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bioRxiv2017

Competing effects of indirect protection and clustering on the power of cluster-randomized controlled vaccine trials

Power considerations for trials evaluating vaccines against infectious diseases are complicated by indirect protective effects of vaccination. While cluster-randomized trials (cRCTs) are less statistically efficient than individually randomized trials (iRCT), a cRCTs ability to measure direct and indirect vaccine effects may mitigate the loss of efficiency due to clustering. Within cRCTs, the number and size of clusters affects three determinants of power: the effect size being measured, disease incidence, and intra-cluster correlation. We simulate trials conducted in a collection of small communities to assess how indirect protection and clustering affect the power of cRCTs and iRCTs during an emerging epidemic. Across diverse parameters, we find that within the same trial population, cRCTs are never more powerful than iRCTs, although the difference can be small. We also identify two effects that attenuate the loss of cRCT power traditionally associated with increased cluster size. First, if enrollment of fewer, larger clusters is performed to achieve higher vaccine coverage within vaccinated communities, this increases the effect to be measured and, consequently, power. Second, the greater rate of imported transmission in larger communities may increase the attack rate and similarly mitigate loss of power relative to a trial in many, smaller communities.

epidemiology↗

bioRxiv2017

Quantification of anti-parasite and anti-disease immunity to malaria as a function of age and exposure

Malaria immunity is complex and multi-faceted, and fundamental gaps remain in our understanding of how it develops. Here, we use detailed clinical and entomological data from three parallel cohort studies conducted across the malaria transmission spectrum in Uganda to quantify the development of immunity against symptomatic Plasmodium falciparum as a function of age and transmission intensity. We focus on: anti-parasite immunity (i.e; ability to control parasite densities) and anti-disease immunity (i.e; ability to tolerate higher parasite densities without fever). Our findings suggest a strong effect of age on both types of immunity, that remains significant after adjusting for cumulative exposure. They also show a non-linear effect of transmission intensity, where children experiencing the lowest transmission appear to develop immunity faster than those experiencing higher transmission. These findings illustrate how anti-parasite and anti-disease immunity develop in parallel, reducing the probability of experiencing symptomatic malaria upon each subsequent P. falciparum infection.

epidemiology↗

bioRxiv2017

Spillover effects of a combined water, sanitation, and handwashing intervention in rural Bangladesh: a randomized controlled trial

BackgroundWater, sanitation, and handwashing (WSH) interventions may confer indirect benefits (\"spillovers\") on neighbors of recipients by interrupting pathogen transmission. We measured geographically local spillovers in WASH Benefits, a cluster-randomized trial in rural Bangladesh, by comparing outcomes among neighbors of intervention vs. control participants.\n\nMethodsWASH Benefits had randomly allocated geographically-defined clusters to a compound-level intervention (chlorinated drinking water, upgraded sanitation, and handwashing promotion) or control and followed children for two years. We enrolled neighboring children age-matched to trial participants that would have been eligible for WASH Benefits had they been conceived slightly earlier or later. After 28 months of intervention, we quantified fecal indicator bacteria in toy rinse and drinking water samples, measured soil-transmitted helminth infections, and recorded caregiver-reported diarrhea and respiratory illness. Neither fieldworkers nor participants were masked. Analysis was intention-to-treat.\n\nResultsWe enrolled neighbors of WASH Benefits participants in 90 control (N=900) and 90 intervention clusters (N=899). Neighbors characteristics were balanced across arms. The prevalence of any detectable E. coli in tubewell samples was lower for neighbors of intervention vs. control (prevalence ratio=0.83; 0.73, 0.95). There was no difference in E. coli and coliform prevalence between arms for other environmental samples. Disease prevalence was similar in neighbors of intervention vs. control participants: Ascaris (prevalence difference [PD]=0.00; -0.07, 0.08), hookworm (PD=0.01; -0.01, 0.04), Trichuris (PD=0.02; -0.02, 0.05), diarrhea (PD=0.00; -0.02,0.03), respiratory illness (PD=-0.01; -0.04, 0.03).\n\nConclusionsWe found spillover effects of a compound-level combined WSH intervention for tubewell water contamination but not for child health outcomes.\n\nKey MessagesO_LIWater, sanitation, and handwashing (WSH) interventions may confer indirect benefits (\"spillovers\") on neighbors of recipients by interrupting pathogen transmission, reducing environmental contamination, or spurring the adoption of health behaviors.\nC_LIO_LIWe conducted a randomized trial in rural Bangladesh to measure whether neighbors of a compound-level WSH intervention improved hygiene behaviors and had lower prevalence environmental contamination, soil-transmitted helminth infection, diarrhea, and respiratory illness among children under 5 years after two years of intervention.\nC_LIO_LIWe did not find evidence of intervention adoption or improved hygiene behavior among neighbors of a WSH intervention delivered for 2 years.\nC_LIO_LIThe WSH intervention reduced fecal contamination of neighbors tubewell water but did not lead to spillovers for other proximal measures of contamination in the domestic environment or for child health outcomes. For proximal spillover effects to translate to distal spillover effects, improvements in neighbors health behaviors may have been necessary.\nC_LI

