National Institute Of Allergy And Infectious Diseases Research Articles

Phylogenetic Analysis of HIV from People Who Inject Drugs in Indonesia, Ukraine, and Vietnam: HPTN 074

Background: HPTN 074 evaluated an HIV prevention intervention for persons who inject drugs (PWID) that included support for HIV and substance use treatment. The study enrolled HIV-infected index participants and HIV-uninfected injection partners (up to five per index) in Indonesia, Ukraine, and Vietnam. Seven partners acquired HIV infection during the study. We analyzed the relationship between HIV strains in this cohort. Methods: HIV from index participants and their partners was sequenced using the ViroSeq HIV-1 Genotyping System. Phylogenetic trees were constructed using RAxML v8.2.10. Pol sequence clusters were identified that had a genetic distance ≤1.5% with ≥90% branch support. Next generation sequencing (NGS, env region) was also performed for the seven seroconverters and the corresponding index participants (index-partner pairs) and from other index participants in pol sequence clusters. Participants were classified as having linked infections if their env sequences formed a distinct monophyletic cluster with ≥90% bootstrap support Findings: Phylogenetic analysis included pol sequences from 445 of 502 index participants and all seven HIV-infected partners. The median pairwise genetic distance at the three study sites ranged from 2.9% to 3.3% with no evidence of large discrete subclades. Eighteen pol clusters were identified, including two of the seven index-partner pairs, one pair of partners enrolled with different indexes, and 15 index-only groups including 36 participants (2-7 index participants per cluster). NGS-env analysis confirmed linkage for both index-partner clusters, the partner-partner cluster, and 11 index-index clusters. Interpretation: Only two of the seven index-partner pairs in this study had genetically-linked HIV infections. Clusters were also identified that included two partners enrolled with different indexes, and groups of 2-7 index participants. These findings suggest that individuals in these PWID communities have exposure to multiple sources of HIV infection. This should be considered when designing strategies for HIV prevention in these high-risk populations. Trial Registration Number: In this report, we analyzed HIV from PWID enrolled in a randomized clinical trial conducted in Indonesia, Ukraine, and Vietnam (HIV Prevention Trials Network [HPTN] 074) Funding Statement: National Institute of Allergy and Infectious Diseases (NIAID), National Institute on Drug Abuse (NIDA), and Office of AIDS Research, of the National Institutes of Health (NIH). Declaration of Interests: None of the authors has a conflict of interest or potential conflict of interest, with the following exceptions: Susan Eshleman has collaborated on research studies with investigators from Abbott Laboratories (distributor of the ViroSeq HIV-1 Genotyping System); Abbott Laboratories has provided reagents for collaborative research studies. Ethics Approval Statement: Written informed consent was signed by each participant in the HPTN 074 trial. The study was approved by institutional review boards and ethics committees of the participating institutions in the United States and at each study site.

Neutropenia Is an Under-Recognized Finding in Pediatric Primary Immunodeficiency Diseases: An Analysis of the United States Immunodeficiency Network Registry

