• Dry

• Wet

Get Cakes

GET https://api.cakes.com/v1/cakes/:id

This endpoint allows you to get free cakes.

Path Parameters

Query Parameters

Headers

Collaboration

All Things gLAMP

Can I become who I want to be?

That's a tough question but thankfully, our team is on it. Please bear with us while we're investigating.

Getting Super Powers

Becoming a super hero is a fairly straight forward process:

• Computational (non-web resources, ex. bioinformatics)

• Web

Contributor Comments

Community Comments

gLAMP

Global LAMP Consortium

The Global LAMP (gLAMP) Consortium was founded in April 2020, in the midst of the COVID-19 pandemic as a diverse group of stakeholders including scientists, engineers, physicians, educators, government officials, philanthropists, and more, who came together to address the global challenges in detecting SARS-CoV-2. As new results kept being reported on pre-prints posted on bioRxiv and medRxiv, it quickly became clear that LAMP technology showed great potential in providing rapid, accurate, and scalable diagnostics. Indeed, there are several different applications and approaches to LAMP methods that can be modified and adapted to various testing goals such as point-of-care clinical testing, community screening, monitoring city sewage samples, or swabbing urban spaces. gLAMP currently has over 300 members spanning academic labs, industry teams, non-profit, community biology, and government agencies. The group meets virtually every week to share IRB protocols, best practices, latest results from pilot experiments, reagent suppliers, and logistic experiences. The goal is to create an open environment where results can be shared to accelerate research as fast as possible and deploy the most optimal testing methods to the field.

gLAMP Central

gLAMP Central refers to planning around the creation of companion infrastructure to benefit ongoing gLAMP calls, in the spirit of "rough consensus and working code".

gLAMP Review

The gLAMP review is the first project resulting from gLAMP Central planning discussion. It is a collaborative synopsis of the key methods and developments shared over the course of 2020.

Getting Involved

There are multiple ways to get involved in gLAMP's ongoing efforts.

Assets

Summary

This page lists the annotated references of the manuscript. Annotations emphasize a subset of the bibliography entries. Each annotated entry receives:

1. Prioritization on a 3-point scale as one of the following:

   1. a work of interest (•)

   2. a work of special interest (••)

   3. a work of outstanding interest (•••)

The 3-point scale takes after the conventions of series such as Annual Reviews and Current Opinions. The descriptions follow an Elsevier Highlights rubric.

ATTN JBT and Publisher

1. An earlier FAQ, detailing further information, is available.

   See: .

2. The Typesetting Sample subpage here describes the source material and desired output. See:

3. The Items subpage here contains the fullest non-.bib draft of all annotated references.

   See:

Guide

Time-Sensitive Claims

Over the course of a series of writing and discussion sessions, we systematically audited the work for time-sensitive claims. Our essential objectives were the following:

Changelog Format

Boilerplate

Legend

X.Y - YYYY-MM-DD

Does this version affect...

• Frontmatter?

• Bodymatter?

• Topics?

• Backmatter?

Added

• Added the platypus. That should keep them second-guessing for a while.

Changed

• Animals are now super cute, all of them.

Fixed

• Patched a bug where humans would develop language & tools, organize, and destroy each other.

Removed

• Removed deadly solar radiation.

Attachments

Files accompanying this revision/release will be found below:

Sample Information

Citekey

For illustrative purposes, we have selected Maranhao2020.

Source

Our bibliography is a .bib database. Each entry is structured data in bibtex format. An annotated entry's source is stored like so:

In this source, the annote field contains the annotations.

1. \onestar is priority 1 on the 1-3 scale, where 3 is highest.

2. \\ is a line-separator.

