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bioRxiv2019

Illuminance affects epidemiological parameters of banana Yellow Sigatoka in Brazil

The Sigatoka leaf spots are among the most important banana diseases. Although less damaging than black sigatoka, yellow sigatoka (Pseudocercospora musae) still prevails in some regions. This study aimed at testing the hypothesis of light interference in monocyclic parameters of yellow sigatoka epidemics. Grande Naine plantlets kept under contrasting shading conditions had their leaves 1 and 2 inoculated. Evaluations were performed for 60 days. For each inoculated leaf, the time until symptom onset (incubation), presence of infectious lesions (latency), and disease severity (extensive leaf necrosis) according to Stovers scale modify per Gauhl (1994), called here only Stovers scale, were registered. Logistic regression was used to assess the relative occurrence risk and survival analysis was used to check the effects of variables on relevant epidemiological parameters. The risks of sporulation and of reaching high severities were lower for plants kept under shading regardless of the acclimation conditions and no effect of leaf age was detected. The logistic regression showed symptoms appearing in both conditions (p=0,85), but have significance difference in occurrence of latent lesions (p=0,013) and necrosis (p<0,0001). The necrosis risk in non-shaded environment arrived 66%. The survival analysis showed significance difference in the time to appear the symptom evaluated in all tested variables (p<0,0001) in function of the cropping system. Lower illuminance negatively affected the incubation, latency and infectious periods, and severity. A shaded system could be tested to produce organic bananas in areas of high risk of occurrence of Yellow sigatoka disease.\n\nSignificance and Impact of the StudyYellow Sigatoka (Pseudocercospora musae) is a banana disease that can cause severe damage if left uncontrolled. Its control is based mostly on fungicides.Our results show that shading downregulates the epidemiological parameters of that disease such as incubation, latent and infectious periods, and symptoms severity. These results can be the basis for testing alternative cropping systems and producing organic bananas.

microbiology↗

bioRxiv2026

Global genomic epidemiology of Candida auris: analysis of 12,644 whole genome sequences from 1997-2024

Candida auris is a critical priority fungal pathogen (World Health Organization) that has emerged into human populations pre-1996 from an unknown environmental reservoir. Genomic sequencing data has been used extensively in the last decade, leading to a largely unharnessed dataset with potential to unlock understanding of emerging fungal pathogen evolution. Here, we compiled publicly available Illumina paired-end whole genome sequences (WGS) for variant calling, supplemented by isolates from the worlds first four-clade single-facility outbreak in Algeria (n = 7), totaling 12,644 WGS. We describe the geographic, clinical, and temporal epidemiology of the outbreak across the globe between 1997 and 2024, indicating a conserved six-clade structure. Despite the evidence of earlier species diversity in low- and lower-middle income countries (LLMIC), the majority of WGS derived from high-income (12,035, 93.2%) and upper-middle-income countries (719, 5.57%), where cases are believed to be imported from endemic regions, with few from lower-middle-income countries (165, 1.28%) and none from lower-income countries. Copy number variation was present, including azole drug target ERG11, with seven isolates displaying ten to fifteen copies. Alarmingly, the standing variation of C. auris reveals emerging variation in hot-spots of the echinocandin drug target FKS1, which encodes a {beta}-1,3-glucan synthase. Eighteen emerging FKS1 hot-spot variants have not been detected or described in databases, and mostly occured in Northern America (57/61, 93.4%), where echinocandin monotherapy is standard treatment. Well-studied FKS1 variants known to cause resistance are significantly more common in clade I isolates derived from urine compared to blood, consistent with a role for the urinary niche as a low echinocandin concentration safe-haven for the development of resistance. The insights from this global genomic epidemiology survey of C. auris highlight sequencing inequality and detect ongoing genomic innovation in clinical settings, raising predictable and urgent concerns around the ongoing use of echinocandin monotherapy and potential emerging antifungal drug resistance-related genotypes in high-income settings.

