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Non-Hodgkin lymphomas (NHL) commonly occur in immunodeficient patients, both those infected by human immunodeficiency virus (HIV) and those who have been transplanted, and are often driven by Epstein-Barr virus (EBV) with cerebral localization, raising the question of tumor immunogenicity, a critical issue for treatment responses. We investigated the immunogenomics of 68 lymphoproliferative disorders from 51 immunodeficient (34 post-transplant, 17 HIV+) and 17 immunocompetent patients. Overall, 72% were large B-cell lymphoma and 25% were primary central nervous system lymphoma, while 40% were EBV+. Tumor whole-exome and RNA sequencing, along with a bioinformatics pipeline allowed analysis of tumor mutational burden, tumor landscape and tumor microenvironment and prediction of tumor neoepitopes. Both tumor mutational burden (2.2 vs. 3.4/Mb, P=0.001) and numbers of neoepitopes (40 vs. 200, P=0.00019) were lower in EBV+ than in EBV- NHL, regardless of the immune status. In contrast both EBV and the immune status influenced the tumor mutational profile, with HNRNPF and STAT3 mutations observed exclusively in EBV+ and immunodeficient NHL, respectively. Peripheral blood T-cell responses against tumor neoepitopes were detected in all EBV- cases but in only half of the EBV+ ones, including responses against IgH-derived MHC-class-II restricted neoepitopes. The tumor microenvironment analysis showed higher CD8 T-cell infiltrates in EBV+ versus EBV- NHL, together with a more tolerogenic profile composed of regulatory T cells, type-M2 macrophages and an increased expression of negative immune-regulators. Our results highlight that the immunogenomics of NHL in patients with immunodeficiency primarily relies on the tumor EBV status, while T-cell recognition of tumor- and IgH-specific neoepitopes is conserved in EBV- patients, offering potential opportunities for future T-cell-based immune therapies.

Background: Early neurodevelopmental risks, compounded with traumatic medical experiences, contribute to emotional and behavioral challenges in as many as 1 in 2 children with congenital heart disease (CHD). Parents report a strong need for supports; yet, there remains a lack of accessible, evidence-based behavioral interventions available for children with CHD and their families. I-InTERACT-North is a web-based stepped-care mental health program designed to support family well-being and reduce behavioral concerns through positive parenting for children with early medical complexity. In previous pilot studies, the program was effective in increasing positive parenting skills and decreasing child behavior problems, with high parent-reported acceptability. This paper presents the protocol for the first randomized study of stepped-care parent support for families of children with CHD., Objective: This study will involve a single-site, 2-arm, single-blind randomized controlled trial to evaluate (1) the feasibility and acceptability of a web-based stepped-care parent support program (I-InTERACT-North) and (2) the effectiveness of the program in enhancing positive parenting skills and reducing behavioral concerns among families of children with CHD., Methods: Families will be randomized (1:1) to either receive treatment or continue with care as usual for 12 months. Randomization will be stratified by child's sex assigned at birth and baseline parent-reported child behavior intensity. Primary outcomes include positive parenting skills and child behavior at baseline, 3 months, 6 months, and 12 months. Secondary outcomes include parental mental health, quality of life, service usage, and feasibility including program reach and adherence. A sample size of 244 families will provide >95% power to detect an effect size of d=0.64. Based on attrition data from pilot studies, a target of 382 families will be enrolled. Parent reports of acceptability, adoption, and suggested adaptability of the program will be examined using cross-case thematic analyses. Primary efficacy analysis will be conducted using an intent-to-treat approach. Generalized estimating equations will be used to examine changes in positive parenting. Child behavior, quality of life, and parent mental health will be tested with repeated-measures analyses. Additional sensitivity and replication analyses will also be carried out., Results: Recruitment began in February 2024, and recruitment and follow-up will continue until January 2029. We anticipate results in late 2029., Conclusions: This study aims to test the effectiveness of I-InTERACT-North web-based stepped-care parent support in improving positive parenting skills and reducing child behavior problems in families of children with CHD compared with a care as usual control group. Results will inform future clinical implementation and expansion of this program among families of children with early medical conditions., Trial Registration: ClinicalTrials.gov NCT06075251; https://clinicaltrials.gov/study/NCT06075251., International Registered Report Identifier (irrid): DERR1-10.2196/64216., (©Marin Taylor, Bianca Christina Bondi, Brendan F Andrade, Stephanie H Au-Young, Vann Chau, Ashley Danguecan, Naddley Désiré, Ting Guo, Dragana Ostojic-Aitkens, Shari Wade, Steven Miller, Tricia Samantha Williams. Originally published in JMIR Research Protocols (https://www.researchprotocols.org), 04.10.2024.)

