Inherited chromosomally integrated human herpesvirus 6: regional variation in prevalence, association with angina, and identification of ancestral viral lineages in two large UK studies.

Tens of millions of people worldwide have inherited chromosomally integrated human herpesvirus 6 (iciHHV-6), yet we know little about the consequences. iciHHV-6-positive individuals inherit the genome of HHV-6A or HHV-6B in the germline, and viral genomes are therefore present in every nucleated cell. To investigate the epidemiology of iciHHV-6 in the UK, almost 32,000 individuals were screened from two volunteer research studies: the family-based Generation Scotland: Scottish Family Health Study (GS:SFHS) and the Breakthrough Generations Study (BGS).

Causal inference over stochastic networks.

Claiming causal inferences in network settings necessitates careful consideration of the often complex dependency between outcomes for actors. Of particular importance are treatment spillover or outcome interference effects. We consider causal inference when the actors are connected via an underlying network structure.

Modeling State Firearm Law Adoption Using Temporal Network Models.

Unlabelled: Policy Points Promoting healthy public policies is a national priority, but state policy adoption is driven by a complex set of internal and external factors. This study employs new social network methods to identify underlying connections among states and to predict the likelihood of new firearm-related policy adoption given changes to this interstate network. This approach could be used to assess the likelihood that a given state will adopt a specific new firearm-related law and to identify points of influence that could either inhibit or promote wider diffusion of specific laws.

The Diffusion of Punitive Firearm Preemption Laws Across U.S. States.

Introduction: Firearm violence is a public health crisis. Most states prohibit local firearm laws, but some states have laws that allow for lawsuits and other penalties against local governments and lawmakers who pass firearm laws deemed preempted. These punitive firearm preemptive laws may reduce firearm policy innovation, discussion, and adoption beyond preemption alone.

Comparing the Real-World Performance of Exponential-family Random Graph Models and Latent Order Logistic Models for Social Network Analysis.

Exponential-family Random Graph models (ERGM) are widely used in social network analysis when modelling data on the relations between actors. ERGMs are typically interpreted as a snapshot of a network at a given point in time or in a final state. The recently proposed Latent Order Logistic model (LOLOG) directly allows for a latent network formation process.

What factors drive state firearm law adoption? An application of exponential-family random graph models.

Guns are a ubiquitous feature of contemporary US culture, driven, at least partly, by firearms' constitutional enshrinement. However, the majority of laws intended to restrict or expand firearm access and use are formulated and passed in the states, leading to 50 different firearm-related legal environments. To date, little is known about why some states pass more restrictive or permissive firearm laws than others.

Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes.

Human cytomegalovirus (HCMV) infects most of the population worldwide, persisting throughout the host's life in a latent state with periodic episodes of reactivation. While typically asymptomatic, HCMV can cause fatal disease among congenitally infected infants and immunocompromised patients. These clinical issues are compounded by the emergence of antiviral resistance and the absence of an effective vaccine, the development of which is likely complicated by the numerous immune evasins encoded by HCMV to counter the host's adaptive immune responses, a feature that facilitates frequent super-infections.

Astrovirus VA1/HMO-C: an increasingly recognized neurotropic pathogen in immunocompromised patients.

Background: An 18-month-old boy developed encephalopathy, for which extensive investigation failed to identify an etiology, 6 weeks after stem cell transplant. To exclude a potential infectious cause, we performed high-throughput RNA sequencing on brain biopsy.

Methods: RNA-Seq was performed on an Illumina Miseq, generating 20 million paired-end reads.

Evaluation of non-extracted genital swabs for real-time HSV PCR.

Nucleic acid extraction of clinical samples is accepted as a key requirement in molecular diagnostics. At Barts Health NHS Trust, swabs taken from patients with clinical suspicion of HSV infection were routinely extracted on the Qiagen MDx BioRobot prior to testing with a real-time triplex PCR for HSV1, HSV2, and VZV. The aim of this study was to adapt an existing HSV1/HSV2/VZV real-time PCR by replacing VZV with phocine herpesvirus 1 (PhHV) as an internal control (IC) and evaluate whether this adapted assay required the nucleic acid extraction step for predominantly genital swabs.

