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

Access this dataset at Dryad: DOI: 10.5061/dryad.z08kprrsh

This dataset includes RT-PCR testing data and sequencing data for the ABCTL SARS-CoV-2 testing and sequencing project performed at ASU.

## Data and file structure:

Surveillance_data_v2.csv: RT-PCR testing data and NGS sequencing data

In all fields, where data was missing, unavailable, or inapplicable, cell values have been filled with 'Blank'. A cell with this value should not be interpreted as a participant response or metadata characteristic, test result, or cohort descriptor. It is recommended to replace this value with a NA/NaN/blank when performing future analysis.

For RTPCR values, during the study period, primary qPCR testing migrated from TaqPath COVID-19 Combo Kit (hereafter TaqPath 1.0) testing to TaqPath COVID-19 Fast PCR Combo Kit 2.0 (hereafter TaqPath 2.0) testing. Ct values prefaced with \"Seq_\" are Ct values ...,