Zinc Fingers in HIV-1 Gag Precursor Are Not Equivalent for gRNA Recruitment at the Plasma Membrane

The human immunodeficiency virus type 1 Gag precursor specifically selects the unspliced viral genomic RNA (gRNA) from the bulk of cellular and spliced viral RNAs via its nucleocapsid (NC) domain and drives gRNA encapsidation at the plasma membrane (PM). To further identify the determinants governing the intracellular trafficking of Gag-gRNA complexes and their accumulation at the PM, we compared, in living and fixed cells, the interactions between gRNA and wild-type Gag or Gag mutants carrying deletions in NC zinc fingers (ZFs) or a nonmyristoylated version of Gag. Our data showed that the deletion of both ZFs simultaneously or the complete NC domain completely abolished intracytoplasmic Gag-gRNA interactions. Deletion of either ZF delayed the delivery of gRNA to the PM but did not prevent Gag-gRNA interactions in the cytoplasm, indicating that the two ZFs display redundant roles in this respect. However, ZF2 played a more prominent role than ZF1 in the accumulation of the ribonucleoprotein complexes at the PM. Finally, the myristate group, which is mandatory for anchoring the complexes at the PM, was found to be dispensable for the association of Gag with the gRNA in the cytosol.

Identification of the initial nucleocapsid recognition element in the HIV-1 RNA packaging signal

Understanding the molecular determinants of retroviral genome packaging is important for drug discovery and development of vectors for gene delivery. We show that the HIV-1 leader, which contains the RNA elements necessary for genome packaging, binds approximately two dozen copies of the cognate NC protein with affinities ranging from ∼40 nM to 1.4 µM. Binding to the four highest-affinity “initial” binding sites occurs with endothermic energetics attributed to NC-induced localized RNA melting. Mutations that stabilize these sites inhibit NC binding in vitro and RNA packaging in transfected cells. A small-molecule inhibitor of RNA packaging binds specifically to the initial NC binding sites and stabilizes the RNA structure. Our findings identify a potential RNA Achilles’ heel for HIV therapeutic development.

Selective packaging of the HIV-1 genome during virus assembly is mediated by interactions between the dimeric 5ʹ-leader of the unspliced viral RNA and the nucleocapsid (NC) domains of a small number of assembling viral Gag polyproteins. Here, we show that the dimeric 5′-leader contains more than two dozen NC binding sites with affinities ranging from 40 nM to 1.4 μM, and that all high-affinity sites (K_d ≲ 400 nM) reside within a ∼150-nt region of the leader sufficient to promote RNA packaging (core encapsidation signal, Ψ^CES). The four initial binding sites with highest affinity reside near two symmetrically equivalent three-way junction structures. Unlike the other high-affinity sites, which bind NC with exothermic energetics, binding to these sites occurs endothermically due to concomitant unwinding of a weakly base-paired [UUUU]:[GGAG] helical element. Mutations that stabilize base pairing within this element eliminate NC binding to this site and severely impair RNA packaging into virus-like particles. NMR studies reveal that a recently discovered small-molecule inhibitor of HIV-1 RNA packaging that appears to function by stabilizing the structure of the leader binds directly to the [UUUU]:[GGAG] helix. Our findings suggest a sequential NC binding mechanism for Gag-genome assembly and identify a potential RNA Achilles’ heel to which HIV therapeutics may be targeted.

Mucosal-associated invariant T (MAIT) cells provide B-cell help in vaccinated and subsequently SIV-infected Rhesus Macaques

Mucosal-associated invariant T (MAIT) cells help combat opportunistic infections. Thus, MAIT cells are of interest in HIV/SIV vaccination and infection. We investigated MAIT cell dynamics and function in rhesus macaque blood and bronchoalveolar lavage (BAL) following mucosal adenovirus (Ad)-SIV recombinant priming, intramuscular SIV envelope boosting and infection following repeated low-dose intravaginal SIV exposures. Increased frequencies of blood MAIT cells over the course of vaccination were observed, which were maintained even 12-weeks post-SIV infection. BAL MAIT cells only increased after the first Ad immunization. Vaccination increased MAIT cell levels in blood and BAL expressing the antiviral cytokine IFN-γ and TNF-α and the proliferation marker Ki67. Upon T cell-specific α-CD3, α-CD28 stimulation, MAIT cells showed a greater capacity to secrete cytokines/chemokines associated with help for B cell activation, migration and regulation compared to CD3⁺MR1⁻ cells. Culture of MAIT cell supernatants with B cells led to greater tissue like memory B cell frequencies. MAIT cell frequencies in blood and BAL correlated with SIV-specific antibody levels in rectal secretions and with SIV-specific tissue resident memory B cells. Overall, SIV vaccination influenced MAIT cell frequency and functionality. The potential for MAIT cells to provide help to B cells was evident during both vaccination and infection.

Validation of a Non-Laboratory Based Screening Tool for Predicting Non-Alcoholic Fatty Liver Disease in an Egyptian Setting

BACKGROUND

Non-alcoholic fatty liver disease (NAFLD) is a common chronic liver disorder in more than 20% of the general population worldwide.  Several combinations of non-invasive factors and scoring models were investigated as indicators of NAFLD. This study aimed to validate and adapt an established fatty liver score, which allows the identification of NAFLD based on routinely available clinical and laboratory data.

MATERIALS AND METHODS

The study cohort comprised 190 adults seeking health check-up at the out-patient clinic of a tertiary care hospital in Alexandria, Egypt. Anthropometric, clinical, and laboratory data were recorded and the status of fatty liver was diagnosed by abdominal ultrasound. A logistic regression model was built to determine the predictors of NAFLD. The performance of the derived risk scores was compared to other existing models.

RESULTS

Obesity (60.0%), metabolic syndrome (42.6%), and NAFLD (56.8%) were predominant features among the study population. Smoking [OR (95% CI) = 4.4 (0.9-21.4)], obesity [OR (95% CI) = 4.0 (1.7-9.7)], hypertension [OR (95% CI) = 2.4 (1.03-5.5)], elevated serum total cholesterol [OR (95% CI) = 4.8 (1.8-13.1)], triglycerides [OR (95% CI) = 11.8 (2.3-661.02)], and ALT [OR (95% CI) = 4.8 (1.8-13.1)] were multivariate predictors of NAFLD. A NAFLD screening questionnaire with values applicable for Egyptians was adapted from an existing model after validation. A total score ≥7 was suggestive of NAFLD [AUC = 0.810 (0.749-0.871); sensitivity = 87.0%; specificity = 62.2%; PPV = 75.2%; NPV = 78.5%].

CONCLUSIONS

NAFLD can be sufficiently predicted among apparently healthy Egyptians by a tempted simple and non-invasive scoring index although external validation is warranted.

From the Argonauts Mythological Sailors to the Argonautes RNA-Silencing Navigators: Their Emerging Roles in Human-Cell Pathologies

Regulation of gene expression has emerged as a fundamental element of transcript homeostasis. Key effectors in this process are the Argonautes (AGOs), highly specialized RNA-binding proteins (RBPs) that form complexes, such as the RNA-Induced Silencing Complex (RISC). AGOs dictate post-transcriptional gene-silencing by directly loading small RNAs and repressing their mRNA targets through small RNA-sequence complementarity. The four human highly-conserved family-members (AGO1, AGO2, AGO3, and AGO4) demonstrate multi-faceted and versatile roles in transcriptome’s stability, plasticity, and functionality. The post-translational modifications of AGOs in critical amino acid residues, the nucleotide polymorphisms and mutations, and the deregulation of expression and interactions are tightly associated with aberrant activities, which are observed in a wide spectrum of pathologies. Through constantly accumulating information, the AGOs’ fundamental engagement in multiple human diseases has recently emerged. The present review examines new insights into AGO-driven pathology and AGO-deregulation patterns in a variety of diseases such as in viral infections and propagations, autoimmune diseases, cancers, metabolic deficiencies, neuronal disorders, and human infertility. Altogether, AGO seems to be a crucial contributor to pathogenesis and its targeting may serve as a novel and powerful therapeutic tool for the successful management of diverse human diseases in the clinic.

Fibrocytes, Wound Healing, and Corneal Fibrosis

Purpose

This review highlights the roles of fibrocytes—their origin, markers, regulation and functions—including contributions to corneal wound healing and fibrosis.

Methods

Literature review.

Results

Peripheral blood fibroblast-like cells, called fibrocytes, are primarily generated as mature collagen-producing cells in the bone marrow. They are likely derived from the myeloid lineage, although the exact precursor remains unknown. Fibrocytes are identified by a combination of expressed markers, such as simultaneous expression of CD34 or CD45 or CD11b and collagen type I or collagen type III. Fibrocytes migrate into the wound from the blood where they participate in pathogen clearance, tissue regeneration, wound closure and angiogenesis. Transforming growth factor beta 1 (TGF-β₁) and adiponectin induce expression of α-smooth muscle actin and extracellular matrix proteins through activation of Smad3 and adenosine monophosphate-activated protein kinase pathways, respectively. Fibrocytes are important contributors to the cornea wound healing response and there are several mechanisms through which fibrocytes contribute to fibrosis in the cornea and other organs, such as their differentiation into myofibroblasts, production of matrix metalloproteinase, secretion of tissue inhibitor of metalloproteinase, and release of TGF-β₁. In some tissues, fibrocytes may also contribute to the basement membrane regeneration and to the resolution of fibrosis.