Classification of HHV-6A and HHV-6B as distinct viruses.

Shortly after the discovery of human herpesvirus 6 (HHV-6), two distinct variants, HHV-6A and HHV-6B, were identified. In 2012, the International Committee on Taxonomy of Viruses (ICTV) classified HHV-6A and HHV-6B as separate viruses. This review outlines several of the documented epidemiological, biological, and immunological distinctions between HHV-6A and HHV-6B, which support the ICTV classification.

Genome Sequence of Human Herpesvirus 7 Strain UCL-1.

The sequence of human herpesvirus 7 (HHV-7) strain UCL-1 was determined using target enrichment and next-generation sequencing methods. We have identified 86 putative open reading frames (ORFs), and comparative sequence analyses demonstrate that this strain is closely related to the previously sequenced HHV-7 strains RK and JI.

Human telomeres that carry an integrated copy of human herpesvirus 6 are often short and unstable, facilitating release of the viral genome from the chromosome.

Linear chromosomes are stabilized by telomeres, but the presence of short dysfunctional telomeres triggers cellular senescence in human somatic tissues, thus contributing to ageing. Approximately 1% of the population inherits a chromosomally integrated copy of human herpesvirus 6 (CI-HHV-6), but the consequences of integration for the virus and for the telomere with the insertion are unknown. Here we show that the telomere on the distal end of the integrated virus is frequently the shortest measured in somatic cells but not the germline.

Universal extraction method for gastrointestinal pathogens.

A universal stool extraction method for recovery of nucleic acids (NAs) from gastrointestinal pathogens was developed to support rapid diagnostics for the London 2012 Olympics. The method involved mechanical disruption (bead beating) of the stools, followed by automated extraction and detection using real-time PCR. This method had been used extensively in the Second Infectious Intestinal Disease Study (IID2) for the isolation of NA from bacteria and parasites (and was effective for the robust recovery of Cryptosporidium spp.

Disease Progression in HIV-1-Infected Viremic Controllers.

Background: The mechanism of CD4 T-cell decline in HIV-1 infection is unclear, but the association with plasma viral RNA load suggests viral replication is involved. Indeed, viremic controller patients with low viral RNA loads typically maintain high CD4 T-cell counts. Within a local cohort of 86 viremic controllers, we identify a subgroup (18 "discord controllers") with low CD4 T-cell counts that present clinical uncertainty.

Comparison of the rate and size of HIV-1 viral load blips with Roche COBAS TaqMan HIV-1 versions 1.0 and 2.0 and implications for patient management.

Background: The Roche COBAS TaqMan HIV-1 version 1.0 (v1.0) real-time PCR test detects more low level viral loads (VL) compared to the previous Roche Amplicor version 1.

Comparative evaluation of the QIAGEN QIAsymphony® SP system and bioMérieux NucliSens easyMAG automated extraction platforms in a clinical virology laboratory.

Background: The QIAGEN QIAsymphony(®) SP is an automated system that can process a variety of different sample types for nucleic acid extraction.

Objectives: To compare this system against the bioMérieux NucliSens easyMAG using a range of common clinical sample types.

Study Design: Nucleic acid extracts were tested on 6 in-house real time viral PCR assays: quantitative cytomegalovirus (CMV); respiratory and enteric multiplex (10 viruses); influenza A H1N1 2009 specific H1 and N1 assays (sH1/N1); herpes simplex virus (HSV) 1, HSV 2 and varicella zoster virus (VZV) multiplex; norovirus genogroups I and II (Noro GI/II) multiplex.

Comparative evaluation of the Seegene Seeplex RV15 and real-time PCR for respiratory virus detection.

