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CONTENT

# _archive-combined-files_papers-lamp_8k (3 files, 7,791 tokens)

# 3,732  _AI_Literature Review - LAMP Large-Scale Testing and Pandemic Preparedness.md
METADATA
last updated: 2026-02-23 AI
file_name: _AI_Literature Review - RT-LAMP Large-Scale Testing and Pandemic Preparedness.md
file_date: 2026-02-23
title: FloodLAMP Literature Review - RT-LAMP Large-Scale Testing and Pandemic Preparedness
category: various
subcategory: papers-lamp
tags: rt-lamp, large-scale-testing, pandemic-preparedness, screening, literature-review
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license: CC BY 4.0 - https://creativecommons.org/licenses/by/4.0/
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notes: Created by ChatGPT 5.2 Pro Extended during archive preparation. **NOT HUMAN VERIFIED - MAY CONTAIN ERRORS** AI-generated annotated literature review of 20 key LAMP/RT-LAMP papers relevant to large-scale testing, screening, and pandemic preparedness, covering population-scale/high-throughput approaches, scalable sample-to-answer workflows, real-world screening evaluations, multiplex respiratory panels, and foundational pandemic-era assay papers. No source files were included in context; the response was generated from the model's training data with an exclusion list of papers already in the archive.
summary_short: Literature Review - RT-LAMP Large-Scale Testing and Pandemic Preparedness surveys 20 LAMP/RT-LAMP papers prioritized for large-scale testing/screening and pandemic preparedness, organized by theme (population-scale barcoded/sequenced LAMP, scalable sample-to-answer workflows, real-world screening evaluations, variant-robust multiplex panels, and foundational pandemic-era assays), with PubMed-linked citations and importance summaries for each paper.


CONTENT

## Prompt (Verbatim)
Your task is to source the 20 most important papers related to lamp molecular testing. This is loop mediated isothermal amplification. And focus on the pandemic and forward. I'm including a list of papers I already have so don't include these and give the citations for the papers in the same format as what's here and then give a couple sentence summary of each paper and why it's important. I'll place a particular focus on tests and papers that relate to large-scale testing and screening for pandemic preparedness and response.

## Prompt (Cleaned)
Identify and annotate 20 key LAMP/RT-LAMP papers (COVID-19 pandemic through present) prioritized for large-scale testing/screening and pandemic preparedness, excluding papers already in the archive collection. Organize by theme and provide PubMed links and importance summaries for each.

**Files included in context window:**
_citations_papers-lamp.md

## AI Response (ChatGPT 5.2 Pro Extended)
Below are **20 LAMP/RT-LAMP papers (COVID-19 pandemic --> present)** that I'd prioritize for **large-scale testing/screening and pandemic preparedness**, **excluding** the papers in the list you provided.

### Population-scale & high-throughput LAMP (barcoding/sequencing/automation)

1. [Ludwig KU, Schmithausen RM, Li D, et al. LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding. *Nat Biotechnol*. 2021;39(12):1556-1562.](https://pubmed.ncbi.nlm.nih.gov/34188222/) ([PubMed][1])
   **Summary/importance:** Introduces **LAMP-Seq**, pairing **RT-LAMP with molecular barcodes** and a sequencing readout to enable massively multiplexed testing. It's important because it lays a credible technical path to **population-scale pooled testing** while maintaining molecular sensitivity. ([PubMed][1])

2. [Warneford-Thomson R, Shah PP, Lundgren P, et al. A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva. *eLife*. 2022;11:e69949.](https://pubmed.ncbi.nlm.nih.gov/35532013/) ([PubMed][2])
   **Summary/importance:** Describes **COV-ID**, combining **RT-LAMP + deep sequencing** with multi-dimensional barcoding, and demonstrates **co-detection** (SARS-CoV-2 + influenza) from saliva. It's important for preparedness because it supports **thousands of samples per sequencing run** and **multiplex pathogen surveillance** in one workflow. ([PubMed][2])

