GLUE: A flexible software system for virus sequence data

Singer, Joshua B.; Thomson, Emma C.; McLauchlan, John; Hughes, Joseph; Gifford, Robert J.

doi:10.1101/269274

Cited by 30 publications

(68 citation statements)

References 36 publications

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“…The analysis of public HCV sequence data was performed within Genes Linked by Underlying Evolution (GLUE) ( 28 ). GLUE is an open source, data-centric bioinformatics environment specialized for the analysis of virus genomic sequence data.…”

Section: Methodsmentioning

confidence: 99%

Predicting the Effectiveness of Hepatitis C Virus Neutralizing Antibodies by Bioinformatic Analysis of Conserved Epitope Residues Using Public Sequence Data

et al. 2018

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Hepatitis C virus (HCV) is a global health issue. Although direct-acting antivirals are available to target HCV, there is currently no vaccine. The diversity of the virus is a major obstacle to HCV vaccine development. One approach toward a vaccine is to utilize a strategy to elicit broadly neutralizing antibodies (bNAbs) that target highly-conserved epitopes. The conserved epitopes of bNAbs have been mapped almost exclusively to the E2 glycoprotein. In this study, we have used HCV-GLUE, a bioinformatics resource for HCV sequence data, to investigate the major epitopes targeted by well-characterized bNAbs. Here, we analyze the level of conservation of each epitope by genotype and subtype and consider the most promising bNAbs identified to date for further study as potential vaccine leads. For the most conserved epitopes, we also identify the most prevalent sequence variants in the circulating HCV population. We examine the distribution of E2 sequence data from across the globe and highlight regions with no coverage. Genotype 1 is the most prevalent genotype worldwide, but in many regions, it is not the dominant genotype. We find that the sequence conservation data is very encouraging; several bNAbs have a high level of conservation across all genotypes suggesting that it may be unnecessary to tailor vaccines according to the geographical distribution of genotypes.

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Section: Methodsmentioning

confidence: 99%

Predicting the Effectiveness of Hepatitis C Virus Neutralizing Antibodies by Bioinformatic Analysis of Conserved Epitope Residues Using Public Sequence Data

et al. 2018

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“…Reverse transcription was carried out via SuperScript IV and cDNA was posteriorly amplified using Q5 R High-Fidelity DNA Polymerase (NEB) with the AR-TIC nCov-2019 primers and following the recommendations in the sequencing protocol of the ARTIC Network (https://artic.network/ncov-2019). Samples were multiplexed following the manufacturer's recommendations using the Oxford Nanopore Native Barcoding Expansion kits NBD104 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12) and NBD114 (13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24), in conjunction with Ligation Sequencing Kit 109 (Oxford Nanopore). Sequencing was carried out on a MinION sequencer using R9.4.1 flow cells and MinKNOW 2.0 software.…”

Section: Discussionmentioning

confidence: 99%

A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages

Dellicour

Durkin

Hong

et al. 2020

Preprint

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Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of the causative virus (SARS-CoV-2) have been generated and shared with the scientific community. The unparalleled volume of available genetic data presents a unique opportunity to gain real-time insights into the virus transmission during the pandemic, but also a daunting computational hurdle if analysed with gold-standard phylogeographic approaches. We here describe and apply an analytical pipeline that is a compromise between fast and rigorous analytical steps. As a proof of concept, we focus on the Belgium epidemic, with one of the highest spatial density of available SARS-CoV-2 genomes. At the global scale, our analyses confirm the importance of external introduction events in establishing multiple transmission chains in the country. At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage dispersal velocity and the long-distance dispersal events within Belgium. Our pipeline has the potential to be quickly applied to other countries or regions, with key benefits in complementing epidemiological analyses in assessing the impact of intervention measures or their progressive easement.

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“…Sequences in this dataset were aligned using a combination of MUSCLE (14) and Pal2Nal (15). We used GLUE – a data-centric bioinformatics framework for working with virus sequence data (16) – to capture the relationships between sequences, alignments and associated tabular data utilised in our investigation. The resultant resource is publicly available via GitHub (https://github.com/giffordlabcvr/SRLV-GLUE).…”

Section: Methodsmentioning

confidence: 99%

An investigation into the origins and history of pandemic small ruminant lentivirus infection

Carrozza

Niewiadomska

Mazzei

et al. 2018

Preprint

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GLUE: A flexible software system for virus sequence data

Abstract: Background: Virus genome sequences, generated in ever-higher volumes, can

Cited by 30 publications

References 36 publications

Predicting the Effectiveness of Hepatitis C Virus Neutralizing Antibodies by Bioinformatic Analysis of Conserved Epitope Residues Using Public Sequence Data

Predicting the Effectiveness of Hepatitis C Virus Neutralizing Antibodies by Bioinformatic Analysis of Conserved Epitope Residues Using Public Sequence Data

A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages

An investigation into the origins and history of pandemic small ruminant lentivirus infection

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