C65 POST–DISCHARGE ARRHYTHMIC RISK STRATIFICATION OF PATIENTS WITH ACUTE MYOCARDITIS AND LIFE–THREATENING VENTRICULAR TACHYARRHYTHMIAS

Aims

The outcomes of patients presenting with acute myocarditis and life–threatening ventricular arrhythmias (LT–VA) are unclear. The aim of this study was to assess the incidence and predictors of recurrent major arrhythmic events (MAEs) after hospital discharge in this patient population.

Methods and Results

We retrospectively analysed 156 patients (median age 44 years; 77% male) discharged with a diagnosis of acute myocarditis and LT–VA from 16 hospitals worldwide. Diagnosis of myocarditis was based on histology or the combination of increased markers of cardiac injury and cardiac magnetic resonance (CMR) Lake Louise criteria. MAEs were defined as the relapse, after discharge, of sudden cardiac death or successfully defibrillated ventricular fibrillation, or sustained ventricular tachycardia (sVT) requiring implantable cardioverter–defibrillator therapy or synchronized external cardioversion. Median follow–up was 23months [first to third quartile (Q1–Q3) 7–60]. Fifty–eight (37.2%) patients experienced MAEs after discharge, at a median of 8 months (Q1–Q3 2.5–24.0 months; 60.3% of MAEs within the first year). At multivariable Cox analysis, variables independently associated with MAEs were presentation with sVT [hazard ratio (HR) 2.90, 95% confidence interval (CI) 1.38–6.11]; late gadolinium enhancement involving ≥2 myocardial segments (HR 4.51, 95% CI 2.39–8.53), and absence of positive short–tau inversion recovery (STIR) (HR 2.59, 95% CI 1.40–4.79) at first CMR.

Conclusions

In this international multicentre study, patients discharged free from HTx or LVAD after an acute myocarditis complicated by LT–VA had a recurrence of MAEs during follow–up of 37.2%, after a median time of 8 months. Initial CMR pattern and sVT at presentation stratify the risk of arrhythmia recurrence.

Estimating the cost of interventions to improve water, sanitation and hygiene in healthcare facilities across India

Introduction

Despite increasing utilisation of institutional healthcare in India, many healthcare facilities (HCFs) lack access to basic water, sanitation and hygiene (WASH) services. WASH services protect patients by improving infection prevention and control (IPC), which in turn can reduce the burden of healthcare-associated infections (HAIs). However, data on the cost of implementing WASH interventions in Indian HCFs are limited.

Methods

We surveyed 32 HCFs across India, varying in size, type and setting to obtain the direct costs of providing improved water supply, sanitation and IPC-supporting infrastructure. We calculated the average costs of WASH interventions and the number of HCFs nationwide requiring investments in WASH to estimate the financial cost of improving WASH across India’s public healthcare system over 1 year.

Results

Improving WASH across India’s public healthcare sector and sustaining services among upgraded facilities for 1 year would cost US$354 million in capital costs and US$289 million in recurrent costs from the provider perspective. The most costly interventions were those on water (US$238 million), linen reprocessing (US$112 million) and sanitation (US$104 million), while the least costly were interventions on hand hygiene (US$52 million), medical device reprocessing (US$56 million) and environmental surface cleaning (US$80 million). Overall, investments in rural HCFs would account for 64.4% of total costs, of which 52.3% would go towards primary health centres.

Conclusion

Improving IPC in Indian public HCFs can aid in the prevention of HAIs to reduce the spread of antimicrobial resistance. Although WASH is a necessary component of IPC, coverage remains low in HCFs in India. Using ex-post costs, our results estimate the investment levels needed to improve WASH across the Indian public healthcare system and provide a basis for policymakers to support IPC-related National Action Plan activities for antimicrobial resistance through investments in WASH.

Utilization of cardiac MRI for the assessment of suspected rejection with negative biopsy in heart transplant recipients

Background

Heart transplant (HTx) patients can develop graft dysfunction (GD) without biopsy evidence of cell or antibody mediated rejection. Cardiac MRI (CMR) can detect inflammatory or infiltrative causes of cardiomyopathy however CMR findings in HTx recipients with GD have not been previously described.

Purpose

We sought to identify CMR characteristics of HTx patients with GD, and evaluate its additive value in its diagnosis and prognosis.

