Rapid diagnostics of novel coronavirus infection by loop-mediated isothermal amplification

Khafizov, K.; Petrov, Vadim V.; Krasovitov, K. V.; Zolkina, M V; Акимкин, В. Г.

doi:10.36233/0507-4088-42

Cited by 9 publications

(3 citation statements)

References 65 publications

(84 reference statements)

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“…CRIE specialists have developed the AmpliSens ® SARS-CoV-2-N501Y-IT reagent kit aimed at detecting the N501Y mutation using the loop-mediated isothermal amplification (LAMP) method. The use of this kit in practice has made it possible to drastically reduce the number of samples submitted for whole-genome sequencing in order to identify and monitor strains containing the S:N501Y mutation [ 15 ]. However, the further emergence of strains characterized by the appearance of additional mutations in the S-protein gene showed that genomic substitutions at the sites of LAMP primers can reduce the effectiveness of this technique [ 16 ].…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 Variants Monitoring Using Real-Time PCR

et al. 2022

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According to the temporary recommendations of the 2021 World Health Organization (WHO), in addition to whole-genome sequencing, laboratories in various countries can also screen for known mutations utilizing targeted RT-PCR-based mutation detection assays. The aim of this work was to generate a laboratory technique to differentiate the main circulating SARS-CoV-2 variants in 2021–2022, when a sharp increase in morbidity was observed with the appearance of the Omicron variant. Real-time PCR methodology is available for use in the majority of scientific and diagnostic institutions in Russia, which makes it possible to increase the coverage of monitoring of variants in the territories of all 85 regions in order to accumulate information for the Central Services and make epidemiological decisions. With the methodology developed by the Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (FSSCRP Human Wellbeing) (CRIE), more than 6000 biological samples have been typed, and 7% of samples with the Delta variant and 92% of samples with the Omicron variant have been identified as of 25 August 2022. Reagents for 140,000 definitions have been supplied to regional organizations.

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Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 Variants Monitoring Using Real-Time PCR

et al. 2022

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“…A great number of recent publications on RCA-mediated analysis indicate an increasing interest in, and a significant practical potential of, the RCA reaction; however, the share of studies on its application for the quantification of bioanalytes in real samples is not large enough. In addition, as distinct from other isothermal amplification methods [ 137 – 139 ], RCA has not yet found application in the molecular diagnosis of the SARS-CoV-2 coronavirus. Apparently, further studies are needed to improve and optimize the corresponding RCA-mediated techniques, to test them on clinical material, to simplify, if possible, some technologies and methods, and to search for, or create novel molecular tools that broaden the potential of RCA.…”

Section: Discussionmentioning

confidence: 99%

Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets

et al. 2021

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— Detection and quantification of biotargets are important analytical tasks, which are solved using a wide range of various methods. In recent years, methods based on the isothermal amplification of nucleic acids (NAs) have been extensively developed. Among them, a special place is occupied by rolling circle amplification (RCA), which is used not only for the detection of a specific NA but also for the analysis of other biomolecules, and is also a versatile platform for the development of highly sensitive methods and convenient diagnostic devices. The present review reveals a number of methodical aspects of RCA-mediated analysis; in particular, the data on its key molecular participants are presented, the methods for increasing the efficiency and productivity of RCA are described, and different variants of reporter systems are briefly characterized. Differences in the techniques of RCA-mediated analysis of biotargets of various types are shown. Some examples of using different RCA variants for the solution of specific diagnostic problems are given.

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“…In addition, three variants (“alpha”, “beta” and “gamma”) have the N501Y mutation in the S-protein gene, which is associated with increased affinity for the angiotensin-converting enzyme 2 (ACE2) receptor, which possibly contributes to the increased transmissibility of the virus (Nelson et al 2021; Tian et al 2021). Earlier, specialists from the Central Research Institute of Epidemiology of Rospotrebnadzor developed a set of reagents for the rapid detection of the N501Y mutation in the virus genome using the isothermal loop amplification method (Khafizov et al 2021), which dramatically reduced the number of samples transferred for whole genome sequencing in order to identify and monitor new strains containing the above mutation. However, the emergence of new strains, including those characterized by other mutations in the S-protein gene, showed that genomic substitutions at the sites of LAMP primer annealing can reduce the effectiveness of the technique.…”

Section: Introductionmentioning

confidence: 99%

Monitoring the spread of SARS-CoV-2 variants in Moscow and the Moscow region using targeted high-throughput sequencing

Borisova

Kotov

Kolesnikov

et al. 2021

Preprint

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Since the outbreak of the COVID-19 pandemic caused by the SARS-CoV-2 coronavirus, the international community has been concerned about the emergence of mutations that alter the biological properties of the pathogen, for example, increasing its infectivity or virulence. In particular, since the end of 2020, several variants of concern have been identified around the world, including variants alpha (B.1.1.7, British), beta (B.1.351, South African), gamma (P.1, Brazilian) and delta (B.1.617.2, Indian). However, the existing mechanism for searching for important mutations and identifying strains may not be effective enough, since only a relatively small fraction of all identified pathogen samples can be examined for genetic changes by whole genome sequencing due to its high cost. In this study, we used the method of targeted high-throughput sequencing of the most significant regions of the gene encoding the S-glycoprotein of the SARS-CoV-2 virus, for which a primer panel was developed. Using this technique, we examined 579 random samples obtained from patients in Moscow and the Moscow region with coronavirus infection from February to June 2021. The study demonstrated the dynamics of the representation in the Moscow region of a number of SARS-CoV-2 strains and its most significant individual mutations in the period from February to June 2021. It was found that the strain B.1.617.2 began to spread rapidly in Moscow and the Moscow region in May, and in June it became dominant, partially displacing other varieties of the virus. The results obtained make it possible to accurately determine the belonging of the samples to the abovementioned and some other strains. The approach can be used to standardize the procedure for searching for new and existing epidemiologically significant mutations in certain regions of the SARS-CoV-2 genome, which allows studying a large number of samples in a short time and to get a more detailed picture of the epidemiological situation in the region.

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Rapid diagnostics of novel coronavirus infection by loop-mediated isothermal amplification

Cited by 9 publications

References 65 publications

SARS-CoV-2 Variants Monitoring Using Real-Time PCR

SARS-CoV-2 Variants Monitoring Using Real-Time PCR

Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets

Monitoring the spread of SARS-CoV-2 variants in Moscow and the Moscow region using targeted high-throughput sequencing

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