PDF(Pubmed)
Abstract：
OBJECTIVE: This 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 4684 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 was 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).
CONCLUSIONS: This 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.
METHODS: In 2022, a total of 4684 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 was 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).
CONCLUSIONS: This 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.
摘要：
目的：这项研究旨在描述整个2022年香港当地社区中流行的SARS-CoV-2谱系的变化。我们研究了检疫安排的调整如何影响Omicron变种在当时具有相对严格的社会距离措施的城市中的传播模式。
方法：2022年，使用牛津纳米孔GridION测序仪对总共4684个本地SARS-CoV-2基因组进行了测序。SARS-CoV-2共有基因组由MAFFT产生，使用IQ-TREE确定这些基因组的最大似然系统发育。在Nextstrain创建的时间树中描述了谱系的动态变化。进行统计分析以评估谱系数量变化与检疫安排调整之间的相关性。
结果：到2022年底，在社区中总共确定了83个SARS-CoV-2谱系。新谱系数量的增加与检疫安排的放松显着相关（单向方差分析，F(5,47)=18.233,p<0.001)。随着时间的推移,OmicronBA.5子谱系取代了BA.2.2，成为香港主要的Omicron变体。新谱系的涌入重塑了社区中Omicron变体的动态，而不会波动死亡率和住院率（单向方差分析，F(5,47)=2.037,p=0.091)。
结论：这项研究表明，即使入境旅客的强制隔离期延长，完全防止高传染性Omicron变种的引入和随后的社区传播可能是不可行的。持续的COVID-19分子监测对于监测新重组变体的出现仍然至关重要。
方法：2022年，使用牛津纳米孔GridION测序仪对总共4684个本地SARS-CoV-2基因组进行了测序。SARS-CoV-2共有基因组由MAFFT产生，使用IQ-TREE确定这些基因组的最大似然系统发育。在Nextstrain创建的时间树中描述了谱系的动态变化。进行统计分析以评估谱系数量变化与检疫安排调整之间的相关性。
结果：到2022年底，在社区中总共确定了83个SARS-CoV-2谱系。新谱系数量的增加与检疫安排的放松显着相关（单向方差分析，F(5,47)=18.233,p<0.001)。随着时间的推移,OmicronBA.5子谱系取代了BA.2.2，成为香港主要的Omicron变体。新谱系的涌入重塑了社区中Omicron变体的动态，而不会波动死亡率和住院率（单向方差分析，F(5,47)=2.037,p=0.091)。
结论：这项研究表明，即使入境旅客的强制隔离期延长，完全防止高传染性Omicron变种的引入和随后的社区传播可能是不可行的。持续的COVID-19分子监测对于监测新重组变体的出现仍然至关重要。
