A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants-Reference-Cited by-同舟云学术

A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants

Published:2023-02-23 Issue:1 Volume:8 Page:
ISSN:2379-5077
Container-title:mSystems
language:en
Short-container-title:mSystems

Author:

Albright Jack¹,Mick Eran¹²³,Sanchez-Guerrero Estella²,Kamm Jack¹,Mitchell Anthea¹⁴,Detweiler Angela M.¹,Neff Norma¹,Tsitsiklis Alexandra²,Hayakawa Serpa Paula²,Ratnasiri Kalani¹,Havlir Diane⁵,Kistler Amy¹,DeRisi Joseph L.¹⁴,Pisco Angela Oliveira¹,Langelier Charles R.¹²^ORCID

Affiliation:

1. Chan Zuckerberg Biohub, San Francisco, California, USA

2. Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, California, USA

3. Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA

4. Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA

5. Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA

Abstract

In this work, we study upper respiratory tract gene expression to develop and validate a 2-gene host-based COVID-19 diagnostic classifier and then demonstrate its implementation in a clinically practical qPCR assay. We find that the host classifier has utility for mitigating false-negative results, for example due to SARS-CoV-2 variants harboring mutations at primer target sites, and for mitigating false-positive viral PCR results due to laboratory cross-contamination.

Funder

Chan Zuckerberg Biohub

HHS | NIH | National Heart, Lung, and Blood Institute

Publisher

American Society for Microbiology

Subject

Computer Science Applications,Genetics,Molecular Biology,Modeling and Simulation,Ecology, Evolution, Behavior and Systematics,Biochemistry,Physiology,Microbiology

Link

https://journals.asm.org/doi/pdf/10.1128/msystems.00671-22

Reference23 articles.

1. World Health Organization. 2021. WHO COVID-19 dashboard. https://covid19.who.int/.

2. False-negative results of initial RT-PCR assays for COVID-19: A systematic review

3. Occurrence and Timing of Subsequent Severe Acute Respiratory Syndrome Coronavirus 2 Reverse-transcription Polymerase Chain Reaction Positivity Among Initially Negative Patients

4. False negative rate of COVID-19 PCR testing: a discordant testing analysis

5. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2

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