EVALUATION OF THE DETERMINE™ HBsAG RAPID TEST AS A POINT-OF-CARE SCREENING TOOL FOR THE DIAGNOSIS OF HEPATITIS B VIRUS INFECTION

The aim of this study was to compare the performance characteristics of the Determine HBsAg Rapid test with the automated AxSYM® HBsAg assay (Abbott Laboratories, Abbott Park, IL USA) and the manual Murex HBsAg Version 3 (DiaSorin S.p.A, Saluggia, Italy) assay

Oxford Screening of CSF and Respiratory Samples ('OSCAR'): Supplementary resources for a project using Next Generation Sequencing (NGS) for identification of viruses from clinical laboratory samples

<p>This is a file set that describes the methods used in a small pilot study to investigate 'next generation sequencing' (NGS) derived from an Illumina platform, applied to clinical diagnostic samples following routine testing in a UK microbiology laboratory.</p><p>We briefly summarise the benefits and challenges of an NGS approach to diagnostics, and conclude with some potential methodological improvements.</p><p>The file set includes anonymised metadata for the samples tested (10 respiratory and 10 CSF).</p><p>Results have been made available through a separate DOI: 10.6084/m9.figshare.5712091 and the entire genomic metadata have been submitted to European Nucleotide Archive (ENA); (primary accession PRJEB22949). </p><p>This study was approved through the UK integrated research application system (REC reference 14/LO/1077).</p

Oxford Screening of CSF and Respiratory Samples ('OSCAR'): interactive data visualisation using Krona to display results from a pilot project using Next Generation Sequencing (NGS) for identification of viruses from clinical laboratory samples

This is an html file that allows visualisation of metagenomic dataset from a pilot project to screen CSF and respiratory samples using Illumina HiSeq after completion of routine diagnostic testing in a UK microbiology laboratory.<div><br></div><div>Methods and underlying metadata are available through a separate DOI (<a rel="noreferrer noopener" target="_blank">10.6084/m9.figshare.5670007). The entire metagenomic dataset has been uploaded to the European Nucleotide Archive (</a>primary accession PRJEB22949). <a rel="noreferrer noopener" target="_blank">A subset of these data have been used for a project to identify human herpesvirus 6 (HHV-6) in clinical samples; this manuscript is available on BioRxiv (</a>https://doi.org/10.1101/236083).</div><div><div><div><div><br></div></div><div>This study was approved through the UK integrated research application system (REC reference 14/LO/1077).</div></div></div

HCV+ Subjects 14.08.18.xlsx

We performed a retrospective study of HCV infection in a UK teaching hospital to evaluate and compare the performance of different laboratory tests, to describe the population with active HCV infection and to determine the proportion of these individuals who access clinical review and treatment. Microbiology records for all HCV screening tests performed at Oxford University Hospitals within two defined time-intervals (Group 1 - 18 months; Jan 2013 - June 2014, Group 2 - 15 months; Jan 2015 - March 2016) were studied . For those testing positive we collected follow-up testing data. We recorded patient age, sex, and the location from which the sample was sent. We used an analytical tool to estimate ethnicity applying Onolytics software for all patients whom a full name was part of the electronic record. Ethics approval was not required, as this study was undertaken as a departmental quality improvement exercise within microbiology using anonymised patient data, and completed the audit cycle for previously approved audit projects. Data for Onolytics analysis were handled separately and were subject to a confidential disclosure agreement drawn up by University of Oxford Research Services (February 2016). <div><div><br><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div></div

'Hepitopes': A Database of HLA Class I Epitopes in Hepatitis B Virus

This is a spreadsheet containing the results of a systematic literature review to identify and curate all known and putative HLA Class I epitopes in hepatitis B virus (HBV). <div> <p>We performed our literature review in January 2016, searching Medline and Embase via the OVID search interface made available by the University of Oxford. No date restrictions were imposed; Medline was searched from 1946-2016 and Embase from 1974-2016. The relevant subject headings for Epitopes, HLA Antigens, CD8 Antigens and Hepatitis B from the thesauri (MESH and EMTREE) were exploded and searched. In addition the terms epitope* (to pick up singular and plural) and Hepatitis B and HBV were searched in the title and abstract fields. We also identified additional references by searching the bibliographies of relevant articles. </p><p>As well as details of each citation, we recorded the HBV protein and sequence-numbered location of each epitope (based on a published reference strain; Liu WC, et al. Aligning to the sample-specific reference sequence to optimize the accuracy of next-generation sequencing analysis for hepatitis B virus. <i>Hepatol Int</i> 2016;10:147-157).</p> <p>Each citation was reviewed by a primary reviewer and then again by a second expert to ensure the records are as accurate as possible. </p><p>Over time, we aim to update and refine the dataset such that it becomes a growing resource for virologists, immunologists and those in the field of vaccine design.</p><p>A live interactive version can be viewed at http://www.expmedndm.ox.ac.uk/hepitopes.</p><p>The visualisation code can be viewed at <a href="https://github.com/ox-it/hepitopes" rel="noreferrer" target="_blank">https://github.com/ox-it/hepitopes</a>. </p><p>As the database is updated and refined, we will submit updated versions to Figshare. In parallel, we have uploaded a static version to Oxford Research Archive (ORA) at the point of initial publication; DOI: 10.5287/bodleian:zr0VAr78q</p> </div

