Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Transmission Patterns of Co-Circulation of Omicron Sub-Lineages in Hong Kong SAR, China, a City with Rigorous Social Distancing Measures, in 2022

Ning Chow
ORCID logo ,
Teng Long
,
Lam-Kwong Lee
,
Ivan Tak-Fai Wong
,
Annie Wing-Tung Lee
,
Wing-Yin Tam
,
Harmen Fung-Tin Wong
,
Jake Siu-Lun Leung
,
Franklin Wang-Ngai Chow
,
Kristine Shik Luk
,
Alex Yat-Man Ho
,
Jimmy Yiu-Wing Lam
,
Miranda Chong-Yee Yau
,
Tak-Lun Que
,
Kam-Tong Yip
,
Viola Chi-Ying Chow
,
River Chun-Wai Wong
,
Bobo Wing-Yee Mok
ORCID logo ,
Honglin Chen
ORCID logo ,
Gilman Kit-Hang Siu
*
Version 1 : Received: 8 April 2024 / Approved: 8 April 2024 / Online: 9 April 2024 (07:22:06 CEST)

A peer-reviewed article of this Preprint also exists.

Chow, N.; Long, T.; Lee, L.-K.; Wong, I.T.-F.; Lee, A.W.-T.; Tam, W.-Y.; Wong, H.F.-T.; Leung, J.S.-L.; Chow, F.W.-N.; Luk, K.S.; Ho, A.Y.-M.; Lam, J.Y.-W.; Yau, M.C.-Y.; Que, T.-L.; Yip, K.-T.; Chow, V.C.-Y.; Wong, R.C.-W.; Mok, B.W.-Y.; Chen, H.-L.; Siu, G.K.-H. Transmission Patterns of Co-Circulation of Omicron Sub-Lineages in Hong Kong SAR, China, a City with Rigorous Social Distancing Measures, in 2022. Viruses 2024, 16, 981. Chow, N.; Long, T.; Lee, L.-K.; Wong, I.T.-F.; Lee, A.W.-T.; Tam, W.-Y.; Wong, H.F.-T.; Leung, J.S.-L.; Chow, F.W.-N.; Luk, K.S.; Ho, A.Y.-M.; Lam, J.Y.-W.; Yau, M.C.-Y.; Que, T.-L.; Yip, K.-T.; Chow, V.C.-Y.; Wong, R.C.-W.; Mok, B.W.-Y.; Chen, H.-L.; Siu, G.K.-H. Transmission Patterns of Co-Circulation of Omicron Sub-Lineages in Hong Kong SAR, China, a City with Rigorous Social Distancing Measures, in 2022. Viruses 2024, 16, 981.

Abstract

Objective: The study aimed to characterize the changing landscape of circulating SARS-CoV-2 lineages in the local community of Hong Kong throughout 2022. We examined how adjustments to quarantine arrangements influenced the transmission pattern of Omicron variants in a city with relatively rigorous social distancing measures at that time. Methods: In 2022, a total of 4,684 local SARS-CoV-2 genomes were sequenced using the Oxford Nanopore GridION sequencer. SARS-CoV-2 consensus genomes were generated by MAFFT, and the maximum likelihood phylogeny of these genomes were determined using IQ-TREE. The dynamic changes in lineages were depicted in a time tree created by Nextstrain. Statistical analysis was conducted to assess the correlation between changes in the number of lineages and adjustments to quarantine arrangements. Results: By the end of 2022, a total of 83 SARS-CoV-2 lineages were identified in the community. The increase in the number of new lineages was significantly associated with the relaxation of quarantine arrangements (One-way ANOVA, F(5,47)=18.233, p<0.001)). Over time, Omicron BA.5 sub-lineages replaced BA.2.2 and became the predominant Omicron variants in Hong Kong. The influx of new lineages reshaped the dynamics of Omicron variants in the community without fluctuating the death rate and hospitalization rate (One-way ANOVA, F(5,47)=2.037, p=0.091). Conclusion: The study revealed that even with an extended mandatory quarantine period for incoming travelers, it may not be feasible to completely prevent the introduction and subsequent community spread of highly contagious Omicron variants. Ongoing molecular surveillance of COVID-19 remains essential to monitor the emergence of new recombinant variants.

Keywords

COVID-19; Omicron; co-circulation; social distancing; quarantine arrangements

Subject

Public Health and Healthcare, Public Health and Health Services

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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