3. Further lines are highlight bullets on the cited work.

Usage

Inline Use

We cite Maranhao2020 by its citekey, Maranhao2020. We do this using the \cite command, as in:

Lorem ipsum dolor sit amet.\cite{Maranhao2020}

In References

Once rendered, this turns into a numeric value in brackets. If Maranhao2020 is reference number 4, for instance, the output is:

Lorem ipsum dolor sit amet.[4]

Appearance

Current Appearance

In our working draft's References section, Maranhao2020 renders like so:

[4] Andre Maranho, Sanchita Bhadra, Inyup Paik, David Walker, and Andrew D. Ellington. 2020. An improved and readily available version of Bst DNA Polymerase for LAMP, and applications to COVID-19 diagnostics. (oct 2020). We can change this ourselves to achieve the desired appearance. Our understanding is that the publisher will not be retaining LaTeX-based styles, however.

Desired Appearance

We would like to see the priority (● - ●●●) prefixed prior to the reference's author(s) field. Additionally, we ask that the highlight bullets not make use of a circular item label, for clarity. An alternative shape, such as a diamond or square, would assist in providing contrast:

[4] ● Andre Maranho, Sanchita Bhadra, Inyup Paik, David Walker, and Andrew D. Ellington. 2020. An improved and readily available version of Bst DNA Polymerase for LAMP, and applications to COVID-19 diagnostics. (oct 2020). ◇ Protein engineering fusion improves function of Bst DNA polymerase in LAMP ◇ Modifying Bst DNA polymerase significantly improves reverse transcriptase activity ◇ Further improves LAMP-OSD detection in pre-heated saliva without RNA extraction

Fallback Appearance

• If the is not possible:

  • Styles closer to the Current Opinions style are acceptable to us.

  • These styles are well-suited to flowing prose annotations.

[4] Andre Maranho, Sanchita Bhadra, Inyup Paik, David Walker, and Andrew D. Ellington. 2020. An improved and readily available version of Bst DNA Polymerase for LAMP, and applications to COVID-19 diagnostics. (oct 2020). ● Protein engineering fusion improves function of Bst DNA polymerase in LAMP Modifying Bst DNA polymerase significantly improves reverse transcriptase activity Further improves LAMP-OSD detection in pre-heated saliva without RNA extraction

Rubrics

Annotations contain two parts: a priority and outline-style highlights. Therefore there are two rubrics.

Highlights Rubric

• 3-5 bullets

• 85 character limit, including whitespace

• no end punctuation

Examples

• • Metastases mostly disseminate late from primary breast tumors, keeping most drivers

  • Drivers at relapse sample from a wider range of cancer genes than in primary tumors

Priorities Rubric

Preparation

• Each reference contains provenance tagging by section.

• This group field allows us to analyze our citations.

• We fetched further informative metadata via:

Calculation

We then tabulated two levels of citation analysis:

1. First, we looked at descriptive statistics.

2. Next, we calculated a few nontrivial measures.

3. Finally, we did a qualitative rundown of known-significant works and how we cited them.

Descriptive Stats

Descriptive stats of relevance include:

1. citation frequency,

2. citation centrality,

3. between-section differences, and so forth.

Statistical Measures

Statistical measures of relevance include:

1. mutual and interaction information,

2. graphical properties — especially cliques and skew partitions,

3. "standard" citation analysis benchmarks, and so forth.

4. Finally, we

• This ultimately the combined multi-bibliography by factors like:

• • citation frequency,

  • citation centrality, and

Evolution

About

What is the gLAMP Review?

See: About § gLAMP Review

When are things happening?

2020 schedules were not carried over from prior docs.

Authorship

What is the authorship model?

1. ‘Football team’ of co-authors and supporting contributors.

2. Co-authors help to write, collate, and synthesize contributions.

3. Sections prioritize topics of importance to the collective.

Who is a section lead?

Section Leads are corresponding authors for their respective sections.

Who is a contributor?

Volunteering Contributors write one or more elements for inclusion (½-¾ page each). We expect these contributions to be ‘close to home’ for the contributor and hence not a significant overhead to write. These can be a cliff note summary of a contributor’s presentation to a Thursday gLAMP, of a preprint, or a summary of an aspect of LAMP testing literature that they have particularly focused on.

Solicited Contributors are individuals that section leads will contact with a request for ½-¾ page on a particular topic for which we currently do not have coverage. If subsequent encouragement is needed, please let us know.