Drug therapy used to treat HBV.

<p>Costing is based on the International Medical Products Price Guide: <a href="http://mshpriceguide.org/en" target="_blank">http://mshpriceguide.org/en</a> (data accessed May 2017. Price for lamivudine (3TC)—South Africa Department of Health; Price for tenofovir (TDF)—Supply Chain Management Project; price for HBV immunoglobulin (HBIG)—Sudan Medicins Sans Frontieres). WHO essential medicines: <a href="http://who.int/medicines/publications/essentialmedicines/EML_2015_FINAL_amended_NOV2015.pdf?ua=1" target="_blank">http://who.int/medicines/publications/essentialmedicines/EML_2015_FINAL_amended_NOV2015.pdf?ua=1</a>.</p

Resource gap in research funding allocations and academic publications for hepatitis B virus (HBV), hepatitis C virus (HCV), HIV, and malaria.

<p>Panels A/C: funding data from the United States National Institutes for Health (NIH) estimated funding for research, condition, and disease categories 2013–2018 (*projected figures for 2017 and 2018), available at <a href="https://report.nih.gov/categorical_spending.aspx" target="_blank">https://report.nih.gov/categorical_spending.aspx</a>, downloaded June 2017. For the projected funding allocation for 2018, HCV will receive 2.3-fold HBV funding, malaria 4.8-fold, and HIV 66.8-fold. Research into “malaria” and “malaria vaccine” are subdivided in the source data set but have been pooled in this graphic. Panels B/D: We recorded the number of publications listed on NCBI PubMed based on the search terms “HIV,” “HBV,” “HCV,” and “malaria” for each year from 2007–2016. Example search string for HBV publications in 2016: (HBV[Title]) AND ("2016/01/01"[Date—Publication]: "2016/12/31"[Date—Publication]). Data are represented as absolute numbers (panels A and B) and the proportion of the whole (panels C and D). For hepatitis delta virus (HDV), funding allocation data are not available, and we identified <25 publications/year (range 7–23).</p

The hepatitis B virus (HBV) cascade.

<p>Diagrammatic representation of the total burden of HBV infection and the subsets of individuals who are diagnosed (orange), linked to care (green), engaged with care (blue), on treatment (light purple), and have suppressed viremia (dark purple). An estimate of the proportion of cases undiagnosed versus diagnosed (91% versus 9%, respectively) is based on the WHO fact sheet [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005842#pntd.0005842.ref003" target="_blank">3</a>]. The proportion who flow from each pool to the next is otherwise represented by a question mark, as these numbers are not represented by robust data.</p

A package of interventions to move towards elimination of hepatitis B virus (HBV) infection as a public health threat.

<p>Suggested measures are aligned with WHO interventions for neglected tropical diseases (NTDs).</p

Randomized controlled trial of molnupiravir SARS-CoV-2 viral and antibody response in at-risk adult outpatients.

Viral clearance, antibody response and the mutagenic effect of molnupiravir has not been elucidated in at-risk populations. Non-hospitalised participants within 5 days of SARS-CoV-2 symptoms randomised to receive molnupiravir (n = 253) or Usual Care (n = 324) were recruited to study viral and antibody dynamics and the effect of molnupiravir on viral whole genome sequence from 1437 viral genomes. Molnupiravir accelerates viral load decline, but virus is detectable by Day 5 in most cases. At Day 14 (9 days post-treatment), molnupiravir is associated with significantly higher viral persistence and significantly lower anti-SARS-CoV-2 spike antibody titres compared to Usual Care. Serial sequencing reveals increased mutagenesis with molnupiravir treatment. Persistence of detectable viral RNA at Day 14 in the molnupiravir group is associated with higher transition mutations following treatment cessation. Viral viability at Day 14 is similar in both groups with post-molnupiravir treated samples cultured up to 9 days post cessation of treatment. The current 5-day molnupiravir course is too short. Longer courses should be tested to reduce the risk of potentially transmissible molnupiravir-mutated variants being generated. Trial registration: ISRCTN30448031