News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

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Clinical Laboratories and Pathology Groups

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New CDC-led Genomics Consortium That Harnessed Genetic Sequencing to Track the SARS-CoV-2 Coronavirus includes Clinical Laboratories and IVD Firms

Medical laboratories are already using gene sequencing as part of a global effort to identify new variants of the coronavirus and their genetic ancestors

Thanks to advances in genetic sequencing technology that enable medical laboratories to sequence organisms faster, more accurately, and at lower cost than ever before, clinical pathology laboratories worldwide are using that capability to analyze the SARS-CoV-2 coronavirus and identify variants as they emerge in different parts of the world.

The US Centers for Disease Control and Prevention (CDC) now plans to harness the power of gene sequencing through a new consortium called SPHERES (SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance) to “coordinate SARS-CoV-2 sequencing across the United States,” states a CDC news release. The consortium is led by the CDC’s Advanced Molecular Detection (AMD) program and “aims to generate information about the virus that will strengthen COVID-19 mitigation strategies.”

The consortium is comprised of 11 federal agencies, 20 academic institutions, state public health laboratories in 21 states, nine non-profit research organizations, and 14 lab and IVD companies, including:

  • Abbott Diagnostics
  • bioMérieux
  • Color Genomics
  • Ginkgo Bioworks
  • IDbyDNA
  • Illumina
  • In-Q-Tel
  • LabCorp
  • One Codex
  • Oxford Nanopore Technologies
  • Pacific Biosciences
  • Qiagen
  • Quest Diagnostics
  • Verily Life Sciences

‘Fundamentally Changing How Public Health Responds’

Gene sequencing and related technologies have “fundamentally changed how public health responds in terms of surveillance and outbreak response,” said Duncan MacCannell, PhD, Chief Science Officer for the CDC’s Office of Advanced Molecular Detection (OAMD), in an April 30 New York Times (NYT) article, which stated that the CDC SPHERES program “will help trace patterns of transmission, investigate outbreaks, and map how the virus is evolving, which can affect a cure.”

The CDC says that rapid DNA sequencing of SARS-CoV-2 will help monitor significant changes in the virus, support contact tracing efforts, provide information for developers of diagnostics and therapies, and “advance public health research in the areas of transmission dynamics, host response, and evolution of the virus.”

The sequencing laboratories in the consortium have agreed to “release their information into the public domain quickly and in a standard way,” the NYT reported, adding that the project includes standards for what types of information medical laboratories should submit, including, “where and when a sample was taken,” and other critical details.

Even in its early phase, the CDC’s SPHERES project has “made a tangible impact in the number of sequences we’re able to deposit and make publicly available on a daily basis,” said Pavitra Roychoudhury, PhD (above), Acting Instructor and Senior Fellow at the University of Washington, and Research Associate at Fred Hutchinson Cancer Research Center, in an e-mail to the NYT. “What we’re essentially doing is reading these small fragments of viral material and trying to jigsaw puzzle the genome together,” said Roychoudhury in an April 28 New York Times article which covered in detail how experts are tracking the coronavirus since it arrived in the US. (Photo copyright: LinkedIn.)

Sharing Data Between Sequencing Laboratories and Biotech Companies

The CDC announced the SPHERES initiative on April 30, although it launched in early April, the NYT reported.

According to the CDC, SPHERES’ objectives include:

  • To bring together a network of sequencing laboratories, bioinformatics capacity and subject matter expertise under the umbrella of a massive and coordinated public health sequencing effort.
  • To identify and prioritize capabilities and resource needs across the network and to align sources of federal, non-governmental, and private sector funding and support with areas of greatest impact and need.
  • To improve coordination of genomic sequencing between institutions and jurisdictions and to enable more resilience across the network.
  • To champion concepts of openness, standards-based analysis, and rapid data sharing throughout the United States and worldwide during the COVID-19 pandemic response.
  • To accelerate data generation and sharing, including the rapid release of high-quality viral sequence data from clinical and public health laboratories into both the National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing All Influenza Data (GISAID) repositories in near-real time.
  • To provide a common forum for US public, private, and academic institutions to share protocols, methods, bioinformatics tools, standards, and best practices.
  • To establish consistent data and metadata standards, including streamlined repository submission processes, sample prioritization criteria, and a framework for shared, privacy-compliant unique case identifiers.
  • To align with other national sequencing and bioinformatics networks, and to support global efforts to advance the use of standards and open data in public health.

Implications for Developing a Vaccine

As the virus continues to mutate and evolve, one question is whether a vaccine developed for one variant will work on others. However, several experts told The Washington Post that the SARS-CoV-2 coronavirus is relatively stable compared to viruses that cause seasonal flu (influenza).

“At this point, the mutation rate of the virus would suggest that the vaccine developed for SARS-CoV-2 would be a single vaccine, rather than a new vaccine every year like the flu vaccine,” Peter Thielen, a molecular biologist at the Johns Hopkins University Applied Physics Laboratory, told the Washington Post.