Who gets writing credit?

Everyone who contributes to the review will receive authorship credit.

Guidelines

Instructions for Authors?

For various other matters, refer to journal guides:

• ​ [​ , ​]

• [​ , ​]

• [​​]

Tools for figures?

Biorender and any visualization tool you might require.

Can contributions be graphical abstracts?

Yes.

More

Looking for old notes?

Early notes were collated at .

Looking for something else?

We have everything from the duration of the gLAMP review writing period. Are you looking for something that seems to be missing? Let Jeremy and Keith know. We'll make it more visible.

Overview

The gLAMP Review is a multi-component project. It consists of a variety of files and moving parts. We have used certain conventions to aid in tracking these parts.

• The overall assembly is partitioned into four (4) parts.

• Each part contains sections.

• Every element has an index in a sectioning scheme.

• This scheme consists of indices of the form DD.DD.DD.

Table of Contents

• Front Matter

  • 00 Metadata

    • 00.01 People

Authorship

Scope

*Emerging Technologies

• What happened to the Emerging Technologies section?

  • The following sections merged, forming Infrastructure:

    • Emerging Technologies

There are 36 annotated items in total.

Annotated References

Alekseenko, A., Barrett, D., Pareja-Sanchez, Y., Howard, R. J., Strandback, E., Ampah-Korsah, H., Rovšnik, U., Zuniga-Veliz, S., Klenov, A., Malloo, J., Ye, S., Liu, X., Reinius, B., Elsässer, S. J., Nyman, T., Sandh, G., Yin, X., & Pelechano, V. (2021). Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples. Scientific reports, 11(1), 1820. https://doi.org/10.1038/s41598-020-80352-8

• STARS: 2

• ANNOTE

  • RT-LAMP detects medium-high viral loads in swabs without RNA extraction and purification

  • Describes homebrew production of B.stearothermophilus Bst-LF ‘v5.9’ from Ellington et al

  • Provides an alternative to commercial reagents for RT-LAMP based SARS-COv2 detection.

Becherer, L N. Borst, M. Bakheit, S. Frischmann, R. Zengerle, and F. von Stetten, “Loop-mediated isothermal amplification (LAMP) – review and classification of methods for sequence-specific detection,” Analytical Methods, vol. 12, no. 6, pp. 717–746, 2020.

• STARS: 2

• ANNOTE

  • LAMP has a propensity to create non-specific amplicons caused by mis-priming

  • Sequence-specific amplicon detection can significantly increase LAMP specificity

Ben-Assa, N et al. , “Direct on-the-spot detection of SARS-CoV-2 in patients,” Experimental Biology and Medicine; , vol. 245, no. 14, pp. 1187–1193, jul 2020.

• STARS: 1

• ANNOTE

  • An early report of the use of saliva (cf. UTM/VTM) in pH-based colourimetric RT-LAMP

  • Simplified sample processing with proteinase K prior to heating and the RT-LAMP test

Bektas, A., Covington, M., Aidelberg, G., Arce, A., Matute, T., N\'u\~nez, I., Walsh, J., Boutboul, D., Lindner, A., Federici, F., & Jayaprakash, A. (2021). Accessible LAMP-Enabled Rapid Test (ALERT) for detecting SARS-CoV-2. medRxiv.

• STARS: 3

• ANNOTE

  • ALERT: a streamlined process that improves overall LAMP performance and usability

  • Separating RT reaction from LAMP significantly improves limit of detection

Bhadra, S., Riedel, T., Lakhotia,S., Tran, N.D., and Ellington, A. High-surety isothermal amplification and detection of SARS-CoV-2, including with crude enzymes bioRxiv 2020.04.13.039941; doi: ; Now accepted for publication in mSphere

• STARS: 3

• ANNOTE

  • Converts three assays using non-specific to a sequence-specific fluorescence readout

  • One-strand displacement (OSD) creates a stable, multicolor readout for saliva LAMP

Broughton, J et al. , “CRISPR–cas12-based detection of SARS-CoV-2,” Nature Biotechnology , vol. 38, no. 7, pp. 870–874, apr 2020.

