A qualitative RT-PCR assay for the specific identification of the SARS-CoV-2 B.1.1.529 (Omicron) Variant of Concern

Corbisier, Philippe; Petrillo, Mauro; Marchini, Antonio; Querci, Maddalena; Buttinger, Gerhard; Bekliz, Meriem; Spieß, Katja; Polacek, Charlotta; Fomsgaard, Anders; Eede, Guy Van den

doi:10.1016/j.jcv.2022.105191

Cited by 19 publications

(10 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The JRC-CoV-UCE assay can be used to monitor the emergence of a potential novel VOC by coupling their usage with those of VOC-specific detection methods. For example, as Omicron is presently the dominant circulating VOC, a collected sample can be quickly screened by JRC-CoV-UCE and tested simultaneously with an Omicron-specific detection method, such as OmMet [ 25 ]. If their relative ratios are in the same range, it is likely that the sample contains predominantly Omicron-related variants.…”

Section: Discussionmentioning

confidence: 99%

“…The reactions were considered positive if the cycle threshold was below 40 cycles. In addition, the samples were also analyzed by the specific Omicron OmMet assay [ 25 ].…”

Section: Methodsmentioning

confidence: 99%

“…Continued evaluation of the performance of established tests together with the development of novel updated and reliable tests should go hand-in-hand with the evolution of SARS-CoV-2. We have recently described a one-step RT-PCR assay for the specific detection of Omicron [ 25 ]. In contrast to other RT-PCR assays based on the deletion H69–/V70, we have proven that this assay was also able to detect Omicron BA.1 and BA.2 and the currently dominant BA.4 and BA.5 lineages.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

New RT-PCR Assay for the Detection of Current and Future SARS-CoV-2 Variants

Marchini

Petrillo

Parrish

et al. 2023

Viruses

Self Cite

View full text Add to dashboard Cite

Multiple lineages of SARS-CoV-2 have been identified featuring distinct sets of genetic changes that confer to the virus higher transmissibility and ability to evade existing immunity. The continuous evolution of SARS-CoV-2 may pose challenges for current treatment options and diagnostic tools. In this study, we have first evaluated the performance of the 14 WHO-recommended real-time reverse transcription (RT)-PCR assays currently in use for the detection of SARS-CoV-2 and found that only one assay has reduced performance against Omicron. We then developed a new duplex real-time RT-PCR assay based on the amplification of two ultra-conserved elements present within the SARS-CoV-2 genome. The new duplex assay successfully detects all of the tested SARS-CoV-2 variants of concern (including Omicron sub-lineages BA.4 and BA.5) from both clinical and wastewater samples with high sensitivity and specificity. The assay also functions as a one-step droplet digital RT-PCR assay. This new assay, in addition to clinical testing, could be adopted in surveillance programs for the routine monitoring of SARS-CoV-2’s presence in a population in wastewater samples. Positive results with our assay in conjunction with negative results from an Omicron-specific assay may provide timely indication of the emergence of a novel SARS-CoV-2 variant in a certain community and thereby aid public health interventions.

show abstract

Section: Discussionmentioning

confidence: 99%

“…The reactions were considered positive if the cycle threshold was below 40 cycles. In addition, the samples were also analyzed by the specific Omicron OmMet assay [ 25 ].…”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

New RT-PCR Assay for the Detection of Current and Future SARS-CoV-2 Variants

Marchini

Petrillo

Parrish

et al. 2023

Viruses

Self Cite

View full text Add to dashboard Cite

show abstract

“…Recently, several single one-step RT-qPCRs reported for the specific detection of Omicron in clinical and environmental samples have been developed [19][20][21]. As Omicron continues to spread and evolve into several lineages and sub-lineages, these methods suffer, as they are not able to differentiate between multiple Omicron sub-lineages, although they have been described as highly specific and sensitive for Omicron.…”

Section: Discussionmentioning

confidence: 99%

A RT-qPCR system using a degenerate probe for specific identification and differentiation of SARS-CoV-2 Omicron (B.1.1.529) variants of concern

Jessen

Nielsen²,

Larsen³

et al. 2022

PLoS ONE

Self Cite

View full text Add to dashboard Cite

Fast surveillance strategies are needed to control the spread of new emerging SARS-CoV-2 variants and gain time for evaluation of their pathogenic potential. This was essential for the Omicron variant (B.1.1.529) that replaced the Delta variant (B.1.617.2) and is currently the dominant SARS-CoV-2 variant circulating worldwide. RT-qPCR strategies complement whole genome sequencing, especially in resource lean countries, but mutations in the targeting primer and probe sequences of new emerging variants can lead to a failure of the existing RT-qPCRs. Here, we introduced an RT-qPCR platform for detecting the Delta- and the Omicron variant simultaneously using a degenerate probe targeting the key ΔH69/V70 mutation in the spike protein. By inclusion of the L452R mutation into the RT-qPCR platform, we could detect not only the Delta and the Omicron variants, but also the Omicron sub-lineages BA.1, BA.2 and BA.4/BA.5. The RT-qPCR platform was validated in small- and large-scale. It can easily be incorporated for continued monitoring of Omicron sub-lineages, and offers a fast adaption strategy of existing RT-qPCRs to detect new emerging SARS-CoV-2 variants using degenerate probes.

show abstract

“…Many groups around the world have responded to the emergence of these highly infectious variants by developing several assays to detect viral variants of concern [ 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 ]. In this study, we collaborated with SBC public health officers and clinicians to rapidly develop and implement a simple and highly specific RT-qPCR assay to detect Omicron variants in residual diagnostic clinical samples.…”

Section: Discussionmentioning

confidence: 99%

Efficient Tracing of the SARS-CoV-2 Omicron Variants in Santa Barbara County Using a Rapid Quantitative Reverse Transcription PCR Assay

et al. 2022

View full text Add to dashboard Cite

The emergence of the SARS-CoV-2 Omicron variant in 2021 is associated with a global surge of cases in late 2021 and early 2022. Identifying the introduction of novel SARS-CoV-2 variants to a population is imperative to inform decisions by clinicians and public health officials. Here, we describe a quantitative reverse transcription PCR-based assay (RT-qPCR) targeting unique mutations in the Omicron BA.1/BA1.1 and BA.2 viral genomes. This assay accurately and precisely detect the presence of these Omicron variants in patient samples in less than four hours. Using this assay, we tested 270 clinical samples and detected the introduction of Omicron BA.1/BA1.1 and BA.2 in the Santa Barbara County (SBC) population in December 2021 and February 2022, respectively. Identifying Omicron variants using this RT-qPCR assay showed complete concordance with whole viral genome sequencing; both assays indicated that Omicron was the dominant variant in SB County. Our data substantiate that RT-qPCR-based virus detection assays offer a fast and inexpensive alternative to NGS for virus variant-specific detection approach, which allows streamlining the detection of Omicron variants in patient samples.

show abstract

A qualitative RT-PCR assay for the specific identification of the SARS-CoV-2 B.1.1.529 (Omicron) Variant of Concern

Cited by 19 publications

References 32 publications

New RT-PCR Assay for the Detection of Current and Future SARS-CoV-2 Variants

New RT-PCR Assay for the Detection of Current and Future SARS-CoV-2 Variants

A RT-qPCR system using a degenerate probe for specific identification and differentiation of SARS-CoV-2 Omicron (B.1.1.529) variants of concern

Efficient Tracing of the SARS-CoV-2 Omicron Variants in Santa Barbara County Using a Rapid Quantitative Reverse Transcription PCR Assay

Contact Info

Product

Resources

About