Given the high rates of learning challenges in children with medical conditions, efficient and reliable screening methods are crucial. This study examined whether parent report of daily learning and memory predicts academic achievement in youth. Parents of 213 youth (aged 6-18) with varied medical diagnoses completed the Multidimensional Everyday Memory Ratings for Youth (MEMRY), and youth completed subtests from the Wechsler Individual Achievement Test-Third Edition (WIAT-III) as part of a comprehensive assessment. All scales of the MEMRY (Learning, Daily Memory, Executive/Working Memory) correlated significantly with WIAT-III Spelling, Word Reading, and Numerical Operations, while only the MEMRY Learning subscale correlated significantly with WIAT-III Pseudoword Decoding. Regression analyses indicated that MEMRY Learning significantly predicted WIAT-III Word Reading and Spelling, while both the MEMRY Learning and MEMRY Daily Memory scales significantly predicted WIAT-III Numerical Operations. When Full Scale IQ was entered into the models first, the MEMRY Learning subscale accounted for an additional 4% of variance in WIAT-III Word Reading and 7% of variance in WIAT-III Spelling, but did not account for additional variance in WIAT-III Numerical Operations or Pseudoword Decoding. Analyses in a subset of children with broadly normal intellectual functioning demonstrated very similar results, with even higher variance in academic testing accounted for by the MEMRY. In sum, the MEMRY questionnaire may serve as an efficient screen to identify children at risk for reading, spelling, and math deficits.

This review had three aims: 1) describe the measures used to assess health-related quality of life (HRQL) in pediatric patients diagnosed with sickle cell disease (SCD); 2) document the biopsychosocial factors related to HRQL in pediatric patients diagnosed with SCD; and 3) complete a meta-analysis comparing HRQL in pediatric patients diagnosed with SCD to healthy controls. Included studies were published in English, quantitatively assessed HRQL as a primary aim, in both SCD and controls, and included participants between 0 and 21 years of age. The final review included 66 articles, with a total of 8642 participants with SCD, 4 months-21 years of age, and 62,458 controls, 5-27 years of age. HRQL was predominately measured using the Pediatric Quality of Life Inventory Generic Core and Sickle Cell Disease Module. Meta-analyses revealed children with SCD had significantly worse HRQL compared to healthy controls (standardized mean difference = -0.93, 95% CI = -1.25, -0.61, p < 0.00001). Worse HRQL was associated with more severe SCD, female sex, and pain. The findings indicate that children with SCD are at risk for worse HRQL compared to their healthy peers and their HRQL may be impacted by several biopsychosocial factors. Future research is needed to examine how sociocultural factors uniquely impact this population and their overall quality of life., Competing Interests: Declaration of Competing Interest None., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Background/objectives: Despite advances in the treatment of sickle cell disease (SCD), cerebrovascular and cognitive insults can have lifelong consequences. Hematopoietic cell transplantation (HCT) is an established curative therapy, and recent studies have demonstrated efficacy with reduced toxicity nonmyeloablative (NMA) regimens, but little is known about neuropsychological outcomes. The objective of this study was to describe neuropsychological, behavioral, and quality-of-life outcomes with medical correlates in children with SCD who received an NMA matched sibling donor (MSD) HCT., Design/methods: Retrospective cohort analysis of nine recipients with hemoglobin SS SCD who underwent MSD HCT using the National Institutes of Health (NIH) NMA protocol., Results: Mean full-scale intellectual functioning (FSIQ) was average pre-HCT (FSIQ = 92.1, SD 9.0; n = 8) and 2 years post-HCT (mean FSIQ = 96.6; SD 11.1; N = 9). Neuropsychological functioning was largely average across all cognitive domains, and no pre/post-HCT differences were found to be statistically significant given the small sample size. However, effect sizes revealed moderate improvements in processing speed (Cohen's d = .72) and verbal memory (Cohen's d = .60) post-HCT, and declines in measures of attention (Cohen's d = -.54) and fine motor speed and dexterity (Cohen's d = -.94). Parents endorsed better quality of life (Cohen's d = .91), less impact of SCD on their family, and less worry about their child's future (Cohen's d = 1.44)., Conclusion: Neuropsychological functioning in a sample of children and adolescents treated uniformly with NMA MSD HCT remained stable or improved in most cognitive domains, and improvements in quality of life and family functioning were observed., (© 2022 Wiley Periodicals LLC.)

This study describes the impact of COVID-19 among a clinical research sample of children with early brain injury and associated conditions. Between March 2020 and March 2021, 64 children and their parents participated. Children ranged in age between 3 and 14 years ( M = 6 years, 3 months; SD =  2 years, 4 months) with a range of diagnoses (i.e., neonatal stroke, hypoxic ischemic encephalopathy (HIE), congenital heart disease (CHD) and preterm birth (<32 weeks)). The abbreviated CoRonavIrus Health Impact Survey (CRISIS) was completed by parents as part of their child's routine intake for neuropsychological services. Questions included COVID-19 specific ratings of child mental health impact, child, and parent stressors, with open-ended questions regarding negative and positive COVID-19 related changes. Over 40% of parents described moderate to extreme influence of COVID-19 on their child's mental health. Common child stressors reported included restrictions on leaving the home and social isolation. Among parents, the most common stress reported was caring for their child's education and daily activities. Children's mental health impact was associated with social isolation, parent mental health, COVID-19 economic concern, and number of siblings in the home. Child's age, sex, brain injury severity, or intellectual functioning were not associated with reported COVID-19 mental health impact. Some COVID-19 positives were identified, namely increased quality family time. Findings reflect the significant pandemic mental health impact among neurologically at-risk children and their families. Implications to future clinical needs and considerations for neuropsychological practice are discussed.

