Low-Coordinate Magnesium Sulfide and Selenide Complexes.

The reactions of [{(NacNac)Mg}] (nacnac = HC(iPrCNDip)) with PhP═O at 100 °C afforded the phosphinate complex [(NacNac)Mg(OPPh)(OPPh)] . Reactions of with PhP═E (E = S, Se) proceeded rapidly at room temperature to low-coordinate chalcogenide complexes [{(NacNac)Mg}(μ-S)] and [{(NacNac)Mg}(μ-Se)] , respectively. Similarly, reactions of NHC═S ((MeCNR)C═S with R = Me, Et, or Pr) with afforded NHC adducts of magnesium sulfide complexes, [{(NacNac)Mg(NHC)}(μ-S){Mg(NacNac)}] , that could alternatively be obtained by adding the appropriate NHC to sulfide complex .

Nosocomial transmission of influenza: A retrospective cross-sectional study using next generation sequencing at a hospital in England (2012-2014).

Background: The extent of transmission of influenza in hospital settings is poorly understood. Next generation sequencing may improve this by providing information on the genetic relatedness of viral strains.

Objectives: We aimed to apply next generation sequencing to describe transmission in hospital and compare with methods based on routinely-collected data.

Ultra-rapid, sensitive and specific digital diagnosis of HIV with a dual-channel SAW biosensor in a pilot clinical study.

Despite widened access to HIV testing, around half of those infected worldwide are unaware of their HIV-positive status and linkage to care remains a major challenge. Current rapid HIV tests are typically analogue risking incorrect interpretation, no facile electronic data capture, poor linkage to care and data loss for public health. Smartphone-connected diagnostic devices have potential to dramatically improve access to testing and patient retention with electronic data capture and wireless connectivity.

Minor groove binder modification of widely used TaqMan hydrolysis probe for detection of dengue virus reduces risk of false-negative real-time PCR results for serotype 4.

Dengue is a vector-transmitted viral infection that is a significant cause of morbidity and mortality in humans worldwide, with over 50 million apparent cases and a fatality rate of 2.5 % of 0.5 million severe cases per annum in recent years.

Use of Whole-Genome Sequencing in the Investigation of a Nosocomial Influenza Virus Outbreak.

Traditional epidemiological investigation of nosocomial transmission of influenza involves the identification of patients who have the same influenza virus type and who have overlapped in time and place. This method may misidentify transmission where it has not occurred or miss transmission when it has. We used influenza virus whole-genome sequencing (WGS) to investigate an outbreak of influenza A virus infection in a hematology/oncology ward and identified 2 separate introductions, one of which resulted in 5 additional infections and 79 bed-days lost.

A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project.

Background & Methods: The ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from next-generation sequencing (NGS) data.

A Phylogenetic Analysis of Human Immunodeficiency Virus Type 1 Sequences in Kiev: Findings Among Key Populations.

Background: The human immunodeficiency virus (HIV) epidemic in Ukraine has been driven by a rapid rise among people who inject drugs, but recent studies have shown an increase through sexual transmission.

Methods: Protease and reverse transcriptase sequences from 876 new HIV diagnoses (April 2013-March 2015) in Kiev were linked to demographic data. We constructed phylogenetic trees for 794 subtype A1 and 64 subtype B sequences and identified factors associated with transmission clustering.

Instability of 8E5 calibration standard revealed by digital PCR risks inaccurate quantification of HIV DNA in clinical samples by qPCR.

Establishing a cure for HIV is hindered by the persistence of latently infected cells which constitute the viral reservoir. Real-time qPCR, used for quantification of this reservoir by measuring HIV DNA, requires external calibration; a common choice of calibrator is the 8E5 cell line, which is assumed to be stable and to contain one HIV provirus per cell. In contrast, digital PCR requires no external calibration and potentially provides 'absolute' quantification.

Emergence of a novel subclade of influenza A(H3N2) virus in London, December 2016 to January 2017.

