Clinical surveillance identifies SARS-CoV-2 outbreaks and emergence of novel variants in real-time

Monitoring community health and tracking SARS-CoV-2 evolution were
critical priorities throughout the COVID-19 pandemic. However, widespread
shortages of personal protective equipment, the necessity for social
distancing, and the redeployment of healthcare personnel to clinical
duties presented significant barriers to traditional sample collection. In
this study, we evaluated the feasibility of using self-collected saliva
specimens for the qualitative detection of SARS-CoV-2 infection. Following
confirmation of reliable viral detection in saliva, we established a
large-scale surveillance program in Arizona, USA, to enable clinical
diagnosis and genomic sequencing from self-collected samples. Between
April 2020 and December 2023, we tested approximately 1.4 million saliva
samples using RT-PCR, identifying 94,330 SARS-CoV-2 infections. Whole
genome sequencing was performed on 69,595 samples, yielding 54,040
high-quality consensus genomes. This surveillance approach enabled
real-time monitoring of infection trends, outbreak detection within
specific populations, and the identification of novel viral lineages over
the course of the pandemic. The co-location of clinical testing and
sequencing capabilities within the same facility significantly reduced
turnaround time from the identification of positive cases to the
generation of sequencing data. Our findings support the use of
self-collected saliva as a scalable, cost-effective, and practical
strategy for infectious disease surveillance in future pandemics.