Conclusions

New methods that block fibrocyte generation, fibrocyte migration, and their differentiation into myofibroblasts, as well as their production of matrix metalloproteinases, tissue inhibitor of metalloproteinase, and TGF-β₁, have therapeutic potential to reduce the accumulation of collagens, maintain tissue integrity and retard or prevent the development of fibrosis.

Cognitive and Emotional Aspects of Cupping Therapy

Cupping therapy has recently gained public attention and is widely used in many regions. Some patients are resistant to being treated with cupping therapy, as visually unpleasant marks on the skin may elicit negative reactions. This study aimed to identify the cognitive and emotional components of cupping therapy. Twenty-five healthy volunteers were presented with emotionally evocative visual stimuli representing fear, disgust, happiness, neutral emotion, and cupping, along with control images. Participants evaluated the valence and arousal level of each stimulus. Before the experiment, they completed the Fear of Pain Questionnaire-III. In two-dimensional affective space, emotional arousal increases as hedonic valence ratings become increasingly pleasant or unpleasant. Cupping therapy images were more unpleasant and more arousing than the control images. Cluster analysis showed that the response to cupping therapy images had emotional characteristics similar to those for fear images. Individuals with a greater fear of pain rated cupping therapy images as more unpleasant and more arousing. Psychophysical analysis showed that individuals experienced unpleasant and aroused emotional states in response to the cupping therapy images. Our findings suggest that cupping therapy might be associated with unpleasant-defensive motivation and motivational activation. Determining the emotional components of cupping therapy would help clinicians and researchers to understand the intrinsic effects of cupping therapy.

Performance and modification of EGCRISC among hepatitis C virus high-risk groups

We have previously shown that the Egyptian Hepatitis C Virus Risk Score (EGCRISC), an Egyptian hepatitis C virus (HCV) risk-based screening tool, to be valid and cost-effective. Certain behaviours, occupations and diseases have been shown to be associated with an increased risk of exposure to HCV infection and constitute a major population reservoir of HCV infection. This study investigated the efficacy of EGCRISC in selected high-risk groups by testing 863 participants from four groups: slaughterhouse workers, illicit drug users (IDUs), female sex workers and human immune deficiency virus (HIV) patients. Data for this study were collected on EGCRISC and another pre-designed risk factor questionnaire. Sera were tested for HCV antibodies by ELISA. EGCRISC, at lower cut-off points, showed significantly good performance (P < 0.05) in all four groups except for females <45 years, but was reliable in detecting HCV cases (sensitivity: 84.21% and negative predictive value: 94.5%). Specific scores for IDUs and HIV patients were developed that showed high accuracy (P < 0.001). A modified EGCRISC for high-risk groups (EGCRISC-HRGs) was shown to be a valid tool that is recommended for use in high-risk populations if no other specific screening tool is available or universal screening is applied. EGCRISC for IDUs (EGCRISC-IDUs) and EGCRISC for HIV patients (EGCRISC-HIV) are useful tools for preselecting potentially HCV-infected cases for further testing in settings where serological analysis is not readily available or accessible.

Crystal structure of Drosophila Piwi

PIWI-clade Argonaute proteins associate with PIWI-interacting RNAs (piRNAs), and silence transposons in animal gonads. Here, we report the crystal structure of the Drosophila PIWI-clade Argonaute Piwi in complex with endogenous piRNAs, at 2.9 Å resolution. A structural comparison of Piwi with other Argonautes highlights the PIWI-specific structural features, such as the overall domain arrangement and metal-dependent piRNA recognition. Our structural and biochemical data reveal that, unlike other Argonautes including silkworm Siwi, Piwi has a non-canonical DVDK tetrad and lacks the RNA-guided RNA cleaving slicer activity. Furthermore, we find that the Piwi mutant with the canonical DEDH catalytic tetrad exhibits the slicer activity and readily dissociates from less complementary RNA targets after the slicer-mediated cleavage, suggesting that the slicer activity could compromise the Piwi-mediated co-transcriptional silencing. We thus propose that Piwi lost the slicer activity during evolution to serve as an RNA-guided RNA-binding platform, thereby ensuring faithful co-transcriptional silencing of transposons.

Argonaute Proteins: From Structure to Function in Development and Pathological Cell Fate Determination

The highly conserved Argonaute protein family members play a central role in the regulation of gene expression networks, orchestrating the establishment and the maintenance of cell identity throughout the entire life cycle, as well as in several human disorders, including cancers. Four functional Argonaute proteins (AGO1-4), with high structure similarity, have been described in humans and mice. Interestingly, only AGO2 is robustly expressed during human and mouse early development, in contrast to the other AGOs. Consequently, AGO2 is indispensable for early development in vivo and in vitro. Here, we review the roles of Argonaute proteins during early development by focusing on the interplay between specific domains of the protein and their function. Moreover, we report recent works highlighting the importance of AGO posttranslational modifications in cancer.

Systematic review: chronic viral hepatitis and metabolic derangement

BACKGROUND

The liver has a critical role in the metabolism of glucose and lipids. Chronic hepatitis B virus (HBV) or hepatitis C virus (HCV) infection leads to a spectrum of liver disease including chronic hepatitis, cirrhosis and hepatocellular carcinoma. Metabolic syndrome (MetS) has a rising incidence owing to an epidemic of type 2 diabetes mellitus (T2DM) and obesity. Non-alcoholic fatty liver disease is a liver manifestation of MetS and has become the most common cause of chronic liver disease worldwide.

AIM

To summarise the interplay among hepatitis viruses, MetS and its components.

METHODS

We searched the literature about HBV, HCV infection, MetS, fatty liver and its components from PubMed.

RESULTS

With respect to the viral replication cycle, lipids are important mediators between viral entry and hepatocyte in HCV infection, but not in HBV infection. Thus, HCV infection is inversely associated with hyperlipidaemia and lipid rebound occurs following sustained viral response induced by interferon-based therapy or direct antiviral agents. In addition, HCV infection is positively associated with insulin resistance, hepatic steatosis, MetS and the risk of T2DM and atherosclerosis. In contrast, HBV infection may protect infected subjects from the development of MetS and hepatic steatosis. Accumulating evidence suggests that HBV infection is inversely associated with lipid metabolism, and exhibits no conclusive association with insulin resistance or the risk of T2DM and arteriosclerosis.

CONCLUSIONS

In patients with viral hepatitis and concurrent metabolic diseases, a multidisciplinary approach should be given rather than simply antiviral treatment.

Dynamic Light Scattering Analysis on RNA Associated to Proteins

Dynamic light scattering represents an accurate, robust, and reliable technique to analyze molecule size in solution and monitor their interactions in real time. Here, we describe how to analyze by DLS an RNA-protein interaction. In our frame, we studied complexes formed between RNA fragments derived from the genome of HIV-1 in association with the viral precursor Pr55^Gag. These interactions are crucial for the specific selection of the viral genomic RNA (gRNA) from the bulk of the viral spliced and cellular RNAs. This chapter displays how DLS allows to characterize the interactions that regulate the early steps of viral assembly.

The interplay between m6A RNA methylation and noncoding RNA in cancer

N6-methyladenosine (m6A) methylation, one of the most common RNA modifications, has been reported to execute important functions that affect normal life activities and diseases. Most studies have suggested that m6A modification can affect the complexity of cancer progression by regulating biological functions related to cancer. M6A modification of noncoding RNAs regulates the cleavage, transport, stability, and degradation of noncoding RNAs themselves. It also regulates cell proliferation and metastasis, stem cell differentiation, and homeostasis in cancer by affecting the biological function of cells. Interestingly, noncoding RNAs also play significant roles in regulating these m6A modifications. Additionally, it is becoming increasingly clear that m6A and noncoding RNAs potentially contribute to the clinical application of cancer treatment. In this review, we summarize the effect of the interactions between m6A modifications and noncoding RNAs on the biological functions involved in cancer progression. In particular, we discuss the role of m6A and noncoding RNAs as possible potential biomarkers and therapeutic targets in the treatment of cancers.

