Validation of a new strategy for the identification of SARS-CoV-2 variants by sequencing the spike gene by Sanger

Article Multidisciplinary Sciences

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Raquel Viana et al.

Summary: The SARS-CoV-2 epidemic in southern Africa has experienced three distinct waves, driven by different variants. The recently identified Omicron variant has rapidly spread in South Africa and to numerous countries, raising global concern.

NATURE (2022)

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Article Multidisciplinary Sciences

Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan

Ko Ko et al.

Summary: This study developed a feasible and effective universal screening strategy for notable SARS-CoV-2 variants using Sanger Sequencing and successfully applied it in mass screening in Hiroshima, Japan. The study demonstrated the reliability and effectiveness of Sanger sequencing for screening a large number of samples, especially in regions where Next Generation Sequencing is not widely available.

SCIENTIFIC REPORTS (2022)

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Article Multidisciplinary Sciences

Genomic surveillance of SARS-CoV-2 Spike gene by sanger sequencing

Tiago Souza Salles et al.

Summary: This study presents a feasible protocol for complete nucleotide sequencing of the S gene of SARS-CoV-2 using the Sanger technique. This method is important for urgent surveillance and effective monitoring of the virus's spread and evolution.

PLOS ONE (2022)

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Article Cell Biology

SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads

Alexandre Bolze et al.

Summary: This study reports the sequencing of 74,348 SARS-CoV-2 positive samples collected in the United States, showing that the Delta variant became the dominant variant by September 2021 and had a higher viral load compared to the Alpha variant.

CELL REPORTS MEDICINE (2022)

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Review Microbiology

Characteristics of SARS-CoV-2 and COVID-19

Ben Hu et al.

Summary: This review summarizes the research progress on SARS-CoV-2 and COVID-19, including virology characteristics, pathogenesis, and recent advances in treatment methods. Furthermore, it discusses in detail the potential wildlife hosts and zoonotic origin of this emerging virus.

NATURE REVIEWS MICROBIOLOGY (2021)

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Article Biochemistry & Molecular Biology

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Erik Volz et al.

Summary: The study suggests a positive selection for the SARS-CoV-2 spike protein variant D614G in the UK, but no evidence of differences in COVID-19 mortality or clinical severity in patients infected with this variant. 614G is associated with higher viral load and younger age of patients compared to 614D.

CELL (2021)

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Article Infectious Diseases

Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020

Antonin Bal et al.

Summary: The study reported the strategy leading to the first detection of the variant of concern 202012/01 (VOC) in France, by screening for mutations such as Delta H69/Delta V70 associated with VOC and identifying co-occurring mutations like S:N501Y.

EUROSURVEILLANCE (2021)

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Article Biochemistry & Molecular Biology

A rapid and low-cost protocol for the detection of B.1.1.7 lineage of SARS-CoV-2 by using SYBR Green-based RT-qPCR

Fadil Abdel Sater et al.

Summary: The new SARS-CoV-2 variant VOC (202012/01) discovered in the UK is more transmissible and has a higher reproductive number compared to other variants. Scientists in the UK were able to detect this variant through an increase in false negative results for the spike target using a specific RT-PCR assay.

MOLECULAR BIOLOGY REPORTS (2021)

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Article Multidisciplinary Sciences

Development of an efficient Sanger sequencing-based assay for detecting SARS-CoV-2 spike mutations

Ho Jae Lim et al.

Summary: Novel primer pairs were developed to accurately detect key spike mutations of SARS-CoV-2 in this study, showing high specificity and accuracy, which is crucial for virus transmission control and patient management.

PLOS ONE (2021)

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Article Biology

The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types

Zharko Daniloski et al.

Summary: A novel variant of SARS-CoV-2 virus with mutation D614G has been found to be more effective at transducing human cells and showing increased infectivity in human cells compared to the wild-type variant.

ELIFE (2021)

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Article Virology

A Routine Sanger Sequencing Target Specific Mutation Assay for SARS-CoV-2 Variants of Concern and Interest

Sin Hang Lee

Summary: The article introduces a protocol for sequencing ACE2 RBD and S gene NTD to accurately determine variants of SARS-CoV-2.

VIRUSES-BASEL (2021)

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Article Multidisciplinary Sciences

Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7

Nicholas G. Davies et al.

Summary: Studies have shown that the SARS-CoV-2 B.1.1.7 lineage is more transmissible and may cause more severe illness compared to pre-existing variants.

NATURE (2021)

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Article Infectious Diseases

A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern

Matheus Filgueira Bezerra et al.

Summary: This study introduces a rapid and accessible Sanger sequencing protocol based on a single PCR fragment for identifying and distinguishing various SARS-CoV-2 variants of concern. Experimental evaluation on COVID-19 samples from Brazilian patients confirmed the method's accuracy and alignment with whole-genome sequencing results.

INFECTION GENETICS AND EVOLUTION (2021)

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Article Genetics & Heredity

A SARS-CoV-2 mutant from B.1.258 lineage with increment H69/ increment V70 deletion in the Spike protein circulating in Central Europe in the fall 2020

Brona Brejova et al.

Summary: SARS-CoV-2 mutants with H69/V70 deletion emerged in six lineages, including the B.1.1.7 variant. Samples from Slovakia showed a significant presence of the B.1.258 variant, which circulated in Central Europe before the arrival of B.1.1.7.

VIRUS GENES (2021)

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Article Engineering, Environmental

Rapid screening for SARS-CoV-2 variants of concern in clinical and environmental samples using nested RT-PCR assays targeting key mutations of the spike protein

G. La Rosa et al.

Summary: A nested RT-PCR assay was developed to detect key mutations of SARS-CoV-2 variants, showing potential for rapid screening of clinical samples and detection of variants in sewage. The study highlights the importance of wastewater surveillance in exploring SARS-CoV-2 diversity and distribution.

WATER RESEARCH (2021)

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Article Biochemistry & Molecular Biology