3. [Peto L, et al. Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing. *J Clin Microbiol*. 2021;59(6):e03271-20.](https://pubmed.ncbi.nlm.nih.gov/33782112/) ([PubMed][3])
   **Summary/importance:** Clinically evaluates **LamPORE** (RT-LAMP + nanopore sequencing) against RT-PCR on respiratory samples, emphasizing throughput potential on a single instrument. It's important because it's one of the clearer **clinical performance + high-throughput** demonstrations of sequencing-readout RT-LAMP. ([PubMed][3])

4. [Dewhurst RE, et al. Validation of a rapid, saliva-based, and ultra-sensitive SARS-CoV-2 screening system for pandemic-scale infection surveillance. *Sci Rep*. 2022;12(1):5936.](https://pubmed.ncbi.nlm.nih.gov/35395856/) ([PubMed][4])
   **Summary/importance:** Presents an **automated high-throughput saliva RT-LAMP surveillance system** built around the "Sentinel" instrument. It's important because it explicitly targets **pandemic-scale operations** (rapid turnaround, continuous-flow sample handling, very high throughput) rather than small-batch lab demonstrations. ([PubMed][4])

5. [Lou D, Meurer M, Ovchinnikova S, et al. Scalable RT-LAMP-based SARS-CoV-2 testing for infection surveillance with applications in pandemic preparedness. *EMBO Rep*. 2023;24(5):e57162.](https://pubmed.ncbi.nlm.nih.gov/36951170/) ([PubMed][5])
   **Summary/importance:** Provides SOPs + software/logistics for a **gargle-based RT-LAMP testing station**, reporting real-world operation at **>35,000 tests** with rapid turnaround. It's important because it's a rare "end-to-end" blueprint for deploying **scalable LAMP diagnostics** with operational constraints (costs, logistics, reporting) addressed head-on. ([PubMed][5])

### Scalable sample-to-answer LAMP workflows (saliva/gargle/paper)

6. [Lalli MA, Langmade JS, Chen X, et al. Rapid and Extraction-Free Detection of SARS-CoV-2 from Saliva by Colorimetric Reverse-Transcription Loop-Mediated Isothermal Amplification. *Clin Chem*. 2021;67(2):415-424.](https://pubmed.ncbi.nlm.nih.gov/33098427/) ([PubMed][6])
   **Summary/importance:** Optimizes **extraction-free saliva** pretreatment and colorimetric RT-LAMP (with multiple readout modes) and validates on clinical saliva. It's important because **extraction-free saliva** is a cornerstone of low-cost, high-throughput screening, and this paper became a key reference workflow for many scale-up efforts. ([PubMed][6])

7. [Bokelmann L, Nickel O, Maricic T, et al. Point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP. *Nat Commun*. 2021;12(1):1467.](https://pubmed.ncbi.nlm.nih.gov/33674580/) ([PubMed][7])
   **Summary/importance:** Introduces **Cap-iLAMP** (capture + improved RT-LAMP) using gargle lavage, plus **smartphone-based hue scoring** to manage readout variability. It's important for scale because it directly addresses **false positives/specificity** and demonstrates **pooling concepts** that reduce per-person reagent cost for screening. ([PubMed][7])

8. [Yu AD, Galatsis K, Zheng J, et al. Development of a Saliva-Optimized RT-LAMP Assay for SARS-CoV-2. *J Biomol Tech*. 2021;32(3):102-113.](https://pubmed.ncbi.nlm.nih.gov/35027868/) ([PubMed][8])
   **Summary/importance:** Improves practical saliva RT-LAMP deployment by validating a higher-contrast dye and introducing **SalivaBeads** (rapid bead purification) plus a low-cost **StickLAMP** tool to simplify scalable handling. It's important because these are **implementation-enabling** innovations that make saliva RT-LAMP more robust outside highly automated labs. ([PubMed][8])

