VIPR: A probabilistic algorithm for analysis of microbial detection microarrays

<p>Abstract</p> <p>Background</p> <p>All infectious disease oriented clinical diagnostic assays in use today focus on detecting the presence of a single, well defined target agent or a set of agents. In recent years, microarray-based diagnostics have been developed that greatly facilitate the highly parallel detection of multiple microbes that may be present in a given clinical specimen. While several algorithms have been described for interpretation of diagnostic microarrays, none of the existing approaches is capable of incorporating training data generated from positive control samples to improve performance.</p> <p>Results</p> <p>To specifically address this issue we have developed a novel interpretive algorithm, VIPR (<b>V</b>iral <b>I</b>dentification using a <b>PR</b>obabilistic algorithm), which uses Bayesian inference to capitalize on empirical training data to optimize detection sensitivity. To illustrate this approach, we have focused on the detection of viruses that cause hemorrhagic fever (HF) using a custom HF-virus microarray. VIPR was used to analyze 110 empirical microarray hybridizations generated from 33 distinct virus species. An accuracy of 94% was achieved as measured by leave-one-out cross validation. <it>Conclusions</it></p> <p>VIPR outperformed previously described algorithms for this dataset. The VIPR algorithm has potential to be broadly applicable to clinical diagnostic settings, wherein positive controls are typically readily available for generation of training data.</p

West Nile Virus Isolation in Human and Mosquitoes, Mexico

West Nile virus has been isolated for the first time in Mexico, from a sick person and from mosquitoes (Culex quinquefasciatus). Partial sequencing and analysis of the 2 isolates indicate that they are genetically similar to other recent isolates from northern Mexico and the western United States

Bacterial-based systems for expression and purification of recombinant Lassa virus proteins of immunological relevance

<p>Abstract</p> <p>Background</p> <p>There is a significant requirement for the development and acquisition of reagents that will facilitate effective diagnosis, treatment, and prevention of Lassa fever. In this regard, recombinant Lassa virus (LASV) proteins may serve as valuable tools in diverse antiviral applications. Bacterial-based systems were engineered for expression and purification of recombinant LASV nucleoprotein (NP), glycoprotein 1 (GP1), and glycoprotein 2 (GP2).</p> <p>Results</p> <p>Full-length NP and the ectodomains of GP1 and GP2 were generated as maltose-binding protein (MBP) fusions in the Rosetta strains of <it>Escherichia coli </it>(<it>E. coli</it>) using pMAL-c2x vectors. Average fusion protein yields per liter of culture for MBP-NP, MBP-GP1, and MBP-GP2 were 10 mg, 9 mg, and 9 mg, respectively. Each protein was captured from cell lysates using amylose resin, cleaved with Factor Xa, and purified using size-exclusion chromatography (SEC). Fermentation cultures resulted in average yields per liter of 1.6 mg, 1.5 mg, and 0.7 mg of purified NP, GP1 and GP2, respectively. LASV-specific antibodies in human convalescent sera specifically detected each of the purified recombinant LASV proteins, highlighting their utility in diagnostic applications. In addition, mouse hyperimmune ascitic fluids (MHAF) against a panel of Old and New World arenaviruses demonstrated selective cross reactivity with LASV proteins in Western blot and enzyme-linked immunosorbent assay (ELISA).</p> <p>Conclusion</p> <p>These results demonstrate the potential for developing broadly reactive immunological assays that employ all three arenaviral proteins individually and in combination.</p

Vesicular stomatitis virus enables gene transfer and transsynaptic tracing in a wide range of organisms

Current limitations in technology have prevented an extensive analysis of the connections among neurons, particularly within nonmammalian organisms. We developed a transsynaptic viral tracer originally for use in mice, and then tested its utility in a broader range of organisms. By engineering the vesicular stomatitis virus (VSV) to encode a fluorophore and either the rabies virus glycoprotein (RABV-G) or its own glycoprotein (VSV-G), we created viruses that can transsynaptically label neuronal circuits in either the retrograde or anterograde direction, respectively. The vectors were investigated for their utility as polysynaptic tracers of chicken and zebrafish visual pathways. They showed patterns of connectivity consistent with previously characterized visual system connections, and revealed several potentially novel connections. Further, these vectors were shown to infect neurons in several other vertebrates, including Old and New World monkeys, seahorses, axolotls, and Xenopus. They were also shown to infect two invertebrates, Drosophila melanogaster, and the box jellyfish, Tripedalia cystophora, a species previously intractable for gene transfer, although no clear evidence of transsynaptic spread was observed in these species. These vectors provide a starting point for transsynaptic tracing in most vertebrates, and are also excellent candidates for gene transfer in organisms that have been refractory to other methods