Background: Neutropenia is recognized as a defining or common element in a limited number of primary immunodeficiency diseases (PIDDs) (Dotta L et al. Immunol Let 2014; Cham B et al. Semin Hematol 2002); but, the overall prevalence of neutropenia within the more than 300 known PIDDs is not well described. Many of the PIDDs rely on a high index of clinical suspicion for diagnosis which may not be readily apparent to hematologists evaluating a neutropenic patient, underscoring the importance of understanding the rate of neutropenia in PIDDs and impact on clinical outcomes. The goal of this study was to evaluate the frequency and characteristics of neutropenia in a large registry of patients with primary immunodeficiency (PID).Methods: The United States Immunodeficiency Network (USIDNET) is a research consortium that maintains a national registry for the collection of data on patients with PIDDs. The USIDNET was queried for data regarding patients aged 21 years or less. Data utilized included reported PID diagnosis, gene mutation, gender, race, status of patient (living or deceased), year of birth, age at death, age of disease diagnosis, and results of reported complete blood counts (CBCs). PID diagnoses were grouped according to the 2017 International Union of Immunological Societies (IUIS) Phenotypic Classification for Primary Immunodeficiencies (Bousfiha A et al. J Clin Immunol 2018). Mild, moderate, and severe neutropenia were defined as absolute neutrophil counts of 1000-1499 cells/μL, 500-999 cells/μL, and < 500 cells/μL, respectively. Data are presented with descriptive statistics. The frequency of neutropenia was compared between genders and by race using chi-square test analysis.Results: An initial data request resulted in information on 1577 patients; 384 patients were eliminated from analysis given insufficient recorded registry data due to a lack of a documented absolute neutrophil count. An additional 48 patients were excluded given that complete blood cell counts were only reported following hematopoietic stem cell transplantation. Data was thus available for 1145 pediatric patients with PIDDs. A total of 2058 neutrophil values were analyzed with 62.7% (719) patients having only a single neutrophil value available for review. Overall, 15.8% of PIDD pediatric patients in the USIDNET registry had neutropenia, ranging from 12.01% (combined immunodeficiencies with associated or syndromic features) to 66.67% (defects in intrinsic and innate immunity) in IUIS categories (Table 1) and in USIDNET categories from 2.94% (autoimmune lymphoproliferative syndrome) to 75.00% (susceptibility to mycobacterial infections) (Table 2). Of PID patients with neutropenia, 20.4% had severe neutropenia, 33.1% had moderate neutropenia, and 46.4% had mild neutropenia. Neutropenia was most likely to be severe in patients with predisposition to severe viral infections as well as those with a defect in intrinsic and innate immunity (Tables 1-2). There was no statistically significant difference in neutropenia between genders (p = 0.64). However, females were more likely to have severe neutropenia than males (28% versus 16%; p=0.03). Additionally, 28% of African-American patients had recorded neutropenia while only 17% of Caucasians and 2% of Asian/Pacific Islanders were neutropenic (p=0.005). There was no statistically significant difference in severity of neutropenia and death nor in the rate of bacterial and fungal infections detected between neutropenic and non-neutropenic patients with 93% of patients in the dataset living at the time of data collection.Conclusions: The frequency of neutropenia within pediatric patients diagnosed with PIDD is higher and more ubiquitous than previously suspected. Hematologists should consider a PIDD in the assessment of neutropenia, particularly if other concerning signs or symptoms are present. Although this evaluation did not detect a difference in morbidity or mortality, the data set was constrained by a limited number of CBCs per patient and the rarity of the PIDDs. The impact of neutropenia on PIDD outcomes requires further study, ideally through a prospective longitudinal study.Acknowledgments: The U.S. Immunodeficiency Network (USIDNET), a program of the Immune Deficiency Foundation (IDF), is supported by a cooperative agreement, U24AI86837, from the National Institute of Allergy and Infectious Diseases (NIAID). [Display omitted] DisclosuresDale:Athelas, Inc.: Equity Ownership; Amgen: Consultancy, Research Funding; Sanofi-Aventi: Consultancy, Honoraria; Cellerant: Other: Scientific Advisory Board; Hospira: Consultancy; Prolong: Consultancy; Beheringer-Ingelheim: Consultancy; Coherus: Consultancy.

Editorial introductions

Editorial introductions

Flu, Pneumococcal Vaccination Rates on the Rise

Flu, Pneumococcal Vaccination Rates on the Rise

Communicator or Shill?

Communicator or Shill?

Drug Susceptibility Testing and Mortality in Patients Treated for Tuberculosis in High-Burden Countries

