Evidence map›Paper›PMID 32511328›Full record

ArticlebioRxiv : the preprint server for biology2020

DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP.

Emily A Bruce, Meei-Li Huang, Garrett A Perchetti, Scott Tighe, Pheobe Laaguiby, Jessica J Hoffman, Diana L Gerrard, Arun K Nalla, Yulun Wei, Alexander L Greninger and 9 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 82 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

19 authors at 3 institutions in 1 country.

Emily A BruceDepartment of Medicine, Division of Immunobiology, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA.
Meei-Li HuangVirology Division, Department of Laboratory Medicine, University of Washington, Seattle WA 98195, USA.
Garrett A PerchettiVirology Division, Department of Laboratory Medicine, University of Washington, Seattle WA 98195, USA.
Scott TigheVermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA.
Pheobe LaaguibyVermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA.
Jessica J HoffmanVermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA.
Diana L GerrardDepartment of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington VT, 05401, USA.
Arun K NallaVirology Division, Department of Laboratory Medicine, University of Washington, Seattle WA 98195, USA.
Yulun WeiVirology Division, Department of Laboratory Medicine, University of Washington, Seattle WA 98195, USA.
Alexander L GreningerVirology Division, Department of Laboratory Medicine, University of Washington, Seattle WA 98195, USA.
Sean A DiehlDepartment of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA.
David J ShirleyIXIS LLC, Data Science Division, Burlington, VT 05401, USA.
Debra G B LeonardDepartment of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont and the University of Vermont Health Network, Burlington VT, 05405, USA.
Christopher D HustonDepartment of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA.
Beth D KirkpatrickDepartment of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA.
Julie A DragonVermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA.
Jessica W CrothersDepartment of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont and the University of Vermont Health Network, Burlington VT, 05405, USA.
Keith R JeromeVirology Division, Department of Laboratory Medicine, University of Washington, Seattle WA 98195, USA.
Jason W BottenDepartment of Medicine, Division of Immunobiology, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA.
University of Vermont · USUniversity of Washington · USUniversity of Vermont Medical Center · US

Funding

Understanding Factors Influencing COVID-19 Testing and Vaccination in Immigrant Low-income and Homeless Populations and Testing Targeted InterventionsU54GM115516 · NIGMS · MAINEHEALTH · PI Brenda Morissette Joly · 2017 to 2026
$51.6M
Using Dengue Controlled Human Infection Model to Identify Adaptive Immune Correlates of ProtectionP20GM125498 · NIGMS · UNIVERSITY OF VERMONT & ST AGRIC COLLEGE · PI Kristen Pierce · 2018 to 2026
$24.9M
Vermont Immunology/Infectious Diseases CenterP30GM118228 · NIGMS · UNIVERSITY OF VERMONT & ST AGRIC COLLEGE · PI BUDD, RALPH C · 2016 to 2021
$6.8M
Mechanisms of Protection and Durability for a Live Attenuated Tetravalent Dengue VaccineU01AI141997 · NIAID · UNIVERSITY OF VERMONT & ST AGRIC COLLEGE · PI Sean A. Diehl, Anna Palmer Durbin · 2019 to 2026
$5.1M
Therapeutic antibodies for treatment of hantavirus cardiopulmonary syndromeR41AI132047 · NIAID · CELDARA MEDICAL, LLC · PI BOTTEN, JASON W., FANGER, MICHAEL W · 2017 to 2018
$800k
NIAID NIH HHS R41 AI132047NIAID NIH HHS U01 AI141997NIGMS NIH HHS P20 GM125498NIGMS NIH HHS P30 GM118228NIGMS NIH HHS U54 GM115516
6 · The paper itself

Abstract

The ongoing COVID-19 pandemic has caused an unprecedented need for rapid diagnostic testing. The Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) recommend a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. We hypothesized that SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether, and tested this hypothesis on a series of blinded clinical samples. The direct RT-qPCR approach correctly identified 92% of NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Thus, direct RT-qPCR could be a front-line approach to identify the substantial majority of COVID-19 patients, reserving a repeat test with RNA extraction for those individuals with high suspicion of infection but an initial negative result. This strategy would drastically ease supply chokepoints of COVID-19 testing and should be applicable throughout the world.

Identifiers

PMID32511328
PMCPMC7239058
OpenAlexW3011355337

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.