1 May 2021

Phylogenomic analysis of COVID-19 summer and winter outbreaks in Hong Kong: An observational study

A group of experts from HKUMed performed detailed phylogenetic and phylodynamic analyses to compare the third (July 2020) and fourth (November 2020) waves of COVID-19 infection in Hong Kong. A total of 509 SARS-CoV-2 genome sequences, representing 8.1% of all COVID-19 cases in Hong Kong, were analyzed. The purpose of this study was to understand the characteristics of each outbreak to guide public health interventions.


Key takeaways from the study:


  1. 96.6% (259/268) of locally acquired cases from the third wave belonged to the PANGO lineage B.1.1.63. The imported cases in this wave were genetically diverse.
  2. During the fourth wave, strains from 73 locally acquired cases were closely related to the viral genomes from two imported cases who had returned to Hong Kong from Nepal. 50.7% (37/73) of them had identical genomes.
  3. Further analysis revealed that the viral genome from the fourth wave differs from the reference Wuhan-Hu-1 strain by 18 nucleotides.
  4. Single nucleotide polymorphisms were found throughout the entire genome of lineages B.1.1.63 and B.1.36.27 in the third and fourth wave, respectively.
  5. This study showed that the third and fourth waves were caused by distinct viruses from different lineages, suggesting that the third wave subsided before the fourth wave occurred. The B.1.36.27 lineage was found to be in Hong Kong for two months before the fourth wave began. Taken together, this study highlighted the use of genomic analysis to uncover the differences and similarities of the different strains from the third and fourth waves of COVID-19 infection in Hong Kong, which could be useful to inform the success or limitation of control measures.


To read the original article published in The Lancet Regional Health - Western Pacific, click here.