Biochemical changes among municipal solid waste sorting workers: implications for personal protective equipment availability and use

Background. Solid waste management has emerged as one of the greatest challenges facing human and environmental health. Municipal solid waste workers are potentially exposed to a variety of occupational biohazards and safety risks in the workplace. Objective. This study aimed to evaluate the availability and use of personal protective equipment (PPE) and some biochemical changes among solid waste sorting workers. Methods. A group of solid waste sorting workers was interviewed and checked for availability, use and appropriateness of PPE using a structured questionnaire and checklist. Workers were tested for hepatic and renal function parameters and biomarkers of allergy and inflammation. Results. The level of high-sensitivity C-reactive protein (hsCRP) as a biomarker of inflammation was elevated in 12.9% while total serum immunoglobulin E was obviously high among most workers (79.2%). Workers with inadequately available, used or effective PPE were more likely to have morbidities and showed elevated serum levels of serum glutamic pyruvic transaminase, serum glutamic-oxaloacetic transaminase, urea, creatinine, hsCRP and total immunoglobulin E. Conclusions. Elevated biomarkers of allergy and inflammation herald preclinical disease risks that should be included in basic health surveillance. Use of PPE should be emphasized for workers involved in solid waste sorting to effectively protect their health.

Seizure Action Plans for Pediatric Patients With Epilepsy: A Randomized Controlled Trial

OBJECTIVES

Seizure action plans help patients and caregivers better self-manage their epilepsy. We hypothesized that providing pediatric patients and their caregivers with a seizure action plan would reduce unplanned health care utilization and decrease the impact of epilepsy.

METHODS

We developed a seizure action plan for use in pediatric epilepsy patients. A prospective cohort was randomly assigned to receive a seizure action plan in addition to standard epilepsy care or to standard epilepsy care alone. All caregivers were surveyed using the Modified Impact on Families (MIF) questionnaire at enrollment, 3 months, and 12 months. Health care utilization measures and Modified Impact on Families questionnaire scores were compared between the 2 groups.

RESULTS

Fifty-four patients received a seizure action plan and standard care, whereas 48 received standard care alone. The groups had similar demographics. There was a significantly higher proportion of overall clinic appointment no shows in the standard care group vs the seizure action plan group (P = .04); however, other significant differences in health care utilization were not found. Among patients with low seizure frequency (12 or fewer seizures per year), Seizure comfort scores on the Modified Impact on Families questionnaire were significantly higher at 12 months among the seizure action plan group compared to the standard care group.

SIGNIFICANCE

Caregivers for patients with epilepsy receiving a seizure action plan were more comfortable regarding seizure care and missed fewer appointments. However, differences in health care utilization were not present. The seizure action plan appears to have more impact in patients who experience lower seizure frequencies. Further studies evaluating the impact as well as assessing caregivers' perceptions of the seizure action plan using a larger sample are needed.

Hepatitis C Virus Infection in the Dallas County Jail: Implications for Screening, Prevention, and Linkage to Care

OBJECTIVES

Screening for hepatitis C virus (HCV) infection in jail provides an opportunity to educate and offer care to a high-risk population. We aimed to (1) estimate the prevalence of HCV infection in jail; (2) describe the demographic characteristics, risk factors, and pre-incarceration health insurance status associated with HCV infection; and (3) examine the implementation of HCV screening in jail.

METHODS

We conducted a retrospective analysis of an opt-out HCV screening program with HCV RNA confirmation and patient education at the Dallas County Jail from April 1 through November 2, 2017. We extracted data on test results, demographic characteristics, and release destination from electronic medical records. A nurse navigator recorded data on patient self-reported risk factors and pre-incarceration health insurance status.

RESULTS

Of 4089 incarcerated persons screened, 708 (17.3%) had a positive HCV antibody result. Of these, 641 (90.5%) had an HCV RNA test ordered; 576 (89.9%) had RNA tests completed, of whom 413 (71.7%) had a positive HCV RNA result. Of these 413, 352 (85.2%) received patient education. Half of HCV RNA-positive incarcerated persons (n = 207, 50.1%) were born outside the birth cohort (1945-1965). Among those with HCV infection, commonly reported risk factors were injection drug use (168 of 352; 47.8%) and tattoos (82 of 352; 23.4%). Most incarcerated persons with HCV infection (284 of 350; 81.1%) did not have health insurance. HCV antibody prevalence was higher among incarcerated persons released to prison (232 of 961; 24.1%) than to outside agencies (38 of 403; 9.4%) or the community (178 of 1026; 17.4%).

CONCLUSIONS

Screening for HCV with RNA confirmation in jail provides an opportunity for disease education, transmission prevention, and navigation to HCV treatment. Future efforts should examine post-incarceration linkage to care.

Risk Factors Associated with Linkage to Care among Suburban Hepatitis C-Positive Baby Boomers and Injection Drug Users

INTRODUCTION

Suffolk County, located in Eastern Long Island, has been an epicenter for the opioid epidemic in New York State, yet no studies have examined hepatitis C virus (HCV) prevalence in this population. Additionally, few studies have assessed barriers for linkage to care (LTC) to HCV treatment in people who inject drugs (PWID), a high-risk HCV cohort. We aimed to determine prevalence of HCV infection in a suburban medical center and to assess risk factors associated with LTC in HCV-positive baby boomers and young PWID.

METHODS

A retrospective chart review was carried out on adult patients with ICD-9/10 diagnostic codes for HCV from January 2016 to December 2018 at Stony Brook Medicine. Data collected included sociodemographics, RNA serostatus, LTC, health insurance, employment, past medical or psychiatric history, and substance or injection drug use.

RESULTS

Overall, 27,049 individuals were screened for HCV and 1017 were HCV seropositive (3.8%), 437 (42.9%) were HCV RNA-positive and 153 (40.6%) achieved LTC. In multivariate analysis, living with cirrhosis was associated with a positive LTC. Medicaid or Medicare insurance was associated with a negative LTC. Intravenous drug users were more likely to be young and have concomitant polysubstance use and psychiatric disease. A bimodal distribution of HCV-positives is present in our population.

CONCLUSION

Those with liver cirrhosis are more likely to achieve LTC, as are those with private insurance. Public health efforts to promote awareness of HCV and to facilitate access to treatment among PWID are needed.

Retroviral-like determinants and functions required for dimerization of Ty1 retrotransposon RNA

During replication of long terminal repeat (LTR)-retrotransposons, their proteins and genome (g) RNA assemble into virus-like particles (VLPs) that are not infectious but functionally related to retroviral virions. Both virions and VLPs contain gRNA in a dimeric form, but contrary to retroviruses, little is known about how gRNA dimerization and packaging occurs in LTR-retrotransposons. The LTR-retrotransposon Ty1 from Saccharomyces cerevisiae is an informative model for studying LTR-retrotransposon and retrovirus replication. Using structural, mutational and functional analyses, we explored dimerization of Ty1 genomic RNA. We provide direct evidence that interactions of self-complementary PAL1 and PAL2 palindromic sequences localized within the 5′UTR are essential for Ty1 gRNA dimer formation. Mutations disrupting PAL1-PAL2 complementarity restricted RNA dimerization in vitro and Ty1 mobility in vivo. Although dimer formation and mobility of these mutants was inhibited, our work suggests that Ty1 RNA can dimerize via alternative contact points. In contrast to previous studies, we cannot confirm a role for PAL3, tRNA_i^Met as well as recently proposed initial kissing-loop interactions in dimer formation. Our data also supports the critical role of Ty1 Gag in RNA dimerization. Mature Ty1 Gag binds in the proximity of sequences involved in RNA dimerization and tRNA_i^Met annealing, but the 5′ pseudoknot in Ty1 RNA may constitute a preferred Gag-binding site. Taken together, these results expand our understanding of genome dimerization and packaging strategies utilized by LTR-retroelements.

HCV-infected individuals have higher prevalence of comorbidity and multimorbidity: a retrospective cohort study

Background

Almost 1% of Canadians are hepatitis C (HCV)-infected. The liver-specific complications of HCV are established but the extra-hepatic comorbidity, multimorbidity, and its relationship with HCV treatment, is less well known. We describe the morbidity burden for people with HCV and the relationship between multimorbidity and HCV treatment uptake and cure in the pre- and post-direct acting antiviral (DAA) era.

Methods

We linked adults with HCV at The Ottawa Hospital Viral Hepatitis Program as of April 1, 2017 to provincial health administrative data and matched on age and sex to 5 Ottawa-area residents for comparison. We used validated algorithms to identify the prevalence of mental and physical health comorbidities, as well as multimorbidity (2+ comorbidities). We calculated direct age- and sex-standardized rates of comorbidity and comparisons were made by interferon-based and interferon-free, DAA HCV treatments.

Results

The mean age of the study population was 54.5 years (SD 11.4), 65% were male. Among those with HCV, 4% were HIV co-infected, 26% had liver cirrhosis, 47% received DAA treatment, and 57% were cured of HCV. After accounting for age and sex differences, the HCV group had greater multimorbidity (prevalence ratio (PR) 1.38, 95% confidence interval (CI) 1.20 to 1.58) and physical-mental health multimorbidity (PR 2.71, 95% CI 2.29–3.20) compared to the general population. Specifically, prevalence ratios for people with HCV were significantly higher for diabetes, renal failure, cancer, asthma, chronic obstructive pulmonary disease, substance use disorder, mood and anxiety disorders and liver failure. HCV treatment and cure were not associated with multimorbidity, but treatment prevalence was significantly lower among middle-aged individuals with substance use disorders despite no differences in prevalence of cure among those treated.