Background: Drug resistance and HIV co-infection are challenges for the global control of tuberculosis. Methods: We collected Mycobacterium tuberculosis isolates from adult patients in Cote d'Ivoire, Democratic Republic of the Congo, Kenya, Nigeria, South Africa, Peru, and Thailand, stratified by HIV status and tuberculosis drug resistance. Molecular or phenotypic drug susceptibility testing (DST) was done locally and at the Swiss tuberculosis reference laboratory. We examined mortality during treatment according to DST results and treatment adequacy in logistic regression models adjusting for sex, age, sputum microscopy and HIV status. Findings: 634 tuberculosis patients were included; median age was 33.2 years, 239 (37.7%) were female, 272 (42.9%) HIV-positive and 69 (10.9%) patients died. Based on the reference laboratory DST, 394 (62.2%) strains were pan-susceptible, 45 (7.1%) mono-resistant, 163 (25.7%) multidrug-resistant (MDR-TB), and 30 (4.7%) had pre-extensive or extensive drug resistance (pre-XDR/XDR-TB). Results of reference and local laboratories were discordant in 121 (19.1%) cases, corresponding to a sensitivity of 84.3% and a specificity of 90.8%. In patients with drug-resistant tuberculosis, discordant results were associated with increased mortality (risk ratio 1.81; 95% CI 1.07-3.07). In logistic regression, compared to adequately treated patients with pan-susceptible strains, the adjusted odds ratio for death was 4.23 (95% CI 2.16-8.29) for adequately treated patients with drug-resistant strains and 21.54 (95% CI 3.36-138.1) for inadequately treated patients with drug-resistant strains. HIV status was not associated with mortality. Interpretation: Using a reference laboratory standard, inaccurate DST leading to inappropriate treatment of drug-resistant tuberculosis, but not HIV infection, contributed to mortality. Funding Statement: This research was supported by the Swiss National Science Foundation (grant numbers 153442, 310030_166687 and 174281), the National Institutes of Allergy and Infectious Diseases (NIAID) under award numbers U01 AI096299, U01 AI069919, U01 AI069924, U01 AI069911, U01 AI069907, U01 AI096186, and U01 AI069923, and Swiss National Center for Mycobacteria, University of Zurich, Switzerland. Declaration of Interests: AA has received honoraria fees from Jensen-Cilag, Gilead and Bristol-Myers Squibb. All other authors have no conflicts of interest to declare. Ethics Approval Statement:Local institutional review boards or ethics committees approved the study at all participating sites. Informed consent was obtained where requested per local regulations. The study was also approved by the Cantonal Ethics Committee in Bern, Switzerland.

Challenges and Benefits of Repurposing Products for Use during a Radiation Public Health Emergency: Lessons Learned from Biological Threats and other Disease Treatments.

The risk of a radiological or nuclear public health emergency is a major growing concern of the U.S. government. To address a potential incident and ensure that the government is prepared to respond to any subsequent civilian or military casualties, the U.S. Department of Health and Human Services and the Department of Defense have been charged with the development of medical countermeasures (MCMs) to treat the acute and delayed injuries that can result from radiation exposure. Because of the limited budgets in research and development and the high costs associated with bring promising approaches from the bench through advanced product development activities, and ultimately, to regulatory approval, the U.S. government places a priority on repurposing products for which there already exists relevant safety and other important information concerning their use in humans. Generating human data can be a costly and time-consuming process; therefore, the U.S. government has interest in drugs for which such relevant information has been established (e.g., products for another indication), and in determining if they could be repurposed for use as MCMs to treat radiation injuries as well as chemical and biological insults. To explore these possibilities, the National Institute of Allergy and Infectious Diseases (NIAID) convened a workshop including U.S. government, industry and academic subject matter experts, to discuss the challenges and benefits of repurposing products for a radiation indication. Topics covered included a discussion of U.S. government efforts (e.g. funding, stockpiling and making products available for study), as well unique regulatory and other challenges faced when repurposing patent protected or generic drugs. Other discussions involved lessons learned from industry on repurposing pre-license, pipeline products within drug development portfolios. This report reviews the information presented, as well as an overview of discussions from the meeting.

A Genome-wide Study of DNA Methylation in Nasal Epithelium and Atopy and Atopic Asthma in Children

