Design of Specific Primer Set for Detection of B.1.1.7 SARS-CoV-2 Variant using Deep Learning

Lopez-Rincon, Alejandro; Perez-Romero, Carmina Angelica; Tonda, Alberto; Mendoza‐Maldonado, Lucero; Claassen, Eric; Garssen, Johan; Kraneveld, Aletta D.

doi:10.1101/2020.12.29.424715

Cited by 23 publications

(18 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, the P681H mutation of the S protein might influence the cleavage of the S protein due to its proximity to the S1/S2 furin cleavage site [ 18 ]. Identification of new mutations is crucial for designing diagnostic reagents [ 19 ], slowing transmission, and reconfiguring vaccines against new variants. In addition, particular mutations, besides those specific to B.1.1.7, may in the future aid in tracing virus movements across Romania and worldwide.…”

Section: Resultsmentioning

confidence: 99%

Emergence of the First Strains of SARS-CoV-2 Lineage B.1.1.7 in Romania: Genomic Analysis

Lobiuc¹,

Dimian²,

Sturdza³

et al. 2021

JMIRx Med

View full text Add to dashboard Cite

Background The United Kingdom reported the emergence of a new and highly transmissible SARS-CoV-2 variant (B.1.1.7) that rapidly spread to other countries. The impact of this new mutation—which occurs in the S protein—on infectivity, virulence, and current vaccine effectiveness is still under evaluation. Objective The aim of this study is to sequence SARS-CoV-2 samples of cases in Romania to detect the B.1.1.7 variant and compare these samples with sequences submitted to GISAID. Methods SARS-CoV-2 samples were sequenced and amino acid substitution analysis was performed using the CoV-GLUE platform. Results We have identified the first cases of the B.1.1.7 variant in samples collected from Romanian patients, of which one was traced to the region of the United Kingdom where the new variant was originally sequenced. Mutations in nonstructural protein 3 (Nsp3; N844S and D455N) and ORF3a (L15F) were also detected, indicating common ancestry with UK strains as well as remote connections with strains from Nagasaki, Japan. Conclusions These results indicate, for the first time, the presence and characteristics of the new variant B.1.1.7 in Romania and underscore the need for increased genomic sequencing in patients with confirmed COVID-19.

show abstract

Section: Resultsmentioning

confidence: 99%

Emergence of the First Strains of SARS-CoV-2 Lineage B.1.1.7 in Romania: Genomic Analysis

Lobiuc¹,

Dimian²,

Sturdza³

et al. 2021

JMIRx Med

View full text Add to dashboard Cite

show abstract

“…Besides the SGTF tests, two recent preprint papers from the same group describe a deep learning approach that was used to design two primer/probe sets targeting a synonymous mutation C16176T in the ORF1a gene or a nonsynonymous mutation in the spike gene (S982A) that were found to be specific to the B.1.1.7 variant 31,32 . However, the primer design raises questions because both mutations in the ORF1a and S genes appear in the middle of the respective forward primers, making it unlikely that either primer set would specifically amplify only the B.1.1.7 variant, since discrimination of SNPs generally requires the mutated base to be located near the 3'-terminal to inhibit extension by the polymerase.…”

Section: Discussionmentioning

confidence: 99%

Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexed RT-qPCR assay

Kovacova

Boršová

Paul

et al. 2021

Preprint

View full text Add to dashboard Cite

The recent emergence of a novel variant of SARS-CoV-2 called lineage B.1.1.7 has sparked global alarm due to evidence of increased transmissibility, mortality, and uncertainty about vaccine efficacy, thus accelerating worldwide efforts to detect and track the variant. Current approaches to detect the B.1.1.7 variant include sequencing and molecular tests that contain a target assay that fails or results in reduced sensitivity towards the B.1.1.7 variant. Since many countries lack a robust genomic surveillance program and the failed target assays detect multiple unrelated variants that contain similar mutations as B.1.1.7, there is an urgent need to develop molecular tests that can accurately and rapidly identify the B.1.1.7 variant. We have developed a room temperature-stable, multiplexed RT-qPCR test that readily differentiates the B.1.1.7 variant from the most common SARS-CoV-2 variants. The test consists of two assays that target either the common SARS-CoV-2 spike gene or the two deletions in the spike gene (ΔH69/ΔV70 and ΔY144) that are present in the B.1.1.7 variant. Moreover, a simple relative comparison of the Ct values of the two assays permits not only identification of the B.1.1.7 variant but also its differentiation from other variants that harbor only the ΔH69/ΔV70 deletion. Each assay is multiplexed with a human RNase P internal control to assess RNA extraction and assay performance. This test can easily be implemented in diagnostic labs to rapidly scale B.1.1.7 surveillance efforts and is particularly useful in countries with high prevalence of variants possessing only the ΔH69/ΔV70 deletion because current strategies using target failure assays incorrectly identify these as putative B.1.1.7 variants.

show abstract

“…Specifically, some novel mutations of SARS-CoV-2 have already been identified as B.1.1.7, B.1.351, P.1, N501Y, and HV69-70del (74,75). A one-step reverse transcription and real-time PCR (RT-qPCR) test is developed for screening Spike N501Y and HV69-70del mutations in 40 min.…”

Section: Real-time Reverse Transcriptase-polymerase Chain Reaction Analysismentioning

confidence: 99%

Monitoring Coronavirus Disease 2019: A Review of Available Diagnostic Tools

Liu

Chu³

et al. 2021

Front. Public Health

View full text Add to dashboard Cite

Coronavirus disease 2019 (COVID-19) pneumonia is caused by the virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has rapidly become a global public health concern. As the new type of betacoronavirus, SARS-CoV-2 can spread across species and between populations and has a greater risk of transmission than other coronaviruses. To control the spread of SARS-CoV-2, it is vital to have a rapid and effective means of diagnosing asymptomatic SARS-CoV-2-positive individuals and patients with COVID-19, an early isolation protocol for infected individuals, and effective treatments for patients with COVID-19 pneumonia. In this review, we will summarize the novel diagnostic tools that are currently available for coronavirus, including imaging examinations and laboratory medicine by next-generation sequencing (NGS), real-time reverse transcriptase–polymerase chain reaction (rRT-PCR) analysis, immunoassay for COVID-19, cytokine and T cell immunoassays, biochemistry and microbiology laboratory parameters in the blood of the patients with COVID-19, and a field-effect transistor-based biosensor of COVID-19. Specifically, we will discuss the effective detection rate and assay time for the rRT-PCR analysis of SARS-CoV-2 and the sensitivity and specificity of different antibody detection methods, such as colloidal gold and ELISA using specimen sources obtained from the respiratory tract, peripheral serum or plasma, and other bodily fluids. Such diagnostics will help scientists and clinicians develop appropriate strategies to combat COVID-19.

show abstract

Design of Specific Primer Set for Detection of B.1.1.7 SARS-CoV-2 Variant using Deep Learning

Cited by 23 publications

References 16 publications

Emergence of the First Strains of SARS-CoV-2 Lineage B.1.1.7 in Romania: Genomic Analysis

Emergence of the First Strains of SARS-CoV-2 Lineage B.1.1.7 in Romania: Genomic Analysis

Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexed RT-qPCR assay

Monitoring Coronavirus Disease 2019: A Review of Available Diagnostic Tools

Contact Info

Product

Resources

About