niman Posted January 9, 2021 Report Share Posted January 9, 2021 (edited) 47 new cases of B.1.1.7 have been identified, spread across 4 of the 5 states in which we have the statistical power to detect it B.1.1.7 reaffirmed as only a subset of S gene target failure (SGTF) samples B.1.1.7 appears to currently represent 32% of SGTF samples and 0.16% of all positive tests Viral sequencing identified strains carrying the H69/V70 mutation that are not B.1.1.7—these were placed into phylogenetic clades https://blog.helix.com/b117-variant-updated-data/ Edited January 9, 2021 by niman Link to comment Share on other sites More sharing options...
niman Posted January 9, 2021 Author Report Share Posted January 9, 2021 Helix Research Team Nicole Washington, Simon White, Kelly Schiabor Barrett, Elizabeth Cirulli, Alexandre Bolze, James Lu January 6, 2021 Helix, Illumina launch surveillance program as the B.1.1.7 variant of SARS-CoV-2, first identified in the UK, spreads further into the US 51 Cases identified by Helix and Illumina to date Most recent update: January 6th, 2021 What’s new? 47 new cases of B.1.1.7 have been identified, spread across 4 of the 5 states in which we have the statistical power to detect it B.1.1.7 reaffirmed as only a subset of S gene target failure (SGTF) samples B.1.1.7 appears to currently represent 32% of SGTF samples and 0.16% of all positive tests Viral sequencing identified strains carrying the H69/V70 mutation that are not B.1.1.7—these were placed into phylogenetic clades Our current understanding of B.1.1.7 in the United States 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 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 continued to sequence SGTF samples—most recently obtaining 127 new, high-quality, SARS-CoV-2 virus sequences from Illumina’s COVIDSeq Test—which has lead to identification of an additional 47 individuals with the B.1.1.7 variant strain in multiple states, including CA, GA, and PA. We have assigned each of the SGTF sequences to a phylogenetic clade in order to understand the recent evolution of this virus (results shown below). 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 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. Please check back frequently: We will be updating the figures below as our data continues to evolve. This work is being done with the support of the CDC and in partnership with Illumina. 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. Current stats based on Helix data Metric Result Total number of SGTF samples sequenced 158 Total number of B.1.1.7 cases detected 51 Percent of sequenced SGTF samples that are B.1.1.7 32% Percent of positive tests with SGTF (for the week of Dec 28) 0.51% Percent of positive tests with B.1.1.7 (extrapolated) 0.16% Total states with B.1.1.7 to date 4 Total states with at least 5 SGTF samples sequenced (85% power to detect at least 1 B.1.1.7 given the current mean—among sampled states—of 32%) 5 Data visualization Figure 1. Analysis pipeline and SARS-CoV-2 Clades in SGTF samples Breakdown of the analysis pipeline used to identify B.1.1.7 samples from all positive Helix COVID-19 Test samples to date.**Updated 01/06/2020 COVID19COVID19-testing Categorized in: Helix Research Uncategorized Helix Research Team Nicole Washington, Simon White, Kelly Schiabor Barrett, Elizabeth Cirulli, Alexandre Bolze, James Lu January 6, 2021 SARS-CoV-2 UK variant (B.1.1.7) in the US: Four cases identified in Florida and California Also tagged: COVID19 Helix Research Team December 31, 2020 Link to comment Share on other sites More sharing options...