9. [Kundrod KA, Natoli ME, Chang MM, et al. Sample-to-answer, extraction-free, real-time RT-LAMP test for SARS-CoV-2 in nasopharyngeal, nasal, and saliva samples: Implications and use for surveillance testing. *PLoS One*. 2022;17(2):e0264130.](https://pubmed.ncbi.nlm.nih.gov/35213596/) ([PubMed][9])
   **Summary/importance:** Develops a **sample-to-answer**, extraction-free **real-time RT-LAMP** assay validated across **multiple sample types** (NP, nasal, saliva), explicitly framed for **surveillance testing**. It's important because surveillance programs often need flexibility in collection type and workflow simplicity to sustain frequent testing. ([PubMed][9])

10. [Wei S, Suryawanshi H, Djandji A, et al. Field-deployable, rapid diagnostic testing of saliva for SARS-CoV-2. *Sci Rep*. 2021;11(1):5448.](https://pubmed.ncbi.nlm.nih.gov/33750853/) ([PubMed][10])
    **Summary/importance:** Demonstrates a **field-deployable saliva RT-LAMP** approach aimed at minimal infrastructure while still supporting rapid detection. It's important for preparedness because outbreaks frequently require **decentralized testing** when centralized PCR capacity or extraction reagents are constrained. ([PubMed][10])

11. [Davidson JL, Wang J, Maruthamuthu MK, et al. A paper-based colorimetric molecular test for SARS-CoV-2 in saliva. *Biosens Bioelectron X*. 2021;9:100076.](https://pubmed.ncbi.nlm.nih.gov/34423284/) ([PubMed][11])
    **Summary/importance:** Builds a **paper-based** colorimetric RT-LAMP molecular test compatible with saliva, pushing toward low-cost, distributed deployment. It's important because paper-based formats are a credible route to **simplified logistics and scalable access**, particularly for low-resource or community settings. ([PubMed][11])

### Real-world performance & screening-focused evaluations

12. [Brown B, O'Hara RW, Guiver M, et al. Evaluation of a novel direct RT-LAMP assay for the detection of SARS-CoV-2 from saliva samples in asymptomatic individuals. *J Clin Virol Plus*. 2022;2(2):100074.](https://pubmed.ncbi.nlm.nih.gov/35345440/) ([PubMed][12])
    **Summary/importance:** Evaluates **direct saliva RT-LAMP** specifically in **asymptomatic** individuals -- exactly the use-case for proactive screening. It's important because asymptomatic screening is where test speed and simplicity matter most, and real-world evaluation data are essential for deciding if/where LAMP fits in a preparedness toolkit. ([PubMed][12])

13. [Kidd SP, et al. Reverse-Transcription Loop-Mediated Isothermal Amplification Has High Accuracy for Detecting Severe Acute Respiratory Syndrome Coronavirus 2 in Saliva and Nasopharyngeal/Oropharyngeal Swabs from Asymptomatic and Symptomatic Individuals. *J Mol Diagn*. 2022;24(4):320-336.](https://pubmed.ncbi.nlm.nih.gov/35121140/) ([PubMed][13])
    **Summary/importance:** Assesses RT-LAMP accuracy across **saliva and NP/OP swabs**, spanning symptomatic and asymptomatic groups. It's important because mass screening requires performance evidence across **specimen types and clinical presentations**, not just contrived samples. ([PubMed][13])

14. [Allsopp RC, Cowley CM, Barber RC, et al. A rapid RT-LAMP SARS-CoV-2 screening assay for collapsing asymptomatic COVID-19 transmission. *PLoS One*. 2022;17(9):e0273912.](https://pubmed.ncbi.nlm.nih.gov/36048856/) ([PubMed][14])
    **Summary/importance:** Frames RT-LAMP explicitly as a **screening tool** to reduce asymptomatic spread and documents an operational screening approach. It's important because it focuses on **public health impact and screening cadence**, not only analytical sensitivity. ([PubMed][14])