Objective: To report preliminary empirical data on a novel, developmentally appropriate, observational postconcussive symptoms inventory for infants, toddlers, and preschoolers., Setting: Emergency departments of 2 tertiary, urban pediatric hospitals., Participants: Ninety-eight children (0-8 years of age; mean age at injury = 33.00, SD = 24.7 months) with mild traumatic brain injury (concussion) divided into younger (0-2 years) and older (3-8 years) age groups., Design: Observational study., Main Measure: The Report of Early Childhood Traumatic Injury Observations & Symptoms (REACTIONS) documents 17 postconcussive symptoms representing observable manifestations thereof and was completed by parents in the acute (24-48 hours; n = 65), subacute (7-14 days; n = 78), and/or persistent phase (25-35 days; n = 72) post-mild traumatic brain injury., Results: Different patterns of postconcussive symptoms were reported by age group, with behavioral manifestations particularly salient in younger children. More children younger than 2 years had sleep and comfort-seeking symptoms at each of the 3 postinjury time points., Conclusion: Postconcussive symptoms may manifest differently after mild traumatic brain injury sustained during early childhood. To fully understand and address their presence and evolution, developmentally sound measures such as the REACTIONS inventory are required., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

Human Herpesvirus 8 (HHV-8) is associated with three main severe orphan malignancies, Kaposi's sarcoma (KS), multicentric Castleman's disease (MCD), and primary effusion lymphoma (PEL), which present few therapeutic options. We identified the antimalarial primaquine diphosphate (PQ) as a promising therapeutic candidate for HHV-8-associated PEL and KS. Indeed, PQ strongly reduced cell viability through caspase-dependent apoptosis, specifically in HHV-8-infected PEL cells. Reactive oxygen species (ROS)- and endoplasmic reticulum (ER) stress-mediated apoptosis signaling pathways were found to be part of the in vitro cytotoxic effect of PQ. Moreover, PQ treatment had a clinically positive effect in a nonobese diabetic (NOD)/SCID xenograft PEL mouse model, showing a reduction in tumor growth and an improvement in survival. Finally, an exploratory proof-of-concept clinical trial in four patients harboring severe KS was conducted, with the main objectives to assess the efficacy, the safety, and the tolerability of PQ, and which demonstrated a positive efficacy on Kaposi's sarcoma-related lesions and lymphedema.

This study focuses on risk assessment of Cr, V, Ni, Co, Pb, Cu, and Zn in the Mefou River sediments located at Yaoundé, West-Africa. Sediment samples were collected from five stations in the downstream of the Mefou River, which drains the urban area of Yaoundé between latitudes 3°30' and 3°58' North and longitudes 11°20' and 11°40' East. The geochemistry data were analyzed statistically and the pollution indices were calculated in order to identify and estimate the sources of metal contamination in the Mefou River sediments. The results obtained show that the average concentrations of trace metals are almost higher than those of the upper continental crust (UCC) and the metal average in the Simbock Lake cores. However, the concentrations of Ni, Cu, Pb, and Zn in sediments located in most urbanized sites are lower than those of the UCC and the average of Simbock Lake sediments. The pollution indices such as enrichment factor (EF), geo-accumulation index (Igeo), and pollution load index (PLI) showed that trace metals were mainly influenced by human sources, except for Pb, Cu, and Zn, which stemmed from natural sources. The sediments of the Mefou River would therefore be affected with low to moderate pollution levels. The low values of potential ecological risk (RI: 22.36-41.53) suggest a low potential ecological risk effect. The multivariate statistical analysis indicates that Ni, Cu, Pb, Co, and Zn have been derived mainly from natural sources, while V and Cr would partially derive from human activities. The results of this research can be a reference for trace metal pollution along an African urbanized river corridor. This can be considered as an act of prevention of urban watercourses in Cameroon and in other parts of the world, especially in major African urban metropolis., Competing Interests: The authors declare no conflict of interest., (© 2021 The Author(s).)

Pediatric neuropsychologists are increasingly recognizing the importance of performance validity testing during evaluations. The use of such measures to detect insufficient effort is of particular importance in pediatric epilepsy evaluations, where test results are often used to guide surgical decisions and failure to detect poor task engagement can result in postsurgical cognitive decline. The present investigation assesses the utility of the Medical Symptom Validity Test (MSVT) in 104 clinically referred children and adolescents with epilepsy. Though the overall failure rate was 15.4% of the total group, children with 2nd grade or higher reading skills (a requirement of the task) passed at a very high rate (96.6%). Of the three failures, two were unequivocally deemed true positives, while the third failed due to extreme somnolence during testing. Notably, for those with ≥2nd grade reading levels, MSVT validity indices were unrelated to patient age, intellectual functioning, or age of epilepsy onset, while modest relations were seen with specific memory measures, number of epilepsy medications, and seizure frequency. Despite these associations, however, this did not result in more failures in this population of children and adolescents with substantial neurologic involvement, as pass rates exceeded 92% for those with intellectual disability, high seizure frequency, high medication burden, and even prior surgical resection of critical memory structures.