epidemiology↗

bioRxiv2017

The Asian tiger mosquito, Aedes albopictus (Skuse, 1894), a vector of dengue, chikungunya and zika, reaches Portugal

The mosquito Aedes albopictus is here reported for the first time in Portugal, from the south of the country, at least 240km west of the nearest known observation in Spain. A population of more than fifty specimens was spotted within a suburban garden over seven days of survey. As an important vector of Human affecting zoonoses such as dengue, chikungunya and yellow-fever, the presence of this mosquito in Portugal now enhances the outbreak chances for such diseases.

epidemiology↗

bioRxiv2017

Quantifying Seasonal and Diel Variation in Anopheline and Culex Human Biting Rates in Southern Ecuador

BackgroundQuantifying mosquito biting rates for specific locations enables estimation of mosquito-borne disease risk, and can inform intervention efforts. Measuring biting itself is fraught with ethical concerns, so the landing rate of mosquitoes on humans is often used as a proxy measure. Southern coastal Ecuador was historically endemic for malaria (P. falciparum and P. vivax), although successful control efforts in the 2000s eliminated autochthonous transmission (since 2011). This study presents an analysis of data collected during the elimination period.\n\nMethodsWe examined human landing catch (HLC) data for three mosquito taxa: 2 malaria vectors, Anopheles albimanus and Anopheles punctimacula, and grouped Culex spp. These data were collected by the National Vector Control Service of the Ministry of Health over a 5-year time span (2007 - 2012) in five cities in southern coastal Ecuador, at multiple households, in all months of the year, during dusk-dawn (18:00-6:00) hours, often at both indoor and outdoor locations. Hurdle models were used to determine if biting activity was fundamentally different for the three taxa, and to identify spatial and temporal factors influencing bite rate. Due to the many different approaches to studying and quantifying bite rates in the literature, we also created a glossary of terms, to facilitate comparative studies in the future.\n\nResultsBiting trends varied significantly with species and time. All taxa exhibited exophagic feeding behavior, and outdoor locations increased both the odds and incidence of bites across taxa. An. albimanus was most frequently observed biting, with an average of 4.7 bites per hour. The highest and lowest respective months for significant biting activity were March and July for An. albimanus, July and August for An. punctimacula, and February and July for Culex spp.\n\nConclusionsFine-scale spatial and temporal differences exist in biting patterns among mosquito taxa in southern coastal Ecuador. This analysis provides detailed information for targeting vector control and household level behavioral interventions. These data were collected as part of routine vector surveillance conducted by the Ministry of Health, but such data have not been collected since. Reinstating such surveillance measures would provide important information to aid in preventing malaria re-emergence.

epidemiology↗

bioRxiv2017

The impact of surveillance and control on highly pathogenic avian influenza outbreaks in poultry in Dhaka division, Bangladesh

