Rapid and simultaneous identification of three mutations by the Novaplex™ SARS-CoV-2 variants I assay kit

Kami, Wakaki; Kinjo, Takeshi; Arakaki, Wakako; Oki, Hiroya; Motooka, Daisuke; Nakamura, Shota; Fujita, Jiro

doi:10.1016/j.jcv.2021.104877

Cited by 25 publications

(19 citation statements)

References 6 publications

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“…Recent studies have evaluated different screening kits in comparison to NGS. The authors demonstrated a high concordance between the two methods, reinforcing the interest of screening methods [ 20 , 21 , 22 , 23 , 24 ]. Here, we showed that the PerkinElmer kit performed better than the ID Solution kit, avoiding the problem of mutation detection, notably the detection of E484K mutation.…”

Section: Discussionmentioning

confidence: 72%

Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR

et al. 2021

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Since January 2021, the diffusion of the most propagated SARS-CoV-2 variants in France (UK variant 20I/501Y.V1 (lineage B.1.1.7), 20H/H501Y.V2 (lineage B.1.351) and 20J/H501Y.V3 (lineage P.1)) were urgently screened, needing a surveillance with an RT-PCR screening assay. In this study, we evaluated one RT-PCR kit for this screening (ID SARS-CoV-2/UK/SA Variant Triplex®, ID Solutions, Grabels, France) on 2207 nasopharyngeal samples that were positive for SARS-CoV-2. Using ID Solutions kit, 4.1% (92/2207) of samples were suspected to belonged to B.1.351 or P.1 variants. Next-generation sequencing that was performed on 67.4% (62/92) of these samples confirmed the presence of a B.1.351 variant in only 75.8% of the samples (47/62). Thirteen samples belonged to the UK variant (B.1.1.7), and two to A.27 with N501Y mutation. The thirteen with the UK variant presented one mutation in the S-gene, near the ΔH69/ΔV70 deletion (S71F or A67S), which impacted the detection of ΔH69/ΔV70 deletion. Using another screening kit (PKampVariantDetect SARS-CoV-2 RT-PCR combination 1 and 3® PerkinElmer, Waltham, MA, USA) on the misidentified samples, we observed that the two mutations, S71F or A67S, did not impact the detection of the UK variant. In conclusion, this study highlights the limitations of the screening strategy based on the detection of few mutations/deletions as well as it not being able to follow the virus evolution.

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Section: Discussionmentioning

confidence: 72%

Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR

et al. 2021

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“…Whole genome sequencing with next-generation sequencing (NGS) is the gold standard for detection of VOCs, but is less ideal in resource-limited settings as it is time-consuming, costly and requires extensive data processing ( Armstrong et al, 2019 ). Direct PCR-based variant analysis of SARS-CoV-2 is rapid, inexpensive and could be utilised as an alternative to NGS ( Kami et al, 2021 ). In this study, we investigated the emergence of VOCs in Malaysia using two multiplex RT-PCR commercial assays to identify VOC-defining mutations, with further validation using NGS.…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021

Chong

Sam

et al. 2022

Journal of Virological Methods

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Emerging SARS-CoV-2 variants of concern (VOC) have been associated with enhanced transmissibility and immune escape. Next-generation sequencing (NGS) of the whole genome is the gold standard for variant identification for surveillance but is time-consuming and costly. Rapid and cost-effective assays that detect SARS-CoV-2 variants are needed. We evaluated Allplex SARS-CoV-2 Master Assay and Variants I Assay to detect HV69/70 deletion, Y144 deletion, E484 K, N501Y, and P681H spike mutations in 248 positive samples collected in Kuala Lumpur, Malaysia, between January and May 2021. Spike variants were detected in 78/248 (31.5%), comprising 60 VOC B.1.351 (beta) and 18 B.1.1.7 (alpha). With NGS as reference for 115 samples, the sensitivity for detecting the spike mutations was 98.7% with the Master Assay and 100% with the Variants I Assay. The emergence of beta variants correlated with increasing COVID-19 infections in Malaysia. The prevalence of alpha VOC and lineage B.1.466.2 was low. These assays detect mutations present in alpha, beta and gamma VOCs. Of the VOCs which have subsequently emerged, the assays should detect omicron (B.1.1.529) but not B.1.617.2 (delta). In conclusion, spike variant PCR assays can be used to rapidly monitor selected SARS-CoV-2 VOCs in resource-limited settings, but require updates as new variants emerge.

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“…Unlike NGS, only some specific mutations of the spike protein of SARS-CoV-2 are amplified. The Novaplex™ SARS-CoV-2 Variants I Assay diagnoses the presence of E484 K, N501Y mutations and H69/V70 deletion( Kami et al, 2021 ). This test is used as a second line test after a positive SARS-COV-2 molecular test has been found.…”

Section: Discussionmentioning

confidence: 99%

The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another

Blairon

Cupaiolo

Piteüs

et al. 2021

Journal of Virological Methods

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Introduction Following the emergence of SARS-CoV-2 variants of concern (VOCs) worldwide, it is important to monitor local epidemiology to better understand the occurrence of clusters, reinfections, or infection after vaccination. Detecting mutations by specific RT-qPCR is a rapid and affordable alternative to sequencing. However, care must be taken to ensure that the techniques used are up-to-date and adapted to the variants circulating in the studied population. Material and methods All samples tested positive for SARS-CoV-2 were screened for detection of mutations of the spike protein using the Novaplex™ SARS-CoV-2 Variants I Assay from week 11 of 2021. Target sought were deletion H69/V70 and mutations N501Y and E484 K. From week 18 we used in addition the new Novaplex™ SARS-CoV-2 Variants II Assay for samples with no targets found with the Variants I assay or with the mutation E484 K alone, in order to screen the mutations L452R, K417 N/T and W152C. Results Between weeks 11 and 25, 2239 positive samples out of 54317 were tested with the Variants I Assay. Between weeks 18 and 25, 94 samples met the criteria for being tested with the Variants II Assay. Of these, 47 had the L452R mutation without the W152C mutation, typical in the B.1.617 variant. At week 25, this profile was found in 45.5% of the samples and was the most frequent. Conclusion According to our observations, variant B.1.617 has become predominant in our institution and most probably in our region. In the absence of the use of the Variants II Assay, they would have been considered wild.

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Rapid and simultaneous identification of three mutations by the Novaplex™ SARS-CoV-2 variants I assay kit

Cited by 25 publications

References 6 publications

Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR

Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR

SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021

The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another

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