Objective: Concussion in children and adolescents is a prevalent problem with implications for subsequent physical, cognitive, behavioral, and psychological functioning, as well as quality of life. While these consequences warrant attention, most concussed children recover well. This study aimed to determine what pre-injury, demographic, and injury-related factors are associated with optimal outcome ("wellness") after pediatric concussion., Method: A total of 311 children 6-18 years of age with concussion participated in a longitudinal, prospective cohort study. Pre-morbid conditions and acute injury variables, including post-concussive symptoms (PCS) and cognitive screening (Standardized Assessment of Concussion, SAC), were collected in the emergency department, and a neuropsychological assessment was performed at 4 and 12 weeks post-injury. Wellness, defined by the absence of PCS and cognitive inefficiency and the presence of good quality of life, was the main outcome. Stepwise logistic regression was performed using 19 predictor variables., Results: 41.5% and 52.2% of participants were classified as being well at 4 and 12 weeks post-injury, respectively. The final model indicated that children who were younger, who sustained sports/recreational injuries (vs. other types), who did not have a history of developmental problems, and who had better acute working memory (SAC concentration score) were significantly more likely to be well., Conclusions: Determining the variables associated with wellness after pediatric concussion has the potential to clarify which children are likely to show optimal recovery. Future work focusing on wellness and concussion should include appropriate control groups and document more extensively pre-injury and injury-related factors that could additionally contribute to wellness. (JINS, 2019, 25, 375-389).

A significant proportion of children and adolescents report psychological distress following concussion, but little is known about the predictors of these problems. The purpose of this study was to examine predictive factors of psychological distress following pediatric concussion. It was hypothesized that the presence of pre-injury psychological distress would be the strongest predictor of psychological distress post-concussion, with other demographic and acute injury factors adding incrementally to prediction. This is a prospective, multi-center cohort. Children and adolescents (6-17 years old; n = 311) who sustained a concussion and were assessed through four pediatric emergency departments. Participants were reassessed at 4-weeks (n = 275) and 12-weeks (n = 190) post-injury. Emergency department (ED) assessment documented injury mechanism, acute symptomatology, acute cognitive functioning, and pre-injury functioning. Psychological distress at 4- and 12-weeks follow-up was categorized as present if one or more psychological scores from the parent-completed measures (Child Behavior Checklist, Strengths and Difficulties Questionnaire) exceeded established cutoffs. The presence of psychological distress at each follow-up was predicted using multi-variable logistic regressions. Psychological distress was reported in 23% of youth at both 4- and 12-weeks post-concussion. A pre-injury diagnosis of anxiety and acutely forgetting recent information were significant predictors of psychological distress at 4 weeks, whereas worse acute orientation assessment in the ED predicted psychological distress at 12 weeks. Nearly one of four youth experienced psychological distress after concussion. Clinicians in acute care settings should screen for the factors (pre-injury anxiety, acute mental status) associated with post-injury psychological distress and consider proactively referring patients for further assistance.

Background: The large and constantly evolving HIV-1 pandemic has led to an increasingly complex diversity. Because of some taxonomic difficulties among the most diverse HIV-1 subtypes, and taking advantage of the large amount of sequence data generated in the recent years, we investigated novel lineage patterns among the main HIV-1 subtypes., Results: All HIV full-length genomes available in public databases were analysed (n = 2017). Maximum likelihood phylogenies and pairwise genetic distance were obtained. Clustering patterns and mean distributions of genetic distances were compared within and across the current groups, subtypes and sub-subtypes of HIV-1 to detect and analyse any divergent lineages within previously defined HIV lineages. The level of genetic similarity observed between most HIV clades was deeply consistent with the current classification. However, both subtypes A and D showed evidence of further intra-subtype diversification not fully described by the nomenclature system at the time and could be divided into several distinct sub-subtypes., Conclusions: With this work, we propose an updated nomenclature of sub-types A and D better reflecting their current genetic diversity and evolutionary patterns. Allowing a more accurate nomenclature and classification system is a necessary step for easier subtyping of HIV strains and a better detection or follow-up of viral epidemiology shifts.