• STARS: 1

• ANNOTE

  • The CRISPR-Cas system detects E and N gene sequences by using specific guide RNA

  • Once bound to cDNA amplified by RT-LAMP, collateral Cas12 ssDNase activity is activated

Corman, V. M., Landt, O., Kaiser, M., Molenkamp, R., Meijer, A., Chu, D. K., Bleicker, T., Brünink, S., Schneider, J., Schmidt, M. L., Mulders, D. G., Haagmans, B. L., van der Veer, B., van den Brink, S., Wijsman, L., Goderski, G., Romette, J. L., Ellis, J., Zambon, M., Peiris, M., … Drosten, C. (2020). Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 25(3), 2000045.

• STARS: 2

• ANNOTE

  • Early reference paper, endorsed by the WHO, on which many RT-qPCR tests were based

  • Created a workflow for detecting SARS-CoV-2 vs. other human respiratory viruses

de Oliveira Coelho, B., Sanchuki, H., Zanette, D. L., Nardin, J. M., Morales, H., Fornazari, B., Aoki, M. N., & Blanes, L. (2021). Essential properties and pitfalls of colorimetric Reverse Transcription Loop-mediated Isothermal Amplification as a point-of-care test for SARS-CoV-2 diagnosis. Molecular medicine (Cambridge, Mass.), 27(1), 30.

• STARS: 2

• ANNOTE

  • Diagnostic comparison (94% sensitivity, 90% specificity) using RNA extracted from NPS

  • Highlights an intermediate orange result when using a pH sensitive readout (red or yellow)

Ding, Sheng, et al. “Sequence-Specific and Multiplex Detection of COVID-19 Virus (SARS-CoV-2) Using Proofreading Enzyme-Mediated Probe Cleavage Coupled with Isothermal Amplification.” Biosensors & Bioelectronics, vol. 178, Apr. 2021, p. 113041. .

• STARS: 1

• ANNOTE

  • Addresses the false positives arising from lack of sequence-specificity in many LAMP readouts

  • Uses Pfu proof-reading enzyme-mediated probe cleavage (RT-Proofman-LAMP)

Maranhao, Andre, et al. An Improved and Readily Available Version of Bst DNA Polymerase for LAMP, and Applications to COVID-19 Diagnostics. preprint, Infectious Diseases (except HIV/AIDS), 5 Oct. 2020. .

• STARS: 1

• ANNOTE

  • Protein engineering fusion improves function of Bst DNA polymerase in LAMP

  • Modifying Bst DNA polymerase significantly improves reverse transcriptase activity

Fowler, V. L., Armson, B., Gonzales, J. L., Wise, E. L., Howson, E., Vincent-Mistiaen, Z., Fouch, S., Maltby, C. J., Grippon, S., Munro, S., Jones, L., Holmes, T., Tillyer, C., Elwell, J., Sowood, A., de Peyer, O., Dixon, S., Hatcher, T., Patrick, H., Laxman, S., … Kidd, S. P. (2021). A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection. The Journal of infection, 82(1), 117–125.

• STARS: 2

• ANNOTE

  • Reports a novel RT-LAMP assay with 97% and 99% clinical sensitivity and specificity, respectively

  • Almost perfect agreement with RNA RT-LAMP (extracted RNA) and RT-qPCR

Ganguli, A., Mostafa, A., Berger, J., Aydin, M., Sun, F., Valera, E., Cunningham, B. T., King, W. P., & Bashir, R. (2020). Rapid Isothermal Amplification and Portable Detection System for SARS-CoV-2. bioRxiv : the preprint server for biology, 2020.05.21.108381.