In Bangladesh, the poultry industry is an economically and socially important sector, but it is persistently threatened by the effects of H5N1 highly pathogenic avian influenza. Thus, identifying the optimal control policy in response to an emerging disease outbreak is a key challenge for policy-makers. To inform this aim, a common approach is to carry out simulation studies comparing plausible strategies, while accounting for known capacity restrictions. In this study we perform simulations of a previously developed H5N1 influenza transmission model framework, fitted to two separate historical outbreaks, to assess specific control objectives related to the burden or duration of H5N1 outbreaks among poultry farms in the Dhaka division of Bangladesh. In particular, we explore the optimal implementation of ring culling, ring vaccination and active surveillance measures when presuming disease transmission predominately occurs from premises-to-premises, versus a setting requiring the inclusion of external factors. Additionally, we determine the sensitivity of the management actions under consideration to differing levels of capacity constraints and outbreaks with disparate transmission dynamics. While we find that reactive culling and vaccination policies should pay close attention to these factors to ensure intervention targeting is optimised, across multiple settings the top performing control action amongst those under consideration were targeted proactive surveillance schemes. Our findings may advise the type of control measure, plus its intensity, that could potentially be applied in the event of a developing outbreak of H5N1 amongst originally H5N1 virus-free commercially-reared poultry in the Dhaka division of Bangladesh.

epidemiology↗

bioRxiv2017

Insights into Hepatitis C Transmission in Young Persons who Inject Drugs: Results From a Dynamic Modeling Approach Informed by State-Level Public Health Surveillance Data

Rising use of heroin and prescription opioids are major contributors to increases in Hepatitis C Virus (HCV) incidence in US young adults since the late 1990s. How best to interrupt transmission and decrease HCV prevalence in young persons who inject drugs (PWID) is uncertain, but modeling studies in older populations support interventions that increase HCV treatment among all PWID. We developed a transmission model of young (aged 15-30 years) PWID, which we fit to state-level US HCV surveillance data, and simulated the potential impact of primary (reducing injection initiation), secondary (increasing cessation, reducing injection partners, or reducing injection drug use relapse), and tertiary (HCV treatment) interventions on incident and prevalent HCV cases. Interventions with primary prevention initiatives (reducing injection initiation) yielded concurrent reductions to HCV incidence and prevalence. Treatment of former PWID led to prevalence reductions but did not reduce incidence. Treatment of current and former PWID without other interventions led to incidence reductions in scenarios with high injection initiation rates, high syringe sharing, and low relapse rates after injection cessation. While these results are specific to Michigan, our approach could be applied in other states conducting HCV surveillance to identify local-level intervention opportunities.

epidemiology↗

bioRxiv2018

Identifying Critical Points of Trajectories of Depressive Symptoms From Childhood to Young Adulthood: Evidence of Sex Differences from the Avon Longitudinal Study of Parents and Children (ALSPAC)

Depression is a common mental illness associated with increased substance misuse and risk of suicide. Potential risk factors for depression include sex and depressive symptoms in early life, however the mechanisms responsible are not yet understood. Research has focused on late childhood and adolescence as this developmental period may be a modifiable risk factor that prevents or reduces depression at a later stage. It is also important to establish at what ages the level of depression is changing as this will help identify critical points to intervene with treatment. We used multilevel growth-curve models to explore adolescent trajectories of depressive symptoms in the Avon Longitudinal Study of Parents and Children, a UK based pregnancy cohort. Using data from 9301 individuals, trajectories of depressive symptoms were constructed for males and females between 10.6 and 22.8 years old. We calculated the age of peak velocity for depressive symptoms (the age at which depressive symptoms increases most rapidly) and the age of maximum depressive symptoms. Adjusted results suggested that being female was associated with a steeper trajectory compared to being male (per 1 year increase in relation to depressive symptoms: 0.128, SE = 0.035, [95% CI: 0.059, 0.198]; p <0.001). We found evidence suggesting that females had an earlier age of peak velocity of depressive symptoms (females 13.7 years old, SE = 0.321, [95% CI: 12.9, 14.4] and males 16.4 years old, SE = 0.096, [95% CI: 16.2, 16.6]; p <0.001), but weak evidence of an earlier age of maximum depressive symptoms (p = 0.125). Possible mechanisms that underlie this sex difference include the roles of pubertal development and timing. Using multilevel growth curve models to estimate the age of peak velocity and maximum depressive symptoms for different population subgroups may provide useful knowledge for treating and preventing later depression.