Methods

CMR has been performed routinely to evaluate GD at our institutions. There were 37 HTx recipients who presented with acute decline in left ventricular ejection fraction (LVEF) of <50% and >10% from baseline, with no biopsy evidence of rejection between 2007 and 2018. Coronary angiogram with IVUS was done to rule out allograft vasculopathy. Treatment of GD was per discretion of the treating clinician. Responders were defined as those with LVEF improvement >10% at 180 days or greater post-presentation. LV and RV indices, the presence and pattern of late gadolinium enhancement (LGE) were determined by CMR.

Results

There were 34% females and mean age at transplant was 49±13 years. Median time from HTx to GD was 1.2 years. Presenting symptoms were heart failure (n=25), cardiogenic shock (n=1) and 11 patients were asymptomatic. Mean LVEF at presentation was 37±12% and donor specific antibodies were detected in 38% patients. Most patients were treated with steroid bolus (n=29), and/or plasmapheresis (n=23). There were no major changes made in immunosuppression in 6 patients. Delayed enhancement MRI was performed with standard inversion-recovery (IR) gradient echo sequences, between 5 and 20 minutes after institutional-standard protocol administration of IV gadolinium contrast. Biventricular LGE was present in 18/37 (49%) patients with GD and was more prevalent in responders (57%, 13 of 23) than non-responders (35%, 5 of 14), although not statistically significant (p=0.21). There were two patterns of LGE noted: 1) Diffuse epicardial (10 patients out which 9 were responders) and 2) Patchy pattern with non-specific distribution (8 patients out of which 4 were responders). Myocardial edema by triple IR sequencing was seen in 6 patients, all having diffuse epicardial pattern of enhancement matching the delayed enhancement pattern. When comparing different treatment groups, among those treated for GD (n=31), 12 of 21 (57%) responders had LGE and 4 of 10 (40%) non-responders had LGE (p=0.37), a pattern similar to the broader population. Among those not treated for GD (n=6), 1 of 2 responders had LGE and 1 of 4 non-responders had LGE (p=0.5).

Conclusion

CMR identified inflammation as a potential cause of GD in approximately 50% of HTx patients. There are 2 distinct patterns of LGE observed in GD, diffuse epicardial (56%) and patchy (44%). Although the presence of LGE in itself is not associated with myocardial recovery, 90% of patients with a diffuse epicardial pattern have recovery of GD.

Funding Acknowledgement

Type of funding source: None

Sequencing and analysis of globally obtained human parainfluenza viruses 1 and 3 genomes

Human Parainfluenza viruses (HPIV) type 1 and 3 are important causes of respiratory tract infections in young children globally. HPIV infections do not confer complete protective immunity so reinfections occur throughout life. Since no effective vaccine is available for the two virus subtypes, comprehensive understanding of HPIV-1 and HPIV-3 genetic and epidemic features is important for diagnosis, prevention, and treatment of HPIV-1 and HPIV-3 infections. Relatively few whole genome sequences are available for both HPIV-1 and HPIV-3 viruses, so our study sought to provide whole genome sequences from multiple countries to further the understanding of the global diversity of HPIV at a whole-genome level. We collected HPIV-1 and HPIV-3 samples and isolates from Argentina, Australia, France, Mexico, South Africa, Switzerland, and USA from the years 2003-2011 and sequenced the genomes of 40 HPIV-1 and 75 HPIV-3 viruses with Sanger and next-generation sequencing with the Ion Torrent, Illumina, and 454 platforms. Phylogenetic analysis showed that the HPIV-1 genome is evolving at an estimated rate of 4.97 × 10-4 mutations/site/year (95% highest posterior density 4.55 × 10-4 to 5.38 × 10-4) and the HPIV-3 genome is evolving at a similar rate (3.59 × 10-4 mutations/site/year, 95% highest posterior density 3.26 × 10-4 to 3.94 × 10-4). There were multiple genetically distinct lineages of both HPIV-1 and 3 circulating on a global scale. Further surveillance and whole-genome sequencing are greatly needed to better understand the spatial dynamics of these important respiratory viruses in humans.

Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains

The recent emergence of Zika virus (ZIKV) has been concentrated in the Caribbean, Southeastern United States, and South- and Central America; resulting in travel-based cases being reported around the globe. As multi-disciplinary collaborations are combatting the ZIKV outbreak, the need to validate the sequence of existing strains has become apparent. Here, we report high-quality sequence data for multiple ZIKV strains made publicly available through the National Institutes of Health- (NIH) funded biorepository, BEI Resources (www.beiresources.org). Next-generation sequencing, 3' rapid amplification of cDNA ends (RACE), and viral genome annotation pipelines generated GenBank sequence records for 16 BEI Resources strains. Minor variants, consensus mutations, and consensus insertions/deletions were identified within the viral stocks using next-generation sequencing (NGS) and consensus changes were confirmed with Sanger sequencing. Bioinformatics analyses of the sequencing results confirm that the virus stocks available to the scientific research community through BEI Resources adequately represent the viral population diversity of ZIKV.

Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic

Chikungunya virus (CHIKV) has been detected sporadically since the 1950s and includes three distinct co-circulating genotypes. In late 2013, the Asian genotype of CHIKV was responsible for the Caribbean outbreak (CO) that rapidly became an epidemic throughout the Americas. There is a limited understanding of the molecular evolution of CHIKV in the Americas during this epidemic. We sequenced 185 complete CHIKV genomes collected mainly from Nicaragua in Central America and Florida in the United States during the 2014-2015 Caribbean/Americas epidemic. Our comprehensive phylogenetic analyses estimated the epidemic history of the Asian genotype and the recent Caribbean outbreak (CO) clade, revealed considerable genetic diversity within the CO clade, and described different epidemiological dynamics of CHIKV in the Americas. Specifically, we identified multiple introductions in both Nicaragua and Florida, with rapid local spread of viruses in Nicaragua but limited autochthonous transmission in Florida in the US. Our phylogenetic analysis also showed phylogeographic clustering of the CO clade. In addition, we identified the significant amino acid substitutions that were observed across the entire Asian genotype during its evolution and examined amino acid changes that were specific to the CO clade. Deep sequencing analysis identified specific minor variants present in clinical specimens below-consensus levels. Finally, we investigated the association between viral phylogeny and geographic/clinical metadata in Nicaragua. To date, this study represents the largest single collection of CHIKV complete genomes during the Caribbean/Americas epidemic and significantly expands our understanding of the emergence and evolution of CHIKV CO clade in the Americas.

Whole-genome sequencing and analyses identify high genetic heterogeneity, diversity and endemicity of rotavirus genotype P[6] strains circulating in Africa

Rotavirus A (RVA) exhibits a wide genotype diversity globally. Little is known about the genetic composition of genotype P[6] from Africa. This study investigated possible evolutionary mechanisms leading to genetic diversity of genotype P[6] VP4 sequences. Phylogenetic analyses on 167 P[6] VP4 full-length sequences were conducted, which included six porcine-origin sequences. Of the 167 sequences, 57 were newly acquired through whole genome sequencing as part of this study. The other 110 sequences were all publicly-available global P[6] VP4 full-length sequences downloaded from GenBank. The strength of association between the phenotypic features and the phylogeny was also determined. A number of reassortment and mixed infections of RVA genotype P[6] strains were observed in this study. Phylogenetic analyses demostrated the extensive genetic diversity that exists among human P[6] strains, porcine-like strains, their concomitant clades/subclades and estimated that P[6] VP4 gene has a higher substitution rate with the mean of 1.05E-3 substitutions/site/year. Further, the phylogenetic analyses indicated that genotype P[6] strains were endemic in Africa, characterised by an extensive genetic diversity and long-time local evolution of the viruses. This was also supported by phylogeographic clustering and G-genotype clustering of the P[6] strains when Bayesian Tip-association Significance testing (BaTS) was applied, clearly supporting that the viruses evolved locally in Africa instead of spatial mixing among different regions. Overall, the results demonstrated that multiple mechanisms such as reassortment events, various mutations and possibly interspecies transmission account for the enormous diversity of genotype P[6] strains in Africa. These findings highlight the need for continued global surveillance of rotavirus diversity.

Augmentation of hepatitis C virus-specific immunity and sustained virologic response