• STARS: 1

• ANNOTE

  • Introduces an RNA extraction-free method from patient swab samples via heat-lysis

  • Microfluidic-phone camera example of portable hardware system for biosurveillance

Garneret, P., Coz, E., Martin, E., Manuguerra, J. C., Brient-Litzler, E., Enouf, V., González Obando, D. F., Olivo-Marin, J. C., Monti, F., van der Werf, S., Vanhomwegen, J., & Tabeling, P. (2021). Performing point-of-care molecular testing for SARS-CoV-2 with RNA extraction and isothermal amplification. PloS one, 16(1), e0243712.

• STARS: 1

• ANNOTE

  • COVIDISC, a paper-based fabricated portable device for point-of-care testing

  • Combines RNA extraction and running RT-LAMP reactions in one device

James, P., Stoddart, D., Harrington, E., Beaulaurier, J., Ly, L., Reid, S., Turner, D., & Juul, S. (2020). LamPORE: rapid, accurate and highly scalable molecular screening for SARS-CoV-2 infection, based on nanopore sequencing. medRxiv.

• STARS: 2

• ANNOTE

  • LAMPoreTM combines triplexed SARS-CoV-2 detection and nanopore DNA sequencing

  • Performs 96 reactions in two hours with good concordance with RT-qPCR using swab samples

Jureka, A. S., Silvas, J. A., & Basler, C. F. (2020). Propagation, Inactivation, and Safety Testing of SARS-CoV-2. Viruses, 12(6), 622.

• STARS: 1

• ANNOTE

  • Important methods and considerations for live viral manipulation/inactivation

  • Propagation of SARS-CoV-2 in different cell lines to augment supply of control RNA

Kahl, L., Molloy, J., Patron, N. et al. Opening options for material transfer. Nat Biotechnol 36, 923–927 (2018).

• STARS: 2

• ANNOTE

  • Introduces the principles of Open Material Transfer Agreements in the open bioeconomy

  • Relaxes the outdated restrictions on redistribution and commercial use of biological materials

Kellner, M., Ross, J., Schnabl, J., Dekens, M., Heinen, R., Grishkovskaya, I., Bauer, B., Stadlmann, J., Menéndez-Arias, L., Fritsche-Polanz, R., Traugott, M., Seitz, T., Zoufaly, A., Födinger, M., Wenisch, C., Zuber, J., , Pauli, A., & Brennecke, J. (2020). A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing. bioRxiv.

• STARS: 3

• ANNOTE

  • Introduces an extraction-free pH buffered Hydroxynapthol blue (HNB)-based RT-LAMP

  • Highlights the use of the dUTP/UDG system to prevent carryover contamination

Larremore, D., Wilder, B., Lester, E., Shehata, S., Burke, J., Hay, J., Tambe, M., Mina, M., & Parker, R. (2020). Test sensitivity is secondary to frequency and turnaround time for COVID-19 surveillance. medRxiv.

• STARS: 2

• ANNOTE

  • Challenges the assumption that clinical sensitivity is paramount for effective surveillance

  • Highlights the importance of testing frequency and reporting speed

Mina, M. J., Parker, R., & Larremore, D. B. (2020). Rethinking Covid-19 Test Sensitivity - A Strategy for Containment. The New England journal of medicine, 383(22), e120.

• STARS: 3

• ANNOTE

  • Reframes and challenges the current predominant view on COVID-19 testing sensitivity

  • Highlights that analytical sensitivity and clinical sensitivity are not the same

Moehling, T. J., Choi, G., Dugan, L. C., Salit, M., & Meagher, R. J. (2021). LAMP Diagnostics at the Point-of-Care: Emerging Trends and Perspectives for the Developer Community. Expert review of molecular diagnostics, 21(1), 43–61.

• STARS: 1

• ANNOTE

  • Complementary review providing valuable insights on development of LAMP diagnostics

  • Describes advantages and disadvantages of different human samples

Natoli, M., Kundrod, K., Chang, M., Smith, C., Paul, S., Eldin, K., Patel, K., Baker, E., Schmeler, K., & Richards-Kortum, R. (2021). Reverse transcription loop-mediated isothermal amplification (Rt-lamp) for point-of-care detection of SARS-CoV-2: A clinical study to evaluate agreement with RT-qPCR. The Lancet. Global Health, 9, S3.

