Simultaneous detection of omicron and other SARS-CoV-2 variants by multiplex PCR MassARRAY technology

Article Virology

Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays

Izaskun Alejo-Cancho et al.

Summary: This study describes the limitations of using multiplex real-time RT-PCR for detecting SARS-CoV-2 variants and provides a recommendation for distinguishing between the Mu strain and the Beta variant based on specific mutations.

ARCHIVES OF VIROLOGY (2022)

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Article Microbiology

Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants

Vanessa De Pace et al.

Summary: The diagnostic performance of five qualitative RT-PCR tests was evaluated in comparison with next-generation sequencing (NGS) for the detection of SARS-CoV-2 variants. These tests showed high accuracy and user-friendliness, making them suitable as second-level tests in the routine workflow of SARS-CoV-2 laboratory diagnostics.

MICROORGANISMS (2022)

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Article Pathology

A Comparison of Seegene Technologies Novaplex SARS-CoV-2 Variants I, II, and IV Assays with Spike Gene Sequencing for Detection of Known Severe Acute Respiratory Syndrome Coronavirus 2 Variants

Marisa C. Nielsen et al.

Summary: This study evaluated the Novaplex SARS-CoV-2 Variants I, II, and IV assays from Seegene Technologies, which demonstrated good agreement with traditional spike gene Sanger sequencing results, providing an accurate, rapid, and less labor-intensive method for detecting SARS-CoV-2 and identifying known variants of interest and concern.

JOURNAL OF MOLECULAR DIAGNOSTICS (2022)

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Article Biochemical Research Methods

SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021

Jolene Yin Ling Fu et al.

Summary: This study evaluated the ability of two detection methods to identify SARS-CoV-2 variants in positive samples collected in Malaysia. The results showed that both methods had high sensitivity and could detect different types of variants.

JOURNAL OF VIROLOGICAL METHODS (2022)

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Article Multidisciplinary Sciences

Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance

Rebecca J. Rockett et al.

Summary: The study reveals the co-infection of SARS-CoV-2 variants Omicron and Delta in two patients with chronic kidney disease, highlighting the importance of integrated genomic surveillance in vulnerable populations.

NATURE COMMUNICATIONS (2022)

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Article Immunology

On the Origins of Omicron's Unique Spike Gene Insertion

A. J. Venkatakrishnan et al.

Summary: The emergence of the heavily mutated Omicron variant of SARS-CoV-2 has raised global public health concerns. The Spike protein of Omicron carries 26 unique amino acid mutations. One of these mutations, ins214EPE, has not been observed in any other SARS-CoV-2 variant and may have been acquired through template switching. This template-switching event could involve other human coronaviruses that infect the same host cells as SARS-CoV-2 or a human transcript expressed in an Omicron-infected host cell.

VACCINES (2022)

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Article Immunology

SARS-CoV-2 Delta-Omicron Recombinant Viruses, United States

Kristine A. Lacek et al.

Summary: In order to detect new and changing SARS-CoV-2 variants, this study investigated candidate Delta-Omicron recombinant genomes from the national genomic surveillance conducted by the Centers for Disease Control and Prevention. Laboratory and bioinformatic investigations identified and validated 9 genetically related SARS-CoV-2 viruses with a hybrid Delta-Omicron spike protein.

EMERGING INFECTIOUS DISEASES (2022)

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Article Microbiology

Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines

John Mark Velasco et al.

Summary: This study presents the complete genome sequences of 11 SARS-CoV-2 variants from the Philippines, including 3 B.1.1.7 and 8 B.1.351 sequences. One B.1.1.7 sequence carries two additional mutations, with V320F located in the receptor binding domain of the S1 subunit.

MICROBIOLOGY RESOURCE ANNOUNCEMENTS (2021)

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Article Microbiology

A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology

Fei Zhao et al.

Summary: A novel detection strategy using mPCR-MS minisequencing was developed for identifying SARS-CoV-2 variants, demonstrating high specificity and accuracy. This method allows for simultaneous detection of multiple mutation types and can be easily expanded to track new variants. The study highlights the importance of this method for monitoring and managing SARS-CoV-2 infections and emerging variants.

MICROBIOLOGY SPECTRUM (2021)

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Article Microbiology

Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021

Kanyarat Phutthasophit et al.

Summary: This study reports the coding-complete genome sequences of 44 SARS-CoV-2 strains of the alpha and delta variants identified from patients in Kamphaeng Phet, Thailand. Two nonsense mutations were found in the alpha variant sequences, while two lineages of the delta variant were identified as B.1.617.2 and AY.30.

MICROBIOLOGY RESOURCE ANNOUNCEMENTS (2021)

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Article Virology

Superiority of MALDI-TOF Mass Spectrometry over Real-Time PCR for SARS-CoV-2 RNA Detection

Magda Rybicka et al.

Summary: The study compared mass spectrometry with RT-PCR for SARS-CoV-2 detection, showing that mass spectrometry has superior sensitivity and is ideal for detection and discrimination of mutations within the viral genome.

VIRUSES-BASEL (2021)

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Article Virology

Rapid and simultaneous identification of three mutations by the NovaplexTM SARS-CoV-2 variants I assay kit

Wakaki Kami et al.

Summary: The study assessed the utility of the NovaplexTM SARS-CoV-2 Variants I Assay kit in identifying mutations in SARS-CoV-2 variants. Among 30 tested samples, four were determined as variants with specific mutations. The kit-based assay was found to be feasible, convenient, and user-friendly with a turnaround time of only 2 hours.

JOURNAL OF CLINICAL VIROLOGY (2021)

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Review Immunology

SARS-CoV-2 Omicron Mutation Is Faster than the Chase: Multiple Mutations on Spike/ACE2 Interaction Residues

Sinae Kim et al.

Summary: The new SARS-CoV-2 Omicron variant originating from South Africa in mid-November 2021 is highly transmissible and mutates rapidly, posing challenges to existing control measures. Better strategies are needed to address the COVID-19 pandemic.

IMMUNE NETWORK (2021)

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Article Infectious Diseases