COVID-19 Detection

Dr. Pete Vallone 

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Introduction

Applied Genetics Group – Biomolecular Measurement Division

Advancing technology and traceability through quality genetic 

measurements to aid work in Forensic and Clinical Genetics.

Forensic SRMs

• PCR-Based DNA Profiling Standard (2391d)

• Human DNA quantitation standard (2372a)

• Mitochondrial DNA Sequencing (2392, 2392-I)

Clinical SRMs

• BK virus (2365)

• Cytomegalovirus (CMV) (2366a)

• Huntington’s (2393)

• JC virus (coming in FY20!)

Variations on the polymerase chain reaction 

(PCR) technique such as rapid PCR, 

multiplex PCR, real-time PCR, and digital 

PCR are used to genotype, sequence, and 

provide quantitative information

pertaining to an organism's genome.

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Initial questions

Controls and Standards: Survey existing 

commercial controls: format, concentration 

characterization

Stakeholders: Who can we work with? 

Working groups, other NMIs, industry, 

government agencies.

Detection: Focusing on molecular Dx (viral 

RNA detection). 

How are labs performing the analysis?

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https://digitalworldbiology.com/blog/what-best-way-test-covid-19
Initial ideas and measurements

Inclusivity: We work collaboratively. We value diversity of people and 

ideas to attain the best solutions to multidisciplinary challenges. 

Detection: Develop competency on RNA 

detection assays (RT-qPCR). Bring WHO and U.S. 

CDC assays in house.

Controls and Standards: What would a NIST 

SARS-CoV-2 material look like? 

How fast can this be carried out?

Interlaboratory and collaborative studies:

Participation and design of SARS-CoV-2 detection 

studies.

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All evolving in real-time

https://www.cdc.gov/coronavirus/2019-

ncov/images/coronavirus-testkit-sample-5.jpg
Research Grade Testing Material

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Creating RGTM 10169

4kb RNA fragments of the SARS-CoV-2 genome characterized using digital PCR

Goal: to send the RGTM out to commercial 

makers of controls and Dx assays, metrology 

institutes, and government agencies

Target: by the end of June 2020

Supported through CARES Act funds

Figure – David Duewer NIST
Interlaboratory Assessments

INSTAND: We participated in a global EQA – external quality 

assessment for SARS-CoV-2. Inactivated SARS-CoV-2 samples 

were extracted and analyzed. Over 450 labs participated. 

Results were submitted for EQA scheme 340 – summary can be 

downloaded at https://www.instand-ev.de/en/

CCQM: Nucleic acid working group Pilot study P199b will expand 

on capabilities demonstrated in the P199 study (HIV-1 RNA copy 

number quantification) for targeted RNA copy number 

concentration and viral gene quantification. (Measurements will 

be carried out early this summer)

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Supported through CARES Act funds
Dx Assay performance

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All evolving in real-time

• As the genome of SARS-CoV-2 develops 

mutations over the course of the pandemic, 

there is a likelihood that one will fall within the 

targeted regions of the CDC diagnostic tests

• How will mutations affect qPCR assay 

performance?

• How does digital PCR ‘tolerate’ mutations

• Materials in house, will continue after 

production of RGTM 10169

Assay development Currently circulating strains

Accumulations of Mutations over time

Supported through internal and CARES Act funds

https://www.gisaid.org/epiflu-applications/next-hcov-19-app/
Controls and Standards

https://jimb.stanford.edu/covid-19-standards

https://poeli.gitlab.io/collated_vendor_info/ 8

All evolving in real-time

Working towards a minimum information 

standard for SARS-CoV-2 controls

• Type of material

• Genes represented

• Storage

• Amount

• Method of characterization

• Matrix

• Purpose

Supported through CARES Act funds

Website live – working on manuscript to describe the 

“Minimum Information About a Viral Control” or MIAViC
qPCR Data analysis

In collaboration with the NIST ITL: Mathematical approaches to improve 

the sensitivity of qPCR detection methods

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All evolving in real-time

https://arxiv.org/abs/2004.05466

Supported through internal and CARES Act funds

Pre-print currently available
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