About: ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection
Creator	Dor, Yuval Wolf, Dana Klochendler, Agnes Oiknine-Djian, Esther Adam, Miriam Chappleboim, Alon Fialkoff, Gavriel Friedman, Nir Gershon, Omer Habib, Naomi Joseph-Strauss, Daphna Kitsberg, Daniel Lotem, Matan Rahat, Ayelet Sadeh, Ronen Schmidtner, Anna-Kristina Sharkia, Israa
source	MedRxiv
abstract	The global SARS-CoV-2 pandemic led to a steep increase in the need for viral detection tests worldwide. Most current tests for SARS-CoV-2 are based on RNA extraction followed by quantitative reverse-transcription PCR assays that involve a separate RNA extraction and qPCR reaction for each sample with a fixed cost and reaction time. While automation and improved logistics can increase the capacity of these tests, they cannot exceed this lower bound dictated by one extraction and reaction per sample. Multiplexed next generation sequencing (NGS) assays provide a dramatic increase in throughput, and hold the promise of richer information on viral strains and host immune response. Here, we establish a significant improvement of existing RNA-seq detection protocols. Our workflow, ApharSeq, includes a fast and cheap RNA capture step, that is coupled to barcoding of individual samples, followed by sample-pooling prior to the reverse transcription, PCR and massively parallel sequencing. Thus, only one step is performed before pooling hundreds of barcoded samples for subsequent steps and further analysis. We characterize the quantitative aspects of the assay, and test ApharSeq on dozens of clinical samples in a robotic workflow. Our proposed workflow is estimated to reduce costs by 10-50 fold, labor by 5-100 fold, automated liquid handling by 5-10 fold, and reagent requirements by 100-1000 fold compared to existing testing methods.
has issue date	2020-08-13(xsd:dateTime)
bibo:doi	10.1101/2020.08.08.20170746
has license	medrxiv
sha1sum (hex)	f7db6e55f11b538b3fe0056f5269c4ee4dc592fb
schema:url	https://doi.org/10.1101/2020.08.08.20170746
resource representing a document's title	ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection
resource representing a document's body	covid:f7db6e55f11b538b3fe0056f5269c4ee4dc592fb#body_text
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