Genotype 1 and global hepatitis C T-cell vaccines designed to optimize coverage of genetic diversity.

Immunological control of hepatitis C virus (HCV) is possible and is probably mediated by host T-cell responses, but the genetic diversity of the virus poses a major challenge to vaccine development. We considered monovalent and polyvalent candidates for an HCV vaccine, including natural, consensus and synthetic 'mosaic' sequence cocktails. Mosaic vaccine reagents were designed using a computational approach first applied to and demonstrated experimentally for human immunodeficiency virus type 1 (HIV-Delta). Mosaic proteins resemble natural proteins, but are assembled from fragments of natural sequences via a genetic algorithm and optimized to maximize the coverage of potential T-cell epitopes (all 9-mers) found in natural sequences and to minimize the inclusion of rare 9-mers to avoid vaccine-specific responses. Genotype 1-specific and global vaccine cocktails were evaluated. Among vaccine candidates considered, polyvalent mosaic sequences provided the best coverage of both known and potential epitopes and had the fewest rare epitopes. A global vaccine based on conserved proteins across genotypes may be feasible, as a five-antigen mosaic cocktail provided 90, 77 and 70% coverage of the Core, NS3 and NS4 proteins, respectively; protein coverage diminished with increased protein variability, dropping to 38% for NS2. For the genotype 1-specific vaccine, the H77 prototype vaccine sequence matched only 50% of the potential epitopes in the population, whilst a polyprotein three-antigen mosaic cocktail increased potential epitope coverage to 83%. More than 75% coverage of all HCV proteins was achieved with a three-antigen mosaic cocktail, suggesting that genotype-specific vaccines could also include the more variable proteins.

The hepatitis C sequence database in Los Alamos.

The hepatitis C virus (HCV) is a significant public health threat worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. Presently, approximately 50 000 HCV sequences have been published. A central website that provides annotated sequences and analysis tools will be helpful to HCV scientists worldwide. The HCV sequence database collects and annotates sequence data, and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database. The HCV website can be accessed via http://hcv.lanl.gov and http://hcv-db.org.

Web-based design and evaluation of T-cell vaccine candidates.

UNLABELLED: We present a suite of on-line tools to design candidate vaccine proteins, and to assess antigen potential, using coverage of k-mers (as proxies for potential T-cell epitopes) as a metric. The vaccine design tool uses the recently published 'mosaic' method to generate protein sequences optimized for coverage of high-frequency k-mers; the coverage-assessment tools facilitate coverage comparisons for any potential antigens. To demonstrate these tools, we designed mosaic protein sets for B-clade HIV-1 Gag, Pol and Nef, and compared them to antigens used in a recent human vaccine trial. AVAILABILITY: http://hiv.lanl.gov/content/sequence/MOSAIC/.

Los Alamos hepatitis C virus sequence and human immunology databases: an expanding resource for antiviral research.

The hepatitis C virus (HCV) resource at Los Alamos (hcv.lanl.gov) provides access to multiple databases: one containing annotated sequences and the other a repository of immunogenic epitopes. They are derived from databases originally developed for HIV research (hiv.lanl.gov). HCV and HIV are RNA viruses with relatively compact genomes (around 10 kb) that are extraordinarily variable, both within and between hosts. This diversity requires methods to track and exclude variants from an individual infection or from epidemiologically related infections, and tools to analyse the variation. The HCV immunology database contains a curated inventory of immunogenic epitopes and information about their interaction with the host immune system, with associated retrieval and analysis tools. This interactive resource provides flexible retrieval tools for sequences, epitopes, clinical information, and meta-data, as well as utilities for scientific data analysis, to investigators with internet access and a web browser. This paper describes the types of data and the services that these databases offer, the tools they provide, and their configuration and use. Examples of applications to clonal analysis for drug-resistance mutations are shown.

An analysis of Brain Trauma Foundation traumatic brain injury guideline compliance and patient outcome.

