‘CoviSwiftTM’: A point-of-care RT-PCR device for SARS-CoV-2 and its variant detection

Dakhave, Minal; Gadekar, Shruti; Malekar, Asmita; Wankhede, Gautam

doi:10.1016/j.jviromet.2023.114714

Cited by 4 publications

(5 citation statements)

References 19 publications

(20 reference statements)

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“…It adopts an unique Tm signature with a combination of 6 different probes targeting the 3 key spike protein codons (452, 484 and 501). The assay is sensitive, specific and can be performed in a multi-well plate format for high throughput testing in most qRT-PCR instruments once reference Tm values are established, unlike almost all commercial assays 39 , 46 , 47 and other published methods 37 , 39 , 40 , 48 , 49 . Certain instruments such as Qiagen Rotagene-Q as shown in this study may require further optimization.…”

Section: Discussionmentioning

confidence: 99%

An expanded RT-PCR melting temperature coding assay to rapidly identify all known SARS-CoV-2 variants and sub-variants of concern

Banada,

Green,

Streck

et al. 2023

Sci Rep

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The continued emergence of vaccine-resistant SARS-CoV-2 variants of concern (VOC) requires specific identification of each VOC as it arises. Here, we report an expanded version of our previously described sloppy molecular beacon (SMB) melting temperature (Tm) signature-based assay for VOCs, now modified to include detection of Delta (B.1.617.2) and Omicron (B.1.1.529) sub-variants. The SMB-VOC assay targets the signature codons 501, 484 and 452 in the SARS-CoV-2 spike protein which we show can specifically detect and differentiate all known VOCs including the Omicron subvariants (BA.1, BA.2, BA.2.12.1, BA.4/BA.5). The limit of detection (LOD) of the assay was 20, 22 and 36 genomic equivalents (GE) per reaction with the Delta, Omicron BA.1 and BA.2 respectively. Clinical validation of the 3-codon assay in the LC480 instrument showed the assay detected 94% (81/86) of the specimens as WT or VOCs and 6% (5/86) of the tests producing indeterminate results compared to sequencing. Sanger sequencing also failed for four samples. None of the specimens were incorrectly identified as WT or as a different VOC by our assay. Thus, excluding specimens with indeterminant results, the assay was 100% sensitive and 100% specific compared to Sanger sequencing for variant identification. This new assay concept can be easily expanded to add newer variants and can serve as a robust diagnostic tool for selecting appropriate monoclonal antibody therapy and rapid VOC surveillance.

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Section: Discussionmentioning

confidence: 99%

An expanded RT-PCR melting temperature coding assay to rapidly identify all known SARS-CoV-2 variants and sub-variants of concern

Banada,

Green,

Streck

et al. 2023

Sci Rep

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“…With the sequence-specific variant and wildtype probes ( Table S1 ) designed in the same gene region for competitive hybridization to the template, high specificity and explicit results for both positive (bright for variant) and negative (dark for wildtype) samples were obtained. In contrast, although having been adapted for POC testing, the detection of variants using target failure RT-qPCR (e.g., S gene ∆69–70 target failure for Omicron variant detection) [ 27 , 44 ] is implicit and prone to be false-positive.…”

Section: Discussionmentioning

confidence: 99%

“…RT-qPCR has been widely adapted for the point-of-care (POC) testing of SARS-CoV-2 outside of laboratory settings with a reduced sample consumption and short turnaround time [ 22 , 23 , 24 , 25 , 26 ]. Although multiplex RT-qPCR using multiple fluorescence-specific probes can improve the assay accuracy [ 27 ], the demand of POC’s portability could possibly compromise its optical functionalities and multiplexity. In addition, the potential temperature fluctuation and operation error in the scenario of on-site POC testing could cause undesired amplification products and PCR bias due to the complicated primer–probe sets [ 28 , 29 , 30 ].…”

Section: Introductionmentioning

confidence: 99%

Digital Microfluidic Multiplex RT-qPCR for SARS-CoV-2 Detection and Variants Discrimination

Ho,

Ding,

Fan

et al. 2023

Micromachines

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Continuous mutations have occurred in the genome of the SARS-CoV-2 virus since the onset of the COVID-19 pandemic. The increased transmissibility of the mutated viruses has not only imposed medical burdens but also prolonged the duration of the pandemic. A point-of-care (POC) platform that provides multitarget detection will help to track and reduce disease transmissions. Here we detected and discriminated three genotypes of SARS-CoV-2, including the wildtype and two variants of concern (VOCs), the Delta variant and Omicron variant, through reverse transcription quantitative polymerase chain reaction (RT-qPCR) on a digital microfluidics (DMF)-based cartridge. Upon evaluating with the RNA samples of Omicron variant, the DMF RT-qPCR presented a sensitivity of 10 copies/μL and an amplification efficiency of 96.1%, capable for clinical diagnosis. When spiking with SARS-CoV-2 RNA (wildtype, Delta variant, or Omicron variant) and 18S rDNA, the clinical analog samples demonstrated accurate detection and discrimination of different SARS-CoV-2 strains in 49 min.

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“…RNaseP was used as an internal control from within the cell. 92 Hofman et al described the “IdyllaTM SARS-CoV-2 Test,” a near-patient RT-PCR assay that can determine the difference between SARS-CoV-2 positive and negative patients in certain settings. The assay was extremely sensitive, specific, quick, and user-friendly.…”

Section: Introduction: a Demi-decade In Combatting The Sars-cov-2 Out...mentioning

confidence: 99%

Engineered two-dimensional nanomaterials based diagnostics integrated with internet of medical things (IoMT) for COVID-19

Sadique,

Yadav,

Khan

et al. 2024

Chem. Soc. Rev.

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‘CoviSwiftTM’: A point-of-care RT-PCR device for SARS-CoV-2 and its variant detection

Cited by 4 publications

References 19 publications

An expanded RT-PCR melting temperature coding assay to rapidly identify all known SARS-CoV-2 variants and sub-variants of concern

An expanded RT-PCR melting temperature coding assay to rapidly identify all known SARS-CoV-2 variants and sub-variants of concern

Digital Microfluidic Multiplex RT-qPCR for SARS-CoV-2 Detection and Variants Discrimination

Engineered two-dimensional nanomaterials based diagnostics integrated with internet of medical things (IoMT) for COVID-19

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