Direct NP- A cost-effective extraction-free RT-qPCR based test for SARS-CoV-2

Rasesh Y. Parikh; Satish N. Nadig; Shikhar Mehrotra; Philip H. Howe; Vamsi K. Gangaraju

doi:10.1016/j.heliyon.2022.e09735

Direct NP- A cost-effective extraction-free RT-qPCR based test for SARS-CoV-2

Rasesh Y. Parikh^*, Satish N. Nadig, Shikhar Mehrotra, Philip H. Howe, Vamsi K. Gangaraju^*

^*Corresponding author for this work

Surgery, Transplant Surgery Division

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

Over 2.4 million daily total tests are currently being performed for SARS-CoV-2, in the United States. The most common SARS-CoV-2 tests require RNA extraction and purification. Extraction of RNA is a time-consuming and costly step that requires a constant supply of reagents and accessories. With the current testing demand, the supply chain remains the bottleneck for RNA extraction. Here, we report Direct NP- a cost-effective extraction-free RT-qPCR based dualplex test for SARS-CoV-2 from Nasopharyngeal (NP) swab specimens. Direct NP detects SARS-CoV-2 viral RNA from heat-denatured patient specimens using a dualplex RT-qPCR assay. Direct NP showed 92.5% positive percentage agreement (PPA) (95% Confidence Interval (CI) = 79.61%–98.43%) and 97% negative percent agreement (NPA) (95% CI = 89.11–100%) with the CDC assay. Direct NP reduces the cost per test to $2, making it suitable for broad-scale testing while lowering the cost burden on the healthcare system.

Original language	English (US)
Article number	e09735
Journal	Heliyon
Volume	8
Issue number	6
DOIs	https://doi.org/10.1016/j.heliyon.2022.e09735
State	Published - Jun 2022

Funding

This work was funded by the Enterprise Strategic Funding for Pandemic Response from the Medical University of South Carolina .

Keywords

Broad-scale
COVID-19
Dualplex
RT-qPCR
SARS-CoV-2
Test

ASJC Scopus subject areas

General

Access to Document

10.1016/j.heliyon.2022.e09735

Cite this

@article{5410031d5db14de190f256b810baad05,

title = "Direct NP- A cost-effective extraction-free RT-qPCR based test for SARS-CoV-2",

abstract = "Over 2.4 million daily total tests are currently being performed for SARS-CoV-2, in the United States. The most common SARS-CoV-2 tests require RNA extraction and purification. Extraction of RNA is a time-consuming and costly step that requires a constant supply of reagents and accessories. With the current testing demand, the supply chain remains the bottleneck for RNA extraction. Here, we report Direct NP- a cost-effective extraction-free RT-qPCR based dualplex test for SARS-CoV-2 from Nasopharyngeal (NP) swab specimens. Direct NP detects SARS-CoV-2 viral RNA from heat-denatured patient specimens using a dualplex RT-qPCR assay. Direct NP showed 92.5% positive percentage agreement (PPA) (95% Confidence Interval (CI) = 79.61%–98.43%) and 97% negative percent agreement (NPA) (95% CI = 89.11–100%) with the CDC assay. Direct NP reduces the cost per test to $2, making it suitable for broad-scale testing while lowering the cost burden on the healthcare system.",

keywords = "Broad-scale, COVID-19, Dualplex, RT-qPCR, SARS-CoV-2, Test",

author = "Parikh, {Rasesh Y.} and Nadig, {Satish N.} and Shikhar Mehrotra and Howe, {Philip H.} and Gangaraju, {Vamsi K.}",

note = "Funding Information: This work was funded by the Enterprise Strategic Funding for Pandemic Response from the Medical University of South Carolina . Publisher Copyright: {\textcopyright} 2022 The Authors",

year = "2022",

month = jun,

doi = "10.1016/j.heliyon.2022.e09735",

language = "English (US)",

volume = "8",

journal = "Heliyon",

issn = "2405-8440",

publisher = "Elsevier BV",

number = "6",

}

TY - JOUR

T1 - Direct NP- A cost-effective extraction-free RT-qPCR based test for SARS-CoV-2

AU - Parikh, Rasesh Y.

AU - Nadig, Satish N.

AU - Mehrotra, Shikhar

AU - Howe, Philip H.

AU - Gangaraju, Vamsi K.

PY - 2022/6

Y1 - 2022/6

N2 - Over 2.4 million daily total tests are currently being performed for SARS-CoV-2, in the United States. The most common SARS-CoV-2 tests require RNA extraction and purification. Extraction of RNA is a time-consuming and costly step that requires a constant supply of reagents and accessories. With the current testing demand, the supply chain remains the bottleneck for RNA extraction. Here, we report Direct NP- a cost-effective extraction-free RT-qPCR based dualplex test for SARS-CoV-2 from Nasopharyngeal (NP) swab specimens. Direct NP detects SARS-CoV-2 viral RNA from heat-denatured patient specimens using a dualplex RT-qPCR assay. Direct NP showed 92.5% positive percentage agreement (PPA) (95% Confidence Interval (CI) = 79.61%–98.43%) and 97% negative percent agreement (NPA) (95% CI = 89.11–100%) with the CDC assay. Direct NP reduces the cost per test to $2, making it suitable for broad-scale testing while lowering the cost burden on the healthcare system.

AB - Over 2.4 million daily total tests are currently being performed for SARS-CoV-2, in the United States. The most common SARS-CoV-2 tests require RNA extraction and purification. Extraction of RNA is a time-consuming and costly step that requires a constant supply of reagents and accessories. With the current testing demand, the supply chain remains the bottleneck for RNA extraction. Here, we report Direct NP- a cost-effective extraction-free RT-qPCR based dualplex test for SARS-CoV-2 from Nasopharyngeal (NP) swab specimens. Direct NP detects SARS-CoV-2 viral RNA from heat-denatured patient specimens using a dualplex RT-qPCR assay. Direct NP showed 92.5% positive percentage agreement (PPA) (95% Confidence Interval (CI) = 79.61%–98.43%) and 97% negative percent agreement (NPA) (95% CI = 89.11–100%) with the CDC assay. Direct NP reduces the cost per test to $2, making it suitable for broad-scale testing while lowering the cost burden on the healthcare system.

KW - Broad-scale

KW - COVID-19

KW - Dualplex

KW - RT-qPCR

KW - SARS-CoV-2

KW - Test

UR - http://www.scopus.com/inward/record.url?scp=85133267608&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85133267608&partnerID=8YFLogxK

U2 - 10.1016/j.heliyon.2022.e09735

DO - 10.1016/j.heliyon.2022.e09735

M3 - Article

C2 - 35747323

AN - SCOPUS:85133267608

SN - 2405-8440

VL - 8

JO - Heliyon

JF - Heliyon

IS - 6

M1 - e09735

ER -

Direct NP- A cost-effective extraction-free RT-qPCR based test for SARS-CoV-2

Abstract

Funding

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this