BACKGROUND: Up to 10-12% of U.S. children and adolescents report respiratory or skin allergies. Epigenetic mechanisms may alter the airway epithelial barrier and ultimately lead to atopic diseases. Here we aim to identify DNA methylation profiles that are associated with - and accurately classify - atopy and atopic asthma in school-aged children. METHODS: We conducted an epigenome-wide study of DNA methylation in nasal epithelium and atopy or atopic asthma in 482 Puerto Rican children. Significant methylation signals were correlated with gene expression, and top CpGs were validated by pyrosequencing. We then replicated our top methylation findings in a cohort including 72 predominantly African American children, and in another cohort including 432 children of European descent. Next, we tested nasal methylation-based classification models of atopy or atopic asthma in all cohorts. FINDINGS: DNA methylation profiles were markedly different between subjects with and without atopy. After adjustment for covariates and multiple testing, we found 8,664 differentially methylated CpGs by atopy, with P-values ranging from 9·58*e-17 to 2·18*e-22 for the top 30 CpGs. These CpGs are in or near genes relevant to epithelial barrier function, including CDHR3 (cadherin-related family member 3) and CDH26 (cadherin 26), and in other biologically plausible genes like FBXL7 (F-box and leucine-rich repeat protein 7), NTRK1 (neurotrophic receptor tyrosine kinase 1), and SLC9A3 (solute carrier family 9 member A3). Moreover, 28 of the top 30 CpGs replicated in both cohorts. Nasal methylation-based classification models of atopy and atopic asthma performed well in the Puerto Rico cohort (area under the curve=0·93-0·94 and accuracy=85%-88%) and in both replication cohorts (AUC=0·74-0·92, accuracy=68%-82%). INTERPRETATION: We have identified methylation profiles in airway epithelium that are associated with atopy and atopic asthma in children, and a nasal methylation profile that classified children by atopy or atopic asthma. This panel performed well in three independent cohorts from different ethnic/racial backgrounds. Funding: This study was supported by grants HL079966, HL117191, and MD011764 (PI: Celedon JC) from the National Heart, Lung, and Blood Institute (NHLBI) of the U.S. National Institutes of Health (NIH). Dr. Forno’s contribution was supported by NIH grant HL125666. Dr. Celedon’s contribution was additionally supported by The Heinz Endowments. Research operations at the University of Puerto Rico were additionally supported by grant U54MD007587 from the National Institute on Minority Health and Health Disparities (NIMHD) and the National Institute of Allergy and Infectious Diseases (NIAID) of the U.S. NIH. PIAMA was supported by The Netherlands Organization for Health Research and Development; The Netherlands Organization for Scientific Research; The Netherlands Lung Foundation (with methylation studies supported by AF 4.1.14.001); The Netherlands Ministry of Spatial Planning, Housing, and the Environment; and The Netherlands Ministry of Health, Welfare, and Sport. Dr. Qi is supported by a grant from the China Scholarship Council. Declaration of Interest: Dr. Celedon has received research materials from Merck, GSK and Pharmavite, to provide medications free of cost to participants in NIH-funded studies, unrelated to the current work. The other authors report no conflicts of interest. Ethical Approval: The study was approved by the institutional review boards of the University of Puerto Rico (San Juan, PR) and the University of Pittsburgh (Pittsburgh, PA).

Subtype C ALVAC-HIV and bivalent subtype C gp120/MF59 HIV-1 vaccine in low-risk, HIV-uninfected, South African adults: a phase 1/2 trial

SummaryBackgroundModest efficacy was reported for the HIV vaccine tested in the RV144 trial, which comprised a canarypox vector (ALVAC) and envelope (env) glycoprotein (gp120). These vaccine components were adapted to express HIV-1 antigens from strains circulating in South Africa, and the adjuvant was changed to increase immunogenicity. Furthermore, 12-month immunisation was added to improve durability. In the HIV Vaccine Trials Network (HVTN) 100 trial, we aimed to assess this new regionally adapted regimen for advancement to efficacy testing.MethodsHVTN 100 is a phase 1/2, randomised controlled, double-blind trial at six community research sites in South Africa. We randomly allocated adults (aged 18–40 years) without HIV infection and at low risk of HIV infection to either the vaccine regimen (intramuscular injection of ALVAC-HIV vector [vCP2438] at 0, 1, 3, 6, and 12 months plus bivalent subtype C gp120 and MF59 adjuvant at 3, 6, and 12 months) or placebo, in a 5:1 ratio. Randomisation was done by computer-generated list. Participants, investigators, and those assessing outcomes were masked to random assignments. Primary outcomes included safety and immune responses associated with correlates of HIV risk in RV144, 2 weeks after vaccination at 6 months (month 6·5). We compared per-protocol participants (ie, those who completed the first four vaccinations and provided samples at month 6·5) from HVTN 100 with stored RV144 samples assayed contemporaneously. This trial is registered with the South African National Clinical Trials Registry (DOH-27-0215-4796) and ClinicalTrials.gov (NCT02404311).FindingsBetween Feb 9, 2015, and May 26, 2015, 252 participants were enrolled, of whom 210 were assigned vaccine and 42 placebo. 222 participants were included in the per-protocol analysis (185 vaccine and 37 placebo). 185 (100%) vaccine recipients developed IgG binding antibodies to all three vaccine-matched gp120 antigens with significantly higher titres (3·6–8·8 fold; all p<0·0001) than the corresponding vaccine-matched responses of RV144. The CD4+ T-cell response to the ZM96.C env protein in HVTN 100 was 56·4% (n=102 responders), compared with a response of 41·4% (n=79 responders) to 92TH023.AE in RV144 (p=0·0050). The IgG response to the 1086.C variable loops 1 and 2 (V1V2) env antigen in HVTN 100 was 70·5% (95% CI 63·5–76·6; n=129 responders), lower than the response to V1V2 in RV144 (99·0%, 95% CI 96·4–99·7; n=199 responders).InterpretationAlthough the IgG response to the HVTN 100 vaccine was lower than that reported in RV144, it exceeded the predicted 63% threshold needed for 50% vaccine efficacy using a V1V2 correlate of protection model. Thus, the subtype C HIV vaccine regimen qualified for phase 2b/3 efficacy testing, a critical next step of vaccine development.FundingUS National Institute of Allergy and Infectious Diseases (NIAID), and Bill & Melinda Gates Foundation.