We report the molecular investigations of a large influenza A(H3N2) outbreak, in a season characterised by sharp increase in influenza admissions since December 2016. Analysis of haemagglutinin (HA) sequences demonstrated co-circulation of multiple clades (3C.3a, 3C.

Hepatitis C virus quasispecies and pseudotype analysis from acute infection to chronicity in HIV-1 co-infected individuals.

HIV-1 infected patients who acquire HCV infection have higher rates of chronicity and liver disease progression than patients with HCV mono-infection. Understanding early events in this pathogenic process is important. We applied single genome sequencing of the E1 to NS3 regions and viral pseudotype neutralization assays to explore the consequences of viral quasispecies evolution from pre-seroconversion to chronicity in four co-infected individuals (mean follow up 566 days).

Ultra-deep sequencing provides insights into the virology of hepatitis C super-infections in a case of three sequential infections with different genotypes.

The current epidemic of Hepatitis C infection in HIV-positive men who have sex with men is associated with increasing use of recreational drugs. Multiple HCV infections have been reported in haemophiliacs and intravenous drug users. Using ultra-deep sequencing analysis, we present the case of an HIV-positive MSM with evidence of three sequential HCV infections, each occurring during the acute phase of the preceding infection, following risk exposures.

Minor groove binder modification of widely used TaqMan probe for hepatitis E virus reduces risk of false negative real-time PCR results.

Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in many parts of the developing world. It is responsible for both sporadic infections and large scale epidemics and may be associated with significant mortality during pregnancy. Over the past two decades many serological and nucleic acid based diagnostic tests for HEV have been developed, including several reverse transcription real-time polymerase chain reaction assays (RT-qPCR).

Quantitation of hepatitis delta virus using a single-step internally controlled real-time RT-qPCR and a full-length genomic RNA calibration standard.

Quantitation of circulating hepatitis delta virus (HDV) RNA is important for assessing the response to antiviral therapy and for understanding the complex dynamic interactions between hepatitis B virus (HBV) and HDV replication. Although several PCR assays for HDV RNA have been described none of them incorporate an internal control or use a full-length RNA calibration standard for absolute quantitation. This study describes the development and evaluation of a novel single-step real-time RT-qPCR assay for HDV RNA quantitation which incorporates a Brome Mosaic virus internal control to prevent false negatives and under-reporting due to inhibitors or due to inefficient RNA purification, reverse transcription or PCR amplification.

Molecular basis for the high degree of antigenic cross-reactivity between hepatitis B virus capsids (HBcAg) and dimeric capsid-related protein (HBeAg): insights into the enigmatic nature of the e-antigen.

The hepatitis B virus core gene codes for two closely related antigens: a 21-kDa protein that forms dimers that assemble as multimegadalton capsids, and a 17-kDa protein that also forms dimers but that do not assemble. The proteins, respectively referred to as core antigen (HBcAg) and e-antigen (HBeAg), share a sequence of 149 residues but have different amino- and carboxy-termini. Their structural and serological relationship has long been unclear.

The dynamics of appearance and disappearance of HIV-1 integrase mutations during and after withdrawal of raltegravir therapy.

Objectives: To monitor HIV-1 integrase resistance mutations during raltegravir (RAL) therapy, including the impact of RAL interruption.

Design And Method: An analysis of viral load and the HIV-1 integrase gene evolution in 26 HIV-1 treatment-experienced patients undergoing RAL therapy.

Results: Initial suppression of viral load was observed in all patients; however, four patients failed to maintain suppression and subsequently developed resistance at viral load rebound.

Presence of hepatitis B virus core promoter mutations pre-seroconversion predict persistent viral replication after HBeAg loss.

Background: In patients with chronic hepatitis B virus (HBV) infection DNA levels do not always fall after anti-hepatitis B e (anti-HBe) seroconversion.