• STARS: 1

• ANNOTE

  • Evaluates the clinical performance of NPS-based but extraction-free RT-LAMP test

  • Performance (92% sensitivity, 91% specificity) was maintained using a lower-cost reader

Notomi, T., Okayama, H., Masubuchi, H., Yonekawa, T., Watanabe, K., Amino, N., & Hase, T. (2000). Loop-mediated isothermal amplification of DNA. Nucleic acids research, 28(12), E63.

• STARS: 3

• ANNOTE

  • Pioneer LAMP paper: introduces LAMP as a novel DNA amplification method

  • Highly specific and sensitive isothermal amplification with a strand-displacing polymerase

Rabe, B. A., & Cepko, C. (2020). SARS-CoV-2 detection using isothermal amplification and a rapid, inexpensive protocol for sample inactivation and purification. Proceedings of the National Academy of Sciences of the United States of America, 117(39), 24450–24458.

• STARS: 3

• ANNOTE

  • Pivotal paper for low-cost RNA extraction-free methods from human samples

  • A basis for many succeeding papers that uses heat/TCEP/EDTA to inactivate RNases

Sherrill-Mix, S., Duyne, G., & Bushman, F. (2021a). Molecular beacons allow specific RT-LAMP detection of B.1.1.7 variant SARS-CoV-2. medRxiv.

• STARS: 2

• ANNOTE

  • Demonstrates the ability of hybridisation-based molecular beacons to detect variants

  • Pilot study on variant-discrimination for SARS-CoV-2 (S1∆69-70 deletion)

Sherrill-Mix, S., Hwang, Y., Roche, A., Glascock, A., Weiss, S., Li, Y., Haddad, L., Deraska, P., Monahan, C., Kromer, A., Graham-Wooten, J., Taylor, L., Abella, B., Ganguly, A., Collman, R., Van Duyne, G., & Bushman, F. (2021b). LAMP-BEAC: Detection of SARS-CoV-2 RNA Using RT-LAMP and Molecular Beacons. medRxiv.

• STARS: 3

• ANNOTE

  • Excellent example of use of molecular beacons for sequence-specific amplicon detection

  • Addresses the false positives arising LAMP to improve reliability and sensitivity of a test

Snodgrass, R., Gardner, A., Semeere, A., Kopparthy, V. L., Duru, J., Maurer, T., Martin, J., Cesarman, E., & Erickson, D. (2018). A portable device for nucleic acid quantification powered by sunlight, a flame or electricity. Nature biomedical engineering, 2(9), 657–665.

• STARS: 1

• ANNOTE

  • Addresses poor diagnostic infrastructure due unreliable access to electricity in Africa

  • TINY: portable microfluidic LAMP device, operating with electricity and alternative power sources

Tan, S. H.; Allicock, O.; Armstrong-Hough, M. & Wyllie, A. L. Saliva as a gold-standard sample for SARS-CoV-2 detection The Lancet Respiratory Medicine, Elsevier BV, 2021, 9, 562-564

• STARS: 3

• ANNOTE

  • Mini-review summarising the potential and pitfalls of using saliva as a biospecimen

  • Focus is on collection, handling, transport, and storage of saliva relative to NPS

Tanner, N. A., Zhang, Y., & Evans, T. C. (2012). Simultaneous multiple target detection in real-time loop-mediated isothermal amplification. BioTechniques, 53(2), 81–89. https://doi.org/10.2144/0000113902

• STARS: 1

• ANNOTE

  • First report of ‘DARQ’ fluorescent LAMP for multiplexed detection of four targets

  • Initial reports of the widely-used Bst 2.0 and WarmStart Bst 2.0 DNA polymerases

Vogels, C., Watkins, A. E., Harden, C. A., Brackney, D. E., Shafer, J., Wang, J., Caraballo, C., Kalinich, C. C., Ott, I. M., Fauver, J. R., Kudo, E., Lu, P., Venkataraman, A., Tokuyama, M., Moore, A. J., Muenker, M. C., Casanovas-Massana, A., Fournier, J., Bermejo, S., Campbell, M., … Grubaugh, N. D. (2021). SalivaDirect: A simplified and flexible platform to enhance SARS-CoV-2 testing capacity. Med (New York, N.Y.), 2(3), 263–280.e6.

