423 - SARS-CoV-2 NGS Assay Powered by Biotia COVID-DX Software

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Presenting Author(s)

Dorottya Nagy-Szakal

Chief Medical Officer
Biotia Inc.
New York, New York
Disclosure: Biotia (Employee)

Co-Author(s)

MC

Mara Couto-Rodriguez

Clinical Research Scientist
Biotia Inc.
New York, New York
Disclosure: Biotia (Employee)
JB

Joseph Barrows

Director of Software Engineering
Biotia
New York, New York
Disclosure: Biotia, Inc. (Employee, Shareholder)
Heather L. Wells

Consultant
Biotia
New York, New York
Disclosure: Biotia (Consultant)
MD

Marilyne Debieu

Bioinformatics Specialist
Biotia
New York, New York
Disclosure: Biotia (Employee)
CH

Courteny Hager

Project Administrator
Biotia
New York, New York
Disclosure: Biotia (Employee)
KB

Kristin Butcher

Research and Development Scientist
Twist Bioscience
South San Francisco, California
Disclosure: Twist Bioscience (Employee)
SC

Siyuan Chen

Senior Director of R&D
Twist Bioscience
New York, New York
Disclosure: Twist Bioscience (Employee)
RB

Robert Boorstein

Medical Director
Lenco Diagnostic Laboratories
Brooklyn, New York
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
CM

Christopher E. Mason

Co-Founder
Biotia Inc.
New York, New York
Disclosure: Biotia (Board Member, Employee, Shareholder)
NO

Niamh B. O'Hara

Chief Executive Officer and Co-Founder
Biotia Inc.
New York, New York
Disclosure: Biotia (Board Member, Employee, Shareholder)Twist (Other Financial or Material Support, I am CEO of Biotia and Biotia has business partnership with Twist)

Background: COVID-19 had spread quickly, causing an international public health emergency with an alarming global shortage of COVID-19 diagnostic tests. We developed and clinically validated a next-generation sequencing (NGS)-based target enrichment assay with the COVID-DX Software tailored for the detection, characterization, and surveillance of the SARS-CoV-2 viral genome.

Methods: The SARS-CoV-2 NGS assay consists of components including library preparation, target enrichment, sequencing, and a COVID-DX Software analysis tool. The NGS library preparation starts with extracted RNA from nasopharyngeal (NP) swabs followed by cDNA synthesis and conversion to Illumina TruSeq-compatible libraries using the Twist Library Preparation Kit via Enzymatic Fragmentation and Unique Dual Indices (UDI). The library is then enriched for SARS-CoV-2 sequences using a panel of dsDNA biotin-labeled probes, specifically designed to target the SARS-CoV-2 genome, then sequenced on an Illumina NextSeq 550 platform. The COVID-DX Software analyzes sequence results and provides a clinically oriented report, including the presence/absence of SARS-CoV-2 for diagnostic use. An additional research use only report describes the assay performance, estimated viral titer, coverage across the viral genome, genetic variants, and phylogenetic analysis.

Results: The SARS-CoV-2 NGS Assay was validated on 30 positive and 30 negative clinical samples. To measure the sensitivity and specificity of the assay, the positive and negative percent agreement (PPA, NPA) was defined in comparison to an orthogonal EUA RT-PCR assay (PPA [95% CI]: 96.77% [90.56%-100%] and NPA [95% CI]: 100% [100%-100%]). Data reported using our assay defined the limit of detection to be 40 copies/ml using heat-inactivated SARS-CoV-2 viral genome in clinical matrices. In-silico analysis provided >99.9% coverage across the SARS-CoV-2 viral genome and no cross-reactivity with evolutionarily similar respiratory pathogens.

Conclusion: The SARS-CoV-2 NGS Assay powered by the COVID-DX Software can be used to detect the SARS-CoV-2 virus and provide additional insight into viral titer and genetic variants to track transmission, stratify risk, predict outcome and therapeutic response, and control the spread of infectious disease.