microbiology↗

bioRxiv2026

Molecular epidemiology of the globally spreading genetic lineage IV of peste des petits ruminants virus

Peste des petits ruminants (PPR) is a highly contagious viral disease of small ruminants caused by the peste des petits ruminants virus (PPRV), which is classified into four distinct genetic lineages (I-IV). A critical concern in the recent epidemiological history of PPRV is the rapid and widespread expansion of lineage IV (LIV) across West Africa over the past decade. This dominance suggests a potential adaptive advantage of circulating LIV strains in the regions current epidemiological context. In this study, we obtain the genome sequence of 26 new PPRV samples, including historical (pre-2000) and many recent African LIV isolates, offering the first opportunity to investigate the evolutionary history of LIV in Africa and identify genetic events potentially associated with its recent spread. Phylogenomic analyses implemented on a dataset of 167 curated PPRV genome sequences reveal that the most ancestral LIV group comprises strains circulating in Sub-Saharan Africa (designated clade LIVssa), providing robust evidence for an African origin of lineage IV. Our results further indicate that PPRV strains linked to the recent West African expansion of LIV belong to a specific LIVssa subgroup, termed NigB. We identified multiple signatures of selection pressure within the LIVssa sublineage, particularly in the NigB cluster. Several amino acid substitutions unique to LIVssa or NigB were detected, some of which may impact protein function and warrant prioritised investigation. Additional genomic data are required to confirm the association between the NigB group and the ongoing spread of LIV in West Africa. The evolutionary adaptations observed in LIVssa - potentially enhancing transmission efficiency, host range or pathogenicity - could undermine current disease control strategies in regions where PPR poses significant threats to food security and local economies. Author SummaryPeste des petits ruminants virus (PPRV) infects sheep and goats across Africa, Middle East, Asia and Europe, causing disease with major impact on global economy and food security. One genetic lineage of PPRV, called lineage IV (LIV), is at the origin of most recent expansion of the distribution of the disease, including replacement of other lineages in areas of African where PPRV is historically present. Here, we generated genome sequences from PPRV LIV isolates from different dates and places to study the evolution of this genetic lineage and explore whether its recent spread can be associated with the appearance of new mutations in the virus genome. Our results provide evidence that the PPRV LIV originated in Sub-Saharan Africa and identify mutations present only virus isolates currently spready in new regions of Africa. Further research should investigate the impact of these mutations on protein functions and capacity of transmission of PPRV.

evolutionary biology↗

bioRxiv2026

Challenges in establishing epidemiological cut-off values for the Burkholderia cepacia complex

The Burkholderia cepacia complex (BCC) is comprised of 24 species of Gram-negative bacteria that cause opportunistic infections. While antimicrobial susceptibility testing (AST) has historically been used to guide treatment for BCC infections, recent work highlighting problems with AST for these organisms led the Clinical and Laboratory Sciences Institute (CLSI) to remove disk diffusion (DD) and minimal inhibitory concentration (MIC) breakpoints for BCC from its M100 standards document. Epidemiological cut-off values (ECVs) may be helpful to clinicians in the absence of breakpoints, as they may be used to determine whether an isolate has a wild-type or non-wild-type phenotype. Here we present an analysis of BCC ECVs for ceftazidime (CAZ), levofloxacin (LVX), meropenem (MEM), minocycline (MIN), and trimethoprim-sulfamethoxazole (TMP-SMX). ECVs were calculated using MIC data from 3 previous studies and 3 independent laboratories for 1,896 BCC isolates. ECVs were 16 g/ml for CAZ, 8 g/ml for LVX, 16 g/ml for MEM, and 8 g/ml for MIN. The ECV for TMP-SMX varied depending on the analysis from 2 g/ml, 8 g/ml, and 16 g/ml and therefore could not be reliably established. Challenges with establishing ECVs for BCC include limitations with the pooled MIC dataset, broad MIC distributions, and high ECVs that are above the obsolete susceptible MIC breakpoints. These challenges limit the clinical utility of ECVs for these organisms and supported removal of ECVs from the CLSI M100 standards document. IMPORTANCEThe Burkholderia cepacia complex is a group of bacterial species that cause difficult-to-treat opportunistic infections. Recently, clinical breakpoints, which are used to determine whether organisms are susceptible to certain antimicrobials, were removed from Clinical and Laboratory Standards Institute (CLSI) standards for these organisms due to problems with antimicrobial susceptibility testing performance. Clinicians are now faced with the challenge of how to treat these complex infections without clinical breakpoints. Here we determine epidemiological cut-off values (ECVs) for relevant antimicrobials for the B. cepacia complex. While we established ECVs for four antimicrobials, we encountered significant challenges in our analyses, including limitations with data for these organisms and high ECVs that are not clinically useful. These challenges limit the practical use of these ECVs in helping guide clinicians on treatment and supported the eventual removal of ECVs from the CLSI M100 standards document.