Assessing Cat Flea Microbiomes in Northern and Southern California by 16S rRNA Next-Generation Sequencing.

Flea-borne diseases (FBDs) impact both human and animal health worldwide. Because adult fleas are obligately hematophagous and can harbor potential pathogens, fleas act as ectoparasites of vertebrates, as well as zoonotic disease vectors. Cat fleas (Ctenocephalides felis) are important vectors of two zoonotic bacterial genera listed as priority pathogens by the National Institute of Allergy and Infectious Diseases (NIAID-USA): Bartonella spp. and Rickettsia spp., causative agents of bartonelloses and rickettsioses, respectively. In this study, we introduce the first microbiome analysis of C. felis samples from California, determining the presence and abundance of relevant pathogenic genera by characterizing the cat flea microbiome through 16S rRNA next-generation sequencing (16S-NGS). Samples from both northern (NoCal) and southern (SoCal) California were assessed to expand current knowledge regarding FBDs in the state. We identified Rickettsia and Bartonella, as well as the endosymbiont Wolbachia, as the most abundant genera, followed by less abundant taxa. In comparison to our previous study screening Californian cat fleas for rickettsiae using PCR/digestion/sequencing of the ompB gene, the 16S-NGS approach applied herein showed a 95% level of agreement in detecting Rickettsia spp. There was no overall difference in microbiome diversity between NoCal and SoCal samples. Bacterial taxa identified by 16S-NGS in this study may help to improve epidemiological investigations, pathogen surveillance efforts, and clinical diagnostics of FBDs in California and elsewhere.

Use of External Quality Control Material for HIV-1 RNA Testing To Assess the Comparability of Data Generated in Separate Laboratories and the Stability of HIV-1 RNA in Samples after Prolonged Storage

The National Institute of Allergy and Infectious Diseases (NIAID) AIDS Clinical Trials Group (ACTG) stores specimens from its clinical trials in a biorepository and permits the use of these specimens for nonprotocol exploratory studies, once the studies for the original protocol are concluded. We sought to assess the comparability of the data generated from real-time HIV-1 RNA testing during two clinical trials with the data generated from the retesting of different aliquots of the same samples after years of storage at -80°C. Overall, there was 92% agreement in the data generated for 1,570 paired samples (kappa statistic = 0.757; 95% confidence interval [CI], 0.716 to 0.797), where samples were tested in one laboratory using the microwell plate (MWP) version of the Roche HIV-1 Monitor test within 1 to 37 days of collection and retested in another laboratory using the Cobas version of the assay after a median of 6.7 years of storage (range, 5.7 to 8.6 years). Historical external quality control data submitted to the NIAID Virology Quality Assurance program (VQA) by client laboratories using the same two versions of the Monitor assay were used to differentiate between systematic differences in the assays to evaluate the stability of HIV-1 RNA in the stored samples. No significant loss of RNA was noted in samples containing either a low concentration (<50 copies/ml) or a high concentration (≥50 copies/ml) of HIV-1 RNA (P = 0.10 and P = 0.90, respectively) regardless of the time in storage. These data confirm the quality of the plasma samples in the ACTG biorepository following long-term storage.

