screenshot showing allele frequency across several star alleles in 30,000 people

National SARS-Cov-2 Viral Sequencing

Helix and Illumina have partnered together to augment national surveillance infrastructure in the US in order to track the emergence and prevalence of novel strains of SARS-CoV-2. This work is done with support from the CDC. Sequences will be deposited regularly to GISAID and Genbank. As a matter of public health, all B.1.1.7 strains are also reported to relevant public health departments for contact tracing efforts.

Background on B.1.1.7

The SARS-CoV-2 variant (B.1.1.7) strain—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 strain 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.
 
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 missing the other mutations that are characteristic of B.1.1.7. 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 strains harboring the H69/V70 deletion, we will continue to regularly sequence high-quality SGTF samples with N gene Cq<28 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 Tests. We also plan to expand this surveillance program past SGTF samples to proactively monitor for the emergence and flow of new strains.
 
The 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.
 
Below, we highlight B.1.1.7 cases alongside SGTF trends in the US.

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Helix's COVID-19 Sequencing Platform

In addition to viral sequencing, Helix is one of the nation's largest COVID-19 laboratories—funded in part by the CDC's RADxATP program—and is helping to drive several research initiatives.

The Helix COVID-19 Test

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 one of the most sensitive tests on the market in a study conducted by the FDA.
 

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Early identification of B.1.1.7

Bar graph showing that individuals with >5 initial symptoms tend to experience COVID-19 symptoms longer than those with <5 symptoms

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 strains. Subsequent viral sequence analysis of SGTF samples led to the identification of 51 of the US's first confirmed B.1.1.7 cases.
 

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NIH Rapid Acceleration of Diagnostics (RADx) award

Example bar graph communicating risk of breast cancer to would be participants

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.
 

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COVID-19 Research

Bar graph showing variant types in different ACMG 59 genes

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 may contribute to severe COVID-19; and are continuing to collect longitudinal survey data to help in future discoveries.
 

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Bar graph showing that individuals with >5 initial symptoms tend to experience COVID-19 symptoms longer than those with <5 symptoms
Example bar graph communicating risk of breast cancer to would be participants
Bar graph showing variant types in different ACMG 59 genes
Bar graph showing that individuals with >5 initial symptoms tend to experience COVID-19 symptoms longer than those with <5 symptoms
Example bar graph communicating risk of breast cancer to would be participants
Bar graph showing variant types in different ACMG 59 genes