15. [Susnjar U, et al. Colorimetric RT-LAMP for SARS-CoV-2 detection from nasopharyngeal swabs or crude saliva: a multicountry diagnostic accuracy study in Africa. *Lancet Glob Health*. 2025;13(7):e1258-e1267.](https://pubmed.ncbi.nlm.nih.gov/40580991/) ([PubMed][15])
    **Summary/importance:** Large **multicountry diagnostic accuracy** evaluation of colorimetric RT-LAMP using **NP swabs and crude saliva** in African settings. It's important for preparedness because it provides higher-confidence evidence in **resource-variable, real-world contexts** where supply chains and infrastructure constraints are most acute. ([PubMed][15])

### Preparedness-forward: variants, robustness, and multiplex respiratory panels

16. [Dong Y, Zhao Y, Li S, et al. Multiplex, Real-Time, Point-of-Care RT-LAMP for SARS-CoV-2 Detection Using the HFman Probe. *ACS Sens*. 2022;7(3):730-739.](https://pubmed.ncbi.nlm.nih.gov/35192340/) ([PubMed][16])
    **Summary/importance:** Develops a **multiplex real-time RT-LAMP** approach using the HFman probe to support point-of-care detection with improved specificity/interpretability. It's important because more robust signal discrimination and multi-target design help assays stay useful as **variants and assay-interference risks** evolve. ([PubMed][16])

17. [Jee H, Park S, Lee J, et al. Comparative Clinical Evaluation of a Novel FluA/FluB/SARS-CoV-2 Multiplex LAMP and Commercial FluA/FluB/SARS-CoV-2/RSV RT-qPCR Assays. *Diagnostics (Basel)*. 2023;13(8):1432.](https://pubmed.ncbi.nlm.nih.gov/37189533/) ([PubMed][17])
    **Summary/importance:** Clinically evaluates a **multiplex LAMP** assay that differentiates influenza A/B and SARS-CoV-2, benchmarked against a commercial RT-qPCR respiratory panel. It's important because pandemic preparedness increasingly means **multiplex respiratory surveillance** (distinguishing pathogens quickly to guide response and clinical management). ([PubMed][17])

### Foundational pandemic-era RT-LAMP assay papers that shaped downstream scale-up

18. [Yan C, Cui J, Huang L, et al. Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay. *Clin Microbiol Infect*. 2020;26(6):773-779.](https://pubmed.ncbi.nlm.nih.gov/32276116/) ([PubMed][18])
    **Summary/importance:** One of the earliest clinical demonstrations of **rapid, visual RT-LAMP** for SARS-CoV-2 detection. It's important because it helped establish RT-LAMP as a serious alternative molecular modality when PCR capacity was constrained -- setting the stage for later scale-up and screening studies. ([PubMed][18])

19. [Park GS, Ku K, Baek SH, et al. Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assays Targeting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). *J Mol Diagn*. 2020;22(6):729-735.](https://pubmed.ncbi.nlm.nih.gov/32276051/) ([PubMed][19])
    **Summary/importance:** Develops and evaluates RT-LAMP assays/primer sets for SARS-CoV-2 early in the pandemic, including practical readouts. It's important because these assay designs and evaluation approaches became foundational references that many later **saliva, extraction-free, and scaled workflows** built upon or compared against. ([PubMed][19])

20. [Ganguli A, Mostafa A, Berger J, et al. Rapid isothermal amplification and portable detection system for SARS-CoV-2. *Proc Natl Acad Sci U S A*. 2020;117(37):22727-22735.](https://pubmed.ncbi.nlm.nih.gov/32868442/) ([PubMed][20])
    **Summary/importance:** Demonstrates RT-LAMP paired with a **portable cartridge + smartphone-based reader**, showing feasibility of molecular testing without conventional lab infrastructure. It's important for preparedness because large-scale response needs both centralized high-throughput testing **and** credible point-of-collection molecular options for remote, outbreak, or surge contexts. ([PubMed][20])

