About: Utility of Pan-Family Assays for Rapid Viral Screening: Reducing Delays in Public Health Responses During Pandemics

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Utility of Pan-Family Assays for Rapid Viral Screening: Reducing Delays in Public Health Responses During Pandemics
Creator	Chana, Gursharan Erlichster, Michael Goudey, Skafidas, Efstratios Zantomio, Daniela
source	MedRxiv
abstract	Background The SARS-CoV-2 pandemic has highlighted deficiencies in the testing capacity of many developed countries during the early stages of emerging pandemics. Here we describe the potential for pan-family viral assays to improve early accessibility of large-scale nucleic acid testing. Methods Coronaviruses and SARS-CoV-2 were used as a case-study for investigating the utility of pan-family viral assays during the early stages of a novel pandemic. Specificity of a pan-coronavirus (Pan-CoV) assay for viral detection 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 SARS-CoV-2 and 59 other coronavirus species. 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. Findings Due to infection with common HCoV species, a Pan-CoV assay would return a false positive for as few as 1% of asymptomatic adults, but up to 30% of immunocompromised patients displaying symptoms of respiratory disease. Two of the four reported pan-coronavirus assays would have identified SARS-CoV-2 and we demonstrate that with small adjustments to the primers, these assays can accommodate novel variation observed in animal coronaviruses. The assay target region of one well established Pan-CoV assay is highly resistant to mutation compared to regions targeted by other widely applied SARS-CoV-2 RT-PCR assays. Interpretation Pan-family assays have the potential to greatly assist management of emerging public health emergencies through prioritization of high-resolution testing or isolation measures, despite limitations in test specificity due to cross-reactivity with common pathogens. Targeting highly conserved genomic regions make pan-family assays robust and resilient to mutation of a given virus. This approach may be applicable to other viral families and has utility as part of a strategic stockpile of tests maintained to better contain spread of novel diseases prior to the widespread availability of specific assays.
has issue date	2020-05-26(xsd:dateTime)
bibo:doi	10.1101/2020.05.24.20112318
has license	medrxiv
sha1sum (hex)	498e426b7a66e2aa517ccf340cc57f6cbbfa69e1
schema:url	https://doi.org/10.1101/2020.05.24.20112318
resource representing a document's title	Utility of Pan-Family Assays for Rapid Viral Screening: Reducing Delays in Public Health Responses During Pandemics
resource representing a document's body	covid:498e426b7a66e2aa517ccf340cc57f6cbbfa69e1#body_text
is schema:about of	named entity 'preprint' named entity 'Public Health' named entity 'preprint' named entity 'pathogens' named entity 'endemic' »more»

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