Genome-wide association studies of gene-environment interaction (GxE GWAS) are becoming popular. As with main effects GWAS, quantile-quantile plots (QQ-plots) and Genomic Control are being used to ...assess and correct for population substructure. However, in G x E work these approaches can be seriously misleading, as we illustrate; QQ-plots may give strong indications of substructure when absolutely none is present. Using simulation and theory, we show how and why spurious QQ-plot inflation occurs in G x E GWAS, and how this differs from main-effects analyses. We also explain how simple adjustments to standard regression-based methods used in G x E GWAS can alleviate this problem.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Since the introduction of polio vaccines in the 1950's and 60's, eradication of poliovirus from the world has been technically feasible. Progress towards this goal, however, has been uneven and ...influenced by social and political factors that challenge the implementation of robust immunization programs. While violence and insecurity are often cited as barriers to eradication, current global risk models are largely based on virologic and immunologic indicators measured at national levels. In this manuscript, we quantify the relevance of indicators of violence and insecurity on the risk of polio spread.
Using logistic regression models and public data sources, we evaluate the relationship between measures of violence and instability and the location of poliomyelitis cases between 2006 and 2015 at the country-level, both individually and after controlling for more proximal determinants of disease, such as nearby circulating poliovirus and vaccination rates. We found that increases in a country's Fragile States Index (FSI) and Global Peace Index (GPI), aggregate indicators of violence and instability, were associated with the occurrence of poliovirus cases in the subsequent year (p< 0.01), even after controlling for established risk factors. These effects of violence and insecurity must be mediated through immunity and exposure to poliovirus, coarse measures of which are included in our model. This also implies that in our study, and in risk models in general, the interpretation depends on the quality and granularity of available data.
National virologic and immunologic indicators understate the risk of poliovirus spread in areas with violence and insecurity, and the inclusion of such factors improves precision. In addition, the link between violence and incidence of disease highlights the broader challenge of implementing health interventions in conflict areas. We discuss practical implications of this work in understanding and measuring the risks to polio eradication and other global health initiatives, and the policy implications of the need to reach vulnerable populations in conflict zones.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Statistical analyses of genome-wide association studies (GWAS) require fitting large numbers of very similar regression models, each with low statistical power. Taking advantage of repeated ...observations or correlated phenotypes can increase this statistical power, but fitting the more complicated models required can make computation impractical.
In this article, we present simple methods that capitalize on the structure inherent in GWAS studies to dramatically speed up computation for a wide variety of problems, with a special focus on methods for correlated phenotypes.
The R package 'boss' is available on the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/web/packages/boss/
Sensitive surveillance for acute flaccid paralysis (AFP) allows for rapid detection of polio outbreaks and provides essential evidence to support certification of the eradication of polio. However, ...accurately assessing the sensitivity of surveillance systems can be difficult due to limitations in the reliability of available performance indicators, including the rate of detection of non-polio AFP and the proportion of adequate stool sample collection. Recent field reviews have found evidence of surveillance gaps despite indicators meeting expected targets.
We propose two simple new approaches for AFP surveillance performance indicator analysis to supplement standard indicator analysis approaches commonly used by the Global Polio Eradication Initiative (GPEI): (1) using alternative groupings of low population districts in the country (spatial binning) and (2) flagging unusual patterns in surveillance data (surveillance flags analysis). Using GPEI data, we systematically compare AFP surveillance performance using standard indicator analysis and these new approaches.
Applying spatial binning highlights areas meeting surveillance indicator targets that do not when analyzing performance of low population districts. Applying the surveillance flags we find several countries with unusual data patterns, in particular age groups which are not well-covered by the surveillance system, and countries with implausible rates of adequate stool specimen collection.
Analyzing alternate groupings of administrative units is a simple method to find areas where traditional AFP surveillance indicator targets are not reliably met. For areas where AFP surveillance indicator targets are met, systematic assessment of unusual patterns (‘flags’) can be a useful prompt for further investigation and field review.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Circulating vaccine-derived poliovirus outbreaks are spreading more widely than anticipated, which has generated a crisis for the global polio eradication initiative. Effectively responding with ...vaccination activities requires a rapid risk assessment. This assessment is made difficult by the low case-to-infection ratio of type 2 poliovirus, variable transmissibility, changing population immunity, surveillance delays, and limited vaccine supply from the global stockpile. The geographical extent of responses have been highly variable between countries.
We develop a statistical spatio-temporal model of short-term, district-level poliovirus spread that incorporates known risk factors, including historical wild poliovirus transmission risk, routine immunization coverage, population immunity, and exposure to the outbreak virus.
We find that proximity to recent cVDPV2 cases is the strongest risk factor for spread of an outbreak, and find significant associations between population immunity, historical risk, routine immunization, and environmental surveillance (p < 0.05). We examine the fit of the model to type 2 vaccine derived poliovirus spread since 2016 and find that our model predicts the location of cVDPV2 cases well (AUC = 0.96). We demonstrate use of the model to estimate appropriate scope of outbreak response activities to current outbreaks.
As type 2 immunity continues to decline following the cessation of tOPV in 2016, outbreak responses to new cVDPV2 detections will need to be faster and larger in scope. We provide a framework that can be used to support decisions on the appropriate size of a vaccination response when new detections are identified. While the model does not account for all relevant local factors that must be considered in the overall vaccination response, it enables a quantitative basis for outbreak response size.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
In recent years, there has been considerable interest in estimating conditional independence graphs in high dimensions. Most previous work assumed that the variables are multivariate Gaussian or that ...the conditional means of the variables are linearly related. Unfortunately, if these assumptions are violated, the resulting conditional independence estimates can be inaccurate.We propose a semiparametric method, graph estimation with joint additive models, which allows the conditional means of the features to take an arbitrary additive form. We present an efficient algorithm for computation of our estimator, and prove that it is consistent. We extend our method to estimation of directed graphs with known causal ordering. Using simulated data, we show that our method performs better than existing methods when there are nonlinear relationships among the features, and is comparable to methods that assume multivariate normality when the conditional means are linear. We illustrate our method on a cell signalling dataset.
