Probing Loop-Mediated Isothermal Amplification (LAMP) targeting two gene-fragments of rose rosette virus

PLoS One. 2021 Nov 29;16(11):e0256510. doi: 10.1371/journal.pone.0256510. eCollection 2021.

Abstract

This study explores the development of Loop-mediated isothermal amplification (LAMP) for detection of rose rosette virus (RRV), a technique with the potential to be translated to rose nurseries. RRV is a negative-sense, single-stranded RNA virus which is a member of the genus Emaravirus (Family Fimoviridae) and the causal agent of the rose rosette disease (RRD). Although RRV symptoms are characteristics, early visual diagnosis of RRD can be misleading and confusing since it may appear like herbicide damage. Moreover, it may take incubation time for symptoms to appear after virus infection. Two sets of RRV gene sequences RNA3 and RNA4 were analyzed and two sets of four LAMP primers were designed. The direct antigen-capture method for direct trapping of RRV in plastic was used for RNA extraction followed by cDNA synthesis. RT-LAMP reactions were for 1 hour at 64°C (RRV-P3) and 66.5°C (RRV-P4) using either a thermocycler or a portable dry bath. RT-qLAMP was also optimized using DNA polymerase GspSSD LD using the same RRV sets of primers. RRV was detected in symptomatic and non-symptomatic RRD tissue from Oklahoma. The limit of detection (LoD) was 1pg/μL and 1 fg/μL using Bst 2.0 LAMP and GspSSD LD quantitative LAMP, respectively. In visual colorimetric pre- and post-reactions, the LoD was 10 pg/μL and 0.1 pg/μL using hydroxy naphthol blue (HNB, 120 μM) and SYBR green I (1:10 dilution), respectively. No cross-reactivity was detected in the RT-LAMP reaction testing cDNAs of eight commonly co-infecting rose viruses and one virus taxonomically related to RRV. Four different dyes were tested, and visible colorimetric reactions were obtained with RT-LAMP Bst 2.0 combined with SYBR I or HNB. RT-qLAMP with GspSSD2.0 offers LoD equal to RT-PCR and it is faster since it works with RNA directly.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Molecular Diagnostic Techniques*
  • Nucleic Acid Amplification Techniques*
  • Plant Diseases / virology*
  • RNA Virus Infections / genetics*
  • RNA Viruses / genetics*
  • Rosa / virology*
  • Sensitivity and Specificity

Supplementary concepts

  • LAMP assay

Grants and funding

The research was funded by the USDA, NIFA, SCRI grant ‘Combating Rose Rosette Disease: Short Term and Long-Term Approaches’ (2014-51181- 392 22644/SCRI), and the Oklahoma Agricultural Experimental Station, Hatch # Okl 02950 ‘Detection and Diagnostic Methods For Agricultural Biosecurity and Forensic Plant Pathology Applications’. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.