microbiology↗

bioRxiv2026

biomeStat: Using Agentic AI for Scalable Genomic Epidemiology Demonstrated Through End-to-End Analysis of 1,000 Asian Dengue Virus Genomes

Genomic epidemiology workflows typically require expert curation of multiple specialized tools, extensive manual parameter tuning, and access to heterogeneous compute infrastructure. While standard generative AI models often hallucinate in complex biological domains, we introduce biomeStat: an autonomous AI agent that functions as a strict deterministic orchestrator. By automatically writing code to execute established bioinformatics tools in sandboxed environments, biomeStat dynamically provisions compute resources (CPU and GPU) and guarantees reproducibility, making it immediately useful for scientists without requiring command-line expertise. To demonstrate the platform, we performed a fully autonomous genomic epidemiology and structural analysis of 1,000 Dengue virus (DENV) genomes sampled from 16 Asian countries between 2000 and 2025. The agent seamlessly orchestrated phylogenetic reconstruction (IQ-TREE, TreeTime), Bayesian phylodynamics (BEAST2 via NVIDIA H200 GPU), selection pressure analysis (HyPhy), and structural mapping (PyMOL). The analysis was completed in under 24 hours of wall-clock time, revealing endemic stability (R_e [~]1.0) and identifying 1,869 candidate immune escape sites structurally colocalized with B-cell and T-cell epitopes. Furthermore, the agent validated 176 highly conserved drug target residues across the viral replication complex, confirming that resistance-associated positions for emerging antivirals JNJ-1802 and NITD-688 remain absolutely conserved across all four serotypes. By bridging the gap between natural language intent and deterministic computational execution, biomeStat reduces weeks of expert effort into a single-session analysis with full methodological transparency.

bioinformatics↗

bioRxiv2026

HiBASIL: Hierarchical Bayesian Source Inference and Localization for Spatial Epidemiology