epidemiology↗

bioRxiv2017

The GENIUS Approach to Robust Mendelian Randomization Inference

Mendelian randomization (MR) is a popular instrumental variable (IV) approach, in which one or several genetic markers serve as IVs that can be leveraged to recover under certain conditions, valid inferences about a given exposure-outcome causal association subject to unmeasured confounding. A key IV identification condition known as the exclusion restriction states that the IV has no direct effect on the outcome that is not mediated by the exposure in view. In MR studies, such an assumption requires an unrealistic level of knowledge and understanding of the mechanism by which the genetic markers causally affect the outcome, particularly when a large number of genetic variants are considered as IVs. As a result, possible violation of the exclusion restriction can seldom be ruled out in such MR studies, and if present, such violation can invalidate IVbased inferences even if unbeknownst to the analyst, confounding is either negligible or absent. To address this concern, we introduce a new class of IV estimators which are robust to violation of the exclusion restriction under a large collection of data generating mechanisms consistent with parametric models commonly assumed in the MR literature. Our approach which we have named \"MR G-Estimation under No Interaction with Unmeasured Selection\" (MR GENIUS) may in fact be viewed as a modification to Robins G-estimation approach that is robust to both additive unmeasured confounding and violation of the exclusion restriction assumption. We also establish that estimation with MR GENIUS may also be viewed as a robust generalization of the well-known Lewbel estimator for a triangular system of structural equations with endogeneity. Specifically, we show that unlike Lewbel estimation, MR GENIUS is under fairly weak conditions also robust to unmeasured confounding of the effects of the genetic IVs on both the exposure and the outcome, another possible violation of a key IV Identification condition. Furthermore, while Lewbel estimation involves specification of linear models both for the outcome and the exposure, MR GENIUS generally does not require specification of a structural model for the direct effect of invalid IVs on the outcome, therefore allowing the latter model to be unrestricted. Finally, unlike Lewbel estimation, MR GENIUS is shown to equally apply for binary, discrete or continuous exposure and outcome variables and can be used under prospective sampling, or retrospective sampling such as in a case-control study, as well as for right censored time-to-event outcomes under an additive hazards model.

epidemiology↗

bioRxiv2017

Interactions between immunotoxicants and parasite stress: implications for host health

Many organisms face a wide variety of biotic and abiotic stressors which reduce individual survival, interacting synergistically to further reduce fitness. Here we studied the effects of two such synergistically interacting stressors; immunotoxicant exposure and parasite infection. We model the dynamics of a within-host infection and the associated immune response of an individual. We consider both the indirect sub-lethal effects on immunosuppression and the direct effects on health and mortality of individuals exposed to toxicants. We demonstrate that sub-lethal exposure to toxicants can promote infection through the suppression of the immune system. This happens through the depletion of the immune response which causes rapid proliferation in parasite load. In addition, high toxicant exposure can alter cellular regulation and cause the breakdown of normal healthy tissue, from which we infer higher mortality risk of the host. We classify this breakdown into three phases of increasing toxicant stress, and demonstrate the range of conditions under which toxicant exposure causes failure at the within-host level. These phases are determined by the relationship between the immunity status, overall cellular health and the level of toxicant exposure. We discuss the implications of our model in the context of individual honey bee health. Our model provides an assessment of how pesticide stress and infection interact to cause the synergistic breakdown of the within-host dynamics of individual honey bees.

epidemiology↗

bioRxiv2017

Nasal and aerosol shedding of infectious influenza virus - a community based study