Conclusion

People with HCV have a higher prevalence of comorbidity and multimorbidity compared to the general population. While HCV treatment was not associated with multimorbidity, people with substance use disorder were less likely to be treated. Our results point to the need for integrated, comprehensive models of care delivery for people with HCV.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-4315-6) contains supplementary material, which is available to authorized users.

Expression of IL-34 correlates with macrophage infiltration and prognosis of diffuse large B-cell lymphoma

Objectives

Infiltration of macrophages through the tyrosine kinase receptor CSF1R is a poor prognosis factor in various solid tumors. Indeed, these tumors produce CSF1R ligand, macrophage colony‐stimulating factor (M‐CSF) or interleukin‐34 (IL‐34). However, the significance of these cytokines, particularly, the newly discovered IL‐34 in haematological malignancies, is not fully understood. We therefore analysed the role of IL‐34 in diffuse large B‐cell lymphoma (DLBCL), the most common subtype of malignant lymphoma.

Methods

We analysed formalin‐fixed paraffin‐embedded lymphoma tissues of 135 DLBCL patients for the expression of IL‐34 and the number of macrophages, and the survival of these patients. The expression of IL‐34 in DLBCL cell lines and the activity of IL‐34 to induce the migration of monocytic cells were also characterised.

Results

Several lymphoma tissues showed a clear IL‐34 signal, and such signal was detectable in 36% of patients. DLBCL cell lines also expressed IL‐34. Interestingly, the percentage of IL‐34⁺ patients in the activated B‐cell subtype was significantly higher than that in the germinal centre B‐cell subtype. More interestingly, IL‐34⁺ patients showed shorter survival periods and higher number of macrophages in lymphoma tissues. The recruitment of monocytes is likely the first step for the higher macrophage density in the IL‐34⁺ lymphoma tissues. Indeed, IL‐34 induced the migration of monocytic cells.

Conclusion

Our results raise the possibility that IL‐34 in lymphoma tissues of DLBCL patients recruits monocytes, leading to the higher number of macrophages in the tissues and poor prognosis of patients. IL‐34 may be an additional therapeutic target of DLBCL.

Modulation of the HIV nucleocapsid dynamics finely tunes its RNA-binding properties during virion genesis

During HIV-1 assembly and budding, Gag protein, in particular the C-terminal domain containing the nucleocapsid domain (NCd), p1 and p6, is the site of numerous interactions with viral and cellular factors. Most in vitro studies of Gag have used constructs lacking p1 and p6. Here, using NMR spectroscopy, we show that the p1-p6 region of Gag (NCp15) is largely disordered, but interacts transiently with the NCd. These interactions modify the dynamic properties of the NCd. Indeed, using isothermal titration calorimetry (ITC), we have measured a higher entropic penalty to RNA-binding for the NCd precursor, NCp15, than for the mature form, NCp7, which lacks p1 and p6. We propose that during assembly and budding of virions, concomitant with Gag oligomerization, transient interactions between NCd and p1-p6 become salient and responsible for (i) a higher level of structuration of p6, which favours recruitment of budding partners; and (ii) a higher entropic penalty to RNA-binding at specific sites that favours non-specific binding of NCd at multiple sites on the genomic RNA (gRNA). The contributions of p6 and p1 are sequentially removed via proteolysis during Gag maturation such that the RNA-binding specificity of the mature protein is governed by the properties of NCd.

Geospatial epidemiology of hepatitis C infection in Egypt 2017 by governorate

BACKGROUND

Geographic Information Systems (GIS) and spatial epidemiological methods may provide a basis for disease investigation through which hotspots and disease determinants can be identified. Applying these methods for hepatitis C virus (HCV) in Egypt would support a more effective strategy to control its transmission. Therefore, this study used GIS software to draw one of the first HCV maps in Egypt elucidating and analyzing geographical and epidemiological differences in HCV distribution within the country.

METHODS

A cross-sectional survey of 21 governorates (n = 12169, 8080 rural, 3733 urban and 356 slums areas) was completed. All participants were interviewed regarding potential exposures to HCV. Third generation ELISA was used to test serum for HCV antibody. Quantitative real-time RT-PCR was used to test anti-HCV positive subjects for HCV-RNA.

RESULTS

The participants ranged in age from 14-90 years. Overall, anti-HCV sero-prevalence was 14.8%. The prevalence of HCV-RNA, was 9.5%. Proportionally, 65.8% of anti-HCV positives were positive for HCV-RNA. The map of Egyptian governorates highlighted the darkest spot of HCV infection in Menoufeya (37.8%) followed by Beni Suef (29.2%) and Minya (28.6%). Anti-HCV prevalence was higher among males and logistic regression models revealed a strong independent association with increasing age, rural residence and parenteral anti-schistosomal therapy.

CONCLUSIONS

Rural residences and HCV hotspots should be prioritized for HCV prevention programs. The unique age distribution first shown in this study shows that the older age groups (≥60 years old) constitutes a considerable reservoir of infection and must not be neglected.

Purification and Functional Characterization of a Biologically Active Full-Length Feline Immunodeficiency Virus (FIV) Pr50Gag

The feline immunodeficiency virus (FIV) full-length Pr50^Gag precursor is a key player in the assembly of new viral particles. It is also a critical component of the efficient selection and packaging of two copies of genomic RNA (gRNA) into the newly formed virus particles from a wide pool of cellular and spliced viral RNA. To understand the molecular mechanisms involved during FIV gRNA packaging, we expressed the His₆-tagged and untagged recombinant FIV Pr50^Gag protein both in eukaryotic and prokaryotic cells. The recombinant Pr50^Gag-His₆-tag fusion protein was purified from soluble fractions of prokaryotic cultures using immobilized metal affinity chromatography (IMAC). This purified protein was able to assemble in vitro into virus-like particles (VLPs), indicating that it preserved its ability to oligomerize/multimerize. Furthermore, VLPs formed in eukaryotic cells by the FIV full-length Pr50^Gag both in the presence and absence of His₆-tag could package FIV sub-genomic RNA to similar levels, suggesting that the biological activity of the recombinant full-length Pr50^Gag fusion protein was retained in the presence of His₆-tag at the carboxy terminus. Successful expression and purification of a biologically active, recombinant full-length Pr50^Gag-His₆-tag fusion protein will allow study of the intricate RNA-protein interactions involved during FIV gRNA encapsidation.

Increased SLAMF7high monocytes in myelofibrosis patients harboring JAK2V617F provide a therapeutic target of elotuzumab

Monocyte-derived fibrocytes recently garnered attention because the novel pathogenesis of myelofibrosis (MF), and suppression of fibrocyte differentiation by serum amyloid P remarkably improved MF. We previously revealed that human fibrocytes highly expressed signaling lymphocytic activation molecule F7 (SLAMF7) compared with macrophages and that SLAMF7^high monocytes in the peripheral blood (PB) of MF patients were significantly elevated relative to those in healthy controls (HCs). In this study, we evaluated SLAMF7^high monocyte percentage in the PB of HCs, myeloproliferative neoplasm (MPN) patients with MF, and MPN patients without MF by using a cross-sectional approach. We found that MPN patients with MF who harbored JAK2V617F had a significantly elevated SLAMF7^high monocyte percentage, which correlated positively with the JAK2V617F allele burden. In addition, the serum concentration of interleukin-1ra (IL-1ra) was significantly correlated with the SLAMF7^high monocyte percentage and JAK2V617F allele burden. These findings suggest that both SLAMF7^high monocytes and IL-1ra could be useful noninvasive markers of MF onset. Furthermore, the JAK2V617F allele burden of SLAMF7^high monocytes was significantly higher than that of SLAMF7^low monocytes and could be a potential target of elotuzumab (Elo), an anti-SLAMF7 antibody used for treating multiple myeloma. Elo independently inhibited differentiation of fibrocytes derived not only from HCs but also from MF patients in vitro. Elo also ameliorated MF and splenomegaly induced by romiplostim administration in humanized NOG mice. In conclusion, an increase of SLAMF7^high monocytes with higher JAK2V617F allele burden was associated with the onset of MF in MPN patients harboring JAK2V617F, and Elo could be a therapeutic agent for MPN patients with MF who harbor JAK2V617F.

Packaging of Genomic RNA in Positive-Sense Single-Stranded RNA Viruses: A Complex Story

The packaging of genomic RNA in positive-sense single-stranded RNA viruses is a key part of the viral infectious cycle, yet this step is not fully understood. Unlike double-stranded DNA and RNA viruses, this process is coupled with nucleocapsid assembly. The specificity of RNA packaging depends on multiple factors: (i) one or more packaging signals, (ii) RNA replication, (iii) translation, (iv) viral factories, and (v) the physical properties of the RNA. The relative contribution of each of these factors to packaging specificity is different for every virus. In vitro and in vivo data show that there are different packaging mechanisms that control selective packaging of the genomic RNA during nucleocapsid assembly. The goals of this article are to explain some of the key experiments that support the contribution of these factors to packaging selectivity and to draw a general scenario that could help us move towards a better understanding of this step of the viral infectious cycle.

