409 - Rapid Development of a Multiplexed PCR Prototype Method that Offers a Syndromic Diagnostic Option by Integrating Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Detection with Twenty-One Other Common Respiratory Pathogens

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Presenting Author(s)

Usha Spaulding

Senior Scientist
BioFire Diagnostics, LLC
Salt Lake City, Utah
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.

Co-Author(s)

JA

Jeremiah Antosch

Research Associate
BioFire Diagnostics, LLC
Salt Lake City, Utah
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
Js

Jessica stone

Research Associate
BioFire Diagnostics, LLC
Salt Lake City, Utah
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
TR

Tanner Robinson

Research Associate
BioFire Diagnostics, LLC
Salt Lake City, Utah
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
KH

Kerrin Halo

Research Associate
BioFire Diagnostics, LLC
Salt Lake City, Utah
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
IK

Iryna Kavetska

Research Associate
BioFire Diagnostics, LLC
Salt Lake City, Utah
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
TH

Tyler Healy

Research Associate
BioFire Diagnostics, LLC
Salt Lake City, Utah
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
AT

Alex Taylor

Research Associate
BioFire Diagnostics, LLC
Salt Lake City, Utah
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
MJ

Matthew Jones

Associate Director
BioFire Diagnostics, LLC
Salt Lake City, Utah
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
TT

Toma Todorov

Research Associate
BioFire Diagnostics, LLC
Salt Lake City, Utah
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
ZL

Zhenmei Lu

Research Associate
BioFire Diagnostics, LLC
Salt Lake City, Utah
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
JC

Joann Cloud

Scientist II
BioFire Diagnostics, LLC
Salt Lake City, Utah
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
MB

Maggie Buccambuso

Scientist
BioFire Diagnostics, LLC
Salt Lake City, Utah
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
BG

Brad Graham

Senior Scientist
BioFire Diagnostics, LLC
Salt Lake City, Utah
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
JB

Jeremy Boone

Principal Investigator
MRIGlobal
Kansas City, Missouri
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
HW

Hillary Wood

Senior Scientist/BSL-3 Lab Manager
MRIGlobal
Kansas City, Missouri
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
MR

Margarita Rogatcheva

Director of Biochemistry
BioFire Diagnostics, LLC
Salt Lake City, Utah
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.

Background: The US Food and Drug Administration (FDA) has granted Emergency Use Authorization (EUA) for multiple PCR-based tests to aid in the diagnosis and containment of COVID-19. A vast majority of these tests detect only SARS-CoV-2 which causes symptoms similar to those caused by other respiratory pathogens. Hence, other etiologies or co-infections requiring a different therapy may be missed. The prototype BioFire® Respiratory Panel 2.1 (RP2.1) continues the syndromic approach of the FDA-cleared BioFire® Respiratory Panel 2 (RP2), to provide the ability to simultaneously detect 22 common respiratory pathogens, including SARS-CoV-2, from nasopharyngeal swab (NPS) specimens. The goal of this study was to rapidly develop a RP2.1 prototype that contains high-performing SARS-CoV-2 assays and maintains the performance of assays retained from RP2.

Methods: Twelve assays designed for four SARS-CoV-2 genes were tested for compatibility with the RP2 assays and conditions. All retained RP2 assays were evaluated to verify established RP2 performance. The sensitivity of novel SARS-CoV-2 assays was estimated with nucleic acids at BioFire and contrived live virus NPS samples at MRIGlobal. Primer homology of SARS-CoV-2 assays to > 15,000 SARS-CoV-2 genomes from accessible databases was assessed for in silico inclusivity

Results: A prototype multiplexed PCR panel containing assays for 22 pathogens was developed in a 5-week period. Of the 12 SARS-CoV-2 assays, 7 were compatible with the RP2 conditions; 2 were selected for the prototype. No false positive results due to cross-reactivity with unintended analytes or non-specific amplification in negative samples were observed for any assays. All retained RP2 assays were detected at or near their established LoD. The SARS-CoV-2 LoD was estimated at 10³-10²genomes/mL with both nucleic acid and live virus spiked into NPS. Together, the assays are 100% inclusive for all 15,370 complete SARS-CoV-2 genomes assessed in silico for reactivity.

Conclusion: The results of this study indicate a strong potential for RP2.1 to serve as a sensitive comprehensive syndromic option to aid in the diagnosis of COVID-19 as well as respiratory syndromes caused by other pathogens, including co-infections.

This study was performed with a test not cleared for diagnostic use.