Little is known about the amount and infectiousness of influenza virus shed into exhaled breath. This contributes to uncertainty about the importance of airborne influenza transmission. We screened 355 symptomatic volunteers with acute respiratory illness and report 142 cases with confirmed influenza infection who provided 218 paired nasopharyngeal (NP) and 30-minute breath samples (coarse >5 m and fine <5 m fractions) on days 1 to 3 post symptom onset. We assessed viral RNA copy number for all samples and cultured NP swabs and fine aerosols. We recovered infectious virus from 52 (39%) of the fine aerosols and 150 (89%) of the NP swabs with valid cultures. The geometric mean RNA copy numbers were 3.8x104/30-min fine, 1.2x104/30-min coarse aerosol sample, and 8.2x108 per NP swab. Fine and coarse aerosol viral RNA was positively associated with body mass index (fine p<0.05, coarse p<0.10) and number of coughs (fine p<0.001, coarse p<0.01) and negatively associated with increasing days since symptom onset (fine p<0.05 to p<0.01, coarse p<0.10) in adjusted models. Fine aerosol viral RNA was also positively associated with having influenza vaccination for both the current and prior season (p<0.01). NP swab viral RNA was positively associated with upper respiratory symptoms (p<0.01) and negatively associated with age (p<0.01) but was not significantly associated with fine or coarse aerosol viral RNA or their predictors. Sneezing was rare, and sneezing and coughing were not necessary for infectious aerosol generation. Our observations suggest that influenza infection in the upper and lower airways are compartmentalized and independent.\n\nSignificanceLack of human data on influenza virus aerosol shedding fuels debate over the importance of airborne transmission. We provide overwhelming evidence that humans generate infectious aerosols and quantitative data to improve mathematical models of transmission and public health interventions. We show that sneezing is rare and not important for, and that coughing is not required for influenza virus aerosolization. Our findings, that upper and lower airway infection are independent and that fine particle exhaled aerosols reflect infection in the lung, open a new pathway for understanding the human biology of influenza infection and transmission. Our observation of an association between repeated vaccination and increased viral aerosol generation demonstrated the power of our method, but needs confirmation.

epidemiology↗

bioRxiv2017

The relative fitness of drug resistant Mycobacterium tuberculosis: a modelling study of household transmission in Lima, Peru

The relative fitness of drug resistant versus susceptible bacteria in an environment dictates resistance prevalence. Estimates for the relative fitness of resistant Mycobacterium tuberculosis (Mtb) strains are highly heterogeneous and mostly derived from in-vitro experiments. Measuring fitness in the field allows us to determine how the environment influences resistance spread.\n\nWe designed a household structured, stochastic mathematical model to estimate the fitness costs associated with multi-drug resistance (MDR) carriage in Mtb in Lima, Peru between 2010-2013. By fitting the model to data from a large prospective cohort study of TB disease in household contacts we estimated the fitness, relative to susceptible strains with a fitness of 1, of MDR-Mtb to be 0.33 (95% credible interval: 0.17-0.54) or 0.39 (0.26-0.58), if only transmission or progression to disease, respectively, was affected. The relative fitness of MDR-Mtb increased to 0.57 (0.43-0.73) when the fitness cost influenced both transmission and progression to disease equally.\n\nWe found the average relative fitness of MDR-Mtb circulating within households in Lima, Peru between 2010-2013 to be significantly lower than concurrent susceptible-Mtb. If these fitness levels do not change, then existing TB control programmes are likely to keep MDR-TB prevalence at current levels in Lima, Peru.

epidemiology↗

bioRxiv2017

Spatial correlation as an early warning signal of regime shifts in a multiplex disease-behaviour network

Early warning signals of sudden regime shifts are a widely studied phenomenon for their ability to quantify a systems proximity to a tipping point to a new and contrasting dynamical regime. However, this effect has been little studied in the context of the complex interactions between disease dynamics and vaccinating behaviour. Our objective was to determine whether critical slowing down (CSD) occurs in a multiplex network that captures opinion propagation on one network layer and disease spread on a second network layer. We parameterized a network simulation model to represent a hypothetical self-limiting, acute, vaccine-preventable infection with shortlived natural immunity. We tested five different network types: random, lattice, small-world, scale-free, and an empirically derived network. For the first four network types, the model exhibits a regime shift as perceived vaccine risk moves beyond a tipping point from full vaccine acceptance and disease elimination to full vaccine refusal and disease endemicity. This regime shift is preceded by an increase in the spatial correlation in non-vaccinator opinions beginning well before the bifurcation point, indicating CSD. The early warning signals occur across a wide range of parameter values. However, the more gradual transition exhibited in the empirically-derived network underscores the need for further research before it can be determined whether trends in spatial correlation in real-world social networks represent critical slowing down. The potential upside of having this monitoring ability suggests that this is a worthwhile area for further research.