Objective: Reliable detection of HIV minority resistant variants (MRVs) requires bioinformatics analysis with specific algorithms to obtain good quality alignments. The aim of this study was to analyze ultra-deep sequencing (UDS) data using different analysis pipelines., Methods: HIV-1 protease, reverse transcriptase (RT) and integrase sequences from antiretroviral-naïve patients were obtained using GS-Junior® (Roche) and MiSeq® (Illumina) platforms. MRVs were defined as variants harbouring resistance-mutation present at a frequency of 1%-20%. Reads were analyzed using different alignment algorithms: Amplicon Variant Analyzer®, Geneious® compared to SmartGene® NGS HIV-1 module., Results: 101 protease and 51 RT MRVs identified in 139 protease and 124 RT sequences generated with a GS-Junior® platform were analyzed using AVA® and SmartGene® software. The correlation coefficients for the MRVs were R2 = 0.974 for protease and R2 = 0.972 for RT. Discordances (n = 13 in protease and n = 15 in RT) mainly concerned low-level MRVs (i.e., with frequencies of 1%-2%, n = 18/28) and they were located in homopolymeric regions (n = 10/15). Geneious® and SmartGene® software were used to analyze 143 protease, 45 RT and 26 integrase MRVs identified in 172 protease, 69 RT, and 72 integrase sequences generated with a MiSeq® platform. The correlation coefficients for the MRVs were R2 = 0.987 for protease, R2 = 0.995 for RT and R2 = 0.993 for integrase. Discordances (n = 9 in protease, n = 3 in RT, and n = 3 in integrase) mainly concerned low-level MRVs (n = 13/15)., Conclusion: We found an excellent correlation between the various UDS analysis pipelines that we tested. However, our results indicate that specific attention should be paid to low-level MRVs, for which the use of two different analysis pipelines and visual inspection of sequences alignments might be beneficial. Thus, our results argue for use of a 2% threshold for MRV detection, rather than the 1% threshold, to minimize misalignments and time-consuming sight reading steps essential to ensure accurate results for MRV frequencies below 2%., Competing Interests: The authors have declared that no competing interests exist.

Objective: Previous research suggests that neuropsychological outcome after pediatric concussion is determined by unmodifiable, preexisting factors. This study aimed to predict neuropsychological outcome after pediatric concussion by using a sufficiently large sample to explore a vast array of predictors., Method: A total of 311 children and adolescents (6-18 years old) with concussion were assessed in the emergency department to document acute symptomatology and to screen for cognitive functioning. At 4 and 12 weeks postinjury, they completed tests of intellectual functioning, attention/working memory, executive functions, verbal memory, processing speed, and fine motor abilities. Multiple hierarchical logistic and linear regressions were performed to assess the contribution of premorbid factors, acute symptoms, and acute cognitive screening (Standardized Assessment of Concussion-Child) to aspects of neuropsychological outcome: (a) cognitive inefficiency (defined using a modified Neuropsychological Impairment Rule; Beauchamp et al., 2015) and (b) neuropsychological performance (defined using principal component analysis)., Results: Neuropsychological impairment was present in 10.3% and 4.5% of participants at 4 and 12 weeks postinjury, respectively. At 4 weeks postinjury, cognitive inefficiency was predicted by premorbid factors and acute cognitive screening, whereas at 12 weeks it was predicted by acute symptoms. Neuropsychological performance at 4 weeks was predicted by a combination of premorbid factors, acute symptoms, and acute cognitive screening, whereas as at 12 weeks, only acute cognitive screening predicted performance., Conclusions: Neuropsychological outcome after pediatric concussion is not attributable solely to preexisting problems but is instead associated with a combination of preexisting and injury-related variables. Acute cognitive screening appears to be particularly useful in predicting neuropsychological status after concussion. (PsycINFO Database Record, ((c) 2018 APA, all rights reserved).)

Background: Propionibacterium acnes (P. acnes) is an anaerobic, Gram-positive bacteria encountered in inflammatory acne lesions, particularly in the pilosebaceous follicle. P. acnes triggers a strong immune response involving keratinocytes, sebocytes and monocytes, the target cells during acne development. Lipoteicoic acid and peptidoglycan induce the inflammatory reaction, but no P. acnes surface protein interacting with Toll-like receptors has been identified. P. acnes surface proteins have been extracted by lithium stripping and shown to induce CXCL8 production by keratinocytes., Methodology and Principal Findings: Far-western blotting identified two surface proteins, of 24.5- and 27.5-kDa in size, specifically recognized by TLR2. These proteins were characterized, by LC-MS/MS, as CAMP factor 1 devoid of its signal peptide sequence, as shown by N-terminal sequencing. Purified CAMP factor 1 induces CXCL8 production by activating the CXCL8 gene promoter, triggering the synthesis of CXCL8 mRNA. Antibodies against TLR2 significantly decreased the CXCL8 response. For the 27 P. acnes strains used in this study, CAMP1-TLR2 binding intensity was modulated and appeared to be strong in type IB and II strains, which produced large amounts of CXCL8, whereas most of the type IA1 and IA2 strains presented little or no CAMP1-TLR2 binding and low levels of CXCL8 production. The nucleotide sequence of CAMP factor displays a major polymorphism, defining two distinct genetic groups corresponding to CAMP factor 1 with 14 amino-acid changes from strains phylotyped II with moderate and high levels of CAMP1-TLR2 binding activity, and CAMP factor 1 containing 0, 1 or 2 amino-acid changes from strains phylotyped IA1, IA2, or IB presenting no, weak or moderate CAMP1-TLR2 binding., Conclusions: Our findings indicate that CAMP factor 1 may contribute to P. acnes virulence, by amplifying the inflammation reaction through direct interaction with TLR2., Competing Interests: The authors have declared that no competing interests exist.

