LAMP-Seq: Population-Scale COVID-19 Diagnostics Using Combinatorial Barcoding

Schmid-Burgk, Jonathan L.; Schmithausen, Ricarda Maria; Li, David; Hollstein, Ronja; Ben-Shmuel, Amir; Israeli, Ofir; Weiss, Shay; Paran, Nir; Wilbring, Gero; Liebing, Jana; Feldman, David; Słabicki, Mikołaj; Lippke, Bärbel; Sib, Esther; Borrajo, Jacob; Strecker, Jonathan; Reinhardt, Julia; Hoffmann, Per; Cleary, Brian; Hölzel, Michael; Nöthen, Markus M.; Exner, Martin; Ludwig, Kerstin U.; Regev, Aviv; Zhang, Feng

doi:10.1101/2020.04.06.025635

Cited by 85 publications

(105 citation statements)

References 13 publications

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“…Looking forward, we envision that nasal swabs -- self-collected into laboratory ready, barcoded tubes and transported dry -- could potentially serve as a common input to a range of SARS-CoV-2 nucleic acid tests. This includes gold-standard tests like RT-qPCR, but also potentially new, more scalable modalities including RT-LAMP ( 6–8 ) and Swab-Seq ( 11 ). The operationalization of the mass distribution and return of such lab-ready collection devices is a significant effort that should begin now.…”

Section: Discussionmentioning

confidence: 99%

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

Srivatsan

Heidl

Pfau

et al. 2020

Preprint

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The urgent need for massively scaled clinical or surveillance testing for SARS-CoV-2 has necessitated a reconsideration of the methods by which respiratory samples are collected, transported, processed and tested. Conventional testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab, storage of the swab during transport in universal transport medium (UTM), extraction of RNA, and quantitative reverse transcription PCR (RT-qPCR). As testing has scaled across the world, supply chain challenges have emerged across this entire workflow. Here we sought to evaluate how eliminating the UTM storage and RNA extraction steps would impact the results of molecular testing. Using paired mid-turbinate swabs self-collected by 11 individuals with previously established SARS-CoV-2 positivity, we performed a comparison of conventional (swab → UTM → RNA extraction → RT-qPCR) vs. simplified (direct elution from dry swab → RT-qPCR) protocols. Our results suggest that dry swabs eluted directly into a simple buffered solution (TE) can support molecular detection of SARS-CoV-2 via endpoint RT-qPCR without substantially compromising sensitivity. Although further confirmation with a larger sample size and variation of other parameters is necessary, these results are encouraging for the possibility of a simplified workflow that could support massively scaled testing for COVID-19 control. ResultsBased on prior literature ( 1 , 2 ) and the fact that dry swabs are employed for SARS-CoV-2 testing outside of the United States , we know that swabs collected and transported without transport media are amenable to subsequent nucleic acid detection-based diagnostics. We hypothesized that elution of dry swabs directly into a Tris-EDTA (TE) buffer would be compatible with RT-qPCR, i.e. skipping conventional RNA extraction altogether. TE's lower salt Seattle Flu Study Investigators Principal Investigators:

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Section: Discussionmentioning

confidence: 99%

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

Srivatsan

Heidl

Pfau

et al. 2020

Preprint

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“…The most sensitive POCT tests on swabs utilizes isothermal reactions: fewer than 10 copies/reaction of viral targets were detected after brief heating in Hank's medium [153], M-Swab medium [176], or water [177]. Sometimes, entire swab samples can be used in amplification reactions [173], eliminating the loss of starting material that accompanies liquid and hardware transfers. Future developments include direct reactions with swabs that integrate cell lysis, RNA conversion and isothermal amplification, as well as visual or mobile detection in a single tube.…”

Section: E Direct Amplification From Complex Matricesmentioning

confidence: 99%

“…As the pandemic fades away, sample barcoding and high sensitivity NGS assays could potentially be used for national level population screening programs, in which a pooled screening strategy was pursued to increase testing throughput, limit use of reagents, and increase overall testing efficiency at an expected slight loss of sensitivity [173].…”