O_LIIdentifying spatial origins of biological invasions, disease outbreaks, or environmental contaminants is critical for timely intervention. However, existing methods struggle to resolve overlapping signals from multiple sources or account for extreme zero/one inflation in bounded data. C_LIO_LIWe developed HiBASIL (Hierarchical BAyesian Source Inference and Localization), a Bayesian framework that jointly infers source coordinates and mechanistic dispersal kernels from zero-one-inflated spatial observations. We systematically tested HiBASIL across 2,500 simulations spanning localized to long-distance dispersal regimes, various foci weight mixtures (0.5/0.5 to 0.95/0.05), and varying sample sizes (N = 50 to 500) to evaluate geometric sensitivity, spatial robustness, parameter recovery capability, and multi-focal resolution. We applied HiBASIL in tracking cucurbit downy mildew dispersal in field experiments including non-inoculated control, single-focus, and two-foci treatments arranged in a randomized complete block design. To demonstrate broad applicability, we validated HiBASIL with historical London cholera epidemic data to determine whether it could accurately localize the epicenter. C_LIO_LIHiBASIL achieved 100% accuracy in kernel identification under correct model specification, 100% and 98% (2% predictive equivalence) in under- and over-parameterization scenarios, and maintained appropriate parsimony in null scenarios. Source localization was highly precise, with a median bias of 0.11 m, successfully resolving minority sources contributing only 5% of the observations. Importantly, the framework provides intrinsic self-diagnostics, signaling model complexity mismatch through posterior bimodality (under-parameterization) or parameter collapse (over-parameterization). HiBASIL is applicable in various epidemic scenarios, including diffused long-distance dispersal. Under an isotropic process, HiBASIL achieved sub-meter mean errors on two-source localization in cucurbit downy mildew field tests, effectively isolating transmission signals from landscape noise despite sparse sampling. Despite confounding influence of underlying network processes in the historical cholera data, the posterior localized the epicenter to within [~] 33m, demonstrating portability beyond plant disease epidemiology. C_LIO_LIIn summary, HiBASIL can accurately localize multiple sources across various epidemic scenarios, extremely unbalanced foci mixtures, and sparse sampling conditions. HiBASIL also demonstrates wide applicability across agricultural and human disease epidemic systems. By providing an open-source Python implementation, HiBASIL enables rigorous inverse spatial inference for ecology, epidemiology, and environmental monitoring, transforming how discrete transmission sources are identified in complex landscapes. C_LI

ecology↗

bioRxiv2017

Sex differences in the epidemiology of tattoo skin disease in captive common bottlenose dolphins (Tursiops truncatus): are males more vulnerable than females?

The clinical and epidemiological features of tattoo skin disease (TSD), caused by cetacean poxviruses, are reported in 257 common bottlenose dolphins (Tursiops truncatus) held in 31 facilities in the USA and Europe. Photographs and biological data of 146 females and 111 males were analyzed. Dolphins were classified into three age classes (0-3; 4-8; over 9 years), approximating the life stages of calves and young juveniles, juveniles and sub-adults and adults. The youngest dolphins with tattoos were 14 and 15 months old. Minimal TSD persistence varied between 4 and 65 months in 30 dolphins and was over 22 months in those with very large lesions (> 115 mm). In 2012-2014, 20.6% of the 257 dolphins had TSD. Prevalence varied between facilities from 5.6% (n= 18) to 60% (n= 20), possibly reflecting variation in environmental conditions. Prevalence was significantly higher in males (31.5%) than in females (12.3%), a pattern which departs from that observed in free-ranging Delphinidae where there is no gender bias. As with free-ranging Delphinidae, TSD prevalence in captive females varied with age category, being the highest in the 4 to 8 year old. By contrast, prevalence levels in males were high in all age classes. Prevalence of very large tattoos was also higher in males (28.6%, n= 35) than in females (11.1%, n= 18). Combined, these data suggest that captive male T. truncatus are more vulnerable to TSD than females possibly because of differences in immune response and because males may be more susceptible to captivity-related stress than females.

epidemiology↗

bioRxiv2017

Epidemiological and ecological determinants of Zika virus transmission in an urban setting.

Zika has emerged as a global public health concern. Although its rapid geographic expansion can be attributed to the success of its Aedes mosquito vectors, local epidemiological drivers are still poorly understood. The city of Feira de Santana played a pivotal role in the early phases of the Chikungunya and Zika epidemics in Brazil. Here, using a climate-driven transmission model, we show that low Zika observation rates and a high vectorial capacity in this region were responsible for a high attack rate during the 2015 outbreak and the subsequent decline in cases in 2016, when the epidemic was peaking in the rest of the country. Our projections indicate that the balance between the loss of herd-immunity and the frequency of viral re-importation will dictate the transmission potential of Zika in this region in the near future. Sporadic outbreaks are expected but unlikely to be detected under current surveillance systems.

epidemiology↗

bioRxiv2017

The high burden of dengue and chikungunya in southern coastal Ecuador: Epidemiology, clinical presentation, and phylogenetics from a prospective study in Machala in 2014 and 2015