INTRODUCTION: Evidence-based guidelines for the care of severe traumatic brain injury have been available from the Brain Trauma Foundation (BTF) since 1995. A total of 15 recommendations compose the current guidelines. Although each individual guideline has been validated in isolation, to date, little research has examined the guidelines in composite. We examined the relationship between compliance with the BTF severe TBI guidelines and mortality. MATERIALS AND METHODS: In a Pennsylvania-verified, mature Level II trauma centre, patients with an admission Glasgow Coma Scale (GCS) ≤ 8 and an abnormal head CT from 2007 to 2012 were queried from the trauma registry. Exclusion criteria included: patients who sustained a non-survivable injury (AIS head 6), died ≤ 24 h, and/or were transferred to a paediatric trauma centre. Strict adherence to the BTF guidelines was determined in a binary fashion (yes/no). We then calculated each patient's percent compliance with total number of guidelines. Bivariate analysis was used to find significant predictors of mortality (p<0.05), including percent BTF guidelines compliance. Significant factors were added to a multivariable logistic regression model to look at mortality rates across the percent compliance spectrum. RESULTS: 185 Patients met inclusion criteria. Percent compliance ranged from 28.6% to 94.4%, (median=71.4%). Following adjustment for age, AIS head, and GCS motor, patients with 55-75% compliance (AOR: 0.20; 95%CI: 0.06-0.70) and >75% compliance (AOR: 0.27; 95%CI: 0.08-0.94) had reduced odds of mortality, as compared to <55% compliance to the BTF guidelines. When the unadjusted rate of mortality was compared across the compliance spectrum, the odds of mortality decreased as compliance increased until 75%, and then reversed. CONCLUSION: Our data indicate that full compliance with all 15 severe TBI guidelines is difficult to achieve and may not be necessary to optimally care for patients.

Designing and testing broadly-protective filoviral vaccines optimized for cytotoxic T-lymphocyte epitope coverage.

We report the rational design and in vivo testing of mosaic proteins for a polyvalent pan-filoviral vaccine using a computational strategy designed for the Human Immunodeficiency Virus type 1 (HIV-1) but also appropriate for Hepatitis C virus (HCV) and potentially other diverse viruses. Mosaics are sets of artificial recombinant proteins that are based on natural proteins. The recombinants are computationally selected using a genetic algorithm to optimize the coverage of potential cytotoxic T lymphocyte (CTL) epitopes. Because evolutionary history differs markedly between HIV-1 and filoviruses, we devised an adapted computational technique that is effective for sparsely sampled taxa; our first significant result is that the mosaic technique is effective in creating high-quality mosaic filovirus proteins. The resulting coverage of potential epitopes across filovirus species is superior to coverage by any natural variants, including current vaccine strains with demonstrated cross-reactivity. The mosaic cocktails are also robust: mosaics substantially outperformed natural strains when computationally tested against poorly sampled species and more variable genes. Furthermore, in a computational comparison of cross-reactive potential a design constructed prior to the Bundibugyo outbreak performed nearly as well against all species as an updated design that included Bundibugyo. These points suggest that the mosaic designs would be more resilient than natural-variant vaccines against future Ebola outbreaks dominated by novel viral variants. We demonstrate in vivo immunogenicity and protection against a heterologous challenge in a mouse model. This design work delineates the likely requirements and limitations on broadly-protective filoviral CTL vaccines.

Traumatic venous varix causing sciatic neuropathy: case report.

OBJECTIVE AND IMPORTANCE: Sciatic neuropathy rarely presents in nonpenetrating trauma because of protection of the nerve by the pelvis, the gluteal muscles, and the tissues in the posterior thigh. We present the case of a patient who fell and subsequently developed a traumatic venous varix of the inferior gluteal vein that caused compression sciatic neuropathy. CLINICAL PRESENTATION: Seven days after a fall onto her right buttock, the patient developed a painful burning paresthesia in her leg and numbness on the dorsum of her foot. Numerous studies ruled out lumbar spine pathological abnormalities as the cause of the pain. Conventional magnetic resonance imaging revealed a lesion adjacent to the sciatic nerve. Gradient echo and two-dimensional time-of-flight magnetic resonance imaging sequences confirmed this to be a vascular lesion originating from the inferior gluteal vein and compressing the sciatic nerve. INTERVENTION: Operative resection obliterated the venous varix, thereby relieving the patient's pain and neurological deficit. CONCLUSION: No case of a traumatic venous varix of the inferior gluteal vein compressing the sciatic nerve has been reported to date. Surgical resection was successful in obliterating the lesion and relieving the symptoms.