Structural Explorations of NCp7-Nucleic Acid Complexes Give Keys to Decipher the Binding Process

A comprehensive view of all the structural aspects related to NCp7 is essential to understand how this protein, crucial in many steps of the HIV-1 cycle, binds and anneals nucleic acids (NAs), mainly thanks to two zinc fingers, ZF1 and ZF2. Here, we inspected the structural properties of the available experimental models of NCp7 bound to either DNA or RNA molecules, or free of ligand. Our analyses included the characterization of the relative positioning of ZF1 and ZF2, accessibility measurements and the exhaustive, quantitative mapping of the contacts between amino acids and nucleotides by a recent tessellation method, VLDM. This approach unveiled the intimate connection between NA binding process and the conformations explored by the free protein. It also provided new insights into the functional specializations of ZF1 and ZF2. The larger accessibility of ZF2 in free NCp7 and the consistency of the ZF2/NA interface in different models and conditions give ZF2 the lead of the binding process. ZF1 contributes to stabilize the complexes through various organizations of the ZF1/NA interface. This work outcome is a global binding scheme of NCp7 to DNA and RNA, and an example of how protein-NA complexes are stabilized.

Clinical features and outcomes of patients with fever of unknown origin: a retrospective study

BACKGROUND

Few studies have reported the long-term clinical outcome of patients discharged with undiagnosed fever of unknown origin (FUO). In this study, the clinical features and outcomes of patients with unexplained fever were explored to improve our understanding of FUO.

METHOD

Patients diagnosed with FUO at admission and discharged without final diagnoses after systematic examination in the department of infectious diseases at Peking Union Medical College Hospital between 2004 and 2010 were followed up by telephone. Medical records were reviewed, and the clinical features and outcomes of patients for whom follow-up data were available were summarized.

RESULTS

Between 2004 and 2010, 58 patients with follow-up data, who were diagnosed with FUO at admission and did not have a final diagnosis at discharge, were enrolled in this study. The median duration of follow-up was 518 (0.4-830) weeks, and the fever duration was 24.6 (6.7-763.2) weeks. Final diagnoses were established in 11 cases (19%), and the diagnostic methods included clinical diagnosis, diagnostic therapy, genetic screening and biopsy pathology. The fever in 35 patients (60%) subsided during hospitalization or after discharge. Their condition was stable and self-limited after long-term follow-up, and they were ultimately thought to be cured. Two patients had periodic fever during prolonged observation: one patient needed intermittent use of nonsteroidal antiinflammatory drugs (NSAIDs), and the other needed intermittent use of NSAIDs and a steroid. Ten patients died during follow-up, with 9 deaths being caused by severe and worsening conditions related to the febrile illness.

CONCLUSIONS

Long-term follow-up should be performed for patients with undiagnosed FUO. Some patients can obtain a definitive diagnosis by repeated multiple invasive examinations and diagnostic treatment. Most patients have a self-limited illness, and their prognosis is good.

Stabilizing role of structural elements within the 5´ Untranslated Region (UTR) and gag sequences in Mason-Pfizer monkey virus (MPMV) genomic RNA packaging

The Mason-Pfizer monkey virus (MPMV) genomic RNA (gRNA) packaging signal is a highly-structured element with several stem-loops held together by two phylogenetically conserved long-range interactions (LRIs) between U5 and gag complementary sequences. These LRIs play a critical role in maintaining the structure of the 5´ end of the MPMV gRNA. Thus, one could hypothesize that the overall RNA secondary structure of this region is further architecturally held together by three other stem loops (SL3, Gag SL1, and Gag SL2) comprising of sequences from the distal parts of the 5´untranslated region (5' UTR) to ~ 120 nucleotides into gag, excluding gag sequences involved in forming the U5-Gag LRIs. To provide functional evidence for the biological significance of these stem loops during gRNA encapsidation, these structural motifs were mutated and their effects on MPMV RNA packaging and propagation were tested in a single round trans-complementation assay. The mutant RNA structures were further studied by high throughput SHAPE (hSHAPE) assay. Our results reveal that sequences involved in forming these three stem loops do not play crucial roles at an individual level during MPMV gRNA packaging or propagation. Further structure-function analysis indicates that the U5-Gag LRIs have a more important architectural role in stabilizing the higher order structure of the 5´ UTR than the three stem loops which have a more secondary and perhaps indirect role in stabilizing the overall RNA secondary structure of the region. Our work provides a better understanding of the molecular interactions that take place during MPMV gRNA packaging.

Annealing of ssDNA and compaction of dsDNA by the HIV-1 nucleocapsid and Gag proteins visualized using nanofluidic channels

The nucleocapsid protein NC is a crucial component in the human immunodeficiency virus type 1 life cycle. It functions both in its processed mature form and as part of the polyprotein Gag that plays a key role in the formation of new viruses. NC can protect nucleic acids (NAs) from degradation by compacting them to a dense coil. Moreover, through its NA chaperone activity, NC can also promote the most stable conformation of NAs. Here, we explore the balance between these activities for NC and Gag by confining DNA–protein complexes in nanochannels. The chaperone activity is visualized as concatemerization and circularization of long DNA via annealing of short single-stranded DNA overhangs. The first ten amino acids of NC are important for the chaperone activity that is almost completely absent for Gag. Gag condenses DNA more efficiently than mature NC, suggesting that additional residues of Gag are involved. Importantly, this is the first single DNA molecule study of full-length Gag and we reveal important differences to the truncated Δ-p6 Gag that has been used before. In addition, the study also highlights how nanochannels can be used to study reactions on ends of long single DNA molecules, which is not trivial with competing single DNA molecule techniques.

Fib-4 Predicts Early Hematological Adverse Events Induced by Interferon-Based Triple Therapy in Chronic Hepatitis C Virus Patients

Interferon-alpha (IFN-α)-based therapy is associated with several hematological adverse events in hepatitis C virus (HCV)-infected patients with advanced fibrosis. We performed this study to evaluate the association between Fibrosis-4 (Fib-4) index and hematological adverse events in patients with chronic HCV infection, undergoing IFN-α-based triple therapy. We included 120 HCV-infected patients, receiving triple therapy: weekly PegIFN-α, daily ribavirin (1,000-1,200 mg), and daily sofosbuvir (400 mg) for 12 weeks. We compared Fib-4 scores for patients who developed hematological adverse events at weeks 4 (w4) and w12 of treatment and w12 post-treatment versus those who did not. Treatment with the aforementioned triple regimen was associated with a sustained virological response (SVR)-12 rate of 93.9%. We found no significant associations (P > 0.05) between SVR12 rate and the degree of fibrosis or the risk of hematological adverse events. The Fib-4 score could predict patients who developed hematological adverse events (anemia, leukopenia, and neutropenia) in the first month of treatment, but not in later stages. A Fib-4 cutoff value of 3.59 had high specificity for anemia, leukopenia, and neutropenia (85.1%, 87.2%, and 88.2%, respectively), but had low sensitivity for detecting the 3 events. In conclusion, the Fib-4 score may predict early hematological adverse effects in HCV-infected patients on IFN-based triple therapy.

Insulin resistance does not impair response of chronic hepatitis C virus to direct-acting antivirals, and improves with the treatment

BACKGROUND

Insulin resistance (IR) is a common complication in chronic hepatitis C virus (HCV) patients. The impact of IR on outcome of therapy with direct antivirals has not been studied.

AIM

The aim was to assess the impact of direct-acting antiviral (DAA) therapy on IR status in chronic HCV patients.

PATIENTS AND METHODS

A total of 511 patients [mean age: 50.7±10.4 years, 29.7% pegylated interferon and ribavirin (RBV) experienced] were enrolled. Patients with uncontrolled diabetes, decompensated liver disease, or previous nonresponse to DAAs were excluded. Homeostatic model assessment (HOMA) was calculated before and 12 weeks after treatment, and IR was defined as HOMA greater than 1.9. Patients were treated according to the treating physician's choice, and received 12 weeks of either ombitasvir/ritonavir/paritaprevir/RBV (n=28); sofosbuvir (SOF)/simeprevir (n=36); SOF/ravidasvir (n=101); SOF/pegylated interferon/RBV (n=192); or 24 weeks of SOF/RBV (n=154).

RESULTS

Most patients received IR pretreatment (80.6%); 51.3% had fibrosis stage F4 and 24.7% had diabetes. A sustained virological response (SVR) at 12 weeks after treatment (SVR12) was achieved in 465 (91%) patients. SVR12 was achieved in 90.5% of patients with IR and in 92.9% of patients without IR (P=0.560), and pretreatment HOMA was not different in responders and nonresponders (P=0.098). The number of patients with IR decreased significantly in patients who achieved an SVR much more than in nonresponders (P<0.0001) and HOMA improved significantly more in patients with SVR than in nonresponders (P=0.001). All treatment protocols were associated with a comparable improvement in HOMA (P=0.101). Predictors of SVR12 included age, platelets, and liver stiffness, but not pretreatment IR.

