DOI: 10.5061/dryad.z08kprrsh
title: Clinical surveillance identifies SARS-CoV-2 outbreaks and emergence of novel variants in real-time

description: 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.
description: # 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 using TaqPath 1.0 assays run on samples before sequencing.
 After the transition to TaqPath 2.0, samples testing positive were run on
 TaqPath 1.0 to ease future comparisons and test for S gene target failure.
 ### Clarification of database columns: sample_id: randomized tube
 identifier participant_id: randomized patient identifier SEX:
 participant's self-identified SEX RACE: participant's
 self-identified RACE ethnicity: participant's self-identified
 ethnicity bin pt_age: participant's age bin test_invitation: whether
 a sample was included in the invited testing comparison collection_week:
 surveillance week sample was collected pcr_turnaround_hrs: hours between
 sample registration and results returned qpcr_plateid: plate identifier
 for RT-PCR testing N gene: TaqPath 1.0 and 2.0 Ct values for N gene locus
 ORF1ab: TaqPath 1.0 Ct values for ORF1ab locus S gene: TaqPath 1.0 Ct
 values for S gene locus MS2: TaqPath 1.0 internal control ORF1a: TaqPath
 2.0 Ct values for ORF1a locus ORF1b: TaqPath 2.0 Ct values for ORF1b locus
 RNase P: TaqPath 2.0 internal control RESULT: RT-PCR assasy result
 Sequencing_week: surveillance week sample sequencing was performed
 Seq_plate: plate identifier for WGS GISAID_turnaround_days: days elapsed
 from sample registration to GISAID upload GISAID Accession: GISAID sample
 Accession identified Sequence name: GISAID sequence name GISAID_lineage:
 PANGO lineage assigned by GISAID Major_lineage: major PANGO lineage of
 sample genome Genome ambiguity: percentage of ambiguous nucleotides in
 consensus genome Genome_coverage: genome coverage obtained by WGS
 Seq_ORF1ab_ct: TaqPath 1.0 Ct values at ORF1ab locus for samples used in
 sequencing Seq_N_ct: TaqPath 1.0 Ct values at N gene locus for samples
 used in sequencing Seq_S_ct: TaqPath 1.0 Ct values at S gene locus for
 samples used in sequencing ## Sharing/Access information: Contact authors
 for additional information.