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BFBNIB, INZLJ, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK, ZRSKP
Abstract
Background
Novel oral poliovirus vaccine (OPV) type 2 (nOPV2) has been made available for outbreak response under an emergency use listing authorization based on supportive clinical trial ...data. Since 2021 more than 350 million doses of nOPV2 were used for control of a large outbreak of circulating vaccine-derived poliovirus type 2 (cVDPV2) in Nigeria.
Methods
Using a bayesian time-series susceptible-infectious-recovered model, we evaluate the field effectiveness of nOPV2 immunization campaigns in Nigeria compared with campaigns using monovalent OPV type 2 (mOPV2).
Results
We found that both nOPV2 and mOPV2 campaigns were highly effective in reducing transmission of cVDPV2, on average reducing the susceptible population by 42% (95% confidence interval, 28–54%) and 38% (20–51%) per campaign, respectively, which were indistinguishable from each other in this analysis (relative effect, 1.1 .7–1.9). Impact was found to vary across areas and between immunization campaigns.
Conclusions
These results are consistent with the comparable individual immunogenicity of nOPV2 and mOPV2 found in clinical trials but also suggest that outbreak response campaigns may have small impacts in some areas requiring more campaigns than are suggested in current outbreak response procedures.
Using a bayesian time-series susceptible-infectious-recovered model, we evaluated novel oral poliovirus vaccine type 2 (OPV2) in Nigeria and found the impact on disease transmission comparable to that previously achieved with monovalent OPV2.
The global withdrawal of trivalent oral poliovirus vaccine (OPV) (tOPV, containing Sabin poliovirus strains serotypes 1, 2 and 3) from routine immunization, and the introduction of bivalent OPV ...(bOPV, containing Sabin poliovirus strains serotypes 1 and 3) and trivalent inactivated poliovirus vaccine (IPV) into routine immunization was expected to improve population serologic and mucosal immunity to types 1 and 3 poliovirus, while population mucosal immunity to type 2 poliovirus would decline. However, over the period since tOPV withdrawal, the implementation of preventive bOPV supplementary immunization activities (SIAs) has decreased, while outbreaks of type 2 circulating vaccine derived poliovirus (cVDPV2) have required targeted use of monovalent type 2 OPV (mOPV2).
We develop a dynamic model of OPV-induced immunity to estimate serotype-specific, district-level immunity for countries in priority regions and characterize changes in immunity since 2016. We account for the changes in routine immunization schedules and varying implementation of preventive and outbreak response SIAs, assuming homogenous coverages of 50% and 80% for SIAs.
In areas with strong routine immunization, the switch from tOPV to bOPV has likely resulted in gains in population immunity to types 1 and 3 poliovirus. However, we estimate that improved immunogenicity of new schedules has not compensated for declines in preventive SIAs in areas with weak routine immunization. For type 2 poliovirus, without tOPV in routine immunization or SIAs, mucosal immunity has declined nearly everywhere, while use of mOPV2 has created highly heterogeneous population immunity for which it is important to take into account when responding to cVDPV2 outbreaks.
The withdrawal of tOPV and declining allocations of resources for preventive bOPV SIAs have resulted in reduced immunity in vulnerable areas to types 1 and 3 poliovirus and generally reduced immunity to type 2 poliovirus in the regions studied, assuming homogeneous coverages of 50% and 80% for SIAs. The very low mucosal immunity to type 2 poliovirus generates substantially greater risk for further spread of cVDPV2 outbreaks. Emerging gaps in immunity to all serotypes will require judicious targeting of limited resources to the most vulnerable populations by the Global Polio Eradication Initiative (GPEI).
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
•The COVID-19 pandemic disrupted polio immunization activities.•Response to COVID-19 included substantial reductions in people mixing and traveling.•Early resumption of polio immunization activities ...could mitigate the impacts on poliovirus transmission.
In early 2020, the COVID-19 pandemic led to substantial disruptions in global activities. The disruptions also included intentional and unintentional reductions in health services, including immunization campaigns against the transmission of wild poliovirus (WPV) and persistent serotype 2 circulating vaccine-derived poliovirus (cVDPV2). Building on a recently updated global poliovirus transmission and Sabin-strain oral poliovirus vaccine (OPV) evolution model, we explored the implications of immunization disruption and restrictions of human interactions (i.e., population mixing) on the expected incidence of polio and on the resulting challenges faced by the Global Polio Eradication Initiative (GPEI). We demonstrate that with some resumption of activities in the fall of 2020 to respond to cVDPV2 outbreaks and full resumption on January 1, 2021 of all polio immunization activities to pre-COVID-19 levels, the GPEI could largely mitigate the impact of COVID-19 to the delays incurred. The relative importance of reduced mixing (leading to potentially decreased incidence) and reduced immunization (leading to potentially increased expected incidence) depends on the timing of the effects. Following resumption of immunization activities, the GPEI will likely face similar barriers to eradication of WPV and elimination of cVDPV2 as before COVID-19. The disruptions from the COVID-19 pandemic may further delay polio eradication due to indirect effects on vaccine and financial resources.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Highlights • Reliability and comparability of reported polio vaccine dose histories are studied. • In many areas, reported doses have a weak relationship to immunization activities. • Data quality ...may distort risk assessment and immunization activity allocation. • Alternative data should be considered for planning polio immunization activities.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
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