Highly Sensitive Lineage Discrimination of SARS-CoV-2 Variants through Allele-Specific Probe PCR

Ratcliff, Jeremy; Al-Beidh, Farah; Bibi, Sagida; Bonsall, David; Clemens, Sue Ann Costa; Estcourt, Lise J; Evans, Amy; Fish, Matthew; Folegatti, Pedro M.; Gordon, Anthony; Jay, Cecilia; Jennings, A.R.; Laing, Emma; Lambe, Teresa; MacIntyre-Cockett, George; Menon, David; Mouncey, Paul; Nguyen, Dung; Pollard, Andrew J.; Ramasamy, Maheshi; Roberts, David; Rowan, Kathy; Rynne, Jennifer; Shankar-Hari, Manu; Williams, Sarah; Harvala, Heli; Golubchik, Tanya; Simmonds, Peter

doi:10.1128/jcm.02283-21

Cited by 5 publications

(8 citation statements)

References 25 publications

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“…Surveillance of SARS-CoV-2 variants is essential for the timely implementation of public health measures aimed at limiting viral spread and the inevitable impacts of an endemic COVID-19 state ( 6 , 8 – 10 , 12 ). While WGS has proven to be an invaluable tool for the identification of new variants, the cost, turnaround times, and viral load requirements for sequencing and data analysis remain challenging for wide implementation ( 6 , 7 , 9 , 10 , 13 – 15 ). This study demonstrates that genotyping mutation panels offer a fast, reliable, and cost-effective method for monitoring known and unknown SARS-CoV-2 variants in addition to complementary WGS surveillance.…”

Section: Discussionmentioning

confidence: 99%

“…While whole-genome sequencing (WGS) provides invaluable insights in these regards, it is a costly and time-consuming method for high-throughput biosurveillance ( 6 , 7 ). In addition, generating consistent, high-quality WGS data requires samples with high viral loads and significant nucleic acid purification ( 7 – 9 ). Genotyping PCR panels, however, have simpler workflows and allow greater success in determining VOC status with low viral loads ( 6 , 8 , 9 ).…”

Section: Introductionmentioning

confidence: 99%

“…In addition, generating consistent, high-quality WGS data requires samples with high viral loads and significant nucleic acid purification ( 7 – 9 ). Genotyping PCR panels, however, have simpler workflows and allow greater success in determining VOC status with low viral loads ( 6 , 8 , 9 ). Moreover, SNP genotyping panels can be easily tailored to current variant activity in a timely manner ( 8 , 10 ).…”

Section: Introductionmentioning

confidence: 99%

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Comparison of analytical performance and economic value of two biosurveillance methods for tracking SARS-COV-2 variants of concern

Pinkhover,

Pontbriand,

Fletcher

et al. 2024

Microbiol Spectr

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The development of biosurveillance programs with strong analytical performance and economically accessible protocols is essential for monitoring viral pathogens. Throughout the COVID-19 pandemic, whole-genome sequencing (WGS) has been the prevailing technology for SARS-CoV-2 variant of concern (VOC) detection. While WGS offers benefits, it is a lengthy process, financially and technically straining for scalable viral tracking. The aim of this study was to compare the analytical performance and economic feasibility of WGS and PCR mutation panels for distinguishing six known VOCs: Alpha (B.1.1.7 and Q.4), Gamma (P.1), Delta (B.1.617.2 and AY.4.2), and Omicron. (B.1.1.529.1). In all, 78 SARS-CoV-2-positive samples were collected from April to December 2021 at Northeastern University (Cabot Testing Site, Boston, MA, USA) for genotyping PCR and WGS analysis. MagMax Viral/Pathogen II Nucleic Acid Isolation and TaqPath COVID-19 Combo Kits were used for RNA extraction and SARS-CoV-2 confirmation. VOC discrimination was assessed using two TaqMan SARS-CoV-2 single nucleotide polymorphism (SNP) assay layouts, and Ion Torrent WGS. In November 2021, the mutation panel demonstrated marked versatility by detecting the emerging Omicron variant reported by South Africa. SNP panel analysis yielded the following 78 VOC identifications: Alpha B.1.1.7 ( N = 20), Alpha Q.4 ( N = 3), Gamma P.1 ( N = 1), Delta B.1.617.2 ( N = 30), Delta AY.4.2 ( N = 3), and Omicron B.1.1.529.1 ( N = 20) with one undetermined ( N = 1) sample. Genotyping mutation panels designated lineages in 77 of 78 samples, 46/78 were confirmed by WGS, while 32 samples failed WGS lineage assignment. RT-PCR genotyping panels offer pronounced throughput and sensitivity and provide an economically advantageous technique for SARS-CoV-2 biosurveillance. IMPORTANCE The results presented in our manuscript demonstrate how the value of simplistic and reliable molecular assays coupled with the core scientific principle of standardization can be overlooked by the charm of more sophisticated assays and instrumentation. This effect can often be amplified during tumultuous public health events, such as the COVID-19 pandemic. By adapting standardized PCR mutation panels to detect prominently circulating SARS-CoV-2 variants, we were able to better assess the potential health impacts of rising positivity rates and transmission clusters within the Northeastern University population. While several literature publications utilizing genotyping PCR and NGS have a similar scope to ours, many investigations lack sufficiently standardized genotyping PCR and NGS bioinformatics inclusionary/exclusionary criteria for SARS-CoV-2 variant identification. Finally, the economic benefits of standardized PCR mutation panels would allow for global implementation of biosurveillance, rather than reserving biosurveillance to more economically developed nations.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Comparison of analytical performance and economic value of two biosurveillance methods for tracking SARS-COV-2 variants of concern