The emergence of varicella-zoster virus (VZV) resistance to current antivirals as acyclovir (ACV) constitutes a hindrance to antiviral treatment effectiveness of VZV infections, especially in immunocompromised patients. The molecular mechanisms of VZV resistance reported so far rely on the presence of mutations within thymidine kinase (TK, ORF36) and DNA polymerase (ORF28) viral genes. The aim of this work was to develop reliable and complementary diagnostic methods to detect VZV antiviral resistance: (i) a genotypic assay based on TK and DNA polymerase genes sequencing, (ii) a plaque reduction assay to determine antiviral 50% effective concentrations, and (iii) a functional assay to evaluate in vitro phosphorylation activity of recombinant TKs. As a whole, this study included the analysis of 21 VZV clinical isolates and 62 biological samples from patients experiencing VZV infection. Genetic analysis revealed 3 and 9 new amino acid changes that have not been previously described within the highly conserved TK and DNA polymerase, respectively. Then, VZV isolates bearing newly identified mutations considered as natural polymorphisms were characterized as susceptible to ACV using plaque-reduction assay in MeWo cells. In parallel, the impact of TK changes on ACV phosphorylation activity was examined using a nonradioactive in vitro enzymatic assay., (Copyright © 2016. Published by Elsevier B.V.)

Unlabelled: Very low levels of variability have been reported for the herpes simplex virus 2 (HSV-2) genome. We recently described a new genetic variant of HSV-2 (HSV-2v) characterized by a much higher degree of variability for the UL30 gene (DNA polymerase) than observed for the HG52 reference strain. Retrospective screening of 505 clinical isolates of HSV-2 by a specific real-time PCR assay targeting the UL30 gene led to the identification of 13 additional HSV-2v isolates, resulting in an overall prevalence of 2.8%. Phylogenetic analyses on the basis of microsatellite markers and gene sequences showed clear differences between HSV-2v and classical HSV-2. Thirteen of the 14 patients infected with HSV-2v originated from West or Central Africa, and 9 of these patients were coinfected with HIV. These results raise questions about the origin of this new virus. Preliminary results suggest that HSV-2v may have acquired genomic segments from chimpanzee alphaherpesvirus (ChHV) by recombination., Importance: This article deals with the highly topical question of the origin of this new HSV-2 variant identified in patients with HIV coinfection originating mostly from West or Central Africa. HSV-2v clearly differed from classical HSV-2 isolates in phylogenetic analyses and may be linked to simian ChHV. This new HSV-2 variant highlights the possible occurrence of recombination between human and simian herpesviruses under natural conditions, potentially presenting greater challenges for the future., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)

Herpes simplex virus type 2 (HSV-2) is the most common cause of genital ulcer disease worldwide. While the contribution of HSV-2 to acquisition and course of human immunodeficiency virus (HIV) infection has been well described, less attention has been paid to the impact of HIV infection on the variability and the pathophysiology of HSV-2 infection. The goal of the present study was to characterize genotypically and phenotypically HSV-2 strains isolated from 12 patients infected by HIV-1 and from 12 HIV-negative patients. Replication capacity analyses were carried out in Vero cells and full-length nucleotide sequences were determined for glycoproteins B (gB), D (gD), G (gG), thymidine kinase (TK), and DNA polymerase (POL) HSV-2 genes. Sequence alignments and phylogenetic trees were performed. No significant differences were found in terms of replication capacity. The interstrain nucleotide identities of the 3 glycoprotein genes (gB, gC, and gG) ranged from 99.5% to 100% among the 24 HSV-2 strains. The phylogenetic analysis showed no clustering of HSV-2 strains when correlating to the HIV status of the patients. A lower variability was observed for the functional proteins TK and DNA polymerase (98.9% to 100% identity). Genetic analysis of TK evidenced mutations related to acyclovir-resistance in two HSV-2 strains. No specific differences regarding replication capacity and gene sequence were found when comparing HSV-2 strains isolated from patients infected with HIV-1 and HIV-negative patients, suggesting that the virological properties of HSV-2 infection are not influenced by HIV-1 infection among co-infected patients., (© 2014 Wiley Periodicals, Inc.)