CONCLUSION

IR does not impair the response of patients with HCV treated with DAAs, and improves significantly in patients who achieve an SVR.

Apolipoprotein E is an HIV-1-inducible inhibitor of viral production and infectivity in macrophages

Apolipoprotein E (ApoE) belongs to a class of cellular proteins involved in lipid metabolism. ApoE is a polymorphic protein produced primarily in macrophages and astrocytes. Different isoforms of ApoE have been associated with susceptibility to various diseases including Alzheimer's and cardiovascular diseases. ApoE expression has also been found to affect susceptibility to several viral diseases, including Hepatitis C and E, but its effect on the life cycle of HIV-1 remains obscure. In this study, we initially found that HIV-1 infection selectively up-regulated ApoE in human monocyte-derived macrophages (MDMs). Interestingly, ApoE knockdown in MDMs enhanced the production and infectivity of HIV-1, and was associated with increased localization of viral envelope (Env) proteins to the cell surface. Consistent with this, ApoE over-expression in 293T cells suppressed Env expression and viral infectivity, which was also observed with HIV-2 Env, but not with VSV-G Env. Mechanistic studies revealed that the C-terminal region of ApoE was required for its inhibitory effect on HIV-1 Env expression. Moreover, we found that ApoE and Env co-localized in the cells, and ApoE associated with gp160, the precursor form of Env, and that the suppression of Env expression by ApoE was cancelled by the treatment with lysosomal inhibitors. Overall, our study revealed that ApoE is an HIV-1-inducible inhibitor of viral production and infectivity in macrophages that exerts its anti-HIV-1 activity through association with gp160 Env via the C-terminal region, which results in subsequent degradation of gp160 Env in the lysosomes.

Cost-effectiveness of EGCRISC application versus hepatitis C virus mass screening in Egypt

BACKGROUND

The Egyptian model of care against hepatitis C virus (HCV) has a great success in treatment and treatment accessibility, but still screening efforts must be strengthened. HCV is a silent infection when most of infected people are unaware of their infection. EGCRISC is a newly developed and validated risk-based HCV screening tool in Egypt that has shown a considerably good performance but is still underused. This brief communication is to analyze its use cost-effectiveness versus mass screening.

STUDY DESIGN

Mathematical comparative analysis for economic evaluation.

METHODS

Its performance data as published recently were used, and a minimum cost of L.E. 20 was considered per one antibody testing. The 2015 health issue survey and population census were used for estimating the population, infected individuals and susceptibles.

RESULTS

The analysis showed that using EGCRISC would save LE 0.43 billion accounting for about 21,646,227 unnecessary tests, while missing less than 70,000 cases when compared to mass screening.

CONCLUSION

EGCRISC is a cost-effective tool that must be adopted nationwide as soon as possible in Egypt for the best outcome of HCV control.

N6-Methyladenosine-binding proteins suppress HIV-1 infectivity and viral production

The internal N6-methyladenosine (m6A) modification of cellular mRNA regulates post-transcriptional gene expression. The YTH domain family proteins (YTHDF1-3 or Y1-3) bind to m6A-modified cellular mRNAs and modulate their metabolism and processing, thereby affecting cellular protein translation. We previously reported that HIV-1 RNA contains the m6A modification and that Y1-3 proteins inhibit HIV-1 infection by decreasing HIV-1 reverse transcription activity. Here, we investigated the mechanisms of Y1-3-mediated inhibition of HIV-1 infection in target cells and the effect of Y1-3 on viral production levels in virus-producing cells. We found that Y1-3 protein overexpression in HIV-1 target cells decreases viral genomic RNA (gRNA) levels and inhibits both early and late reverse transcription. Purified recombinant Y1-3 proteins preferentially bound to the m6A-modified 5' leader sequence of gRNA compared with its unmodified RNA counterpart, consistent with the strong binding of Y1-3 proteins to HIV-1 gRNA in infected cells. HIV-1 mutants with two altered m6A modification sites in the 5' leader sequence of gRNA exhibited significantly lower infectivity than WT, replication-competent HIV-1, confirming that these sites alter viral infection. HIV-1 produced from cells in which endogenous Y1, Y3, or Y1-3 proteins were knocked down singly or together had increased viral infectivity compared with HIV-1 produced in control cells. Interestingly, we found that Y1-3 proteins and HIV-1 Gag protein formed a complex with RNA in HIV-1-producing cells. Overall, these results indicate that Y1-3 proteins inhibit HIV-1 infection and provide new insights into the mechanisms by which the m6A modification of HIV-1 RNA affects viral replication.

Expression, purification, and characterization of biologically active full-length Mason-Pfizer monkey virus (MPMV) Pr78Gag

MPMV precursor polypeptide Pr78^Gag orchestrates assembly and packaging of genomic RNA (gRNA) into virus particles. Therefore, we have expressed recombinant full-length Pr78^Gag either with or without His₆-tag in bacterial as well as eukaryotic cultures and purified the recombinant protein from soluble fractions of the bacterial cultures. The recombinant Pr78^Gag protein has the intrinsic ability to assemble in vitro to form virus like particles (VLPs). Consistent with this observation, the recombinant protein could form VLPs in both prokaryotes and eukaryotes. VLPs formed in eukaryotic cells by recombinant Pr78^Gag with or without His₆-tag can encapsidate MPMV transfer vector RNA, suggesting that the inclusion of the His₆-tag to the full-length Pr78^Gag did not interfere with its expression or biological function. This study demonstrates the expression and purification of a biologically active, recombinant Pr78^Gag, which should pave the way to study RNA-protein interactions involved in the MPMV gRNA packaging process.

The C-terminal p6 domain of the HIV-1 Pr55Gag precursor is required for specific binding to the genomic RNA

The Pr55^Gag precursor specifically selects the HIV-1 genomic RNA (gRNA) from a large excess of cellular and partially or fully spliced viral RNAs and drives the virus assembly at the plasma membrane. During these processes, the NC domain of Pr55^Gag interacts with the gRNA, while its C-terminal p6 domain binds cellular and viral factors and orchestrates viral particle release. Gag∆p6 is a truncated form of Pr55^Gag lacking the p6 domain usually used as a default surrogate for wild type Pr55^Gag for in vitro analysis. With recent advance in production of full-length recombinant Pr55^Gag, here, we tested whether the p6 domain also contributes to the RNA binding specificity of Pr55^Gag by systematically comparing binding of Pr55^Gag and Gag∆p6 to a panel of viral and cellular RNAs. Unexpectedly, our fluorescence data reveal that the p6 domain is absolutely required for specific binding of Pr55^Gag to the HIV-1 gRNA. Its deletion resulted not only in a decreased affinity for gRNA, but also in an increased affinity for spliced viral and cellular RNAs. In contrast Gag∆p6 displayed a similar affinity for all tested RNAs. Removal of the C-terminal His-tag from Pr55^Gag and Gag∆p6 uniformly increased the Kd values of the RNA-protein complexes by ~ 2.5 fold but did not affect the binding specificities of these proteins. Altogether, our results demonstrate a novel role of the p6 domain in the specificity of Pr55^Gag-RNA interactions, and strongly suggest that the p6 domain contributes to the discrimination of HIV-1 gRNA from cellular and spliced viral mRNAs, which is necessary for its selective encapsidation.

Efficient support of virus-like particle assembly by the HIV-1 packaging signal

The principal structural component of a retrovirus particle is the Gag protein. Retroviral genomic RNAs contain a 'packaging signal' ('Ψ') and are packaged in virus particles with very high selectivity. However, if no genomic RNA is present, Gag assembles into particles containing cellular mRNA molecules. The mechanism by which genomic RNA is normally selected during virus assembly is not understood. We previously reported (<xref ref-type="bibr" rid="bib9">Comas-Garcia et al., 2017</xref>) that at physiological ionic strength, recombinant HIV-1 Gag binds with similar affinities to RNAs with or without Ψ, and proposed that genomic RNA is selectively packaged because binding to Ψ initiates particle assembly more efficiently than other RNAs. We now present data directly supporting this hypothesis. We also show that one or more short stretches of unpaired G residues are important elements of Ψ; Ψ may not be localized to a single structural element, but is probably distributed over >100 bases.

Global epidemiology of viral hepatitis and national needs for complete control

INTRODUCTION

The World Health Organization recognizes that viral hepatitis is not only a massive public health issue but also a huge opportunity to improve quality of life and equity at a global level. Viral hepatitis causes about 1.5 million deaths each year and significantly affects the quality of life of hundreds of millions of people. To date, frail individuals in high-income countries and people living in low-income settings are paying the heaviest tool. Areas covered. Here we present a broad discussion on current knowledge and topical issues about the hepatitis pandemic. The report includes a structured overview of global epidemiology, including the definition of specific local epidemic profiles for each hepatitis agents (HAV, HBV, HCV, and HEV), and a perspective about the critical actions needed for achieving a complete control. Expert commentary. The control of viral hepatitis is currently, ethically urgent and even economically convenient. There is a wide consensus that viral hepatitis can be controlled through comprehensive intervention tailored on local needs addressing the issue of viral hepatitis as a unique public health issue. These strategies should include: (1) primary prevention (including vaccination and improved infection control), (2) improving diagnosis rate, and (3) management of existing cases of infections.