Treatment for chronic hepatitis C virus (HCV) infection has rapidly evolved into interferon-free directly acting antiviral regimens (DAA) that result in high sustained virologic response. DAAs primarily work by suppressing HCV replication and rely less on the immune system than interferon-based therapies. However, it is unclear whether the immune system recovers with suppression of HCV replication and contributes to HCV clearance with DAA therapy. We previously demonstrated HCV clearance is associated with increased HCV-specific immunity in CHCV-GT-1-infected patients during treatment with sofosbuvir (SOF)+ribavirin (RBV). Here, we aimed to analyse changes in HCV-specific immunological responses associated with viral clearance with combination DAA therapy of SOF+ledipasvir (LDV) for 12 weeks in CHCV-GT1 (N=14) patients who relapsed without augmentation of HCV-specific immunity during treatment with SOF+RBV. Phenotypic and functional changes within the T-cell compartment of PBMCs pre- and post-treatment were analysed. Retreatment of relapsers with LDV/SOF resulted in all patients attaining SVR12 . Suppression of HCV was associated with a decline in T-cell exhaustion markers (CD57; Tim3; PD1) along with augmented of HCV-specific T-cell IFN-gamma responses post-treatment. Addition of LDV to SOF was associated with augmentation of HCV-specific immunity and SVR in patients who previously failed SOF+RBV therapy without increased immunity. These findings demonstrate a novel effect of DAA in inducing host immune responses to aid HCV clearance and achieve SVR.

Liver Function Tests Abnormalities and Hepatitis B Virus & Hepatitis C Virus Co-infection in Human Immunodeficiency Virus (HIV)-infected Patients in India

BACKGROUND

While highly active anti-retroviral therapy (HAART) has improved survival of HIV-infected patients, there is increasing liver disease and progressive Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) related liver disease.

AIMS

To study the liver function tests (LFT) and HBV and HCV co-infection in HIV-infected patients.

MATERIAL AND METHODS

All HIV-positive patients presenting to a tertiary level hospital from April 2009 to April 2011 were evaluated. Baseline LFT, CD4/CD8 counts, ultrasound abdomen, HBsAg, IgG anti-HBc, HBVDNA, Anti-HCV and HCVRNA were done in all patients. LFT was repeated monthly or more frequently with anti-tubercular therapy (ATT)/HAART.

RESULTS

Abnormal LFT were seen in 143/320 (44.6%) HIV-infected patients (n = 320; M-282, F-38; mean age-35.4 ± 7.3 years). Baseline LFT was abnormal in 48 (15%) [hepatotropic viruses-19, alcohol-24, NAFLD-1, disseminated TB-1, idiopathic-03). Subsequent LFT derangement developed in 95/272 (34.9%). In the majority, the LFT abnormality was mild (119/143-83.2%) and multi-factorial [HAART 132 (76.4%), alcohol 69 (48.2%), ATT 31 (21.7%), HBV 16 (11.2%), HCV 15 (10.4%)]. Using multivariate analysis, abnormal LFT were associated with HAART (OR, 5.92; 95%CI, 2.83-12.37), ATT (OR, 2.06; 95%CI, 1.06-3.99) or HCV infection (OR, 2.54; 95%CI, 1.03-6.26). Significant hepatotoxicity requiring drug modification was seen in only 7 cases. HBV, HCV and HBV + HCV co-infection were seen in 37 (11.6%), 28 (8.8%) and 2 (0.6%) respectively. Occult co-infections were rare [HBV-1 (0.3%); HCV-3 (0.9%)].

CONCLUSION

While LFT abnormalities in HIV are common, they are usually mild and multifactorial. HBV and HCV co-infections were seen in 11.6% and 8.8%, respectively. Occult HBV and HCV infections were rare.

Ureteral obstruction following renal transplantation: causes, diagnosis and management

Renal transplantation, first performed successfully in the 1950s, is the treatment of choice for most patients with end-stage renal failure. It confers longer term survival and a better quality of life than do both haemodialysis and peritoneal dialysis. The success of renal transplantation is dependent on the preservation of renal graft function and despite the many advances in surgical techniques, immunosuppressive regimens and supportive therapies, many challenges remain including post-operative ureteral obstruction. This complication can pose a risk to graft, and, occasionally, to patient survival. In this pictorial review, we describe the causes of ureteral obstruction following renal transplantation and illustrate the pivotal role of radiology in both diagnosing and managing these complications.

Prevalence of hepatitis A virus, hepatitis B virus, hepatitis C virus, hepatitis D virus and hepatitis E virus as causes of acute viral hepatitis in North India: a hospital based study

CONTEXT

Acute viral hepatitis (AVH) is a major public health problem and is an important cause of morbidity and mortality.

AIM

The aim of the present study is to determine the prevalence of hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV) and hepatitis E virus (HEV) as causes of AVH in a tertiary care hospital of North India.

SETTINGS AND DESIGN

Blood samples and clinical information was collected from cases of AVH referred to the Grade I viral diagnostic laboratory over a 1-year period.