[1]: https://pubmed.ncbi.nlm.nih.gov/34188222/
[2]: https://pubmed.ncbi.nlm.nih.gov/35532013/
[3]: https://pubmed.ncbi.nlm.nih.gov/33782112/
[4]: https://pubmed.ncbi.nlm.nih.gov/35395856/
[5]: https://pubmed.ncbi.nlm.nih.gov/36951170/
[6]: https://pubmed.ncbi.nlm.nih.gov/33098427/
[7]: https://pubmed.ncbi.nlm.nih.gov/33674580/
[8]: https://pubmed.ncbi.nlm.nih.gov/35027868/
[9]: https://pubmed.ncbi.nlm.nih.gov/35213596/
[10]: https://pubmed.ncbi.nlm.nih.gov/33750853/
[11]: https://pubmed.ncbi.nlm.nih.gov/34423284/
[12]: https://pubmed.ncbi.nlm.nih.gov/35345440/
[13]: https://pubmed.ncbi.nlm.nih.gov/35121140/
[14]: https://pubmed.ncbi.nlm.nih.gov/36048856/
[15]: https://pubmed.ncbi.nlm.nih.gov/40580991/
[16]: https://pubmed.ncbi.nlm.nih.gov/35192340/
[17]: https://pubmed.ncbi.nlm.nih.gov/37189533/
[18]: https://pubmed.ncbi.nlm.nih.gov/32276116/
[19]: https://pubmed.ncbi.nlm.nih.gov/32276051/
[20]: https://pubmed.ncbi.nlm.nih.gov/32868442/


# 2,638  _citations_papers-lamp.md
METADATA
last updated: 2026-02-26 RT
file_name: _citations_papers-lamp.md
category: various
subcategory: papers-lamp
words: 851
tokens: 2638


CONTENT

## Color Whitepaper - SARS-CoV-2 LAMP Diagnostic Assay (5-21-2020).pdf
[Color Health, Inc. SARS-CoV-2 LAMP Diagnostic Assay. Company Whitepaper, Version 1.2. Updated May 21, 2020.](https://www.fda.gov/media/138249/download)


## Dao Thi - Preprint - Screening for SARS-CoV-2 infections with colorimetric RT-LAMP and LAMP sequencing (5-5-2020).pdf
[Dao Thi VL, Herbst K, Boerner K, et al. A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples. *Sci Transl Med*. 2020;12(556):eabc7075.](https://pubmed.ncbi.nlm.nih.gov/32719001/)
Publisher: [Science Translational Medicine](https://www.science.org/doi/10.1126/scitranslmed.abc7075)


## Domus Paper - A lyophilized colorimetric RT-LAMP test kit (2022 Nature).pdf
[Song X, Coulter FJ, Yang M, et al. A lyophilized colorimetric RT-LAMP test kit for rapid, low-cost, at-home molecular testing of SARS-CoV-2 and other pathogens. *Sci Rep*. 2022;12:7043.](https://pubmed.ncbi.nlm.nih.gov/35487969/)
Publisher: [Nature Scientific Reports](https://www.nature.com/articles/s41598-022-11144-5)


## Heithoff - Assessment of a Smartphone-Based Loop-Mediated Isothermal Amplification Assay for Detection of SARS-CoV-2 and Influenza Viruses (2022).pdf
[Heithoff DM, Barnes VL, Mahan SP, et al. Assessment of a smartphone-based loop-mediated isothermal amplification assay for detection of SARS-CoV-2 and influenza viruses. *JAMA Netw Open*. 2022;5(1):e2145669.](https://pubmed.ncbi.nlm.nih.gov/35089353/)
Publisher: [JAMA Network Open](https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2788464)


## Hu - Preprint - LAMP (5-29-2020).pdf
[Hu X, Deng Q, Li J, et al. Development and clinical application of a rapid and sensitive loop-mediated isothermal amplification test for SARS-CoV-2 infection. *mSphere*. 2020;5(4):e00808-20.](https://pubmed.ncbi.nlm.nih.gov/32848011/)
Preprint: [medRxiv (2020.05.20.20108530)](https://www.medrxiv.org/content/10.1101/2020.05.20.20108530v1)