Objectives: To follow longitudinally through HB e antigen (HBeAg) loss HBV DNA levels and core promoter/precore sequences in a cohort of 21 chronic HBV carriers.

Study Design: Treatment-naïve HBeAg seropositive HBV carriers were monitored through HBeAg loss for between 2 and 22 years (mean 9.

A low rate of hepatitis B virus vaccine breakthrough infections in Mongolia.

A nation-wide hepatitis B virus (HBV) immunization program of all newborn babies was launched in Mongolia in 1991. However, the continuation of clinical icteric viral hepatitis infections in children led to the investigation to determine whether HBV breakthrough infections were occurring and if any were due to hepatitis B surface antigen (HBsAg) mutants. Hepatitis A virus (HAV) infections accounted for most of these cases with 3% of the jaundiced children shown to have acute hepatitis B.

Development and evaluation of a real-time RT-PCR assay for quantification of cell-free human immunodeficiency virus type 2 using a Brome Mosaic Virus internal control.

Quantification of cell-free virus in plasma is important for monitoring disease progression and for assessing the response to antiretroviral therapy in both human immunodeficiency type 1 and type 2 (HIV-1, HIV-2) infections. Although commercial assays suitable for HIV-1 quantification have been used for more than a decade, no commercial assays are yet available for the measurement of cell-free HIV-2. We have therefore developed a novel real-time RT-PCR assay which, unlike previously described 'in house' assays, incorporates a Brome Mosaic Virus (BMV) internal control to minimise the risk of generating false-negative or falsely low results due to unrecognised problems with viral RNA purification, cDNA synthesis or PCR amplification.

Evaluation of the role of real-time PCR in the diagnosis of invasive aspergillosis.

Recently, two developments relating to the diagnosis of invasive aspergillosis (IA) have occurred. First, the standardisation of criteria for determining the category of this disease according to the European Organisation for Research and Treatment of Cancer/Mycosis (EORTC) Study Group consensus definitions has allowed comparison of results from different studies to be undertaken. The second development is the generation of PCR assays based on real-time technologies that are able to quantify Aspergillus DNA.

Real-time PCR quantitation of hepatitis B virus DNA using automated sample preparation and murine cytomegalovirus internal control.

Quantitation of circulating hepatitis B virus (HBV) DNA is important for monitoring disease progression and for assessing the response to antiviral therapy. Several commercial and 'in house' assays for HBV DNA quantitation have been described but many of these have limitations of relatively low sensitivity and limited dynamic range. This study describes the development and evaluation of a FRET-based real-time PCR assay designed to overcome these limitations and to provide accurate quantitation of DNA from all eight genotypes of HBV (A-H).

A 'first loop' linear epitope accessible on native hepatitis B surface antigen that persists in the face of 'second loop' immune escape.

Murine monoclonal antibodies (mAbs) were raised following immunization with native mutant hepatitis B surface antigen (HBsAg) purified from human sera. A set of antibodies binding to a linear epitope carried between residues 121 and 129 of the s region was demonstrated. These antibodies were shown by cross-competition assays to bind to a single epitope whose antigenicity was influenced by the TTP motif lying between residues 125 and 127.

The prospective evaluation of a nested polymerase chain reaction assay for the early detection of Aspergillus infection in patients with leukaemia or undergoing allograft treatment.

Patients with acute leukaemia or undergoing allogenic bone marrow transplantation at University College London Hospital Trust were screened for the presence of aspergillosis by polymerase chain reaction (PCR). Aspergillus DNA, from whole blood samples, was amplified by nested PCR to detect a 135 bp fragment in the mitochondrial region of Aspergillus fumigatus or A. flavus (121 bp).

Characterisation of a panel of monoclonal antibodies raised against recombinant HCV core protein.

Hepatitis C virus (HCV) has as yet no practical culture system so any antigen or antibody studies must be carried out using recombinant antigens. In this study, HCV core sequence was amplified by PCR, inserted into pRSET, and expressed in E. coli.