Multiple, Switchable Protein:RNA Interactions Regulate Human Immunodeficiency Virus Type 1 Assembly

Human immunodeficiency virus type 1 (HIV-1) particle assembly requires several protein:RNA interactions that vary widely in their character, from specific recognition of highly conserved and structured viral RNA elements to less specific interactions with variable RNA sequences. Genetic, biochemical, biophysical, and structural studies have illuminated how virion morphogenesis is accompanied by dramatic changes in the interactions among the protein and RNA virion components. The 5' leader RNA element drives RNA recognition by Gag upon initiation of HIV-1 assembly and can assume variable conformations that influence translation, dimerization, and Gag recognition. As Gag multimerizes on the plasma membrane, forming immature particles, its RNA binding specificity transiently changes, enabling recognition of the A-rich composition of the viral genome. Initiation of assembly may also be regulated by occlusion of the membrane binding surface of Gag by tRNA. Finally, recent work has suggested that RNA interactions with viral enzymes may activate and ensure the accuracy of virion maturation.

Systematic overview of hepatitis C infection in the Middle East and North Africa

AIM

To assess the quality of and to critically synthesize the available data on hepatitis C infections in the Middle East and North Africa (MENA) region to map evidence gaps.

METHODS

We conducted an overview of systematic reviews (SRs) following an a priori developed protocol (CRD42017076736). Our overview followed the preferred reporting items for systematic reviews and meta-analyses guidelines for reporting SRs and abstracts and did not receive any funding. Two independent reviewers systematically searched MEDLINE and conducted a multistage screening of the identified articles. Out of 5758 identified articles, 37 SRs of hepatitis C virus (HCV) infection in populations living in 20 countries in the MENA region published between 2008 and 2016 were included in our overview. The nine primary outcomes of interest were HCV antibody (anti-) prevalences and incidences in different at-risk populations; the HCV viremic (RNA positive) rate in HCV-positive individuals; HCV viremic prevalence in the general population (GP); the prevalence of HCV co-infection with the hepatitis B virus, human immunodeficiency virus, or schistosomiasis; the HCV genotype/subtype distribution; and the risk factors for HCV transmission. The conflicts of interest declared by the authors of the SRs were also extracted. Good quality outcomes reported by the SRs were defined as having the population, outcome, study time and setting defined as recommended by the PICOTS framework and a sample size > 100.

RESULTS

We included SRs reporting HCV outcomes with different levels of quality and precision. A substantial proportion of them synthesized data from mixed populations at differing levels of risk for acquiring HCV or at different HCV infection stages (recent and prior HCV transmissions). They also synthesized the data over long periods of time (e.g., two decades). Anti-HCV prevalence in the GP varied widely in the MENA region from 0.1% (study dates not reported) in the United Arab Emirates to 2.1%-13.5% (2003-2006) in Pakistan and 14.7% (2008) in Egypt. Data were not identified for Bahrain, Jordan, or Palestine. Good quality estimates of anti-HCV prevalence in the GP were reported for Algeria, Djibouti, Egypt, Iraq, Morocco, Pakistan, Syria, Sudan, Tunisia, and Yemen. Anti-HCV incidence estimates in the GP were reported only for Egypt (0.8-6.8 per 1000 person-year, 1997-2003). In Egypt, Morocco, and the United Arab Emirates, viremic rates in anti-HCV-positive individuals from the GP were approximately 70%. In the GP, the viremic prevalence varied from 0.7% (2011) in Saudi Arabia to 5.8% (2007-2008) in Pakistan and 10.0% (2008) in Egypt. Anti-HCV prevalence was lower in blood donors than in the GP, ranging from 0.2% (1992-1993) in Algeria to 1.7% (2005) in Yemen. The reporting quality of the outcomes in blood donors was good in the MENA countries, except in Qatar where no time framework was reported for the outcome. Some countries had anti-HCV prevalence estimates for children, transfused patients, contacts of HCV-infected patients, prisoners, sex workers, and men who have sex with men.

CONCLUSION

A substantial proportion of the reported outcomes may not help policymakers to develop micro-elimination strategies with precise HCV infection prevention and treatment programs in the region, as nowcasting HCV epidemiology using these data is potentially difficult. In addition to providing accurate information on HCV epidemiology, outcomes should also demonstrate practical and clinical significance and relevance. Based on the available data, most countries in the region have low to moderate anti-HCV prevalence. To achieve HCV elimination by 2030, up-to-date, good quality data on HCV epidemiology are required for the GP and key populations such as people who inject drugs and men who have sex with men.

Addressing hepatitis C in the foreign-born population: A key to hepatitis C virus elimination in Canada

Hepatitis C virus (HCV) is the leading cause of death from infectious disease in Canada. Immigrants are an important group who are at increased risk for HCV; they account for a disproportionate number of all HCV cases in Canada (~30%) and have approximately a twofold higher prevalence of HCV (~2%) than those born in Canada. HCV-infected immigrants are more likely to develop cirrhosis and hepatocellular carcinoma and are more likely to have a liver-related death during a hospitalization than HCV-infected non-immigrants. Several factors, including lack of routine HCV screening programs in Canada for immigrants before or after arrival, lack of awareness on the part of health practitioners that immigrants are at increased risk of HCV and could benefit from screening, and several patient- and health system-level barriers that affect access to health care and treatment likely contribute to delayed diagnosis and treatment uptake. HCV screening and engagement in care among immigrants can be improved through reminders in electronic medical records that prompt practitioners to screen for HCV during clinical visits and implementation of decentralized community-based screening strategies that address cultural and language barriers. In conclusion, early screening and linkage to care for immigrants from countries with an intermediate or high prevalence of HCV would not only improve the health of this population but will be key to achieving HCV elimination in Canada. This article describes the unique barriers encountered by the foreign-born population in accessing HCV care and approaches to overcoming these barriers.

All-oral direct antiviral treatment for hepatitis C chronic infection in a real-life cohort: The role of cirrhosis and comorbidities in treatment response

BACKGROUND

Hepatitis C virus (HCV) infection is the major cause of end-stage liver disease (LD) worldwide. The aim of this study was to assess sustained virological response (SVR) rates in a real-world cohort of patients with HCV infection treated with interferon-free direct antiviral agents (DAA).

PATIENTS AND METHODS

All patients with genotypes 1, 2 or 3 HCV infection who started interferon-free treatment at a university hospital from December 2015 through July 2017 were included. The primary outcome was SVR at post-treatment week 12 by intention-to-treat (ITT) and modified ITT (mITT) analysis.

RESULTS

Five hundred twenty seven patients were enrolled, 51.6% with cirrhosis. Most patients received sofosbuvir + daclatasvir + ribavirin (60.7%) and sofosbuvir + simeprevir (25.6%). Overall SVR rates were 90.5% for ITT and 96% for mITT. SVR rates were higher in non-cirrhotic (94.2% in ITT and 96.8% in mITT) versus cirrhotic patients (87.1% in ITT and 95.2% in mITT). In ITT and mITT assessments, SVR rates were higher in patients with Child-Pugh A (n = 222, 88.7% and 95.7%, respectively) versus Child-Pugh B or C (n = 40, 80% and 90%, respectively); SVR rates were higher in patients with genotype 1 (n = 405, 92.1% and 98.2%), followed by genotype 2 (n = 13, 84.6% and 92.7%) and genotype 3 (n = 109, 84.4% and 88.4%). Lower comorbidity index (p = 0.0014) and absence of cirrhosis (p = 0.0071) were associated with SVR. Among cirrhotic patients, lower Model for End-Stage Liver Disease (p = 0.0258), higher albumin (p = 0.0015), and higher glomerular filtration rate (p = 0.0366) were related to SVR. Twenty-two cirrhotic patients (8%) had clinical liver decompensation during treatment. Complications of advanced LD were responsible for discontinuation of treatment and death in 12 and 7 patients, respectively.

CONCLUSION

Treatment with all-oral DAA achieved high SVR rates, particularly in patients without cirrhosis and few comorbidities. Advanced LD is associated to poor outcome, such as treatment failure and death.

Cupping therapy for treating ankylosing spondylitis: The evidence from systematic review and meta-analysis

OBJECTIVE

Cupping therapy has been widely used in Eastern Asia, the Middle East, or Central and North Europe to manage the symptom of ankylosing spondylitis (AS). The aim of this systematic review was to review data from randomized controlled trials (RCTs) of cupping therapy for treating patients with AS.