## Kellner (Vienna) - Preprint - Open LAMP SARS-CoV-2 assay (7-23-2020).pdf
[Kellner MJ, Ross JJ, Schnabl J, et al. A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing. *Front Mol Biosci*. 2022;9:801309.](https://pubmed.ncbi.nlm.nih.gov/35433827/)
Publisher: [Frontiers in Molecular Biosciences](https://doi.org/10.3389/fmolb.2022.801309)


## Marcello - Diagnostic performance of a colorimetric RT -LAMP in sub-Saharan Africa.pdf
[Baba MM, Bitew M, Fokam J, Lelo EA, et al. Diagnostic performance of a colorimetric RT-LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa. *EClinicalMedicine*. 2021;40:101101.](https://pubmed.ncbi.nlm.nih.gov/34476394/)
Publisher: [Elsevier / EClinicalMedicine](https://doi.org/10.1016/j.eclinm.2021.101101)


## OConnor - Preprint - Initial evaluation of a mobile SARS-CoV-2 RT-LAMP testing strategy (7-28-2020).pdf
[Newman CM, Ramuta MD, McLaughlin MT, et al. Initial evaluation of a mobile SARS-CoV-2 RT-LAMP testing strategy. *J Biomol Tech*. 2021;32(3).](https://pubmed.ncbi.nlm.nih.gov/33655260/)
Publisher: [Journal of Biomolecular Techniques](https://doi.org/10.7171/jbt.21-32-03-009)


## OConnor Dudley - Preprint - Optimizing direct RT-LAMP(8-30-2020).pdf
[Dudley DM, Newman CM, Weiler AM, et al. Optimizing direct RT-LAMP to detect transmissible SARS-CoV-2 from primary nasopharyngeal swab samples. *PLoS ONE*. 2020;15(12):e0244882.](https://pubmed.ncbi.nlm.nih.gov/33382861/)
Publisher: [PLoS ONE](https://doi.org/10.1371/journal.pone.0244882)


## Parra - A Rapid RT-LAMP Assay for SARS-CoV-2 with Colorimetric Detection Assisted by a Mobile Application (2022 Diagnostics).pdf
[Londono-Avendano MA, Libreros G, Osorio L, Parra B. A rapid RT-LAMP assay for SARS-CoV-2 with colorimetric detection assisted by a mobile application. *Diagnostics*. 2022;12(4):848.](https://pubmed.ncbi.nlm.nih.gov/35453896/)
Publisher: [MDPI Diagnostics (Open Access)](https://doi.org/10.3390/diagnostics12040848)


## Prakash (Stanford) - Preprint - Rabe Cepko LAMP w Handyfuge (6-30-20).pdf
[Kothari A, Larson A, Li E, Prakash M. Handyfuge-LAMP: low-cost and electricity-free centrifugation for isothermal SARS-CoV-2 detection in saliva. *medRxiv*. 2020.](https://www.medrxiv.org/content/10.1101/2020.06.30.20143255v1)


## Rabe Cepko - SARS-CoV-2 detection using isothermal amplification (7-8-2020 PNAS Resub).pdf
[Rabe BA, Cepko C. SARS-CoV-2 detection using isothermal amplification and a rapid, inexpensive protocol for sample inactivation and purification. *Proc Natl Acad Sci U S A*. 2020;117(39):24450-24458.](https://pubmed.ncbi.nlm.nih.gov/32900935/)
Publisher: [PNAS](https://www.pnas.org/doi/10.1073/pnas.2011221117)


## Rabe Cepko Anahtar - Clinical Assessment and Validation (12-21-2020).pdf
[Anahtar MN, McGrath GEG, Rabe BA, et al. Clinical assessment and validation of a rapid and sensitive SARS-CoV-2 test using reverse transcription loop-mediated isothermal amplification without the need for RNA extraction. *Open Forum Infect Dis*. 2021;8(2):ofaa631.](https://pubmed.ncbi.nlm.nih.gov/34853795/)
Publisher: [Oxford Academic](https://academic.oup.com/ofid/article/8/2/ofaa631/6042584)