Objectives: The genetic barrier (defined as the number of genetic transitions/transversions needed to produce a resistance mutation) can differ between HIV-1 subtypes. The genetic barrier for the new attachment inhibitor BMS-626529 was evaluated in five HIV-1 subtypes., Methods: Nine substitutions associated with BMS-626529 resistance at seven amino acid positions (116, 204, 375, 426, 434, 475 and 506) were analysed in 300 nucleotide sequences of the env gene encoding the gp120 protein from antiretroviral-naive patients (60 for each subtype and recombinant: B, C, D, CRF01&#95;AE and CRF02&#95;AG)., Results: Differently from the B subtype, some resistance mutations were found as natural polymorphisms in the C and D subtypes and the CRF02&#95;AG and CRF01&#95;AE recombinants for four positions of the env gene encoding the gp120 protein (375, 426, 434 and 475). The majority (five out of seven) of amino acid positions studied (116, 426, 434, 475 and 506) were relatively conserved (>63%) between the five HIV-1 subtypes, leading to a similar genetic barrier to mutations associated with resistance to BMS-626529. However, at positions 116 and 506 a minority of C and CRF02&#95;AG subtypes had codons leading to a higher genetic barrier. Different predominant codons were observed at two out of seven positions (204 and 375) between the subtypes, with no effect on the calculated genetic barrier. However, for position 375, a minority of CRF02&#95;AG sequences showed a lower genetic barrier to S375M/T resistance mutations., Conclusions: In non-B HIV-1 subtypes, four out of seven studied positions presented mutations implicated in BMS-626529 resistance. Despite great variability of the HIV-1 envelope, there was no major impact of polymorphisms on the genetic barrier to acquisition of BMS-626529 resistance., (© The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Background: Presence at the same time of HBsAg and anti-HBs antibodies (HBsAg/Ab) is an entity sometimes encountered in chronic hepatitis B (CHB) carriers., Objectives: This study was designed to characterize such serological profiles and to assess the reliability of serological marker quantification by three commercially available assays in this setting., Study Design: Among 2578 CHB identified patients, 129 (5%) had an HBsAg/Ab profile as determined by Abbott Architect. After exclusion of co-infections (HIV, HCV, HDV), HBV reactivation or HBIg treatment, 101 samples from 62 patients were tested for HBsAg and anti-HBs quantification using Architect, DiaSorin Liaison-XL and Roche Modular-Cobas. Influence of genotype and HBsAg variants was studied in 31 samples with HBV replication., Results: HBsAg detection was confirmed with the 3 techniques for 98% (n = 99) of the samples while the HBsAg/Ab profile was concordant between all techniques for 65% of them. The overall correlation between the 3 HBsAg quantification techniques was good (R(2): 0.94-0.97). The median HBsAg concentration was comparable for the 99 samples whatever the used technique but a bias of -0.11 and 0.02 log IU/mL were noticed for DiaSorin and Roche compared to Abbott, respectively. Anti-HBs quantifications were poorly correlated between techniques with major discrepancies observed. Genotype and substitutions within the "a" determinant showed an impact on HBsAg quantification., Conclusions: The double HBsAg/Ab profile is not an analytical artifact and is confirmed on all commercially available techniques. While such profile does not influence HBsAg quantification, differences of HBsAg quantification were noticed according to HBV genotype or HBsAg variant., (Copyright © 2014 Elsevier B.V. All rights reserved.)

The accuracy and usefulness of laboratory-developed real-time PCR procedures using a Light Cycler instrument (Roche Diagnostics) for detecting and quantifying human immunodeficiency virus type 1 (HIV-1) RNA and DNA as well as herpes simplex virus type 1 (HSV-1)/HSV-2 DNA in cervicovaginal secretions from women coinfected with HIV and HSV were evaluated. For HIV-1, the use of the NEC152 and NEC131 primer set and the NEC-LTR probe in the long terminal repeat gene allowed us to detect accurately the majority of HIV-1 subtypes of group M circulating in sub-Saharan Africa, including subtypes A, B, C, D, and G as well as circulating recombinant forms 02 and 11. The detection threshold of real-time PCR for HIV in cervicovaginal lavage samples was 5 copies per assay for both RNA and DNA; the intra- and interassay coefficients of variation of C(T) values were 1.30% and 0.69% (HIV-1 RNA) and 1.84% and 0.67% (HIV-1 DNA), respectively. Real-time PCR for HSV using primers and probe targeting the HSV DNA polymerase gene allowed both detection and quantification of HSV DNA and also differentiation between HSV-1 and HSV-2 genotypes. The detection threshold of real-time PCR for HSV was 5 copies per assay; the intra- and interassay coefficients of variation of C(T) values were 0.96% and 1.49%, respectively. Both manual and automated silica-based procedures were appropriate for combined extraction of HIV and HSV genomes from female genital secretions. Taken together, these findings indicate that real-time PCR may be used as a unique nucleic acid amplification procedure to detect and quantify HIV and HSV genomes in cervicovaginal secretions and thus to assess at reduced costs the genital shedding of both viruses in women included in intervention studies.

