Rapid Pathogen Sequencing for Health Policy and Care

Lead  Prof. Gilman SIU

Department of Health Technology and Informatics | Otto Poon Charitable Foundation Smart Cities Research Institute

During infectious disease outbreaks, timing is critical. SARS-CoV-2 cases can double within 1.5 to 3 days, and viruses can mutate every 7 days, potentially compromising diagnostics, vaccines, and treatments. Traditional genome sequencing (up to 48 hours) is too slow to prevent exponential spread.

Prof. Gilman Siu’s laboratory pioneered rapid pathogen genome sequencing protocols, reducing diagnostic times from 48–72 to 6–8 hours. This breakthrough enables direct detection of infections from clinical samples without the need for time-consuming laboratory cultures, fundamentally transforming infectious disease surveillance and diagnosis in Hong Kong.

This innovation has delivered significant and measurable impacts across three critical domains: public health policy-making, hospital infection control, and clinical diagnosis.

During the COVID-19 pandemic, Prof. Siu and his team sequenced 20,000+ cases, providing real-time genomic insights that identified outbreak sources and directly informed Hong Kong government policies, including crew quarantine suspensions and hotel quarantine reforms. Their work helped interrupt transmission chains and strengthen the city’s pandemic response.

Rapid genomic surveillance also enabled timely containment of hospital outbreaks, safeguarding routine healthcare services across 13 hospitals serving 5.1 million people.

Since 2022, these protocols have been deployed in public hospitals for culture-independent acute invasive infection diagnosis, benefiting more than 1,000 patients through streamlined antimicrobial treatment while eliminating unnecessary procedures. This successful translation of research into clinical practice has directly improved patient care and outcomes.