Epidemiological and evolutionary dynamics of human respiratory viruses in Hong Kong during COVID-19

Abstract

The COVID-19 pandemic and associated public health measures have had a substantial impact on the epidemiology of respiratory viruses in Hong Kong. A notable decline in hospitalizations related to non-COVID-19 respiratory viruses among children was observed in 2020. However, as social measures were gradually relaxed, enterovirus/rhinovirus emerged as the predominant respiratory virus detected. This thesis aims to investigate the genetic diversity of resurgent human rhinovirus (HRV) and respiratory syncytial virus (RSV) cases among children and adolescents presenting clinical signs of respiratory viral infections. Sequencing of enterovirus/rhinovirus samples obtained from children at Queen Mary Hospital, Hong Kong, between August 2020 and October 2021 was conducted to assess changes in HRV genotypes and elucidate their epidemic characteristics. Additionally, whole genome sequencing of RSV positive samples collected from 2020 to 2022 was performed to examine genetic diversity, prevalence, and patterns of virus introduction. Despite reduced circulation of respiratory viruses, HRV-A and C infections persisted in children, with intermittent detection of HRV-B and other respiratory viruses. A resurgence of HRV-A cases, predominantly genotypes A47 and A101, was observed in November 2020 when public health measures were relaxed between the third and fourth waves of COVID-19. The subsequent restrictions implemented during the fourth wave, including school closures, substantially reduced the circulation of respiratory virus. In May 2021, upon the relaxation of control measures, genotype A49 became predominant, suggesting the persistence of multiple transmission lineages despite strict public health measures. Furthermore, genotyping highlighted the association of genotypes A49 and A47 with upper respiratory tract infections, emphasizing their epidemic potential. RSV case detections were also influenced by COVID-19 and its control measures, with an increase in RSV cases whenever restrictions were eased, followed by a decline in RSV during subsequent COVID-19 waves. This led to winter RSV peaks in 2020–2022 as opposed to the normal spring/summer peak. Twenty RSV-A types were identified, all belonging to genotype GA.2.3.5 or ON-1, and eight RSV-B types, all belonging to genotype GB.5.0.5a or BA. While one large RSV-A cluster was observed, most detected viruses appeared as singletons. Notably, RSV sequences collected in 2021 exhibited close similarity to RSV samples sequenced from China, whereas those collected in late 2022 showed similarities to sequences from abroad, likely due to changes in travel restrictions. The implementation of non-pharmaceutical interventions had an impact on the genetic diversity of circulating HRV and RSV. This study underscores the importance of ongoing surveillance of respiratory viruses to enhance our understanding of transmission dynamics and contribute to the formulation of effective public health interventions.