Determination of polyomavirus BK (BKV) load in urine and plasma has been advocated for monitoring adult renal transplant recipients suffering from BKV-related nephropathy. An "in-house" real-time quantitative PCR assay was developed using the BKV-1/BKV-3 primers set in the large tumor antigen (LT-ag) region to quantitate BK virus loads in plasma and urine in renal transplant patients. This assay was adapted to routine virology laboratory by evaluating two extraction procedures of nucleic acids from urine and plasma, one manual and the other using an automatic extractor, and by evaluating the Light Cycler versus Taqman apparatus. Both the manual and automatic extraction procedures and real-time PCR apparatus were equivalent. The Light Cycler and Taqman instruments allow similarly rapid, accurate, reproducible and specific quantitative detection of the three major BKV subtypes, with a detection limit of 10 BKV DNA copies/ml, and a range from 10(0) to 10(7) copies/ml. Of 855 renal transplant patients, 128 (15%) had BKV DNA in both plasma and urine samples with a mean viral load of 5.1 log/ml in plasma and 6.8 log/ml in urine and in 5 (4%) BKV-associated tubulo-interstitial nephropathy; 332 (39%) BKV DNA was found only in the urine, not in the plasma, without further development of nephropathy and 395 patients had no BKV in plasma and urine. These observations emphasize the usefulness of real-time PCR to assess the BKV load by routine testing, and confirm the need to combine both plasma and urine determinations of the BKV DNA load in order to identify renal transplant patient at high risk for BKV-associated nephropathy.

Background: WBC depletion by filtration may prevent the transmission of HTLV-I, which requires cell-to-cell contact. The removal of HTLV-I-infected cells in routinely filtered blood cell components was measured., Study Design and Methods: The study was conducted in Martinique where systematic screening for HTLV-I and -II and universal leukoreduction are mandatory. HTLV-I was quantified by use of real-time PCR in 8 RBC units and 4 PLT concentrates before and after filtration. HTLV-I proviral load in PBMNCs was determined in five of the eight HTLV-I-infected blood donors., Results: The amount of MNC-associated HTLV-I DNA in RBC units before filtration was 21 x 10(6)+/- 29 x 10(6) copies (mean +/- SD). HTLV-I was detected in 4 of 8 RBC units after filtration, with a number of copies in the MNC fraction ranging from 20 to 140, following a 4.9 to 5.8 log reduction. Flow cytometry analysis performed in 2 of the filtered RBC units containing detectable HTLV-I showed suboptimal and out-of-range leukoreduction (0.56 x 10(6) and 1.22 x 10(6) residual WBCs). HTLV was not detected in filtered RBCs from the blood donor with the highest percentage of HTLV-I-infected PBMCs (9%)., Conclusion: This study confirms that HTLV-I-infected cells can be detected in filtered blood cell components and shows that optimal leukoreduction is critical for HTLV-I removal.

A quantitative real-time PCR assay was developed to measure the proviral load of human T-lymphotropic virus type I (HTLV-I) in peripheral blood mononuclear cells (PBMCs). The HTLV-I copy number was referred to the actual amount of cellular DNA by means of the quantitation of the albumin gene. Ten copies of HTLV-I DNA could be detected with 100% sensitivity, and the assay had a wide range of at least 5 log(10). Intra- and inter-assay reproducibility was evaluated using independent extractions of PBMCs from an HTLV-I-infected patient (coefficients of variation, 24 and 7% respectively). The performance of this TaqMan PCR assay, coupled with its high throughput, thus allows reliable routine follow-up of HTLV-I proviral load in infected patients. Preliminary results using clinical samples indicate a higher proviral load in patients with HTLV-I-associated myelopathy/tropical spastic paraparesis than in asymptomatic carriers, and also suggest the usefulness of this quantitative measurement to assess the etiological link between HTLV-I and adult T-cell leukaemia/lymphoma-like syndromes.

Several reports suggest that HTLV-I/HIV coinfection may be associated with an increased risk of HTLV-I-associated myelopathy/tropical spastic paraparesis (HAM/TSP). In HTLV-I-monoinfected patients, the occurrence of HAM/TSP is associated with high peripheral blood HTLV-I proviral load. Using a real-time quantitative PCR assay, we assessed the proviral DNA load in peripheral blood mononuclear cells (PBMCs) from 15 asymptomatic HTLV-I-monoinfected patients, 15 HTLV-I-monoinfected patients with HAM/TSP, and 25 HTLV-I/HIV-1 coinfected patients, including 4 with HAM/TSP. We also measured HIV-1 proviral DNA load in PBMCs from the coinfected patients. The median HTLV-I proviral loads were 6,800 and 4,100 copies per 10(6) PBMCs in the asymptomatic monoinfected and coinfected groups, and 58,800 and 43,300 copies per 10(6) PBMCs in the monoinfected and coinfected patients with HAM/TSP, respectively. The difference between HTLV-I proviral loads in HAM/TSP and asymptomatic monoinfected patients was statistically significant (p < 0.0001), but there was no difference between the HTLV-I-monoinfected and HTLV-I/HIV-1-coinfected groups. There was no correlation between HTLV-I and HIV-1 proviral load. HTLV-I proviral load did not correlate with the CD4+ T lymphocyte count. Among patients with no HTLV-I disease, the median copy number of HTLV-I per 10(6) circulating CD4+ T cells was 114,000 in the coinfected group and 16,700 in the monoinfected group, but the difference was not significant (p = 0.089). These data do not confirm the hypothesis in which HIV-1 coinfection would increase HTLV-I proviral burden in the PBMCs. However, depletion of the CD4+ T cell subset, the main target of HTLV-I, could be counterbalanced by an up-regulation of HTLV-I replication or by greater resistance of HTLV-I-infected cells to HIV-1-induced destruction.