Assessing effects of behavioral intervention on treatment outcomes among patients initiating HIV care: Rationale and design of iENGAGE intervention trial

During the initial year of HIV diagnosis, while patients are often overwhelmed adjusting to this life changing diagnosis, they must develop self-care behaviors for attending regular medical care visits and antiretroviral therapy (ART) adherence to achieve and sustain viral suppression (VS). Maintaining “HIV adherence” and integrating it into one's daily life is required to sustain VS over time. The HIV care continuum or “treatment cascade,” an epidemiological snapshot of the national epidemic in the United States (US), indicates that a minority of persons living with HIV (PLWH) have achieved VS. Little evidence exists regarding the effects of interventions focusing on PLWH newly initiating outpatient HIV care. An intervention that focuses on both retention in care and ART adherence skills delivered during the pivotal first year of HIV care is lacking.To address this, we developed a theory-based intervention evaluated in the Integrating Engagement and Adherence Goals upon Entry (iENGAGE) study, a National Institute of Allergy and Infectious Diseases (NIAID) funded randomized behavioral intervention trial. Here we present the study objectives, design and rationale, as well as the intervention components, targeting rapid and sustained VS through retention in HIV care and ART adherence during participants' first year of HIV care. The primary outcome of the study is 48-week VS (<200 c/mL). The secondary outcomes are retention in care, including HIV visit adherence and visit constancy, as well as ART adherence.

Identification of Novel 5,6-Dimethoxyindan-1-one Derivatives as Antiviral Agents.

Discovery of novel antiviral agents is essential because viral infection continues to threaten human life globally. Various heterocyclic small molecules have been developed as antiviral agents. The 5,6-dimethoxyindan-1-on nucleus is of considerable interest as this ring is the key constituent in a range of bioactive compounds, both naturally occurring and synthetic, and often of considerable complexity. The main purpose of this research was to discover and develop small molecule heterocycles as broad-spectrum of antiviral agents. A focused small set of 5,6-dimethoxyindan-1-one analogs (6-8) along with a thiopene derivative (9) was screened for selected viruses (Vaccinia virus - VACA, Human papillomavirus - HPV, Zika virus - ZIKV, Dengue virus - DENV, Measles virus - MV, Poliovirus 3 - PV, Rift Valley fever virus - RVFV, Tacaribe virus - TCRV, Venezuelan equine encephalitis virus - VEEV, Herpes simplex virus 1 -HSV-1 and Human cytomegalovirus - HCMV) using the National Institute of Allergy and Infectious Diseases (NIAID)'s Division of Microbiology and Infectious Diseases (DMID) antiviral screening program. These molecules demonstrated moderate to excellent antiviral activity towards variety of viruses. The 5,6-dimethoxyindan-1-one analog (7) demonstrated high efficacy towards vaccinia virus (EC50: <0.05 µM) and was nearly 232 times more potent than the standard drug Cidofovir (EC50: 11.59 µM) in primary assay whereas it demonstrated moderate activity (EC50: >30.00 µM) in secondary plaque reduction assay. The thiophene analog (9) has shown very good viral inhibition towards several viruses such as Human papillomavirus, Measles virus, Rift Valley fever virus, Tacaribe virus and Herpes simplex virus 1. Our research identified a novel 5,6-dimethoxyindan-1-one analog (compound 7), as a potent antiviral agent for vaccinia virus, and heterocyclic chalcone analog (compound 9) as a broad spectrum antiviral agent.

Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis.

Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools. The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights. Nephele integrates common microbiome analysis tools as well as valuable reference datasets like the healthy human subjects cohort of the Human Microbiome Project (HMP). Nephele is built on the Amazon Web Services cloud, which provides centralized and automated storage and compute capacity, thereby reducing the burden on researchers and their institutions. https://nephele.niaid.nih.gov and https://github.com/niaid/Nephele. darrell.hurt@nih.gov.

Editorial introductions

Editorial introductions

A Novel Surface Plasmon Resonance Biosensor for the Rapid Detection of Botulinum Neurotoxins.