Nor, he said, is one variant likely to cause worse clinical outcomes than others. “So far, we don’t have any evidence linking a specific virus [strain] to any disease severity score. Right now, disease severity is much more likely to be driven by other factors.”

That point was echoed by Anthony Fauci, MD, Director of the National Institute of Allergy and Infectious Diseases, in a March 22 interview with CBS News. “I have no doubt it’s mutating as all RNA viruses mutate,” he said. However, he added, “we have not seen thus far any type of change in the way it’s acting.”

Fast improvements in gene sequencing technology have made it faster, more accurate, and cheaper to sequence. Thus, as the COVID-19 outbreak happened, there were many clinical laboratories around the world with the equipment, the staff, and the expertise to sequence the novel coronavirus and watch it mutate from generation to generation and from region to region around the globe. This capability has never been available in outbreaks prior to the current SARS-CoV-2 outbreak.

—Stephen Beale

Related Information:

Genome Canada Leads $40 Million Genomics Initiative to Address COVID-19 Pandemic

COVID-19 Genomics UK

Bad News Wrapped in Protein: Inside the Coronavirus Genome

How Coronavirus Mutates and Spreads

Covid-19 Arrived in Seattle. Where It Went from There Stunned the Scientists

8 Strains of the Coronavirus Are Circling the Globe. Here’s What Clues They’re Giving Scientists

SARS-CoV-2 Genomes Let Researchers Retrace Viral Spread, Mitigation Effects

Varied COVID-19 Strains Not a Problem for Vaccines—For Now

The Coronavirus Mutates More Slowly Than the Flu, Which Means a Vaccine Will Likely Be Effective Long-Term

Response to “On the Origin and Continuing Evolution of SARS-CoV-2”

Comparison of In Vitro Diagnostic Industry’s Top Five Trends for 2015 and 2016 Reveals Rapid Technology Advances Intended to Give Clinical Laboratories New Diagnostic Tools

Of the five trends described in a report published by Kalorama, only two made the list for both years: Consolidation within the IVD industry and growth in molecular point of care

What a difference one year can make in the most significant trends influencing the in vitro diagnostics (IVD) industry, which also influences clinical laboratories, the largest customers of IVD manufacturers. These insights come from comparing the top five IVD trends for 2016 as identified by Kalorama Information from its top five IVD trends that it says dominated during 2015.

Kalorama is a division of MarketResearch.com, a company that publishes market research in the life sciences. In a report titled, “Five IVD Market Trends to Watch for in 2016,” it published its picks for the top five trends in IVD testing for 2016. The five most prominent trends recognized by the healthcare research marketer are as follows: (more…)

Frost & Sullivan Report Identifies Molecular Diagnostics as Fastest-Growing Sector of Clinical Pathology Laboratory Testing

Annual growth rates of 11% or more is predicted for molecular diagnostics in coming years

Just as consolidation and acquisitions reshaped the in vitro diagnostics (IVD) manufacturing industry and concentrated market share among just a handful of multi-billion dollar IVD giants, a similar consolidation can be seen in the molecular diagnostics sector. Today it is estimated that just nine global companies control 75% of the molecular diagnostics market.

That market concentration means clinical laboratories and anatomic pathology groups have a just a handful of primary vendors from which to purchase many of the molecular diagnostic assays and genetic tests that are used most frequently in clinical care.

Frost and Sullivan published a detailed study about the molecular diagnostics marketplace. The consulting firm estimated that worldwide sales of molecular diagnostics totaled $4.1 billion in 2010. By contrast, total IVD sales globally were about $48 billion in 2010. That total includes the routine, reference, and esoteric test kits, reagents, and supplies used every day by medical laboratories.

(more…)

Pathologists and Clinical Labs Can Expect to See More Companion Diagnostic Tests

Pharmaceutical Companies Partnering with IVD Manufacturers to Develop Companion Diagnostic Tests for their Therapeutic Drugs

Growing acceptance of companion diagnostics is a trend with the potential to greatly increase the value that clinical pathology laboratory testing delivers to physicians, patients, and payers. In 2010, it was increasingly common to see a pharmaceutical company announce an agreement with an in vitro diagnostics (IVD) manufacturer to develop a companion diagnostic test specifically for a therapeutic drug under development by that pharmaceutical company.

As most pathologists and clinical managers know, use of a companion diagnostic test is expected to add precision to the physician’s decision to prescribe therapeutic drugs. Thus, the increased number of public announcements during 2010 about companion diagnostic test development deals involving a pharmaceutical company and an IVD manufacturer indicates this trend is establishing solid roots. (more…)

New Technology Stores DNA at Room Temperature, Eliminates Need for Specimen Storage Freezers

There’s a green bonus: GenVault’s new storage systems can reduce a clinical laboratory’s carbon footprint

Innovative laboratory technologies continue to disrupt the status quo as new products and services enter the marketplace. Among them is new dry-storage technology from Carlsbad, California-based GenVault Corp. that allows biological specimens to be stored at room temperature. It is a technology that has applications for medical laboratories and pathology groups.

(more…)

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