Chan Wan-Mui, Ip Jonathan Daniel, Chu Allen Wing-Ho, Tse Herman, Tam Anthony Raymond, Li Xin, Kwan Mike Yat-Wah, Yau Yat-Sun, Leung Wai-Shing, Chik Thomas Shiu-Hong, To Wing-Kin, Ng Anthony Chin-Ki, Yip Cyril Chik-Yan, Poon Rosana Wing-Shan, Chan Kwok-Hung, Wong Sally Cheuk-Ying, Choi Garnet Kwan-Yue, Lung David Christopher, Cheng Vincent Chi-Chung, Hung Ivan Fan-Ngai, Yuen Kwok-Yung, To Kelvin Kai-Wang
State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
Department of Pathology, Hong Kong Children's Hospital, Kowloon, Hong Kong Special Administrative Region, China.
Lancet Reg Health West Pac. 2021 May;10:100130. doi: 10.1016/j.lanwpc.2021.100130. Epub 2021 Mar 23.
Viral genomic surveillance is vital for understanding the transmission of COVID-19. In Hong Kong, breakthrough outbreaks have occurred in July (third wave) and November (fourth wave) 2020. We used whole viral genome analysis to study the characteristics of these waves.
We analyzed 509 SARS-CoV-2 genomes collected from Hong Kong patients between 22nd January and 29th November, 2020. Phylogenetic and phylodynamic analyses were performed, and were interpreted with epidemiological information.
During the third and fourth waves diverse SARS-CoV-2 genomes were identified among imported infections. Conversely, local infections were dominated by a single lineage during each wave, with 96.6% (259/268) in the third wave and 100% (73/73) in the fourth wave belonging to B.1.1.63 and B.1.36.27 lineages, respectively. While B.1.1.63 lineage was imported 2 weeks before the beginning of the third wave, B.1.36.27 lineage has circulated in Hong Kong for 2 months prior to the fourth wave. During the fourth wave, 50.7% (37/73) of local infections in November was identical to the viral genome from an imported case in September. Within B.1.1.63 or B.1.36.27 lineage in our cohort, the most common non-synonymous mutations occurred at the helicase (nsp13) gene.
Although stringent measures have prevented most imported cases from spreading in Hong Kong, a single lineage with low-level local transmission in October and early November was responsible for the fourth wave. A superspreading event or lower temperature in November may have facilitated the spread of the B.1.36.27 lineage.
病毒基因组监测对于了解新型冠状病毒肺炎（COVID - 19）的传播至关重要。在香港，2020年7月（第三波）和11月（第四波）出现了突破性疫情。我们使用全病毒基因组分析来研究这些疫情波次的特征。
我们分析了2020年1月22日至11月29日期间从香港患者中收集的509个严重急性呼吸综合征冠状病毒2（SARS-CoV-2）基因组。进行了系统发育和系统动力学分析，并结合流行病学信息进行解读。
在第三波和第四波疫情期间，输入性感染中鉴定出多种SARS-CoV-2基因组。相反，每一波次的本地感染均由单一谱系主导，第三波中96.6%（259/268）、第四波中100%（73/73）分别属于B.1.1.63和B.1.36.27谱系。虽然B.1.1.63谱系在第三波疫情开始前2周输入，但B.1.36.27谱系在第四波疫情前已在香港传播了2个月。在第四波疫情期间，11月本地感染的50.7%（37/73）与9月一例输入病例的病毒基因组相同。在我们的队列中，B.1.1.63或B.1.36.27谱系中，最常见的非同义突变发生在解旋酶（nsp13）基因。
尽管严格的措施阻止了大多数输入病例在香港传播，但10月和11月初低水平本地传播的单一谱系导致了第四波疫情。11月的一次超级传播事件或较低温度可能促进了B.1.36.27谱系的传播。
