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. 2024 Dec;18(12):e70060.
doi: 10.1111/irv.70060.

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

Hao Yi Tan  1   2 , Nur Huda Khamis  1 , Alvin Goh  1 , Tania K L Mah  1 , Benny Yeo  3 , Jie Yin Ngan  3 , Yichen Ding  3 , Cui Lin  3 , Sae-Rom Chae  1 , Phoebe Lee  1 , Zheng Jie Marc Ho  1   4
Affiliations

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

Hao Yi Tan et al. Influenza Other Respir Viruses. 2024 Dec.

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.

Keywords: Acute Respiratory Infections (ARI); COVID‐19; Emerging infectious diseases; Genomic Surveillance; Health Strategy; Pandemic preparedness; Singapore; Whole genome sequencing (WGS).

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

FIGURE 1
FIGURE 1
Workflow of sampling imported, community and severe COVID‐19 cases for genomic surveillance.
FIGURE 2
FIGURE 2
Area chart plotting the variant distribution of imported, local and severe COVID‐19 cases from 1 February 2022 to 11 February 2023.
FIGURE 3
FIGURE 3
Bar chart plotting the number of reported COVID‐19 cases in Singapore from 1 February 2022 to 11 February 2023, subdivided into variant proportions by colour.
See this image and copyright information in PMC

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