Botulinum neurotoxins (BoNTs) are Category A agents on the NIAID (National Institute of Allergy and Infectious Diseases) priority pathogen list owing to their extreme toxicity and the relative ease of production. These deadly toxins, in minute quantities (estimated human i.v. lethal dose LD50 of 1–2 ng/kg body weight), cause fatal flaccid paralysis by blocking neurotransmitter release. The current gold standard detection method, the mouse-bioassay, often takes days to confirm botulism. Furthermore, there are no effective antidotes known to reverse the symptoms of botulism, and as a result, patients with severe botulism often require meticulous care during the prolonged paralytic illness. To combat potential bio-terrorism incidents of botulinum neurotoxins, their rapid detection is paramount. Surface plasmon resonance (SPR) is a very sensitive technique to examine bio-molecular interactions. The label-free, real-time analysis, with high sensitivity and low sample consumption makes this technology particularly suitable for detection of the toxin. In this study, we demonstrated the feasibility in an assay with a newly designed SPR instrument for the rapid detection of botulinum neurotoxins. The LOD (limit of detection) of the Newton Photonics (NP) SPR based assay is 6.76 pg/mL for Botulinum Neurotoxin type A Light Chain (BoNT/A LC). We established that the detection sensitivity of the system is comparable to the traditional mouse LD50 bioassay in BoNT/A using this SPR technology.

Prediction of promiscuous T cell epitopes in RNA dependent RNA polymerase of Chikungunya virus.

To explore RNA dependent RNA polymerase of Chikungunya virus (CHIKV) and develop T cell based epitopes with high antigenicity and good binding affinity for the human leukocyte antigen (HLA) classes as targets for epitopes based CHIKV vaccine. In this study we downloaded 371 non-structural protein 4 protein sequences of CHIKV belonging to different regions of the world from the US National Institute of Allergy and Infectious Diseases (NIAID) virus pathogen resource database. All the sequences were aligned by using CLUSTALW software and a consensus sequence was developed by using Uni Pro U Gene Software version 1.2.1. Propred I and Propred software were used to predict HLA I and HLA II binding promiscuous epitopes from the consensus sequence of non-structural protein 4 protein. The predicted epitopes were analyzed to determine their antigenicity through Vaxijen server version 2.0. All the HLA I binding epitopes were scanned to determine their immunogenic potential through the Immune Epitope Database (IEDB). All the predicted epitopes of our study were fed to IEDB database to determine whether they had been tested earlier. Twenty two HLA class II epitopes and eight HLA class I epitopes were predicted. The promiscuous epitopes WMNMEVKII at position 486-494 and VRRLNAVLL at 331-339 were found to bind with 37 and 36 of the 51 HLA class II alleles respectively. Epitope MANRSRYQS at position 58-66 and epitopes YQSRKVENM at positions 64-72 were predicted to bind with 12 and 9 HLA II alleles with antigenicity scores of 0.754 9 and 1.013 0 respectively. Epitope YSPPINVRL was predicted to bind 18 HLA I alleles and its antigenicity score was 1.425 9 and immunogenicity score was 0.173 83. This epitope is very useful in the preparation of a universal vaccine against CHIKV infection. Epitopes reported in this study showed promiscuity, antigenicity as well as good binding affinity for the HLA classes. These epitopes will provide the baseline for development of efficacious vaccine for CHIKV.

Endotypes of difficult-to-control asthma in inner-city African American children.

African Americans have higher rates of asthma prevalence, morbidity, and mortality in comparison with other racial groups. We sought to characterize endotypes of childhood asthma severity in African American patients in an inner-city pediatric asthma population. Baseline blood neutrophils, blood eosinophils, and 38 serum cytokine levels were measured in a sample of 235 asthmatic children (6–17 years) enrolled in the NIAID (National Institute of Allergy and Infectious Diseases)-sponsored Asthma Phenotypes in the Inner City (APIC) study (ICAC (Inner City Asthma Consortium)-19). Cytokines were quantified using a MILLIPLEX panel and analyzed on a Luminex analyzer. Patients were classified as Easy-to-Control or Difficult-to-Control based on the required dose of controller medications over one year of prospective management. A multivariate variable selection procedure was used to select cytokines associated with Difficult-to-Control versus Easy-to-Control asthma, adjusting for age, sex, blood eosinophils, and blood neutrophils. In inner-city African American children, 12 cytokines were significant predictors of Difficult-to-Control asthma (n = 235). CXCL-1, IL-5, IL-8, and IL-17A were positively associated with Difficult-to-Control asthma, while IL-4 and IL-13 were positively associated with Easy-to-Control asthma. Using likelihood ratio testing, it was observed that in addition to blood eosinophils and neutrophils, serum cytokines improved the fit of the model. In an inner-city pediatric population, serum cytokines significantly contributed to the definition of Difficult-to-Control asthma endotypes in African American children. Mixed responses characterized by TH2 (IL-5) and TH17-associated cytokines were associated with Difficult-to-Control asthma. Collectively, these data may contribute to risk stratification of Difficult-to-Control asthma in the African American population.

