Singapore's COVID‐19 Genomic Surveillance Programme: Strategies and Insights From a Pandemic Year

• Published in: Influenza and other respiratory viruses 2024-12, Vol.18 (12), p.e70060-n/a
• Main Authors: Tan, Hao Yi, Khamis, Nur Huda, Goh, Alvin, Mah, Tania K. L., Yeo, Benny, Ngan, Jie Yin, Ding, Yichen, Lin, Cui, Chae, Sae‐Rom, Lee, Phoebe, Ho, Zheng Jie Marc
• Format: Article
• Language: English
• Subjects: Acute Respiratory Infections (ARI); Adolescent; Adult; Aged; Aged, 80 and over; Antigens; Child; Child, Preschool; COVID-19; COVID-19 - epidemiology; COVID-19 - transmission; COVID-19 - virology; COVID-19 diagnostic tests; Disease detection; Disease transmission; Emerging infectious diseases; Epidemiological Monitoring; Female; Gene sequencing; Genome, Viral - genetics; Genomes; Genomic Surveillance; Genomics; Global health; Health Strategy; Health surveillance; Heterogeneity; Humans; Infant; Infant, Newborn; Infections; Influenza; Laboratories; Male; Middle Aged; Original; Pandemic preparedness; Pandemics; Pathogens; Primary care; Public Health; Respiratory tract infection; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Severe acute respiratory syndrome coronavirus 2; Singapore; Singapore - epidemiology; Surveillance; Trends; Viruses; Whole Genome Sequencing; Whole genome sequencing (WGS); Young Adult
• ISSN: 1750-2640; 1750-2659; 1750-2659
• DOI: 10.1111/irv.70060

ABSTRACT Background During the COVID‐19 pandemic, genomic surveillance was crucial for monitoring virus spread and identifying variants. Effective surveillance helped understand transmission dynamics. Singapore had success in combating COVID‐19 through its surveillance programmes. This paper outlines Singapore's strategy and its impact on public health during the transition to endemicity over 54 weeks from February 2022 to February 2023. Methods In May 2022, Singapore expanded its acute respiratory infections (ARI) surveillance to enhance COVID‐19 detection. COVID‐19–positive samples from ARI cases were sent to the National Public Health Laboratory for whole genome sequencing (WGS). WGS data informed public health actions based on transmission origins and case severity. Results Over 54 weeks, NPHL sequenced 18,918 (73%) samples. Analysis showed 29% imported and 71% local cases. Severe cases accounted for 12% and were mostly elderly, specifically those aged 80 years old and above. Variant analysis identified 11 predominant variants and 288 subvariants. Omicron BA.2, BA.5 and XBB were initially dominant, followed by increased variant heterogeneity. Severe cases mirrored these trends. Conclusion Genomic surveillance was integral in Singapore's COVID‐19 response, guiding timely public health decisions. Effective variant tracking supported proactive measures. The experience underscores the importance of genomic surveillance for future pandemic preparedness and emerging disease detection, emphasising its role in shaping pandemic responses and global health.