METHODS

Databases that were searched from their inception until December 2017 included: MEDLINE, CINAHL, EMBASE, AMED, Cochrane Central Register of Controlled Trials, four Chinese databases [Chinese BioMedical Database, China National Knowledge Infrastructure, Wan-Fang Data, and the Chinese WeiPu Database], KoreaMed, The Korean National Assembly Library, Japana Centra Revuo Medicina (http://www.jamas.gr.jp/) and CiNii. In this systematic review, only RCTs that were related to the effects of cupping therapy on managing AS were included. A quantitative synthesis of RCTs will be conducted using RevMan 5.3 software. Study selection, data extraction, and validation were performed independently by two reviewers. Quantitative analysis of RCTs were performed using RevMan 5.3 software, and cochrane criteria for risk-of-bias were used to assess the methodological quality of the trials.

RESULTS

A total of 5 RCTs met the inclusion criteria, and most were of low methodological quality. Participants in cupping therapy plus Western medicine group showed significantly greater improvements in the response rate [RR = 1.13, 95%CI (1.06, 1.22), p < 0.01] with low heterogeneity (Chi² = 2.88, p = 0.41, I² = 0%). Moreover, when compared with western medicine alone, meta-analysis indicated favorable statistically significant effects of cupping therapy plus western medicine on the Bath Ankylosing Spondylitis Functional Index (BASFI) [MD = -16.63, 95%CI (-17.75, -15.51), p < 0.01] and Bath Ankylosing Disease Activity Index (BASDAI) [MD = -9.93, 95%CI (-10.34, -9.52), p < 0.01], with low heterogeneity (Chi² = 0.32, p = 0.85, I² = 0% in BASFI; (Chi² = 2.46, p = 0.29, I² = 19% in BASDAI). Furthermore, when compared with western medicine alone, meta-analysis demonstrated statistically significant effects of cupping therapy plus western medicine on the serum level of ESR [MD = -1.28, 95% CI (-1.44, -1.13), p < 0.01] and the serum level of CRP [MD = -3.97, 95%CI (-4.71, -3.22), p < 0.01], with low heterogeneity (Chi² = 0.50, p = 0.78, I² = 0% in the serum level of ESR; Chi² = 0.19, p = 0.91, I² = 0% in the serum level of CRP).

CONCLUSION

Taken together, only weak evidence supported the hypothesis that cupping therapy had potential benefits for patients with AS.

The bifurcated stem loop 4 (SL4) is crucial for efficient packaging of mouse mammary tumor virus (MMTV) genomic RNA

Packaging the mouse mammary tumor virus (MMTV) genomic RNA (gRNA) requires the entire 5' untranslated region (UTR) in conjunction with the first 120 nucleotides of the gag gene. This region includes several palindromic (pal) sequence(s) and stable stem loops (SLs). Among these, stem loop 4 (SL4) adopts a bifurcated structure consisting of three stems, two apical loops, and an internal loop. Pal II, located in one of the apical loops, mediates gRNA dimerization, a process intricately linked to packaging. We thus hypothesized that the bifurcated SL4 structure could constitute the major gRNA packaging determinant. To test this hypothesis, the two apical loops and the flanking sequences forming the bifurcated SL4 were individually mutated. These mutations all had deleterious effects on gRNA packaging and propagation. Next, single and compensatory mutants were designed to destabilize then recreate the bifurcated SL4 structure. A structure-function analysis using bioinformatics predictions and RNA chemical probing revealed that mutations that led to the loss of the SL4 bifurcated structure abrogated RNA packaging and propagation, while compensatory mutations that recreated the native SL4 structure restored RNA packaging and propagation to wild type levels. Altogether, our results demonstrate that SL4 constitutes the principal packaging determinant of MMTV gRNA. Our findings further suggest that SL4 acts as a structural switch that can not only differentiate between RNA for translation versus packaging/dimerization, but its location also allows differentiation between spliced and unspliced RNAs during gRNA encapsidation.

Validation of discharge diagnosis codes to identify serious infections among middle age and older adults

OBJECTIVES

Hospitalisations for serious infections are common among middle age and older adults and frequently used as study outcomes. Yet, few studies have evaluated the performance of diagnosis codes to identify serious infections in this population. We sought to determine the positive predictive value (PPV) of diagnosis codes for identifying hospitalisations due to serious infections among middle age and older adults.

SETTING AND PARTICIPANTS

We identified hospitalisations for possible infection among adults >=50 years enrolled in the Tennessee Medicaid healthcare programme (2008-2012) using International Classifications of Diseases, Ninth Revision diagnosis codes for pneumonia, meningitis/encephalitis, bacteraemia/sepsis, cellulitis/soft-tissue infections, endocarditis, pyelonephritis and septic arthritis/osteomyelitis.

DESIGN

Medical records were systematically obtained from hospitals randomly selected from a stratified sampling framework based on geographical region and hospital discharge volume.

MEASURES

Two trained clinical reviewers used a standardised extraction form to abstract information from medical records. Predefined algorithms served as reference to adjudicate confirmed infection-specific hospitalisations. We calculated the PPV of diagnosis codes using confirmed hospitalisations as reference. Sensitivity analyses determined the robustness of the PPV to definitions that required radiological or microbiological confirmation. We also determined inter-rater reliability between reviewers.

RESULTS

The PPV of diagnosis codes for hospitalisations for infection (n=716) was 90.2% (95% CI 87.8% to 92.2%). The PPV was highest for pneumonia (96.5% (95% CI 93.9% to 98.0%)) and cellulitis (91.1% (95% CI 84.7% to 94.9%)), and lowest for meningitis/encephalitis (50.0% (95% CI 23.7% to 76.3%)). The adjudication reliability was excellent (92.7% agreement; first agreement coefficient: 0.91). The overall PPV was lower when requiring microbiological confirmation (45%) and when requiring radiological confirmation for pneumonia (79%).

CONCLUSIONS

Discharge diagnosis codes have a high PPV for identifying hospitalisations for common, serious infections among middle age and older adults. PPV estimates for rare infections were imprecise.

Biochemical and Functional Characterization of Mouse Mammary Tumor Virus Full-Length Pr77Gag Expressed in Prokaryotic and Eukaryotic Cells

The mouse mammary tumor virus (MMTV) Pr77^Gag polypeptide is an essential retroviral structural protein without which infectious viral particles cannot be formed. This process requires specific recognition and packaging of dimerized genomic RNA (gRNA) by Gag during virus assembly. Most of the previous work on retroviral assembly has used either the nucleocapsid portion of Gag, or other truncated Gag derivatives—not the natural substrate for virus assembly. In order to understand the molecular mechanism of MMTV gRNA packaging process, we expressed and purified full-length recombinant Pr77^Gag-His₆-tag fusion protein from soluble fractions of bacterial cultures. We show that the purified Pr77^Gag-His₆-tag protein retained the ability to assemble virus-like particles (VLPs) in vitro with morphologically similar immature intracellular particles. The recombinant proteins (with and without His₆-tag) could both be expressed in prokaryotic and eukaryotic cells and had the ability to form VLPs in vivo. Most importantly, the recombinant Pr77^Gag-His₆-tag fusion proteins capable of making VLPs in eukaryotic cells were competent for packaging sub-genomic MMTV RNAs. The successful expression and purification of a biologically active, full-length MMTV Pr77^Gag should lay down the foundation towards performing RNA–protein interaction(s), especially for structure-function studies and towards understanding molecular intricacies during MMTV gRNA packaging and assembly processes.

In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging

Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell MIME) as a way to define RNA regulatory landscapes at single nucleotide resolution under native conditions. In cell MIME is based on (i) random mutation of an RNA target, (ii) expression of mutated RNA in cells, (iii) physical separation of RNA into functional and non-functional populations, and (iv) high-throughput sequencing to identify mutations affecting function. We used in cell MIME to define RNA elements within the 5' region of the HIV-1 genomic RNA (gRNA) that are important for viral replication in cells. We identified three distinct RNA motifs controlling intracellular gRNA production, and two distinct motifs required for gRNA packaging into virions. Our analysis reveals the 73AAUAAA78 polyadenylation motif within the 5' PolyA domain as a dual regulator of gRNA production and gRNA packaging, and demonstrates that a functional polyadenylation signal is required for viral packaging even though it negatively affects gRNA production.

Retroviral Gag protein-RNA interactions: Implications for specific genomic RNA packaging and virion assembly

Retroviral Gag proteins are responsible for coordinating many aspects of virion assembly. Gag possesses two distinct nucleic acid binding domains, matrix (MA) and nucleocapsid (NC). One of the critical functions of Gag is to specifically recognize, bind, and package the retroviral genomic RNA (gRNA) into assembling virions. Gag interactions with cellular RNAs have also been shown to regulate aspects of assembly. Recent results have shed light on the role of MA and NC domain interactions with nucleic acids, and how they jointly function to ensure packaging of the retroviral gRNA. Here, we will review the literature regarding RNA interactions with NC, MA, as well as overall mechanisms employed by Gag to interact with RNA. The discussion focuses on human immunodeficiency virus type-1, but other retroviruses will also be discussed. A model is presented combining all of the available data summarizing the various factors and layers of selection Gag employs to ensure specific gRNA packaging and correct virion assembly.