Partnership to Create New Tool for Rapid SARS-CoV-2 Variant Detection

Widespread and scalable surveillance of the SARS-CoV-2 virus on a national basis won’t be possible if identification of the variants and subvariants that keep popping up remains a game of Whac-a-Mole. But help may be on the way. Thermo Fisher Scientific announced that it has teamed with Helix and Rosalind, Inc. on a National Institutes of Health (NIH)-supported project to develop a new SARS-CoV-2 genotyping method allowing for more rapid identification of virus variants.

The Strategic Opportunity

Current detection and tracing of new CoV-2 variants is based on next-generation sequencing (NGS), with roughly 5 percent of randomly selected positive samples in the US sent for variant identification. The problem with NGS is that it’s slow, taking up to 21 days from the date of positive result for variant data to become available in public repositories. Widespread adoption of genotyping-based identification would be much faster, not to mention cheaper since it would enable labs to reduce costs for strain subtyping required for NGS, allowing for classifying a high percentage of positive samples and provide information in just two or three days. Samples that can’t be assigned to a known variant via the genotyping approach would then become prime suspects for new variants. Large numbers of such samples would send up a red flag that a new variant might be emerging and give test and vaccine makers time to analyze and adjust their products accordingly.

The NIH RADx Project

Funded by the NIH Rapid Acceleration of Diagnostics (RADx) Initiative, the Thermo Fisher/Helix/Rosalind project utilizes a polymerase chain reaction (PCR)-based genotyping method that any test lab performing real-time PCR testing can use. Labs can use the Rosalind Tracker website to make the data generated publicly available. “Our approach makes it possible to conduct surveillance testing on a significantly larger number of samples and quickly determine which variant is present in a sample,” said Dr. Eric Lai, one of the co-lead investigators, in a statement. The collaborators used Rosalind’s cloud-based data analytics platform to create a centralized tool that labs can use to aggregate and analyze the data in a real-time dashboard format offering a snapshot of the most current virus strains circulating the country. Thermo Fisher’s role: Supply the tests by updating its TaqMan SARS-CoV-2 Mutation Panel research-use only assay to include the four markers that can detect the Omicron and Delta variants with high precision. Population genomics and viral surveillance company Helix validated the technology. “Our challenge has been staying in front of this pandemic at the rate the virus is evolving,” noted Rosalind CEO Tim Wesselman in a press release. “We’ve demonstrated an approach for maintaining highly accurate markers, rapidly implementing marker updates in manufacturing, and quickly deploying these assays to nationwide testing labs for validating COVID-19 positivity with lineage assignment.” Here’s a summary of some of other key strategic diagnostic deals announced in March 2022:

Strategic Alliances, Partnerships, & Collaborations

Partner 1	Partner(s) 2+	Deal Summary
Thermo Fisher Scientific	Helix and Rosalind	• Objective: Develop new, faster genotyping method for identifying emerging new variants of SARS-CoV-2 virus • Dynamic: Create PCR-based method allowing for variant-agnostic detection of virus and assigning lineages to viral variants • Project funded by National Institute of Biomedical Imaging and Bioengineering under NIH’s RADx initiative to increase SARS-CoV-2 testing capacity
Siemens Healthineers	Proscia	• Objective: Expand Siemens’ position in global digital pathology market • Dynamic: Combine Siemens Healthineers’ Enterprise Imaging offering with Proscia’s Concentriq Dx platform
Centogene	Pfizer	• Objective: Expand existing data access + collaboration agreement • Dynamic: Initial 2019 deal gave Pfizer access to Centogene's bio/databank for discovery and validation of genetic and biochemical targets for rare disease therapies • Under expansion, cohort of patient samples from Centogene's bio/databank will be used to validate rare genetic causes of neurodegenerative diseases as potential drug targets
Lumea	Verily	• Objective: Develop digital pathology products to diagnose, prognose, and guide prostate cancer therapy selection • Dynamic: combine Verily’s artificial intelligence algorithms with Lehi, Lumea’s end-to-end digital pathology platform
Illumina Singapore	Panton Trivitron Healthcare	• Objective: Expand use of NGS-based in vitro diagnostics in India • Dynamic: Four-year deal to develop and distribute suite of IVD assays for oncology, infectious diseases, and prenatal health • Trivitron to manufacture and market tests following regulatory approvals
Biognosys	Kymera Therapeutics'	• Objective: Use Biognosys’ proteomics panels to advance Kymera Therapeutics' drug-discovery and clinical trials • Dynamic: Use Biognosys' newly launched TrueSignature platform to monitor and quantify protein degradation associated with Kymera drug candidates
Ultivue	Sirona Dx	• Objective: Comarket tissue-based spatial multiplexed immunophenotyping products • Dynamic: Offer Ultivue's InSituPlex technology, which uses antibody-DNA barcoding and signal amplification for biomarker detection and analysis in tissue samples, along with contract research organization Sirona Dx's ultra-high parameter, multiplexed imaging services
Sophia Genetics	Realm IDx	• Objective: Codevelop new genomic applications and commercialize multimodal applications to widen use of next-generation sequencing for cancer care • Dynamic: Letter of intent to use Realm IDx’s subsidiary Ambry Genetics’ TumorNEXT-HRD detecting somatic tumor mutations and germline mutations in blood in combination with Sophia's DDM (Data-Driven Medicine) analytics platform to improve detection of homologous recombination deficiency • May use Ambry's lab for sequencing
Audere	Medical Diagnostech	• Objective: Combine Medical Diagnostech’s SARS-CoV-2 antigen test with Audere's HealthPulse app to provide for rapid result interpretation in Africa • Dynamic: Integrate rapid lateral flow test with public health reporting systems in Africa
PathAI	Cleveland Clinic	• Objective: Enable development and usage of artificial intelligence-powered pathology diagnostics to improve patient care • Dynamic: Five-year agreement to digitize pathology specimens across multiple disease areas, with data to be linked with clinical and molecular information from Cleveland Clinic to create a multimodal dataset to conduct research with PathAI's technology platform and algorithms • PathAI to use data from the digitized slides to develop and improve its algorithms
BioReference Laboratories	9am.health	• Objective: Offer at-home lab testing services • Dynamic: 9am.health to offer its customers access to BioReference's Scarlet Health blood-drawing service for $15 per month
Insitro	Genomics England	• Objective: Embed Insitro’s machine learning-powered search capabilities into Genomics England's phenotypic and genomic database • Dynamic: Apply Insitro’s machine learning technology to histopathology images and genomic data in Genomics England’s database to create a multimodal representation of clinical data enabling users to search for images, biopsies, and cases based on semantic similarity rather than visual similarity
Arctoris	Evariste Technologies	• Objective: Identify novel small molecule kinase inhibitors for treatment of patients with non-small cell lung cancer (NSCLC) • Dynamic: Joint venture to combine companies’ respective platforms for AI-guided and robotics-powered drug discovery to develop set of novel kinase inhibitors against cMET
Bruker	Newomics	• Objective: Comarket mass spectrometry solutions for drug discovery • Dynamic: Market Newomics' microflow-nanospray electrospray ionization products with Bruker's maxis II and timsTOF Pro 2 mass spectrometers
Lifebit Biotech	Boehringer Ingelheim	• Objective: Build scalable bioinformatics platform to standardize data sources and types, curate information, and identify data and services that could be moved to the cloud • Dynamic: Platform to be built in Lifebit CloudOS environment and federated to give Boehringer access to data from third-party biobanks without having to move data around
GeneDx	Saol Therapeutics	• Objective: Identify young children with the rare mitochondrial disorder pyruvate dehydrogenase complex deficiency to participate in Phase III clinical study of dichloroacetate (DCA) • Dynamic: Use GeneDx's genetic testing tools to speed recruitment by making physicians treating PDCD aware of trial
Singular Genomics Systems	Roche	• Objective: Ensure Roche’s sample and library preparation kits work with Singular's G4 sequencing platform • Dynamic: Work with Roche to enable Kapa Library Preparation kits, including Kapa EvoPlus and HyperPrep kits with G4
Singular Genomics Systems	Agilent Technologies	• Objective: Ensure Agilent’s sample and library preparation kits work with Singular's G4 sequencing platform • Dynamic: Work with Agilent to validate SureSelect target enrichment products
Singular Genomics Systems	Qiagen	• Objective: Ensure Qiagen’s sample and library preparation kits work with Singular's G4 sequencing platform • Dynamic: Work with Qiagen to validate Qiaseq kits for both DNA and RNA sample prep

Distribution, Sales, & Marketing Agreements

Product Owner	Distributor	Deal Summary
Bioké	Applied Cells	• Products: Bioké’s MARS (multi-physics automated reconfigurable separation) cell isolation and separation instrument • Territory: Belgium, Netherlands, Luxembourg
SphingoTec	Rivaara Labs	• Products: SphingoTec’s Nexus IB10 fully automated rapid immunoassay point-of-care instrument and related tests • Territory: India • Exclusive
Sense Biodetection	Cruinn Diagnostics	• Products: Sense Biodetection’s Veros COVID-19 test, which runs on firm’s single-use, instrument-free Veros point-of-care platform • Territory: Ireland
Saladax Biomedical	Beckman Coulter (owned by Danaher)	• Products: Saladax’s MyCare Psychiatry Laboratory Assays • Territory: Global
Applied BioCode	Hardy Diagnostics	• Products: Applied BioCode's MDx-3000 System and tests for upper respiratory and gastrointestinal infections, and analyte specific reagents (ASRs) • Territory: US • Exclusive
PixCell Medical	Katalyst Diagnostics	• Products: PixCell's HemoScreen complete blood count (CBC) analyzer • Territories: UK, Ireland • Exclusive

Licenses

Licensor	Licensee	Deal Summary
Penn State Research Foundation	Inscripta	Inscripta licenses CRISPR-Cas9 genome editing technology enabling simultaneous use of multiple guide RNAs (gRNAs), which lets researchers target several genes at once
Cornell University	Eurofins Viracor	Exclusive license to sequencing-based liquid biopsy technology for tracking tissue damage in COVID-19 and transplant patients, which Eurofins Viracor intends to use to develop assays to scan for complications of hematopoietic cell transplantation, gauge COVID-19 cell damage, and identify urinary tract infections in kidney transplant patients
Royal Phillips	Novigenix	Novigenix gets access to Philips' technology on tumor-derived immuno-transcriptomic signatures to develop commercial prostate cancer products

Government Contracts

Contractor	Govt. Agency	Contract Summary
Leidos	National Institute of Allergy and Infectious Diseases (NIAD)	$545 million, 7-year contract and will be funded by NIAID, NIH, and Department of Health and Human Services to provide biomedical preclinical and development capabilities