Section: G Next Generation Sequencing and Nanopore Sequencingmentioning

confidence: 99%

“…One of the major bottlenecks lies in the maintenance of isotherm temperature during the course of the biochemical assays. Apart from low cost devices (e.g.sous vide precision cooker) that contain temperature control feedback loops, a USB-powered heating device, or a chemical process buffered by phase change material were trialed (A) [173].…”

Section: Emerging Instrument Free Molecular Assaysmentioning

confidence: 99%

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Navigating the Pandemic Response Life Cycle: Molecular Diagnostics and Immunoassays in the Context of COVID-19 Management

Gharizadeh

Yue

et al. 2021

IEEE Rev. Biomed. Eng.

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Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To counter COVID-19 spreading, an infrastructure to provide rapid and thorough molecular diagnostics and serology testing is the cornerstone of outbreak and pandemic management. We hereby review the clinical insights with regard to using molecular tests and immunoassays in the context of COVID-19 management life cycle: the preventive phase, the preparedness phase, the response phase and the recovery phase. The spatial and temporal distribution of viral RNA, antigens and antibodies during human infection is summarized to provide a biological foundation for accurate detection of the disease. We shared the lessons learned and the obstacles encountered during real world high-volume screening programs. Clinical needs are discussed to identify existing technology gaps in these tests. Leverage technologies, such as engineered polymerases, isothermal amplification, and direct amplification from complex matrices may improve the productivity of current infrastructure, while emerging technologies like CRISPR diagnostics, visual end point detection, and PCR free methods for nucleic acid sensing may lead to at-home tests. The lessons learned, and innovations spurred from the COVID-19 pandemic could upgrade our global public health infrastructure to better combat potential outbreaks in the future.

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“…Moreover, the behavior of the viral infection spread can be modeled and simulated using a Markov chain with binomial distributions, as appears in Figure 1, and this is equivalent to the ODE model in Eq. (2). Using the maximum-likelihood principle and the Johns Hopkins dataset [8] we estimate the SIR-D parameters τ , t 0 , κ, α 0 , β, and γ that maximize the log-likelihood at time t:…”

Section: The Sir-d Differential Equations and The Equivalent Time-varmentioning

confidence: 99%

Poolkeh Finds the Optimal Pooling Strategy for a Population-wide COVID-19 Testing (Israel, UK, and US as Test Cases)

Eliaz

Danovich²,

Gasic

2020

Preprint

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The SARS-CoV-2 pandemic has changed the lifestyle of citizens of the world. In order for decision makers to manage the viral spread of COVID-19 both in the intra-national and the international frontiers, it is essential to operate based on data-driven assessments. It's crucial to do so rapidly and frequently, since the nature of the viral spread grows exponentially and can burst worldwide again. A fast and accurate health status of individuals globally during a pandemic can save many lives and bring life back to a new normal. Herein, we present a data-driven tool to allow decision-makers to assess the spread of the virus among the world population. Our framework allows health agencies to maximize the throughput of COVID-19 tests among the world population by finding the best test pooling that fits the current SIR-D [1] status of the nation. * These authors contributed equally to this work

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LAMP-Seq: Population-Scale COVID-19 Diagnostics Using Combinatorial Barcoding

Abstract: NOTE: This protocol has not been validated with clinical samples. To facilitate collaborations with interested parties to jointly advance the fight against the current coronavirus pandemic, wehave set up a public forum on www.LAMP-Seq.org.

Cited by 85 publications

References 13 publications

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

Navigating the Pandemic Response Life Cycle: Molecular Diagnostics and Immunoassays in the Context of COVID-19 Management

Poolkeh Finds the Optimal Pooling Strategy for a Population-wide COVID-19 Testing (Israel, UK, and US as Test Cases)

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