SUBJECTS AND METHODS

Samples were tested for hepatitis B surface antigen, anti-HCV total antibodies, anti-HAV immunoglobulin M (IgM) and anti-HEV IgM by the enzyme-linked immunosorbent assay. PCR for nucleic acid detection of HBV and HCV was also carried out. Those positive for HBV infection were tested for anti-HDV antibodies.

STATISTICAL ANALYSIS USED

Fisher's exact test was used and a P < 0.05 was considered to be statistically significant.

RESULTS

Of the 267 viral hepatitis cases, 62 (23.22%) patients presented as acute hepatic failure. HAV (26.96%) was identified as the most common cause of acute hepatitis followed by HEV (17.97%), HBV (16.10%) and HCV (11.98%). Co-infections with more than one virus were present in 34 cases; HAV-HEV co-infection being the most common. HEV was the most important cause of acute hepatic failure followed by co-infection with HAV and HEV. An indication towards epidemiological shift of HAV infection from children to adults with a rise in HAV prevalence was seen.

CONCLUSIONS

To the best of our knowledge, this is the first report indicating epidemiological shift of HAV in Uttar Pradesh.

Isolation, propagation, genome analysis and epidemiology of HKU1 betacoronaviruses

From 1 January 2009 to 31 May 2013, 15 287 respiratory specimens submitted to the Clinical Virology Laboratory at the Children's Hospital Colorado were tested for human coronavirus RNA by reverse transcription-PCR. Human coronaviruses HKU1, OC43, 229E and NL63 co-circulated during each of the respiratory seasons but with significant year-to-year variability, and cumulatively accounted for 7.4-15.6 % of all samples tested during the months of peak activity. A total of 79 (0.5 % prevalence) specimens were positive for human betacoronavirus HKU1 RNA. Genotypes HKU1 A and B were both isolated from clinical specimens and propagated on primary human tracheal-bronchial epithelial cells cultured at the air-liquid interface and were neutralized in vitro by human intravenous immunoglobulin and by polyclonal rabbit antibodies to the spike glycoprotein of HKU1. Phylogenetic analysis of the deduced amino acid sequences of seven full-length genomes of Colorado HKU1 viruses and the spike glycoproteins from four additional HKU1 viruses from Colorado and three from Brazil demonstrated remarkable conservation of these sequences with genotypes circulating in Hong Kong and France. Within genotype A, all but one of the Colorado HKU1 sequences formed a unique subclade defined by three amino acid substitutions (W197F, F613Y and S752F) in the spike glycoprotein and exhibited a unique signature in the acidic tandem repeat in the N-terminal region of the nsp3 subdomain. Elucidating the function of and mechanisms responsible for the formation of these varying tandem repeats will increase our understanding of the replication process and pathogenicity of HKU1 and potentially of other coronaviruses.

Visual and digital comparative tooth colour assessment methods and atomic force microscopy surface roughness

This study compared digital and visual colour tooth colour assessment methods in a sample of 99 teeth consisting of incisors, canines and pre-molars. The teeth were equally divided between Control, Ozicure Oxygen Activator bleach and Opalescence Quick bleach and subjected to three treatments. Colour readings were recorded at nine intervals by two assessment methods, VITA Easyshade and VITAPAN 3D MASTER TOOTH GUIDE, giving a total of 1782 colour readings. Descriptive and statistical analysis was undertaken using a GLM test for Analysis of Variance for a Fractional Design set at a significance of P < 0.05. Atomic force micros copy was used to examine treated ename surfaces and establish surface roughness. Visual tooth colour assessment showed significance for the independent variables of treatment, number of treatments, tooth type and the combination tooth type and treatment. Digital colour assessment indicated treatment and tooth type to be of significance in tooth colour change. Poor agreement was found between visual and digital colour assessment methods for Control and Ozicure Oxygen Activator treatments. Surface roughness values increased two-fold for Opalescence Quick specimens over the two other treatments, implying that increased light scattering improved digital colour reading. Both digital and visual colour matching methods should be used in tooth bleaching studies to complement each other and to compensate for deficiencies.