Here we report the findings from the first two years of an arbovirus surveillance study conducted in Machala, Ecuador, a dengue endemic region (2014-2015). Patients with suspected dengue virus (DENV) infections (index cases, n=324) were referred from five Ministry of Health clinical sites. A subset of DENV positive index cases (n = 44) were selected, and individuals from the index household and four neighboring homes within 200-meters were recruited (n = 400). Individuals who entered the study, other than index cases, are referred to as associates. In 2014, 70.9% of index cases and 35.6% of associates had acute or recent DENV infections. In 2015, 28.3% of index cases and 12.8% of associates had acute or recent DENV infections. For every DENV infection captured by passive surveillance, we detected an additional three acute or recent DENV infections in associates. Of associates with acute DENV infections, 68% reported dengue-like symptoms, with the highest prevalence of symptomatic acute infections in children under 10 years of age. The first chikungunya virus (CHIKV) infections were detected on epidemiological week 12 in 2015. 43.1% of index cases and 3.5% of associates had acute CHIKV infections. No Zika virus infections were detected. Phylogenetic analyses of isolates of DENV from 2014 revealed genetic relatedness and shared ancestry of DENV1, DENV2 and DENV4 genomes from Ecuador with those from Venezuela and Colombia, indicating presence of viral flow between Ecuador and surrounding countries. Enhanced surveillance studies, such as this, provide high-resolution data on symptomatic and inapparent infections across the population.

epidemiology↗

bioRxiv2017

Epidemiology of the multidrug-resistant ST131-H30 subclone among extraintestinal Escherichia coli collected from US children

BackgroundE. coli ST131-H30 is a globally important pathogen implicated in rising rates of multidrug resistance among E. coli causing extraintestinal infections. Previous studies have focused on adults, leaving the epidemiology of H30 among children undefined.\n\nMethodsWe used clinical data and isolates from a case-control study of extended-spectrum cephalosporin-resistant E. coli conducted at four US childrens hospitals to estimate the burden and identify host correlates of infection with H30. H30 isolates were identified using two-locus genotyping; host correlates were examined using log-binomial regression models stratified by extended-spectrum cephalosporin resistance status.\n\nResultsA total of 339 extended-spectrum cephalosporin-resistant and 1008 extended-spectrum cephalosporin-susceptible E. coli isolates were available for analyses. The estimated period prevalence of H30 was 5.3% among all extraintestinal E. coli isolates (95% confidence interval [CI] 4.6%-7.1%); H30 made up 43.3% (81/187) of ESBL-producing isolates in this study. Host correlates of infection with H30 differed by extended-spectrum cephalosporin resistance status: among resistant isolates, age [≤]5 years was positively associated with H30 infection (relative risk [RR] 1.83, 95% CI 1.19-2.83); among susceptible isolates, age [≤]5 years was negatively associated with H30 (RR 0.48, 95% CI 0.27-0.87), while presence of an underlying medical condition was positively associated (RR 4.49, 95% CI 2.43-8.31).\n\nConclusionsST131-H30 is less common among extraintestinal E. coli collected from children compared to reported estimates among adults, possibly reflecting infrequent fluoroquinolone use in pediatrics; however, it is similarly dominant among ESBL-producing isolates. The H30 subclone appears to disproportionately affect young children relative to other extendedspectrum cephalosporin-resistant E. coli.\n\nSummaryST131-H30 was responsible for 5.3% of all extraintestinal E. coli infections and 43.3% of ESBL-producing extraintestinal E. coli infections among US children. The clinical and demographic correlates of infection with ST131-H30 differed between extended-spectrum cephalosporin-resistant and -sensitive isolates.

epidemiology↗

bioRxiv2017

A Standard Operating Procedure For Outlier Removal In Large-Sample Epidemiological Transcriptomics Datasets