## Sawyer (Univ Colorado) - Preprint - Saliva 2 Step (v2 7-16-2020).pdf
[Yang Q, Meyerson NR, Clark SK, et al. Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers. *eLife*. 2021;10:e65113.](https://pubmed.ncbi.nlm.nih.gov/33779548/)
Publisher: [eLife](https://elifesciences.org/articles/65113)


## Sherrill-Mix (UPenn) - Preprint - LAMP Molecular Beacons (8-13-2020).pdf
[Sherrill-Mix S, Hwang Y, Roche AM, et al. Detection of SARS-CoV-2 RNA using RT-LAMP and molecular beacons. *Genome Biol*. 2021;22:169.](https://pubmed.ncbi.nlm.nih.gov/34082799/)
Publisher: [Genome Biology / BMC](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02387-y)


## Song (UPenn) - Preprint - Closed Tube Molecular COVID-19 TestRAMP assay (2-19-2020).pdf
[Song J, El-Tholoth M, Li Y, et al. Single and two-stage, closed-tube, point-of-care, molecular detection of SARS-CoV-2. *Anal Chem*. 2021;93(38):13063-13071.](https://pubmed.ncbi.nlm.nih.gov/34541844/)
Publisher: [ACS Analytical Chemistry](https://pubs.acs.org/doi/10.1021/acs.analchem.1c03016)


## Springer (Harvard) - Preprint - FIND An enhanced isothermal amplification assay for viral detection (5-28-2020).pdf
[Qian J, Boswell SA, Chidley C, et al. An enhanced isothermal amplification assay for viral detection. *Nat Commun*. 2020;11:5920.](https://pubmed.ncbi.nlm.nih.gov/33219228/)
Publisher: [Nature Communications](https://doi.org/10.1038/s41467-020-19258-y)


## Tanner (NEB and Mirimus) - Preprint - Extraction-Free Saliva SARS-CoV-2 RT-LAMPWorkflow for Workplace Surveillance (3-11-2022).pdf
[Li Z, Bruce JL, Cohen B, et al. Development and implementation of a simple and rapid extraction-free saliva SARS-CoV-2 RT-LAMP workflow for workplace surveillance. *PLoS ONE*. 2022;17(5):e0268692.](https://pubmed.ncbi.nlm.nih.gov/35617204/)
Publisher: [PLoS ONE](https://doi.org/10.1371/journal.pone.0268692)


## Tanner (NEB) - Current Protocols Loop-Mediated Isothermal Amplification for Detection of Nucleic Acids (2014).pdf
[Tanner NA, Evans TC Jr. Loop-mediated isothermal amplification for detection of nucleic acids. *Curr Protoc Mol Biol*. 2014;105:15.14.1-15.14.14.](https://pubmed.ncbi.nlm.nih.gov/24510439/)
Publisher: [Wiley / Current Protocols](https://doi.org/10.1002/0471142727.mb1514s105)


## Tanner Zhang (NEB) - Preprint - Enhancing Colorimetric LAMP Amplification Speed and Sensitivity with Guanidine Chloride (6-3-2020).pdf
[Zhang Y, Ren G, Buss J, Barry AJ, Patton GC, Tanner NA. Enhancing colorimetric loop-mediated isothermal amplification speed and sensitivity with guanidine chloride. *BioTechniques*. 2020;69(3):178-185.](https://pubmed.ncbi.nlm.nih.gov/32635743/)
Publisher: [BioTechniques](https://doi.org/10.2144/btn-2020-0078)