Increased regulatory T cells and impaired functions of circulating CD8 T lymphocytes is associated with viral persistence in Hepatitis B virus-positive newborns

Hepatitis B Virus (HBV) infection in infancy or early childhood leads to high rate of persistent infection (25-90%). The immunological basis of high rate of viral persistence in vertically acquired HBV infections is not completely understood. CD8 T cells play a pivotal role in clearing the Hepatitis B virus infection in adults. Herein, we sought to delineate the role of T cells in viral persistence in HBsAg+ve newborns. At birth peripheral and cord blood of HBsAg+ve (N = 12), HBsAg-ve (N = 10) and healthy newborns (HC: N = 15) were evaluated for T-cell frequency and functionality by flow cytometry. No significant differences were observed in the frequency of CD8 and CD4 T cells in all the three groups. However, significantly higher frequency of FoxP3 expressing regulatory T cells were observed in HBsAg+ve (63.79%) compared with HBsAg-ve (28.12%) and HC (11.06%) (P < 0.05). Moreover, HBsAg+ve newborns showed functional defect in CD8 T cells by decreased IFN-γ production and lower CD107A expression (cytotoxic capacity) compared with HBsAg-ve and HC, which positively correlated with decreased TCRζ-chain expression CD8 T cells (r(2) > 0.93, P < 0.05). Despite equal frequency of CD8 T cells in all the three groups, CD8 T cells in HBsAg+ve newborns are dysfunctional. An expansion of regulatory T cells and impaired TCR signalling may represent the immune tolerant state of the adaptive immune system in response to chronic HBV infection.

Analysis of whole genome sequences of 16 strains of rubella virus from the United States, 1961-2009

Rubella virus is the causative agent of rubella, a mild rash illness, and a potent teratogenic agent when contracted by a pregnant woman. Global rubella control programs target the reduction and elimination of congenital rubella syndrome. Phylogenetic analysis of partial sequences of rubella viruses has contributed to virus surveillance efforts and played an important role in demonstrating that indigenous rubella viruses have been eliminated in the United States. Sixteen wild-type rubella viruses were chosen for whole genome sequencing. All 16 viruses were collected in the United States from 1961 to 2009 and are from 8 of the 13 known rubella genotypes. Phylogenetic analysis of 30 whole genome sequences produced a maximum likelihood tree giving high bootstrap values for all genotypes except provisional genotype 1a. Comparison of the 16 new complete sequences and 14 previously sequenced wild-type viruses found regions with clusters of variable amino acids. The 5' 250 nucleotides of the genome are more conserved than any other part of the genome. Genotype specific deletions in the untranslated region between the non-structural and structural open reading frames were observed for genotypes 2B and genotype 1G. No evidence was seen for recombination events among the 30 viruses. The analysis presented here is consistent with previous reports on the genetic characterization of rubella virus genomes. Conserved and variable regions were identified and additional evidence for genotype specific nucleotide deletions in the intergenic region was found. Phylogenetic analysis confirmed genotype groupings originally based on structural protein coding region sequences, which provides support for the WHO nomenclature for genetic characterization of wild-type rubella viruses.

Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

BACKGROUND

In a high-throughput environment, to PCR amplify and sequence a large set of viral isolates from populations that are potentially heterogeneous and continuously evolving, the use of degenerate PCR primers is an important strategy. Degenerate primers allow for the PCR amplification of a wider range of viral isolates with only one set of pre-mixed primers, thus increasing amplification success rates and minimizing the necessity for genome finishing activities. To successfully select a large set of degenerate PCR primers necessary to tile across an entire viral genome and maximize their success, this process is best performed computationally.

RESULTS

We have developed a fully automated degenerate PCR primer design system that plays a key role in the J. Craig Venter Institute's (JCVI) high-throughput viral sequencing pipeline. A consensus viral genome, or a set of consensus segment sequences in the case of a segmented virus, is specified using IUPAC ambiguity codes in the consensus template sequence to represent the allelic diversity of the target population. PCR primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the full length of the specified target region. As part of the tiling process, primer pairs are computationally screened to meet the criteria for successful PCR with one of two described amplification protocols. The actual sequencing success rates for designed primers for measles virus, mumps virus, human parainfluenza virus 1 and 3, human respiratory syncytial virus A and B and human metapneumovirus are described, where >90% of designed primer pairs were able to consistently successfully amplify >75% of the isolates.

CONCLUSIONS

Augmenting our previously developed and published JCVI Primer Design Pipeline, we achieved similarly high sequencing success rates with only minor software modifications. The recommended methodology for the construction of the consensus sequence that encapsulates the allelic variation of the targeted population and is a key step prior to designing degenerate primers is also formally described.

