ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection

Editorial Material Medicine, General & Internal

Genetic Variants of SARS-CoV-2-What Do They Mean?

Adam S. Lauring et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2021)

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Article Immunology

COVID-19 evolution during the pandemic – Implications of new SARS-CoV-2 variants on disease control and public health policies

Cock van Oosterhout et al.

Virulence (2021)

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Article Microbiology

Optimization and Clinical Validation of Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification, a Fast, Highly Sensitive and Specific COVID-19 Molecular Diagnostic Too That Is Robust to Detect SARS-CoV-2 Variants of Concern

Pedro A. Alves et al.

Summary: The study validated a pH-dependent colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for SARS-CoV-2 detection, showing good sensitivity and specificity, suitable for large-scale COVID-19 testing.

FRONTIERS IN MICROBIOLOGY (2021)

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Article Biochemical Research Methods

HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences

Phuoc Thien Truong Nguyen et al.

Summary: Research related to SARS-CoV-2 has become increasingly important globally since December 2019, with the emergence of new variants like the UK variant B.1.1.7, the South African variant B1.351 and the Brazilian variant P.1. The open-source bioinformatic pipeline HAVoC has been developed to assemble raw sequences and identify lineages of SARS-CoV-2 variants. HAVoC is particularly useful for detecting and monitoring the spread of SARS-CoV-2 variants during local outbreaks and is currently being used in Finland for this purpose.

BMC BIOINFORMATICS (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 Virology

Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70-and N501Y variants such as B.1.1.7

Dominik Noerz et al.

Summary: New SARS-CoV-2 variants like B.1.1.7 and B.1.351 have raised global concern, highlighting the need for rapid, sensitive, and high-throughput detection methods. This study presents a highly sensitive multiplex PCR assay capable of detecting and distinguishing SARS-CoV-2 mutations, allowing for high-throughput screening of relevant variants in clinical samples before sequencing.

JOURNAL OF CLINICAL VIROLOGY (2021)

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Article Biochemistry & Molecular Biology

COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence

Felipe Gomes Naveca et al.

Summary: Analysis of circulating SARS-CoV-2 viruses during the first and second waves of COVID-19 in Amazonas, Brazil, shows successive lineage replacements led to predominance of the variant of concern P.1 and are associated with variable levels of social distancing.

NATURE MEDICINE (2021)

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Article Genetics & Heredity

poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing

Christian Brandt et al.

Summary: In response to the SARS-CoV-2 pandemic, there has been a significant increase in global sequencing efforts to track viral evolution. While technologies like nanopore sequencing are used for genome generation, bioinformatics remains a bottleneck for many labs, requiring specific long-read tools and parameter settings to accurately reconstruct SARS-CoV-2 genomes. A new workflow, poreCov, aims to streamline this process and facilitate rapid analysis of raw sequence data or genomes.

FRONTIERS IN GENETICS (2021)

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Article Virology

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool

Aine O'Toole et al.

Summary: The global virus genomics community has responded unprecedentedly to the SARS-CoV-2 pandemic, leading to significant advances in 'real-time' generation and sharing of genomic data. The development of new analytical methods, such as pangolin, has been necessary to handle the rapid growth in virus genome data production. Pangolin has processed nearly two million virus genomes, aiding in SARS-CoV-2 genomic epidemiology and providing researchers with valuable information about the pandemic's transmission lineages.

VIRUS EVOLUTION (2021)

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Article Virology

The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the spike protein

Paola Cristina Resende et al.

Summary: Mutations in both the receptor-binding domain (RBD) and the amino-terminal domain (NTD) of the SARS-CoV-2 Spike glycoprotein can alter its antigenicity, with Brazilian lineages showing convergent deletions and insertions in the NTD region, potentially impacting antibody neutralization.

VIRUS EVOLUTION (2021)

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Article Immunology

Genomic Diversity of Severe Acute Respiratory Syndrome-Coronavirus 2 in Patients With Coronavirus Disease 2019

Zijie Shen et al.

CLINICAL INFECTIOUS DISEASES (2020)

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Article Multidisciplinary Sciences

A new coronavirus associated with human respiratory disease in China

Fan Wu et al.

NATURE (2020)

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Review Chemistry, Medicinal

Clinical and Laboratory Diagnosis of SARS-CoV-2, the Virus Causing COVID-19

Severino Jefferson Ribeiro da Silva et al.

ACS INFECTIOUS DISEASES (2020)

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Article Biochemical Research Methods

Ion torrent-based nasopharyngeal swab metatranscriptomics in COVID-19

Gubio S. Campos et al.

JOURNAL OF VIROLOGICAL METHODS (2020)

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Article Genetics & Heredity

Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic

Sureshnee Pillay et al.

GENES (2020)

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Article Virology

Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation

Caroline Charre et al.

Summary: Four Next-Generation Sequencing methods have shown excellent performance in SARS-CoV-2 whole-genome sequencing, demonstrating high concordance and suitability for samples with different viral loads. However, it is important to consider the characteristics and validation requirements of each method.

VIRUS EVOLUTION (2020)

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Article Virology