Waning Immunity and Microbial Vaccines-Workshop of the National Institute of Allergy and Infectious Diseases.

Since the middle of the 20th century, vaccines have made a significant public health impact by controlling infectious diseases globally. Although long-term protection has been achieved with some vaccines, immunity wanes over time with others, resulting in outbreaks or epidemics of infectious diseases. Long-term protection against infectious agents that have a complex life cycle and antigenic variation remains a key challenge. Novel strategies to characterize the short- and long-term immune responses to vaccines and to induce immune responses that mimic natural infection have recently emerged. New technologies and approaches in vaccinology, such as adjuvants, delivery systems, and antigen formulations, have the potential to elicit more durable protection and fewer adverse reactions; together with in vitro systems, these technologies have the capacity to model and accelerate vaccine development. The National Institute of Allergy and Infectious Diseases (NIAID) held a workshop on 19 September 2016 that focused on waning immunity to selected vaccines (for Bordetella pertussis, Salmonella enterica serovar Typhi, Neisseria meningitidis, influenza, mumps, and malaria), with an emphasis on identifying knowledge gaps, future research needs, and how this information can inform development of more effective vaccines for infectious diseases.

A Web-Based Data Collection Platform for Multisite Randomized Behavioral Intervention Trials: Development, Key Software Features, and Results of a User Survey.

BackgroundMeticulous tracking of study data must begin early in the study recruitment phase and must account for regulatory compliance, minimize missing data, and provide high information integrity and/or reduction of errors. In behavioral intervention trials, participants typically complete several study procedures at different time points. Among HIV-infected patients, behavioral interventions can favorably affect health outcomes. In order to empower newly diagnosed HIV positive individuals to learn skills to enhance retention in HIV care, we developed the behavioral health intervention Integrating ENGagement and Adherence Goals upon Entry (iENGAGE) funded by the National Institute of Allergy and Infectious Diseases (NIAID), where we deployed an in-clinic behavioral health intervention in 4 urban HIV outpatient clinics in the United States. To scale our intervention strategy homogenously across sites, we developed software that would function as a behavioral sciences research platform.ObjectiveThis manuscript aimed to: (1) describe the design and implementation of a Web-based software application to facilitate deployment of a multisite behavioral science intervention; and (2) report on results of a survey to capture end-user perspectives of the impact of this platform on the conduct of a behavioral intervention trial.MethodsIn order to support the implementation of the NIAID-funded trial iENGAGE, we developed software to deploy a 4-site behavioral intervention for new clinic patients with HIV/AIDS. We integrated the study coordinator into the informatics team to participate in the software development process. Here, we report the key software features and the results of the 25-item survey to evaluate user perspectives on research and intervention activities specific to the iENGAGE trial (N=13).ResultsThe key features addressed are study enrollment, participant randomization, real-time data collection, facilitation of longitudinal workflow, reporting, and reusability. We found 100% user agreement (13/13) that participation in the database design and/or testing phase made it easier to understand user roles and responsibilities and recommended participation of research teams in developing databases for future studies. Users acknowledged ease of use, color flags, longitudinal work flow, and data storage in one location as the most useful features of the software platform and issues related to saving participant forms, security restrictions, and worklist layout as least useful features.ConclusionsThe successful development of the iENGAGE behavioral science research platform validated an approach of early and continuous involvement of the study team in design development. In addition, we recommend post-hoc collection of data from users as this led to important insights on how to enhance future software and inform standard clinical practices.Trial RegistrationClinicaltrials.gov NCT01900236; (https://clinicaltrials.gov/ct2/show/NCT01900236 (Archived by WebCite at http://www.webcitation.org/6qAa8ld7v)