Respiratory virus infections contribute substantially both to hospitalizations of young children, and to morbidity in immunocompromised patients such as those with hematological malignancies. Their rapid and accurate diagnosis is essential to patient management. To evaluate the prospective utility of Seeplex® DPO technology in respiratory virus diagnosis, a panel of 99 respiratory samples positive by real-time RT-PCR for one or more viruses was assayed by the Seegene Seeplex® RV12 system.

Extensive human cytomegalovirus (HCMV) genomic DNA in the renal tubular epithelium early after renal transplantation: Relationship with HCMV DNAemia and long-term graft function.

Human cytomegalovirus (HCMV) infection is associated with a series of direct and indirect effects following renal transplantation. However, the presence of HCMV in the kidney and its relationship with acute rejection and long-term graft function remain to be fully elucidated. Sixty-two biopsies derived from 30 renal transplant recipients with signs of clinical rejection were analyzed for HCMV using a sensitive in situ DNA hybridization method.

Importance of chromosomally integrated HHV-6A and -6B in the diagnosis of active HHV-6 infection.

Human herpesvirus-6 (HHV-6) exists as two closely related variants: A and B. Whereas no disease has been firmly associated with HHV-6A, variant B causes febrile illness in young children and is pathogenic in immunosuppressed transplant recipients. Chromosomally integrated HHV-6 (with either variant A or B) occurs in a minority of people.

Microarray-based determination of the lytic cascade of human herpesvirus 6B.

The lytic gene expression of several members of the human herpesvirus family has been profiled by using gene-expression microarrays; however, the lytic cascade of roseoloviruses has not been studied in similar depth. Based on the complete DNA genome sequences of human herpesvirus 6 variant A (HHV-6A) and variant B (HHV-6B), we constructed a cDNA microarray containing DNA probes to their predicted open reading frames, plus 914 human genes. Gene-expression profiling of HHV-6B strain Z29 in SupT1 cells over a 60 h time-course post-infection, together with kinetic classification of the HHV-6B genes in the presence of either cycloheximide or phosphonoacetic acid, allowed the placement of HHV-6B genes into defined kinetic classes.

Human herpesvirus 6 integrates within telomeric regions as evidenced by five different chromosomal sites.

Fluorescent in situ hybridization (FISH) was used to investigate the chromosomal integration sites of human herpesvirus 6 (HHV-6) in phytohemagglutinin-stimulated leukocytes and B lymphocytes from Epstein-Barr virus transformed lymphoblastoid cell lines (LCLs). Five different chromosomal integration sites were found in nine individuals. Only one site was identified in each individual, each site was in the vicinity of the telomeric region and was on either the p or q arm of only one of the two chromosome homologues.

Comparative evaluation of the automated Roche TaqMan real-time quantitative human immunodeficiency virus type 1 RNA PCR assay and the Roche AMPLICOR Version 1.5 conventional PCR assay.

The need to evaluate antiviral treatment response and the emergence of resistance have made the human immunodeficiency virus (HIV) viral load assay a major feature of the diagnostic monitoring of HIV-infected individuals. The objective of this study was to evaluate the utility of the recently In Vitro Diagnostic Medical Devices Directive-approved Roche COBAS AmpliPrep/TaqMan96 real-time PCR assay by comparison with the existing Roche COBAS AmpliPrep/AMPLICOR MONITOR conventional PCR assay. EDTA-treated plasma samples from 191 HIV-1-infected individuals were tested for HIV-1 RNA by the AMPLICOR assay and the TaqMan assay.

Human herpesvirus 6 DNA levels in cerebrospinal fluid due to primary infection differ from those due to chromosomal viral integration and have implications for diagnosis of encephalitis.

The prevalence and concentration of human herpesvirus 6 (HHV-6) DNA in the cerebrospinal fluid (CSF) of the immunocompetent in primary infection was compared with that in viral chromosomal integration. Samples from 510 individuals with suspected encephalitis, 200 young children and 310 older children and/or adults, and 12 other patients were tested. HHV-6 DNA concentration (log(10) copies/ml) was measured in CSF, serum, and whole blood using PCR.