Pinkhover,

Pontbriand,

Fletcher

et al. 2024

Microbiol Spectr

View full text Add to dashboard Cite

show abstract

“…For example, the Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV system (CA, USA) can provide rapid detection of SARS-CoV-2 in 25 min and provide results for four pathogens in 36 min, with less than 1 min hands-on time. Moreover, the Abbott's ID NOWTM system (IL, USA) adopts isothermal amplification technology, and it can process (Berenger et al, 2021;Borsova et al, 2021;Hale et al, 2021;Fu et al, 2022;Oh et al, 2022;Ratcliff et al, 2022), beta (Hale et al, 2021;Dikdan et al, 2022;Fu et al, 2022), gamma (Hale et al, 2021;Ratcliff et al, 2022), delta (Berenger et al, 2021;Hale et al, 2021;Norz et al, 2021;Oh et al, 2022;Rosato et al, 2022), and omicron (Bloemen et al, 2022;Dachert et al, 2022;Rasmussen et al, 2022).…”

Section: Biosensors and Microfluidicsmentioning

confidence: 99%

“…NTD, N-terminal domain; RBD, receptor-binding domain; RBM, receptor-binding motif; FP, fusion peptide; CD, connecting domain; TM, transmembrane domain; CT, cytoplasmic tail. Alpha(Berenger et al, 2021;Borsova et al, 2021;Hale et al, 2021;Fu et al, 2022;Oh et al, 2022;Ratcliff et al, 2022), beta(Hale et al, 2021;Dikdan et al, 2022;Fu et al, 2022), gamma(Hale et al, 2021;Ratcliff et al, 2022), delta(Berenger et al, 2021;Hale et al, 2021; Norz et al, 2021;Oh et al, 2022;Rosato et al, 2022), and omicron(Bloemen et al, 2022;Dachert et al, 2022;Rasmussen et al, 2022).…”

mentioning

confidence: 99%

Nucleic acid testing of SARS-CoV-2: A review of current methods, challenges, and prospects

Zhu

Zhang

et al. 2022

Front. Microbiol.

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Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has brought a huge threat to public health and the global economy. Rapid identification and isolation of SARS-CoV-2-infected individuals are regarded as one of the most effective measures to control the pandemic. Because of its high sensitivity and specificity, nucleic acid testing has become the major method of SARS-CoV-2 detection. A deep understanding of different diagnosis methods for COVID-19 could help researchers make an optimal choice in detecting COVID-19 at different symptom stages. In this review, we summarize and evaluate the latest developments in current nucleic acid detection methods for SARS-CoV-2. In particular, we discuss biosensors and CRISPR-based diagnostic systems and their characteristics and challenges. Furthermore, the emerging COVID-19 variants and their impact on SARS-CoV-2 diagnosis are systematically introduced and discussed. Considering the disease dynamics, we also recommend optional diagnostic tests for different symptom stages. From sample preparation to results readout, we conclude by pointing out the pain points and future directions of COVID-19 detection.

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Rapid and Technically Simple Detection of SARS-CoV-2 Variants Using CRISPR Cas12 and Cas13

et al. 2023

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Highly Sensitive Lineage Discrimination of SARS-CoV-2 Variants through Allele-Specific Probe PCR

Cited by 5 publications

References 25 publications

Comparison of analytical performance and economic value of two biosurveillance methods for tracking SARS-COV-2 variants of concern

Comparison of analytical performance and economic value of two biosurveillance methods for tracking SARS-COV-2 variants of concern

Nucleic acid testing of SARS-CoV-2: A review of current methods, challenges, and prospects

Rapid and Technically Simple Detection of SARS-CoV-2 Variants Using CRISPR Cas12 and Cas13

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