Negeviruses reduce replication of alphaviruses during co-infection

Negeviruses are a group of insect-specific virus (ISV) that have been found in many arthropods. Their presence in important vector species led us to examine their interactions with arboviruses during co-infections. Wild-type negeviruses reduced the replication of several alphaviruses during co-infections in mosquito cells. Negev virus (NEGV) isolates were also used to express GFP and anti-chikungunya virus (CHIKV) antibody fragments during co-infections with CHIKV. NEGV expressing anti-CHIKV antibody fragments was able to further reduce replication of CHIKV during co-infections, while reductions of CHIKV with NEGV expressing GFP were similar to titers with wild-type NEGV alone. These results are the first to show that negeviruses induce superinfection exclusion of arboviruses and to demonstrate a novel approach to deliver anti-viral antibody fragments with paratransgenic ISVs. The ability to inhibit arbovirus replication and express exogenous proteins in mosquito cells make negeviruses a promising platform for control of arthropod-borne pathogens

West Nile Virus Infection among the Homeless, Houston, Texas1

Among 397 homeless participants studied, the overall West Nile virus (WNV) seroprevalence was 6.8%. Risk factors for WNV infection included being homeless >1 year, spending >6 hours outside daily, regularly taking mosquito precautions, and current marijuana use. Public health interventions need to be directed toward this high-risk population

From causes to solutions - insights from lay knowledge about health inequalities

<p>Abstract</p> <p>Background</p> <p>This paper reports on a qualitative study of lay knowledge about health inequalities and solutions to address them. Social determinants of health are responsible for a large proportion of health inequalities (unequal levels of health status) and inequities (unfair access to health services and resources) within and between countries. Despite an expanding evidence base supporting action on social determinants, understanding of the impact of these determinants is not widespread and political will appears to be lacking. A small but growing body of research has explored how ordinary people theorise health inequalities and the implications for taking action. The findings are variable, however, in terms of an emphasis on structure versus individual agency and the relationship between being 'at risk' and acceptance of social/structural explanations.</p> <p>Methods</p> <p>This paper draws on findings from a qualitative study conducted in Adelaide, South Australia, to examine these questions. The study was an integral part of mixed-methods research on the links between urban location, social capital and health. It comprised 80 in-depth interviews with residents in four locations with contrasting socio-economic status. The respondents were asked about the cause of inequalities and actions that could be taken by governments to address them.</p> <p>Results</p> <p>Although generally willing to discuss health inequalities, many study participants tended to explain the latter in terms of individual behaviours and attitudes rather than social/structural conditions. Moreover, those who identified social/structural causes tended to emphasise individualized factors when describing typical pathways to health outcomes. This pattern appeared largely independent of participants' own experience of advantage or disadvantage, and was reinforced in discussion of strategies to address health inequalities.</p> <p>Conclusions</p> <p>Despite the explicit emphasis on social/structural issues expressed in the study focus and framing of the research questions, participants did not display a high level of knowledge about the nature and causes of place-based health inequalities. By extending the scope of lay theorizing to include a focus on solutions, this study offers additional insights for public health. Specifically it suggests that a popular constituency for action on the social determinants of health is unlikely to eventuate from the current popular understandings of possible policy levers.</p

Encephalomyocarditis virus may use different pathways to initiateinfection of primary human cardiomyocytes

Encephalomyocarditis virus (EMCV) caninfect a wide range of vertebrate species including swineand non-human primates, but few data are available forhumans. We therefore wanted to gain further insight intothe mechanisms involved in EMCV infection of humancells. For this purpose, we analyzed the permissiveness ofprimary human cardiomyocytes towards two strains ofEMCV; a pig myocardial strain (B279/95) and a rat strain(1086C). In this study, we show that both strains productivelyinfect primary human cardiomyocytes and inducecomplete cytolysis. Binding and infection inhibitionexperiments indicated that attachment and infection areindependent of sialic acid and heparan sulfate for B279/95and dependent for 1086C. Sequence comparison betweenthe two strains and three-dimensional analysis of the capsidrevealed that six of the seven variable residues are surfaceexposed,suggesting a role for these amino acids in binding.Moreover, analysis of variants isolated from the 1086Cstrain revealed the importance of lysine 231 of VP1 in theattachment of EMCV to cell-surface sialic acid residues.Together, these results show a potential for EMCV strainsto use at least two different binding possibilities to initiateinfection and provide new insights into the mechanismsinvolved in primary human cell recognition by EMCV