2021
DOI: 10.1038/s41467-021-21653-y
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A multiplexed, next generation sequencing platform for high-throughput detection of SARS-CoV-2

Abstract: Population scale sweeps of viral pathogens, such as SARS-CoV-2, require high intensity testing for effective management. Here, we describe “Systematic Parallel Analysis of RNA coupled to Sequencing for Covid-19 screening” (C19-SPAR-Seq), a multiplexed, scalable, readily automated platform for SARS-CoV-2 detection that is capable of analyzing tens of thousands of patient samples in a single run. To address strict requirements for control of assay parameters and output demanded by clinical diagnostics, we employ… Show more

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Cited by 41 publications
(34 citation statements)
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“…Screening for variants of concern (VOCs) was conducted using the C19-SPAR-Seq platform, a multiplex RT-PCR method using primers corresponding to the RNA-dependent RNA polymerase, S-receptor-binding domain, envelope, nucleocapsid, and 2 regions of the spike gene. 4 Whole-genome sequencing (WGS) was conducted at the Hospital for Sick Children.…”
Section: Methodsmentioning
confidence: 99%
“…Screening for variants of concern (VOCs) was conducted using the C19-SPAR-Seq platform, a multiplex RT-PCR method using primers corresponding to the RNA-dependent RNA polymerase, S-receptor-binding domain, envelope, nucleocapsid, and 2 regions of the spike gene. 4 Whole-genome sequencing (WGS) was conducted at the Hospital for Sick Children.…”
Section: Methodsmentioning
confidence: 99%
“…Multiple differences exist between recently published NGS-based diagnostic assays (8)(9)(10)(11)(12)(13)(14)(15)(16), including sample type (e.g., saliva, nasal swab) and reaction type (e.g., RT-PCR, LAMP). Early hybridization and pooling as implemented in ApharSeq are compatible with various extraction methods, enzymatic reactions, and protocols.…”
Section: Discussionmentioning
confidence: 99%
“…In the last decade, next generation sequencing (NGS) has replaced RT-qPCR and microarrays as the assay of choice for quantifying RNA molecules in research. During the COVID-19 pandemic, different NGS-based assays have been proposed to measure the presence and abundance of the viral genome in samples (8)(9)(10)(11)(12)(13)(14)(15)(16). In addition to detection and quantification, these assays can provide near real-time sequence information and provide epidemiologists with data on the emergence of new variants (17,18).…”
Section: Introductionmentioning
confidence: 99%
“…This technique was used by Zhou and coworkers to acquire viruses from seven patients with severe pneumonia, and full-length sequencing was performed on an RNA sample (Zhou et al 2020). Aynaud et al also report "Systematic Parallel Analysis of RNA connected to Sequencing for COVID-19 screening" (C19-SPAR-Seq) that can analyze a huge number of infected individual samples in one run with a sensitivity of 91 to > 95% and a specificity of 100% (Aynaud et al 2021). In general, this technology is insufficient when quick analysis and results are needed compared to RT-PCR (Thorburn et al 2015).…”
Section: Next-generation Sequencing (Ngs) and Sars-cov-2 Detectionmentioning
confidence: 99%