Helix SARS-CoV-2 Surveillance

Helix® is currently working with public health agencies to sequence COVID-19 samples to monitor evolution and spread of SARS-CoV-2 variants.

Note that positivity_by_time.csv and positivity_by_age.csv are the only datasets currently being updated.

The files counts_by_state.csv and sequencing_results.csv are not up to date.

For Helix's latest SARS-CoV-2 variant frequencies, please see the Helix COVID-19 Surveillance Dashboard.

This data is being made available via the Creative Commons Attribution Share Alike license

📚 Datasets

positivity_by_time.csv 📃

• This file contains positivity rates for COVID-19 and FluA from Helix's diagnostic testing operation. Helix's diagnostic test simultaneously assays for COVID-19 and Flu.

Column Name	Description
collection_date	Date sample collected
positive_result	Diagnostic test result
positive_tests	Number of tests with that test result
total_tests	Total number of tests collected that day
positivity	Positivity rate corresponding to test result
positivity_7day	7-day rolling average positivity rate

positivity_by_age.csv 📃

• This file contains 7-day rolling average positivity rates for COVID-19 and FluA, by age group, from Helix's diagnostic testing operation. Helix's diagnostic test simultaneously assays for COVID-19 and Flu.

Column Name	Description
age_bin	Age group: <18, 18-24, 25-44, 45-64, and ≥65 year-olds
collection_date	Date sample collected
positive_result	Diagnostic test result
positivity_7day	7-day rolling average positivity rate

counts_by_state.csv 📃

• This file contains counts of test results aggregated by state and collection date.
• Records with fewer than 3 positives are removed to protect privacy.
• All records have a qPCR quantification cycle (Cq) of less than 27 for the N gene target.

Column Name	Description
state	Patient state of residence
collection_date	Date of specimen collection
positive	Number of positive test results
all_SGTF	Number of positive test results with S gene target failure
sequenced_SGTF	Number of sequenced test results with S gene target failure
B117	Number of positive test results that were sequenced and known to be of the B.1.1.7 lineage

sequencing_results.csv 📃

• This file contains metadata for individual sequenced specimens, including GenBank Accession numbers and other GenBank metadata to facilitate retrieval of the viral genome sequence data.
• Samples without GenBank Accession numbers have been sequenced but are not yet submitted to or approved by GenBank.

Column Name	Description
STM_id	Specimen ID
GISAID_virus_name	GISAID Virus Name
sex	Patient sex
state	Patient state of residence
lineage	Pangolin assigned SARS-CoV-2 lineage
clade	Nextclade assigned SARS-CoV-2 clade
age_bracket	Patient's age bracket at time of specimen collection
ncbi_accession_id	NCBI GenBank Accession ID
extra	Additional GenBank identifiers
subname	GenBank subname
sequence_length	GenBank sequence length
createdate	GenBank record creation date (YYYY/MM/DD)
updatedate	GenBank record update date (YYYY/MM/DD)