epidemiology↗

bioRxiv2017

Metabolic characterization of menopause: cross-sectional and longitudinal evidence

BackgroundIt remains elusive whether the changes in cardiometabolic biomarkers during the menopausal transition are due to ovarian aging or chronological aging. Well-conducted longitudinal studies are required to determine this. The aim of this study was to explore the cross-sectional and longitudinal associations of reproductive status defined according to the 2012 Stages of Reproductive Aging Workshop criteria with 74 metabolic biomarkers, and establish whether any associations are independent of age related changes.\n\nMethodsWe determined cross-sectional associations of reproductive status with metabolic profiling in 3,312 UK midlife women. In a subgroup of 1,492 women who had repeat assessments after 2.5 years, we assessed how change in reproductive status was associated with the changes in metabolic biomarkers. Metabolic profiles were measured by high-throughput quantitative serum NMR metabolomics. In longitudinal analyses, we compared the change in metabolic biomarkers for each reproductive status category change to that in the reference of being pre-menopausal at both time points. As all women aged by a similar amount during follow-up, these analyses contribute to distinguish age related changes from those related to change in reproductive status.\n\nResultsConsistent cross-sectional and longitudinal associations of menopause with a wide range of metabolic biomarkers were observed, suggesting transition to menopause induces multiple metabolic changes independent of chronological aging. The metabolic changes included increased concentrations of very small VLDL, IDL and LDL subclasses, remnant and LDL cholesterol, and reduced LDL particle size, all towards an atherogenic lipoprotein profile. Increased inflammation was suggested via an inflammatory biomarker, glycoprotein acetyls, but not via C-reactive protein. Also, levels of glutamine and albumin were increased during the transition. Most of these metabolic changes seen at the time of becoming post-menopausal remained or became slightly stronger during the post-menopausal years.\n\nConclusionsTransition to post-menopause has effects on multiple circulating metabolic biomarkers, over and above the underlying age trajectory. The adverse changes in multiple apolipoprotein-B containing lipoprotein subclasses and increased inflammation may underlie womens increased cardiometabolic risk in post-menopausal years.\n\nAbbreviations

epidemiology↗

bioRxiv2018

Detection of Plasmodium berghei infected Anopheles stephensi using near-infrared spectroscopy

BackgroundThe proportion of mosquitoes infected with malaria is an important entomological metric used to assess the intensity of transmission and the impact of vector control interventions. Currently the prevalence of mosquitoes with salivary gland sporozoites is estimated by dissecting mosquitoes under a microscope or using molecular methods. These techniques are laborious, subjective, and require either expensive equipment or training. This study evaluates the potential of near infra-red spectroscopy (NIRS) to identify laboratory reared mosquitoes infected with rodent malaria.\n\nMethodsAnopheles stephensi mosquitoes were reared in the laboratory and fed on Plasmodium berghei infected blood. After 12 and 21 days post-feeding mosquitoes were killed, scanned and analysed using NIRS and immediately dissected by microscopy to determine the number of oocysts on the midgut wall or sporozoites in the salivary glands. A predictive classification model was used to determine parasite prevalence and intensity status from spectra.\n\nResultsThe predictive model correctly classifies infectious and uninfectious mosquitoes with an overall accuracy of 72%. The false negative and false positive rates are, respectively, 30% and 26%. While NIRS was able to differentiate between uninfectious and highly infectious mosquitoes, differentiating between mid-range infectious groups was less accurate. Multiple scans of the same specimen, with repositioning the mosquito between scans, is shown to improve accuracy. On a smaller dataset NIRS was unable to predict whether mosquitoes harboured oocysts.\n\nConclusionsWe provide the first evidence that NIRS can differentiate between infectious and uninfectious mosquitoes. Currently the method has moderate accuracy and distinguishing between different intensities of infection is challenging. The classification model provides a flexible framework and allows for different error rates to be optimised, enabling the sensitivity and specificity of the technique to be varied according to requirements.