• STARS: 2

• ANNOTE

  • First saliva-based SARS-CoV-2 detection to be granted EUA by the FDA

  • Led to increased awareness and interest in saliva as a biospecimen type

Wang, Rui, et al. “OpvCRISPR: One-Pot Visual RT-LAMP-CRISPR Platform for SARS-Cov-2 Detection.” Biosensors and Bioelectronics, vol. 172, Jan. 2021, p. 112766. .

• STARS: 2

• ANNOTE

  • CRISPR incorporates gRNA for specificity with enzymatic amplification to increase sensitivity.

  • Incorporating CRISPR-Cas12a improves LAMP sensitivity by a factor of 10

Wölfel, R., Corman, V.M., Guggemos, W. et al. Virological assessment of hospitalized patients with COVID-2019. Nature 581, 465–469 (2020).

• STARS: 2

• ANNOTE

  • Early report monitoring the viral load, replication rates and clinical symptoms from nine COVID cases

  • Respiratory samples with < 10^6 copies per mL did not yield a replicative isolate

Yan, C., et al. “Rapid and Visual Detection of 2019 Novel Coronavirus (SARS-CoV-2) by a Reverse Transcription Loop-Mediated Isothermal Amplification Assay.” Clinical Microbiology and Infection, vol. 26, no. 6, June 2020, pp. 773–79. .

• STARS: 2

• ANNOTE

  • Thorough description of primer design strategy to create primer sets for orf1ab and S genes.

  • First to demonstrate 100% sensitivity and 100% specificity on clinical samples via visual readout

Yang, Q., Meyerson, N. R., Clark, S. K., Paige, C. L., Fattor, W. T., Gilchrist, A. R., Barbachano-Guerrero, A., Healy, B. G., Worden-Sapper, E. R., Wu, S. S., Muhlrad, D., Decker, C. J., Saldi, T. K., Lasda, E., Gonzales, P., Fink, M. R., Tat, K. L., Hager, C. R., Davis, J. C., … Sawyer, S. L. (2021). Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers. ELife, 10, e65113. .

• STARS: 1

• ANNOTE

  • Saliva-based detection of SARS-CoV-2 in asymptomatic individuals at 94% sensitivity

  • Neutralising saliva stabilisation solution with Proteinase K for saliva-based RT-LAMP

Yaren, O., McCarter, J., Phadke, N., Bradley, K. M., Overton, B., Yang, Z., Ranade, S., Patil, K., Bangale, R., & Benner, S. A. (2021). Ultra-rapid detection of SARS-CoV-2 in public workspace environments. PloS one, 16(2), e0240524.

• STARS: 3

• ANNOTE

  • Development of a sequence-specific method for amplicon detection (displaceable probe, DP)

  • Reports successful use of two COVID-19 primer sets with Rnase P and DP in a single tube assay

Zhang, Y., Odiwuor, N., Xiong, J., Sun, L., Nyaruaba, R., Wei, H., & Tanner, N. (2020). Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP. medRxiv.

• STARS: 2

• ANNOTE

  • An early paper demonstrating the feasibility of SARS-CoV-2 detection using RT-LAMP

  • Vital study that designed five LAMP primer sets targeting SARS-CoV-2 RNA

Zhang, Yinhua, and Nathan A. Tanner. Development of Multiplexed RT-LAMP for Detection of SARS-CoV-2 and Influenza Viral RNA. preprint, Epidemiology, 27 Oct. 2020. .

• STARS: 3

• ANNOTE

  • Describes application of DARQ for sequence-specific detection of SARS-CoV2 amplicons

  • Multiplexing of SARS-CoV2 and influenza virus as pathogens leading to similar symptoms