Comparative genome analysis of 19 Ureaplasma urealyticum and Ureaplasma parvum strains

Background

Ureaplasma urealyticum (UUR) and Ureaplasma parvum (UPA) are sexually transmitted bacteria among humans implicated in a variety of disease states including but not limited to: nongonococcal urethritis, infertility, adverse pregnancy outcomes, chorioamnionitis, and bronchopulmonary dysplasia in neonates. There are 10 distinct serotypes of UUR and 4 of UPA. Efforts to determine whether difference in pathogenic potential exists at the ureaplasma serovar level have been hampered by limitations of antibody-based typing methods, multiple cross-reactions and poor discriminating capacity in clinical samples containing two or more serovars.

Results

We determined the genome sequences of the American Type Culture Collection (ATCC) type strains of all UUR and UPA serovars as well as four clinical isolates of UUR for which we were not able to determine serovar designation. UPA serovars had 0.75−0.78 Mbp genomes and UUR serovars were 0.84−0.95 Mbp. The original classification of ureaplasma isolates into distinct serovars was largely based on differences in the major ureaplasma surface antigen called the multiple banded antigen (MBA) and reactions of human and animal sera to the organisms. Whole genome analysis of the 14 serovars and the 4 clinical isolates showed the mba gene was part of a large superfamily, which is a phase variable gene system, and that some serovars have identical sets of mba genes. Most of the differences among serovars are hypothetical genes, and in general the two species and 14 serovars are extremely similar at the genome level.

Conclusions

Comparative genome analysis suggests UUR is more capable of acquiring genes horizontally, which may contribute to its greater virulence for some conditions. The overwhelming evidence of extensive horizontal gene transfer among these organisms from our previous studies combined with our comparative analysis indicates that ureaplasmas exist as quasi-species rather than as stable serovars in their native environment. Therefore, differential pathogenicity and clinical outcome of a ureaplasmal infection is most likely not on the serovar level, but rather may be due to the presence or absence of potential pathogenicity factors in an individual ureaplasma clinical isolate and/or patient to patient differences in terms of autoimmunity and microbiome.

Treatment of Stage I Seminoma testis with extended field adjuvant radiation

With an aim to analyze and document the outcome of Stage I Seminoma patients we undertook a retrospective analysis of patients treated between January 1990 and December 1998. The treatment charts of patients treated between January 1990 and December 1998 were reviewed. Patient and tumor characteristics, treatment details, relapse rates, late toxicities, or occurrence of second primary was noted. Royal Marsden Staging System was utilized because of its simplicity and wide-use in the above period. Out of 137 patients, 41 (30%) patients did not receive any further treatment, 96 (70%) patients received prophylactic radiotherapy to para-aortic and pelvic nodes. The observation group patients had a median follow-up 20 months, 9 patients had nodal relapse with 7 in retroperitoneal nodes and 2 patients in inguinal nodes. Of these, 7 patients received BEP chemotherapy and 2 patients Chemoradiation. Four patients had complete remission while remaining 5 patients had partial response. The histopathologies of all the 5 patients with partial response were reviewed to reconfirm the diagnosis. Patients of prophylactic radiotherapy group had a follow-up of 33 months, 6 patients relapsed, RP nodal disease in 5 patients and distant metastasis in 1 patient. All these patients received BEP chemotherapy. One had complete response and remaining 5 patients had partial response. The group of patients under observation had a significantly higher relapse rate and lower disease free compared to the adjuvant radiotherapy group (73.5% vs. 91% at five years, p value 0.004). Disease specific survivals for the two groups were however similar (89% vs. 93%) at five years, p value 0.18). We conclude that Stage I Seminoma patients treated with prophylactic radiation to paraaortic and pelvic region had better outcome.

CharProtDB: a database of experimentally characterized protein annotations

CharProtDB (http://www.jcvi.org/charprotdb/) is a curated database of biochemically characterized proteins. It provides a source of direct rather than transitive assignments of function, designed to support automated annotation pipelines. The initial data set in CharProtDB was collected through manual literature curation over the years by analysts at the J. Craig Venter Institute (JCVI) [formerly The Institute of Genomic Research (TIGR)] as part of their prokaryotic genome sequencing projects. The CharProtDB has been expanded by import of selected records from publicly available protein collections whose biocuration indicated direct rather than homology-based assignment of function. Annotations in CharProtDB include gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession. Each annotation is referenced with the source; ideally a journal reference, or, if imported and lacking one, the original database source.

Fertility, developmental toxicity and teratogenicity in albino rats treated with methanol sub-fraction of Carica papaya seeds

Objective:

To evaluate the status of fertility, developmental stages during gestation and teratological changes, if any, following oral administration of methanol sub-fraction (MSF) of the benzene chromatographic fraction of the chloroform extract of the seeds of Carica papaya in rats.

