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  1. Article ; Online: Erratum to “A Bioinformatics Pipeline for the Analyses of Viral Escape Dynamics and Host Immune Responses during an Infection”

    Preston Leung / Rowena Bull / Andrew Lloyd / Fabio Luciani

    BioMed Research International, Vol

    2014  Volume 2014

    Keywords Medicine ; R
    Language English
    Publishing date 2014-01-01T00:00:00Z
    Publisher Hindawi Limited
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: A Bioinformatics Pipeline for the Analyses of Viral Escape Dynamics and Host Immune Responses during an Infection

    Preston Leung / Rowena Bull / Andrew Lloyd / Fabio Luciani

    BioMed Research International, Vol

    2014  Volume 2014

    Abstract: Rapidly mutating viruses, such as hepatitis C virus (HCV) and HIV, have adopted evolutionary strategies that allow escape from the host immune response via genomic mutations. Recent advances in high-throughput sequencing are reshaping the field of immuno- ...

    Abstract Rapidly mutating viruses, such as hepatitis C virus (HCV) and HIV, have adopted evolutionary strategies that allow escape from the host immune response via genomic mutations. Recent advances in high-throughput sequencing are reshaping the field of immuno-virology of viral infections, as these allow fast and cheap generation of genomic data. However, due to the large volumes of data generated, a thorough understanding of the biological and immunological significance of such information is often difficult. This paper proposes a pipeline that allows visualization and statistical analysis of viral mutations that are associated with immune escape. Taking next generation sequencing data from longitudinal analysis of HCV viral genomes during a single HCV infection, along with antigen specific T-cell responses detected from the same subject, we demonstrate the applicability of these tools in the context of primary HCV infection. We provide a statistical and visual explanation of the relationship between cooccurring mutations on the viral genome and the parallel adaptive immune response against HCV.
    Keywords Medicine ; R
    Subject code 570
    Language English
    Publishing date 2014-01-01T00:00:00Z
    Publisher Hindawi Limited
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Impact of sequencing depth and read length on single cell RNA sequencing data of T cells

    Simone Rizzetto / Auda A. Eltahla / Peijie Lin / Rowena Bull / Andrew R. Lloyd / Joshua W. K. Ho / Vanessa Venturi / Fabio Luciani

    Scientific Reports, Vol 7, Iss 1, Pp 1-

    2017  Volume 11

    Abstract: Abstract Single cell RNA sequencing (scRNA-seq) provides great potential in measuring the gene expression profiles of heterogeneous cell populations. In immunology, scRNA-seq allowed the characterisation of transcript sequence diversity of functionally ... ...

    Abstract Abstract Single cell RNA sequencing (scRNA-seq) provides great potential in measuring the gene expression profiles of heterogeneous cell populations. In immunology, scRNA-seq allowed the characterisation of transcript sequence diversity of functionally relevant T cell subsets, and the identification of the full length T cell receptor (TCRαβ), which defines the specificity against cognate antigens. Several factors, e.g. RNA library capture, cell quality, and sequencing output affect the quality of scRNA-seq data. We studied the effects of read length and sequencing depth on the quality of gene expression profiles, cell type identification, and TCRαβ reconstruction, utilising 1,305 single cells from 8 publically available scRNA-seq datasets, and simulation-based analyses. Gene expression was characterised by an increased number of unique genes identified with short read lengths (<50 bp), but these featured higher technical variability compared to profiles from longer reads. Successful TCRαβ reconstruction was achieved for 6 datasets (81% − 100%) with at least 0.25 millions (PE) reads of length >50 bp, while it failed for datasets with <30 bp reads. Sufficient read length and sequencing depth can control technical noise to enable accurate identification of TCRαβ and gene expression profiles from scRNA-seq data of T cells.
    Keywords Medicine ; R ; Science ; Q
    Subject code 612
    Language English
    Publishing date 2017-10-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Transmission of Hepatitis C Virus among Prisoners, Australia, 2005–2012

    Neil Arvin Bretaña / Lies Boelen / Rowena Bull / Suzy Teutsch / Peter A. White / Andrew R. Lloyd / Fabio Luciani

    Emerging Infectious Diseases, Vol 21, Iss 5, Pp 765-

    2015  Volume 774

    Abstract: Hepatitis C virus (HCV) is predominantly transmitted between persons who inject drugs. For this population, global prevalence of HCV infection is high and incarceration is common and an independent risk factor for HCV acquisition. To explore HCV ... ...

    Abstract Hepatitis C virus (HCV) is predominantly transmitted between persons who inject drugs. For this population, global prevalence of HCV infection is high and incarceration is common and an independent risk factor for HCV acquisition. To explore HCV transmission dynamics in incarcerated populations, we integrated virus sequences with risk behavior and spatiotemporal data and analyzed transmission clusters among prisoners in Australia. We detected 3 clusters of recent HCV transmission consisting of 4 likely in-custody transmission events involving source/recipient pairs located in the same prison at the same time. Of these 4 events, 3 were associated with drug injecting and equipment sharing. Despite a large population of prisoners with chronic HCV, recent transmission events were identified in the prison setting. This ongoing HCV transmission among high-risk prisoners argues for expansion of prevention programs to reduce HCV transmission in prisons.
    Keywords hepatitis C virus ; transmission ; phylogenetics ; clustering ; injecting drug use ; prisons ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
    Subject code 360
    Language English
    Publishing date 2015-05-01T00:00:00Z
    Publisher Centers for Disease Control and Prevention
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Emergence and antibody evasion of BQ, BA.2.75 and SARS-CoV-2 recombinant sub-lineages in the face of maturing antibody breadth at the population levelResearch in context

