Rapid Detection of the Omicron (B.1.1.529) SARS-CoV-2 Variant Using a COVID-19 Diagnostic PCR Assay

Ippoliti, Chiara; Maio, Flavio De; Santarelli, Giulia; Marchetti, Simona; Vella, Antonietta; Santangelo, Rosaria; Sanguinetti, Maurizio; Posteraro, Brunella

doi:10.1128/spectrum.00990-22

Cited by 13 publications

(9 citation statements)

References 13 publications

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“…The study also reported that the mutant's infectivity was higher than that of the wild-type variant measured in Vero E6 and Calu-3 cells, and the mutations enhanced disease severity in the hamster model. Other studies later showed that R203K and G204R mutations can also be found in the B.1.1.529 and BA (Omicron) variants as well ( Hossain et al 2022 ; Ippoliti et al 2022 ; Jung et al 2022 ). While it is unclear if the mutations observed herein have similar effects to the R203K|G204R mutations, this finding warrants further investigation of the effects of mutations on nucleocapsid protein's linker domain on the virus.…”

Section: Resultsmentioning

confidence: 94%

Systematic Exploration of SARS-CoV-2 Adaptation to Vero E6, Vero E6/TMPRSS2, and Calu-3 Cells

Aiewsakun

Phumiphanjarphak

Ludowyke

et al. 2023

Genome Biology and Evolution

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread globally, and scientists around the world are currently studying the virus intensively in order to fight against the on-going pandemic of the virus. To do so, SARS-CoV-2 is typically grown in the lab to generate viral stocks for various kinds of experimental investigations. However, accumulating evidence suggests that such viruses often undergo cell culture adaptation. Here, we systematically explored cell culture adaptation of two SARS-CoV-2 variants, namely the B.1.36.16 variant and the AY.30 variant, a sub lineage of the B.1.617.2 (Delta) variant, propagated in three different cell lines, including Vero E6, Vero E6/TMPRSS2, and Calu-3 cells. Our analyses detected numerous potential cell culture adaptation changes scattering across the entire virus genome, many of which could be found in naturally circulating isolates. Notable ones included mutations around the spike glycoprotein's multibasic cleavage site, and the Omicron-defining H655Y mutation on the spike glycoprotein, as well as mutations in the nucleocapsid protein's linker region, all of which were found to be Vero E6-specific. Our analyses also identified deletion mutations on the non-structural protein 1 and membrane glycoprotein as potential Calu-3-specific adaptation changes. S848C mutation on the non-structural protein 3, located to the protein's papain-like protease domain, was also identified as a potential adaptation change, found in viruses propagated in all three cell lines. Our results highlight SARS-CoV-2 high adaptability, emphasize the need to deep-sequence cultured viral samples when used in intricate and sensitive biological experiments, and illustrate the power of experimental evolutionary study in shedding lights on the virus evolutionary landscape.

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Section: Resultsmentioning

confidence: 94%

Systematic Exploration of SARS-CoV-2 Adaptation to Vero E6, Vero E6/TMPRSS2, and Calu-3 Cells

Aiewsakun

Phumiphanjarphak

Ludowyke

et al. 2023

Genome Biology and Evolution

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“…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

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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.

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“…As these samples were obtained in a period completely dominated by the Omicron variant (see below for identification details), the sample size in the second period was somewhat comparable with that of single non-Omicron variants (see below for identification details) in the first period. We had also studied part of these samples previously ( 24 ).…”

Section: Methodsmentioning

confidence: 99%

“…We used the CleanPlex SARS-CoV-2 panel (Paragon Genomics, Hayward, CA) or the SARS-CoV-2 S gene kit (Arrows Diagnostics, Genoa, Italy) for samples ( n = 67 and n = 64, respectively) collected before 1 July 2021 and the COVIDSeq assay kit (Illumina, San Diego, CA) for samples ( n = 234) collected after 1 July 2021. This was the date of implementing the whole-genome sequencing (WGS)-based SARS-CoV-2 variant surveillance program in the Lazio Region in Italy ( 24 ), which is our study’s location. For the groups of 67 and 234 samples mentioned above, WGS data were also available (see Table S1 in the supplemental material).…”

Section: Methodsmentioning

confidence: 99%

Two-Period Study Results from a Large Italian Hospital Laboratory Attesting SARS-CoV-2 Variant PCR Assay Evolution

et al. 2022

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Omicron variants of SARS-CoV-2 pose more important public health concerns than the previously circulating Alpha or Delta variants, particularly regarding the efficacy of anti-SARS-CoV-2 vaccines and therapeutics. Precise identification of these variants highly requires performant PCR-based assays that allow us to reduce the reliance on NGS-based assays, which remain the reference method in this topic.

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Rapid Detection of the Omicron (B.1.1.529) SARS-CoV-2 Variant Using a COVID-19 Diagnostic PCR Assay

Cited by 13 publications

References 13 publications

Systematic Exploration of SARS-CoV-2 Adaptation to Vero E6, Vero E6/TMPRSS2, and Calu-3 Cells

Systematic Exploration of SARS-CoV-2 Adaptation to Vero E6, Vero E6/TMPRSS2, and Calu-3 Cells

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

Two-Period Study Results from a Large Italian Hospital Laboratory Attesting SARS-CoV-2 Variant PCR Assay Evolution

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