epidemiology↗

bioRxiv2017

Parallel progress in perceived age and life expectancy

Human life expectancy continues to rise in most populations. This rise not only leads to longer lives but is also accompanied by improved health at a given age, i.e. we see a reduction of biological age for a given chronological age in recent cohorts. Despite or even because of the diversity of biomarkers of aging, an accurate quantification of a general shift in biological age across time has been challenging. By comparing age perception of images taken in 2001 over a decade, we show that age perception changes substantially across time and parallels the progress in life expectancy. In 2012, people aged 70+ needed to look 2.3 years younger to be rated the same age as in 2002. Our results further suggest that age perception reflects the past life events better than predicts future length of life, i.e. it is written in your face how much you have aged so far, but does not predict well how fast you will age in the future. We draw this conclusion since age perception among elderly paralleled changes in life expectancy at birth but not changes in remaining life expectancies. We illustrate advantages of perceived age as a biomarker of aging and suggest that changes in age perception should be explored for younger age classes to inform on aging processes, including whether aging is delayed or slowed with increasing life expectancy.

epidemiology↗

bioRxiv2017

A 30-minute nucleic acid amplification point-of-care test for genital Chlamydia trachomatis infection in women: a prospective, multi-centre study of diagnostic accuracy

BackgroundRapid Point-Of-Care Tests (POCTs) for Chlamydia trachomatis (CT) may reduce onward transmission and reproductive sexual health (RSH) sequelae by reducing turnaround times between diagnosis and treatment. The io(R) single module system (Atlas Genetics Ltd) runs clinical samples through a microfluidic CT cartridge, delivering results in 30 minutes. We evaluated its performance on female genital samples in four UK Genito-Urinary Medicine (GUM)/RSH clinics.\n\nMethodsProspective diagnostic accuracy study, using BD ProbeTec CT/GC assay as the routine clinic nucleic acid amplification test (NAAT) as the initial comparator test, and the QIAgen Artus CT assay to resolve discrepancies. In these instances, the reference standard was defined as the resolved result when two out of three assay results concurred. Female participants aged [≥]16 provided additional-to-routine self-collected vulvovaginal swabs. Samples were tested fresh with the io(R) CT assay within 7 days of collection, or were frozen at -80{degrees}C for later testing. Participant clinical, demographic and behavioural characteristics were collected to assess risk factors associated with CT infection.\n\nResultsOf 785 participants recruited, final analyses were conducted on 709 (90.3%). CT prevalence was 7.2% (51/709) overall. Sensitivity, specificity, positive and negative predictive values of the io(R) CT assay were, respectively, 96.1% (95% Confidence Interval (CI): 86.5-99.5), 97.7% (95%CI: 96.3-98.7), 76.6% (95%CI: 64.3-86.2) and 99.7% (95%CI: 98.9-100). There was no significant difference in performance measures between fresh and frozen samples, or between symptomatic and asymptomatic participants (p>0.05). The only risk factor associated with CT infection was being a sexual contact of an individual with CT.\n\nConclusionsThe io(R) CT-assay is the only 30-minute, fully automated, high-performing NAAT currently CE-marked for CT diagnosis in women, making it a highly promising diagnostic to enable specific treatment, initiation of partner notification and appropriately intensive health promotion at the point of care. Future research is required to evaluate acceptability by clinicians and patients in GUM/RSH clinics, impact on clinical pathways and patient management, and cost-effectiveness.

epidemiology↗

bioRxiv2017

90-90-90, epidemic control, and ending AIDS: review of global situation and recommendations

HIV remains a devastating pandemic HIV remains a devastating... Ending AIDS The prevention vs. treatment... Economics of ending AIDS Major innovations accelerating... HIV self-tests Universal treatment regimen Comprehensive community-based... Standardized M and E... Unification of global leadership... Last mile strategies,... Conclusion References Although human immunodeficiency virus (HIV) first came to our attention thirty-seven years ago, the acquired immunodeficiency syndrome (AIDS) which it causes is, without treatment, 100% fatal with devastating consequences for millions of people1. More than 35 million people have already died of ...

epidemiology↗