niman Posted January 9, 2021 Author Report Share Posted January 9, 2021 Illumina and Helix Collaborate to Assess Prevalence of New SARS-CoV-2 UK Variant (B.1.1.7) in the US and Develop National Surveillance Infrastructure With support from the Centers for Disease Control and Prevention (CDC), Illumina and Helix have already identified more than 50 cases of the new variant in the US January 05, 2021 07:00 PM Eastern Standard Time SAN DIEGO--(BUSINESS WIRE)--Illumina, Inc. (Nasdaq: ILMN) and Helix today announced a collaboration to augment national surveillance infrastructure in the US to track the emergence and prevalence of novel strains of SARS-CoV-2 with support from the CDC. The combination of Illumina’s sequencing technology and expertise and Helix’s national COVID-19 testing footprint will significantly expand the country’s existing surveillance efforts to detect and characterize emerging variants of SARS-CoV-2. “Genomic surveillance is essential in fighting the pandemic. Illumina is pleased to partner with the CDC and Helix to provide accurate sequencing that can contribute to rapidly scaling genomic surveillance in the US to better understand the presence of B.1.1.7 and other variants as they emerge in our communities” Tweet this The collaboration has already demonstrated results – identifying 51 of the first 54 cases of B.1.1.7, the highly transmissible variant first found in the UK, reported in the US. Over the past several weeks, Helix has analyzed recent positive samples and identified those with ‘S gene dropout’ on their diagnostic PCR assay, indicating the potential presence of the emerging B1.1.7 variant in different regions in the US. Illumina then sequenced a subset of these ‘S gene dropout’ samples using Illumina’s COVIDSeq Test, which identified the B.1.1.7 variant in 4 samples from California and Florida. “Genomic surveillance is essential in fighting the pandemic. Illumina is pleased to partner with the CDC and Helix to provide accurate sequencing that can contribute to rapidly scaling genomic surveillance in the US to better understand the presence of B.1.1.7 and other variants as they emerge in our communities,” said Dr. Phil Febbo, M.D., Chief Medical Officer of Illumina. “Having a robust surveillance effort in place is critical to understanding how the SARS-CoV-2 virus is evolving, and how our public health response needs to adapt,” said Dr. James Lu, M.D., Ph.D., co-founder and President of Helix. “By bringing together the strengths of Helix, Illumina, and the CDC, we were able to quickly evaluate the prevalence of this new variant and take learnings from this effort to better and more proactively characterize future strains that will emerge.” Helix and Illumina are expanding the scope of their collaboration to examine a higher volume of samples on an ongoing basis for both the presence of B.1.1.7 and new strains. This will empower public and private entities to react quickly to any potential changes in pathogenicity of the virus or effectiveness of diagnostics, therapeutics, and vaccines. About Illumina Illumina is improving human health by unlocking the power of the genome. Our focus on innovation has established us as the global leader in DNA sequencing and array-based technologies, serving customers in the research, clinical, and applied markets. Our products are used for applications in the life sciences, oncology, reproductive health, agriculture, and other emerging segments. To learn more, visit www.illumina.com and connect with us on Twitter, Facebook, LinkedIn, Instagram, and YouTube. About Helix Helix is the leading population genomics company operating at the intersection of clinical care, research, and genomics. Its end-to-end platform enables health systems, life sciences companies, and payers to advance genomic research and accelerate the integration of genomic data into clinical care. Powered by one of the world’s largest CLIA / CAP next-generation sequencing labs and its proprietary Exome+® assay, Helix supports all aspects of population genomics including recruitment and engagement, clinically actionable disease screening, return of results, and basic and translational research. In response to the COVID-19 public health crisis, Helix has launched a sensitive and scalable end-to-end COVID-19 test system to meet the needs of health systems, employers, governments, and other organizations across the country. Learn more at www.helix.com. Contacts Illumina Media Dr. Karen Birmingham 646.355.2111[email protected] Investor Relations Juliet Cunningham 858.200.6583[email protected] Helix Sarah Bobulsky VP, Strategy & Marketing[email protected] https://www.businesswire.com/news/home/20210105006007/en/Illumina-and-Helix-Collaborate-to-Assess-Prevalence-of-New-SARS-CoV-2-UK-Variant-B.1.1.7-in-the-US-and-Develop-National-Surveillance-Infrastructure Link to comment Share on other sites More sharing options...
niman Posted January 9, 2021 Author Report Share Posted January 9, 2021 Link to comment Share on other sites More sharing options...
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