TY - JOUR
T1 - Improving Performance of a SARS-CoV-2 RT-LAMP Assay for Use With a Portable Isothermal Fluorimeter
T2 - Towards a Point-of-Care Molecular Testing Strategy
AU - Natoli, Mary E.
AU - Kundrod, Kathryn A.
AU - Chang, Megan M.
AU - Smith, Chelsey A.
AU - Paul, Sai
AU - Coole, Jackson B.
AU - Butlin, Nathaniel G.
AU - Tanner, Nathan A.
AU - Baker, Ellen
AU - Schmeler, Kathleen M.
AU - Richards-Kortum, Rebecca
N1 - Funding Information:
We thank the numerous collaborators who contributed to clinical sample collection: Rebecca Elias for assistance with institutional review board protocol submissions; Liam Sweeney, Charles Swope, Kaye Tryels, Sonya Polk-Davis, Angela Muhammad-Ali, Shayla Elliot, Lara Medina, Chelsea Ja’nae, Jessica Thornell, Olalekan Ojeshina, and Nancy Arevalo for their assistance in obtaining samples for initial test development; and Arturo Barrera, Jessica Gallegos, Cindy Melendez, Ana López, Keiry Paiz, Jose Garcia, and Anthony Price for clinical coordination at Lyndon B. Johnson Hospital. Funding for this work was provided from the American people by USAID through an IAVI research grant CCID 9204 under award AID-OAA-A16-00032 between IAVI and USAID, as well as from Rice University internal funding.
Publisher Copyright:
© 2021 ABRF.
PY - 2021/9
Y1 - 2021/9
N2 - Frequent and accessible testing is a critical tool to contain the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To develop low-cost rapid tests, many researchers have used reverse transcription loop-mediated isothermal amplification (RT-LAMP) with fluorescent readout. Fluorescent LAMP-based assays can be performed using cost-effective, portable, isothermal instruments that are simpler to use and more rugged than polymerase chain reaction (PCR) instruments. However, false-positive results due to nonspecific priming and amplification have been reported for a number of LAMP-based assays. In this report, we implemented a RT-LAMP assay for SARS-CoV-2 on a portable isothermal fluorimeter and a traditional thermocycler; nonspecific amplification was not observed using the thermocycler but did occur frequently with the isothermal fluorimeter. We explored 4 strategies to optimize the SARS-CoV-2 RT-LAMP assay for use with an isothermal fluorimeter and found that overlaying the reaction with mineral oil and including the enzyme Tte UvrD helicase in the reaction eliminated the problem. We anticipate these results and strategies will be relevant for use with a wide range of portable isothermal instruments.
AB - Frequent and accessible testing is a critical tool to contain the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To develop low-cost rapid tests, many researchers have used reverse transcription loop-mediated isothermal amplification (RT-LAMP) with fluorescent readout. Fluorescent LAMP-based assays can be performed using cost-effective, portable, isothermal instruments that are simpler to use and more rugged than polymerase chain reaction (PCR) instruments. However, false-positive results due to nonspecific priming and amplification have been reported for a number of LAMP-based assays. In this report, we implemented a RT-LAMP assay for SARS-CoV-2 on a portable isothermal fluorimeter and a traditional thermocycler; nonspecific amplification was not observed using the thermocycler but did occur frequently with the isothermal fluorimeter. We explored 4 strategies to optimize the SARS-CoV-2 RT-LAMP assay for use with an isothermal fluorimeter and found that overlaying the reaction with mineral oil and including the enzyme Tte UvrD helicase in the reaction eliminated the problem. We anticipate these results and strategies will be relevant for use with a wide range of portable isothermal instruments.
UR - http://www.scopus.com/inward/record.url?scp=85123459172&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85123459172&partnerID=8YFLogxK
U2 - 10.7171/jbt.21-3203-013
DO - 10.7171/jbt.21-3203-013
M3 - Article
C2 - 35027875
AN - SCOPUS:85123459172
SN - 1524-0215
VL - 32
SP - 180
EP - 185
JO - Journal of Biomolecular Techniques
JF - Journal of Biomolecular Techniques
IS - 3
ER -