruoxuan Xiang & Je-Nie Phue & Rong-Fong Shen & James Rozzelle & Neeraj Kapoor & Taylor Rabara & Jeff Fairman & Hang Xie, 2021. "SARS-CoV-2 B.1.1.7 (alpha) and B.1.351 (beta) variants induce pathogenic patterns in K18-hACE2 transgenic mice distinct from early strains," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    20. Bruno Palialol & Paula Pereda & Carlos Azzoni, 2020. "Does weather influence COVID‐19 transmission?," Regional Science Policy & Practice, Wiley Blackwell, vol. 12(6), pages 981-1004, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28420-7. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.