Evaluation of the clinical and analytical performance of the Seegene allplex™ SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI)

Caza, Mélissa; Hogan, Catherine A.; Jassem, Agatha N; Prystajecky, Natalie; Hadzic, Amir; Wilmer, Amanda

doi:10.1016/j.jcv.2021.104996

Cited by 16 publications

(13 citation statements)

References 35 publications

(22 reference statements)

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“…Commercial PCR kits for variant detection are currently available. However, these kits also target a few mutation markers originating from SARS-CoV-2 lineages of interest ( 23 – 25 ). As we showed above, targeting a single mutation might make the assay less accurate in certain regions due to the presence of other lineages that have the same mutation.…”

Section: Discussionmentioning

confidence: 99%

Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics

Sashittal

Zhou

et al. 2022

Appl Environ Microbiol

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Section: Discussionmentioning

confidence: 99%

Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics

Sashittal

Zhou

et al. 2022

Appl Environ Microbiol

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“…Commercial multiplex PCR genotyping kits can be combined to maximize variant detection capacity and identify novel variants. There are a number of variant PCR assays which, when combined, allow for detection of multiple SAR-CoV-2 variants [21,22,28,29,33,34].…”

Section: Plos Onementioning

confidence: 99%

Evaluation of a commercial SARS-CoV-2 multiplex PCR genotyping assay for variant identification in resource-scarce settings

Umunnakwe¹,

Makatini

Maphanga³

et al. 2022

PLoS ONE

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The rapid emergence and spread of numerous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants across the globe underscores the crucial need for continuous SARS-CoV-2 surveillance to ensure that potentially more pathogenic variants are detected early and contained. Whole genome sequencing (WGS) is currently the gold standard for COVID-19 surveillance; however, it remains cost-prohibitive and requires specialized technical skills. To increase surveillance capacity, especially in resource-scarce settings, supplementary methods that are cost- and time-effective are needed. Real-time multiplex PCR genotyping assays offer an economical and fast solution for screening circulating and emerging variants while simultaneously complementing existing WGS approaches. In this study we evaluated the AllplexTM SARS-CoV-2 Variants II multiplex real-time PCR genotyping assay, Seegene (South Korea), and implemented it in retrospectively characterizing circulating SARS-CoV-2 variants in a rural South African setting between April and October 2021, prior to the emergence of the Omicron variant in South Africa. The AllplexTM SARS-CoV-2 Variants II real-time PCR assay demonstrated perfect concordance with whole-genome sequencing in detecting Beta and Delta variants and exhibited high specificity, sensitivity and reproducibility. Implementation of the assay in characterization of SARS-CoV-2 variants between April and October 2021 in a rural South African setting revealed a rapid shift from the Beta to the Delta variant between April and June. All specimens successfully genotyped in April were Beta variants and the Delta variant was not detected until May. By June, 78% of samples genotyped were Delta variants and in July >95% of all genotyped samples were Delta variants. The Delta variant continued to predominate through to the end of our analysis in October 2021. Taken together, a commercial SARS-CoV-2 variant genotyping assay detected the rapid rate at which the Delta variant displaced the Beta variant in Limpopo, an under-monitored province in South Africa. Such assays provide a quick and cost-effective method of monitoring circulating variants and should be used to complement genomic sequencing for COVID-19 surveillance especially in resource-scarce settings.

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“…To identify potential SARS-CoV-2 variants of concern (VOCs), self-collected specimens yielding the highest concentration of SARS-CoV-2 RNA of each individual were further screened for the presence of the N501Y, del69/70, and E484K spike mutations using the Allplex™ SARS-CoV-2 Variants I Assay (Seegene Inc., Seoul, South Korea) [18] on the CFX96 Touch Real-Time PCR Detection System (Bio-Rad Laboratories Inc., Hercules, CA, USA). The assay was used according to the manufacturer's protocol.…”

Section: Mutation Screening Of Self-collected Specimensmentioning

confidence: 99%

Self-Collected Samples to Detect SARS-CoV-2: Direct Comparison of Saliva, Tongue Swab, Nasal Swab, Chewed Cotton Pads and Gargle Lavage

Kohmer

Eckermann

Böddinghaus³

et al. 2021

JCM

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Testing for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by RT-PCR is a vital public health tool in the pandemic. Self-collected samples are increasingly used as an alternative to nasopharyngeal swabs. Several studies suggested that they are sufficiently sensitive to be a useful alternative. However, there are limited data directly comparing several different types of self-collected materials to determine which material is preferable. A total of 102 predominantly symptomatic adults with a confirmed SARS-CoV-2 infection self-collected native saliva, a tongue swab, a mid-turbinate nasal swab, saliva obtained by chewing a cotton pad and gargle lavage, within 48 h of initial diagnosis. Sample collection was unsupervised. Both native saliva and gargling with tap water had high diagnostic sensitivity of 92.8% and 89.1%, respectively. Nasal swabs had a sensitivity of 85.1%, which was not significantly inferior to saliva (p = 0.092), but 16.6% of participants reported they had difficult in self-collection of this sample. A tongue swab and saliva obtained by chewing a cotton pad had a significantly lower sensitivity of 74.2% and 70.2%, respectively. Diagnostic sensitivity was not related to the presence of clinical symptoms or to age. When comparing self-collected specimens from different material, saliva, gargle lavage or mid-turbinate nasal swabs may be considered for most symptomatic patients. However, complementary experiments are required to verify that differences in performance observed among the five sampling modes were not attributed to collection impairment.

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Evaluation of the clinical and analytical performance of the Seegene allplex™ SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI)

Cited by 16 publications

References 35 publications

Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics

Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics

Evaluation of a commercial SARS-CoV-2 multiplex PCR genotyping assay for variant identification in resource-scarce settings

Self-Collected Samples to Detect SARS-CoV-2: Direct Comparison of Saliva, Tongue Swab, Nasal Swab, Chewed Cotton Pads and Gargle Lavage

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