Large-Scale Saliva-Based Clinical Surveillance Enables Real Time SARS-CoV-2 Outbreak Detection and Genomic Tracking...

Area of Science:

• Virology
• Public Health
• Genomic Surveillance

Background:

• Traditional sample collection for COVID-19 surveillance faced challenges due to PPE shortages and social distancing.
• Healthcare personnel redeployment also impacted routine sample collection efforts.

Purpose of the Study:

• To evaluate the feasibility of self-collected saliva for SARS-CoV-2 detection.
• To establish a large-scale surveillance program using self-collected saliva for diagnosis and genomic sequencing.

Main Methods:

• 1.4 million saliva samples were tested for SARS-CoV-2 using RT-PCR between April 2020 and December 2023.
• Whole genome sequencing was performed on over 69,000 samples to track viral evolution.
• S gene target failure was monitored on a commercial assay for genotyping accuracy.

Main Results:

• Real-time monitoring of infection trends aligned with regional case counts.
• Multiple waves of viral lineage introductions were identified.
• The assay demonstrated high positive predictive value (PPV=0.98) and negative predictive value (NPV=0.94) for genotyping.
• Low turnaround time (median 12 days) from collection to sequencing data.

Conclusions:

• Self-collected saliva is a practical and scalable strategy for infectious disease surveillance.
• This method offers a cost-effective alternative for future pandemic preparedness.
• The study demonstrates the utility of saliva-based surveillance for both clinical diagnosis and genomic tracking.