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
- 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 |
- 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 |
- 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 |
- 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) |