Transcriptome measurements and other -omics type data are increasingly more used in epidemiological studies. Most of omics studies to date are small with samples sizes in the tens, or sometimes low hundreds, but this is changing. Our Norwegian Woman and Cancer (NOWAC) datasets are to date one or two orders of magnitude larger. The NOWAC biobank contains about 50000 blood samples from a prospective study. Around 125 breast cancer cases occur in this cohort each year. The large biological variation in gene expression means that many observations are needed to draw scientific conclusions. This is true for both microarray and RNA-seq type data. Hence, larger datasets are likely to become more common soon.\n\nTechnical outliers are observations that somehow were distorted at the lab or during sampling. If not removed these observations add bias and variance in later statistical analyses, and may skew the results. Hence, quality assessment and data cleaning are important. We find common quality assessment libraries difficult to work with for large datasets for two reasons: slow execution speed and unsuitable visualizations.\n\nIn this paper, we present our standard operating procedure (SOP) for large-sample transcriptomics datasets. Our SOP combines automatic outlier detection with manual evaluation to avoid removing valuable observations. We use laboratory quality measures and statistical measures of deviation to aid the analyst. These are available in the nowaclean R package, currently available on GitHub (https://github.com/3inar/nowaclean). Finally, we evaluate our SOP on one of our larger datasets with 832 observations.

epidemiology↗

bioRxiv2017

Using epidemiological principles to explain fungicide resistance management strategies: why do mixtures outperform alternations?

O_LIWhether fungicide resistance management is optimised by spraying chemicals with different modes of action as a mixture (i.e. simultaneously) or in alternation (i.e. sequentially) has been studied by experimenters and modellers for decades, largely inconclusively.\nC_LIO_LIWe use previously-parameterised and validated mathematical models of wheat septoria leaf blotch and grapevine powdery mildew to test which strategy provides better resistance management, using the total yield before fungicide-resistance causes disease control to become economically-ineffective (\"lifetime yield\") to measure effectiveness.\nC_LIO_LILifetime yield is optimised by spraying as much low-risk fungicide as is permitted, combined with slightly more high-risk fungicide than needed for acceptable initial disease control, applying these fungicides as a mixture. This is invariant to model parameterisation and structure, as well as the pathosystem in question. However if comparison focuses on other metrics, for example lifetime yield at full label dose, either mixtures or alternation can be optimal.\nC_LIO_LIOur work shows how epidemiological principles can explain the evolution of fungicide resistance, and highlights a theoretical framework to address the question of whether mixtures or alternation provide better resistance management. Our work also demonstrates that precisely how spray strategies are compared must be given extremely careful consideration.\nC_LI

epidemiology↗

bioRxiv2017

Dengue modeling in rural Cambodia: statistical performance versus epidemiological relevance

Dengue dynamics are shaped by the complex interplay between several factors, including vector seasonality, interaction between four virus serotypes, and inapparent infections. However, paucity or quality of data do not allow for all of these to be taken into account in mathematical models. In order to explore separately the importance of these factors in models, we combined surveillance data with a local-scale cluster study in the rural province of Kampong Cham (Cambodia), in which serotypes and asymptomatic infections were documented. We formulate several mechanistic models, each one relying on a different set of hypotheses, such as explicit vector dynamics, transmission via asymptomatic infections and coexistence of several virus serotypes. Models are confronted with the observed time series using Bayesian inference, through Markov chain Monte Carlo. Model selection is then performed using statistical information criteria, but also by studying the coherence of epidemiological characteristics (reproduction numbers, incidence proportion, dynamics of the susceptible class) in each model. Considering the available data, our analyses on transmission dynamics in a rural endemic setting highlight both the importance of using two-strain models with interacting effects and the lack of added value of incorporating vector and explicit asymptomatic components.

epidemiology↗

bioRxiv2017

Hepatitis C Virus (HCV) diagnosis, epidemiology and access to treatment in a UK cohort

