SARS-CoV-2 Variants of Concern
Note: These numbers are continually being updated. Because of this, the most recent datapoint on the dashboard should be cautiously interpreted—we may still be processing data from that time point. Also, these numbers only reflect cases identified by Helix and do not include cases identified by other organizations. Numbers may differ from other publicly reported dashboards due to a time lag from detection to reporting of the cases. The numbers displayed in the map graphic above show the total number of non-SGTF samples sequenced, NOT the total number of VOCs.
Helix is working together with the CDC, local public health agencies, and other organizations on national viral surveillance efforts. Drawing from samples collected during routine lower-nasal swab COVID-19 testing, typically at Helix-supported testing sites across the country, a subset of positive samples are chosen for follow-on sequencing based on demographics, sample quality, test characteristics, or simply random selection.
Once raw sequencing data is generated, Helix uses Pangolin and Nextclade to identify which strain of the SARS-COV-2 virus is present in each sample, as well as its recent evolutionary relationship to other strains. The results of this work are shown in the above dashboard.
For Variants of Concern (VOC), we further notify State Departments of Health for contact tracing within 24 hours of receipt of sequencing results.
A downloadable version of the data presented above can be found here.
Note: These numbers only reflect cases identified by Helix and do not include cases identified by other organizations. Numbers may differ from other publicly reported dashboards due to a time lag from detection to reporting of the cases.
The SARS-CoV-2 variant (B.1.1.7)—first identified in the United Kingdom—has garnered much of the world’s attention in recent weeks. This variant is known to carry several mutations that culminate in a more infectious variant of the virus and presents a significant threat to public health.
We first reported the potential spread of the B.1.1.7 variant in the United States based on the occurrence of S gene dropout—a phenomenon where qRT-PCR testing fails to detect the presence of the virus’ S gene, owing to a deletion mutation affecting amino acids H69 and V70 (this is also known as S gene target failure, or SGTF). This deletion is one of several mutations that distinguish the B.1.1.7 from other SARS-CoV-2 strains. In these cases, qRT-PCR testing is still able to identify the presence of the virus thanks to two other targets on the virus: the N gene and ORF1 gene.
Subsequent viral sequence analysis of SGTF samples using Illumina’s COVIDSeq Test confirmed that only a subset of these samples harbored all variants that define B.1.1.7. The remaining SGTF samples were other variants of the virus. We have assigned each of the SGTF sequences to a phylogenetic clade in order to understand the recent evolution of this virus.
To monitor trends in B.1.1.7 transmission, as well as the dynamics of other variants harboring the H69/V70 deletion, we will continue to regularly sequence high-quality SGTF samples with N gene Cq<27* from our lab and place these strains on the SARS-CoV-2 phylogeny. While growing in prevalence, SGTF samples represent a small subset of all positive Helix® COVID-19 Test results. We are also expanding this surveillance program beyond SGTF samples to proactively monitor for the emergence and spread of new variants.
The interactive dashboards provided above and below are updated on a weekly basis. The above dashboard serves to specifically highlight B.1.1.7 cases in the US.
*Cq is defined by the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines as the quantification cycle and is equivalent to quantification threshold (Ct)
If you use the Helix® COVID-19 Surveillance Dashboard in your research, we ask that you cite its use and include a link to this page.
Example: Data sourced from the Helix® COVID-19 Surveillance Dashboard. Accessed at Helix.com/covid19db on [date].
Helix and Illumina, with support from the CDC, are collaborating to augment national surveillance infrastructure in the US to track the emergence and prevalence of novel variants of SARS-CoV-2. Sequences are deposited regularly to GISAID and Genbank by the CDC. All B.1.1.7 variants are also reported to relevant public health departments for contact tracing efforts.
In addition to conducting viral sequencing, Helix is one of the nation's largest COVID-19 laboratories—funded in part by the NIH's RADxATP program—and is helping to drive several research initiatives.
The Helix® COVID-19 Test is a real-time RT-PCR test that received Emergency Use Authorization from the FDA in July of 2020. This expanded EUA enables both supervised and unsupervised self-collection on-site—meaning no healthcare professional is required to be on-site—our partners significantly streamline their operations and decrease their collection costs.
Clinical performance studies show a consistent limit of detection (LoD) of 1000 Viral copies / mL and was recently found to be one of the most sensitive tests on the market in a study conducted by the FDA.
Helix researchers first reported the potential spread of the B.1.1.7 variant in the United States based on the occurrence of S gene dropout—a phenomenon where qRT-PCR testing fails to detect the presence of the virus’ S gene, owing to a deletion mutation affecting amino acids H69 and V70 (this is also known as S gene target failure, or SGTF). This deletion is one of several mutations that distinguish the B.1.1.7 from other SARS-CoV-2 variants. Subsequent viral sequence analysis of SGTF samples led to the identification of 51 of the US's first confirmed B.1.1.7 cases.
Helix has been awarded $33.4 M in funding from the National Institutes of Health (NIH) under the Rapid Acceleration of Diagnostics (RADx) program. These funds will support rapid scaling of our COVID-19 infrastructure and operations, with a goal of reaching a capacity of 100,000 COVID-19 tests per day.
As this pandemic continues to unfold, Helix researchers are working with international collaborators to advance our understanding of COVID-19. Helix researchers have helped shed light on the drawbacks of saliva as a COVID-19 sample source; identify genetic factors that contribute to severe COVID-19; and are continuing to collect longitudinal survey data to help in future discoveries.
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