## Wang (UI Chicago) - Developing RT-LAMP assays for rapid diagnosis of SARS-CoV-2 in saliva (2022).pdf
[Huang X, Tang G, Ismail N, Wang X. Developing RT-LAMP assays for rapid diagnosis of SARS-CoV-2 in saliva. *eBioMedicine*. 2022;75:103736.](https://pubmed.ncbi.nlm.nih.gov/34922321/)
Publisher: [eBioMedicine / The Lancet](https://doi.org/10.1016/j.ebiom.2021.103736)


# 773  _context-commentary_various-papers-lamp.md
METADATA
last updated: 2026-02-23 RT
file_name: _context-commentary_various-papers-lamp.md
category: various
subcategory: papers-lamp
words: 552
tokens: 773


CONTENT

## Context
The papers-lamp subcategory contains a curated selection of published papers on RT-LAMP (reverse transcription loop-mediated isothermal amplification) tests for SARS-CoV-2 detection. The collection includes work from academic groups and commercial entities whose efforts were particularly relevant to FloodLAMP's development and operations during the pandemic. This is not a comprehensive literature review — it is a somewhat haphazard selection of papers that intersected directly with FloodLAMP's work or that represent notable milestones in LAMP-based COVID-19 testing.


## Commentary Points
The foundational paper in the collection is Rabe and Cepko (2020, PNAS), which describes the assay that FloodLAMP adopted as the basis for its testing protocol. The Rabe-Cepko test offered both a purified version — using a low-cost "glass milk" silica purification method — and a direct (extraction-free) version. FloodLAMP initially used the purified version before transitioning to the direct protocol for its subsequent clinical validation and FDA submissions as well as all of its surveillance pilot testing programs. A companion clinical validation paper (Anahtar, Rabe, et al., 2021) further established the assay's performance. In this archive's lamp-tech subcategory there is additional technical background on this assay, including an interview with Brian Rabe about the test's development.

Several papers represent groups that were central to the open-source LAMP testing community. The Kellner et al. paper from the Vienna BioCenter describes an open RT-LAMP assay developed by a group that was a prominent contributor to the gLAMP (Global LAMP) consortium. The Vienna group established rtlamp.org, a resource hosting open protocols, background information, how-to guides, and eventually distributing test kits. The various/glamp subcategory of this archive provides more information. Dave O'Connor's group at the University of Wisconsin contributed multiple papers on direct RT-LAMP evaluation and optimization. O'Connor also shared surveillance program documentation that is cross-referenced elsewhere in the archive. Nathan Tanner and colleagues at New England Biolabs (NEB) published papers on both foundational LAMP methodology and practical applications — including an extraction-free saliva RT-LAMP workflow for workplace surveillance conducted in partnership with Mirimus. Tanner was a key contributor to the GLAMP community, and NEB's colorimetric LAMP master mix reagent was a critical supply for FloodLAMP and many other LAMP-based testing efforts.

On the commercial side, Color Genomics obtained FDA Emergency Use Authorization for a purified, fluorometric LAMP assay read on a PCR thermal cycler. Color's test was widely deployed in screening programs across the San Francisco Bay Area, including at Stanford University and numerous companies. Its authorization and scale of deployment served as an important validation that LAMP-based molecular testing could function as a practical alternative to RT-PCR in large screening programs. The collection also includes a paper from Domus, which developed a lyophilized colorimetric RT-LAMP kit; Domus was a recipient of late-stage RADx (Rapid Acceleration of Diagnostics) funding from NIH.

Additional papers in the collection represent other notable academic efforts in LAMP-based SARS-CoV-2 detection, including work from Stanford (Prakash, using the Rabe-Cepko protocol with a low-cost centrifuge), UPenn (Sherrill-Mix on molecular beacons; Song on closed-tube detection), University of Chicago (Wang, saliva-based assays), and groups working in sub-Saharan Africa (Marcello et al., multicenter evaluation). An AI-generated literature review included in the subcategory extends coverage to 20 additional papers prioritized for large-scale testing and pandemic preparedness. The subcategory also includes a citations file with full bibliographic references and links for all papers in the collection.