Materials and Methods:

The MSF was administered at the doses of 50 mg contraceptive dose (CD), 100 mg (2× CD), 250 mg (5× CD) and 500 mg (10× CD)/kg body wt/day along with vehicle-treated control using 10 male and 20 female Wistar rats in each group. Necropsies were performed one day before the expected parturition. Status of gravid/non-gravid uterus, the number of corpora lutea in the ovary, implantation status, fetal wellbeing, fetal resorption, fetal body weight, external, visceral and skeletal malformations were recorded.

Results:

Pregnancies were recorded in vehicle-treated control animals and in the animals treated with 50 mg/kg body wt/day. The animals treated with 2× CD, 5× CD and 10× CD did not get pregnant. The fetuses and the status of the ovary, uterus and implantation, fetal body weight, soft tissues and skeletal structures were recorded normal. Data were comparable to those of control.

Conclusion:

The results suggest that the test substance had no developmental toxicity and teratogenicity which could affect pregnancy, implantation and gestation.

A comparison of functional and physical properties of self-expanding intracranial stents [Neuroform3, Wingspan, Solitaire, Leo+, Enterprise]

PURPOSE

5 self-expanding intracranial stents Neuroform (N), Wingspan (W), Solitaire (S), Leo(+) (L), and Enterprise (E) were subjected to an in vitro examination and comparison of their physical features and functional properties in order to better understand the clinical advantages and potential limitations of each device.

MATERIAL AND METHODS

The following features were examined for each stent: visual appearance, radial strength, wall apposition, bending stiffness, gator backing, kink resistance, ovalization, vessel wall coverage, cell size, ease of delivery.

RESULTS

Given are rankings for the 5 stents: radial force at 50% oversizing: L<N<E<S<W; radial force at 15% oversizing L<E<S<N<W; wall apposition: E<N=W<S; bending stiffness: N<L<W<S<E; gator backing: N and W only; kink resistance: N=W<E<S<L; ovalization: W<L<S<N<E; vessel wall coverage: S<E<N<W<L; cell size: L<W<E<N<S; ease of delivery: W<N<L<E<S. A comparative analysis of the in vitro test results with the clinical experience of the authors is presented in this paper.

CONCLUSION

The 5 stents have fundamentally different features and there is no stent that is superior in all tested aspects. The selection in an individual treatment should be based on clinical and technical requirements.

Three-dimensional trans-esophageal Echocardiographic Evaluation of Atrial Septal Defects: A Pictorial Essay

This pictorial assay illustrates the methodology of evaluating the atrial septal defects by three dimensional transesophageal echocardiography with the help of representative images. The article starts by discussing the technical details of how to acquire and crop the dataset to reconstruct the transesophageal three dimensional echocardiographic images of the inter atrial septum. Next, the anatomical details of the normal inter atrial septum are illustrated, followed by representative examples of all the possible defects of inter atrial septum. All the images have been reproduced in a uniform pattern which is similar to the view of the inter atrial septum that is seen in the real life situation by the surgeon.

A novel device for the revascularization in acute ischemic stroke patients

SUMMARY

This article provides insights into how the authors developed the Solitaire™ FR revascularization device and associated procedure including commentary on the mechanism of revascularization and future of device development in this area. The article is intended to give research-minded physicians a view into the device development world by sighting examples of this novel device for revascularizing patients with acute ischemic stroke.

Exogenous interferon-gamma immunotherapy for invasive fungal infections in kidney transplant patients

The incidence of invasive fungal infections (IFIs) in nonneutropenic solid organ transplant patients is increasing. We report our clinical experience with the use of interferon-gamma (IFN-gamma) immunotherapy in seven renal transplant patients who developed life threatening, disseminated IFIs refractory to conventional antifungal drug therapy. The infections were all microbiologically and histologically proven. The rapid cure of these disseminated infections with exogenous IFN-gamma injections was not associated with impaired kidney allograft function despite the use of liposomal amphotericin B in all cases. No clinical toxicity from the IFN-gamma immunotherapy was seen and no IFI relapsed during long-term follow-up. Our experience is both uncontrolled and in patients with unpredictable fungal infection-related outcomes. However, compared to standard approaches, the accelerated cure of life threatening, disseminated IFIs with 6 weeks of combination antifungal drug therapy and IFN-gamma immunotherapy saved lives, retained allograft function and led to substantial cost savings in this small patient group.