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Title: Pan-Family Assays for Rapid Viral Screening: Reducing Delays in Public Health Responses During Pandemics.
Authors: Erlichster, Michael;Chana, Gursharan;Zantomio, Daniela;Goudey, Benjamin;Skafidas, Efstratios
Affiliation: IBM Research Australia, Southbank, Victoria, Australia
Department of Haematology, Austin Health, Heidelberg, Victoria, Australia
MX3 Diagnostics, Melbourne, Victoria, Australia
Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Victoria, Australia
Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Melbourne, Victoria, Australia
Department of Electrical and Electronic Engineering, Melbourne School of Engineering, The University of Melbourne, Melbourne, Victoria, Australia
Issue Date: 20-Jul-2020
EDate: 2020-07-20
Citation: Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020; online first: 20 July
Abstract: COVID-19 has highlighted deficiencies in the testing capacity of many developed countries during the early stages of pandemics. Here we describe a strategy utilizing pan-family viral assays to improve early accessibility of large-scale nucleic acid testing. Coronaviruses and SARS-CoV-2 were used as a case-study for assessing utility of pan-family viral assays during the early stages of a novel pandemic. Specificity of a pan-coronavirus (Pan-CoV) assay for a novel pathogen was assessed using the frequency of common human coronavirus (HCoV) species in key populations. A reported Pan-CoV assay was assessed to determine sensitivity to 60 reference coronaviruses, including SARS-CoV-2. The resilience of the primer target regions of this assay to mutation was assessed in 8893 high-quality SARS-CoV-2 genomes to predict ongoing utility during pandemic progression. Due to common HCoV species, a Pan-CoV assay would return false positives for as few as 1% of asymptomatic adults, but up to 30% of immunocompromised patients with respiratory disease. Half of reported Pan-CoV assays identify SARS-CoV-2 and with small adjustments can accommodate diverse variation observed in animal coronaviruses. The target region of one well established Pan-CoV assay is highly resistant to mutation compared to species-specific SARS-CoV-2 RT-PCR assays. Despite cross-reactivity with common pathogens, pan-family assays may greatly assist management of emerging pandemics through prioritization of high-resolution testing or isolation measures. Targeting highly conserved genomic regions make pan-family assays robust and resilient to mutation. A strategic stockpile of pan-family assays may improve containment of novel diseases prior to the availability of species-specific assays.
DOI: 10.1093/cid/ciaa1028
PubMed URL: 32687168
Type: Journal Article
Subjects: Pan-Family Assays
Viral Screening
Appears in Collections:Journal articles

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