    Anouschka Akerman / Vanessa Milogiannakis / Tyra Jean / Camille Esneau / Mariana Ruiz Silva / Timothy Ison / Christina Fichter / Joseph A. Lopez / Deborah Chandra / Zin Naing / Joanna Caguicla / Daiyang Li / Gregory Walker / Supavadee Amatayakul-Chantler / Nathan Roth / Sandro Manni / Thomas Hauser / Thomas Barnes / Anna Condylios /
    Malinna Yeang / Maureen Wong / Charles S.P. Foster / Kenta Sato / Sharon Lee / Yang Song / Lijun Mao / Allison Sigmund / Amy Phu / Ann Marie Vande More / Stephanie Hunt / Mark Douglas / Ian Caterson / Warwick Britton / Kerrie Sandgren / Rowena Bull / Andrew Lloyd / Jamie Triccas / Stuart Tangye / Nathan W. Bartlett / David Darley / Gail Matthews / Damien J. Stark / Kathy Petoumenos / William D. Rawlinson / Ben Murrell / Fabienne Brilot / Anthony L. Cunningham / Anthony D. Kelleher / Anupriya Aggarwal / Stuart G. Turville

    EBioMedicine, Vol 90, Iss , Pp 104545- (2023)

    2023  

    Abstract: Summary: Background: The Omicron era of the COVID-19 pandemic commenced at the beginning of 2022 and whilst it started with primarily BA.1, it was latter dominated by BA.2 and the related sub-lineage BA.5. Following resolution of the global BA.5 wave, a ... ...

    Abstract Summary: Background: The Omicron era of the COVID-19 pandemic commenced at the beginning of 2022 and whilst it started with primarily BA.1, it was latter dominated by BA.2 and the related sub-lineage BA.5. Following resolution of the global BA.5 wave, a diverse grouping of Omicron sub-lineages emerged derived from BA.2, BA.5 and recombinants thereof. Whilst emerging from distinct lineages, all shared similar changes in the Spike glycoprotein affording them an outgrowth advantage through evasion of neutralising antibodies. Methods: Over the course of 2022, we monitored the potency and breadth of antibody neutralization responses to many emerging variants in the Australian community at three levels: (i) we tracked over 420,000 U.S. plasma donors over time through various vaccine booster roll outs and Omicron waves using sequentially collected IgG pools; (ii) we mapped the antibody response in individuals using blood from stringently curated vaccine and convalescent cohorts. (iii) finally we determine the in vitro efficacy of clinically approved therapies Evusheld and Sotrovimab. Findings: In pooled IgG samples, we observed the maturation of neutralization breadth to Omicron variants over time through continuing vaccine and infection waves. Importantly, in many cases, we observed increased antibody breadth to variants that were yet to be in circulation. Determination of viral neutralization at the cohort level supported equivalent coverage across prior and emerging variants with isolates BQ.1.1, XBB.1, BR.2.1 and XBF the most evasive. Further, these emerging variants were resistant to Evusheld, whilst increasing neutralization resistance to Sotrovimab was restricted to BQ.1.1 and XBF. We conclude at this current point in time that dominant variants can evade antibodies at levels equivalent to their most evasive lineage counterparts but sustain an entry phenotype that continues to promote an additional outgrowth advantage. In Australia, BR.2.1 and XBF share this phenotype and, in contrast to global variants, are ...
    Keywords SARS-CoV-2 ; Variants ; TMPRSS2 ; Covid-19 ; Neutralising antibodies ; Sotrovimab ; Medicine ; R ; Medicine (General) ; R5-920
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Norovirus Recombination in ORF1/ORF2 Overlap

    Rowena Bull / Grant S. Hansman / Leighton E. Clancy / Mark M. Tanaka / William D. Rawlinson / Peter A. White

    Emerging Infectious Diseases, Vol 11, Iss 7, Pp 1079-

    2005  Volume 1085

    Abstract: Norovirus (NoV) genogroups I and II (GI and GII) are now recognized as the predominant worldwide cause of outbreaks of acute gastroenteritis in humans. Three recombinant NoV GII isolates were identified and characterized, 2 of which are unrelated to any ... ...

    Abstract Norovirus (NoV) genogroups I and II (GI and GII) are now recognized as the predominant worldwide cause of outbreaks of acute gastroenteritis in humans. Three recombinant NoV GII isolates were identified and characterized, 2 of which are unrelated to any previously published recombinant NoV. Using data from the current study, published sequences, database searches, and molecular techniques, we identified 23 recombinant NoV GII and 1 recombinant NoV GI isolates. Analysis of the genetic relationships among the recombinant NoV GII isolates identified 9 independent recombinant sequences; the other 14 strains were close relatives. Two of the 9 independent recombinant NoV were closely related to other recombinants only in the polymerase region, and in a similar fashion 1 recombinant NoV was closely related to another only in the capsid region. Breakpoint analysis of recombinant NoV showed that recombination occurred in the open reading frame (ORF)1/ORF2 overlap. We provide evidence to support the theory of the role of subgenomic RNA promoters as recombination hotspots and describe a simple mechanism of how recombination might occur in NoV.
    Keywords Keywords: gastroenteritis ; Recombinant norovirus ; phylogenetic analysis ; breakpoint ; reverse transcriptase polymerase chain reaction ; subgenomic RNA ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
    Subject code 580
    Language English
    Publishing date 2005-07-01T00:00:00Z
    Publisher Centers for Disease Control and Prevention
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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