BackgroundAs direct acting antiviral (DAA) therapy is progressively rolled out for patients with hepatitis C virus (HCV) infection, careful scrutiny of HCV epidemiology, diagnostic testing, and access to care is crucial to underpin improvements in delivery of treatment.\n\nMethodsWe performed a retrospective study of HCV infection in a UK teaching hospital to evaluate the performance of different diagnostic laboratory tests, to describe the population with active HCV infection, and to determine the proportion of these individuals who access clinical care.\n\nResultsOver a total time period of 33 months between 2013 and 2016, we tested 38,510 individuals for HCV infection and confirmed a new diagnosis of active HCV infection (HCV-Ag+ and/or HCV RNA+) in 359 (positive rate 0.9%). Our in-house HCV-Ab test had a positive predictive value of 87% when compared to repeat HCV-Ab testing in a regional reference laboratory, highlighting the potential for false positives to arise based on a single round of antibody-based screening. Of those confirmed Ab-positive, 70% were HCV RNA positive. HCV-Ag screening performed well, with 100% positive predictive value compared to detection of HCV RNA. There was a strong correlation between quantitative HCV-Ag and HCV RNA viral load (p<0.0001). Among the 359 cases of infection, the median age was 37 years, 85% were male, and 36% were in prison. Among 250 infections for which genotype was available, HCV genotype-1 (n=110) and genotype-3 (n=111) accounted for the majority. 117/359 (33%) attended a clinic appointment and 48 (13%) had curative treatment defined as sustained virologic response at 12 weeks (SVR12).\n\nConclusionsHCV-Ab tests should be interpreted with caution as an indicator of population prevalence of HCV infection, both as a result of the detection of individuals who have cleared infection and due to false positive test results. We demonstrate that active HCV infection is over-represented among men and in the prison population. A minority of patients with a diagnosis of HCV infection access clinical care and therapy; enhanced efforts are required to target diagnosis and providing linkage to clinical care within high risk populations.\n\nABBREVIATIONS

epidemiology↗

bioRxiv2018

Heterogeneous susceptibility to rotavirus infection and gastroenteritis in two birth cohort studies: parameter estimation and epidemiological implications

Variation in susceptibility is a known contributor to bias in studies estimating immune protection acquired from vaccination or natural infection. However, difficulty measuring this heterogeneity hinders assessment of its influence on estimates. Cohort studies, randomized trials, and post-licensure studies have reported reduced natural and vaccine-derived protection against rotavirus gastroenteritis in low- and middle-income countries (LMICs). We sought to understand differences in susceptibility among children enrolled in two birth-cohort studies of rotavirus in LMICs, and to explore the implications for estimation of immune protection. We re-analyzed data from studies conducted in Mexico City, Mexico and Vellore, India. Cumulatively, 573 unvaccinated children experienced 1418 rotavirus infections and 371 episodes of rotavirus gastroenteritis (RVGE) over 17,636 child-months. We developed a model characterizing susceptibility to rotavirus infection and RVGE among children, accounting for aspects of the natural history of rotavirus and differences in transmission rates between settings, and tested whether modelgenerated susceptibility measurements were associated with demographic and anthropometric factors. We identified greater variation in susceptibility to rotavirus infection and RVGE in Vellore than in Mexico City. In both cohorts, susceptibility to rotavirus infection and RVGE were associated with male sex, lower birth weight, lower maternal education, and having fewer siblings; within Vellore, susceptibility was also associated with lower socioeconomic status. Children who were more susceptible to rotavirus also experienced higher rates of diarrhea due to other causes. Simulations suggest that discrepant estimates of naturally-acquired immunity against RVGE can be attributed, in part, to between-setting differences in transmission intensity and susceptibility of children. We found that more children in Vellore than in Mexico City belong to a high-risk group for rotavirus infection and RVGE, and demonstrate that bias owing to differences in rotavirus transmission intensity and population susceptibility may hinder comparison of estimated immune protection against RVGE.\n\nAuthor summaryDifferences in susceptibility can help explain why some individuals, and not others, acquire infection and exhibit symptoms when exposed to infectious disease agents. However, it is difficult to distinguish between differences in susceptibility versus exposure in epidemiological studies. We developed a modeling approach to distinguish transmission intensity and susceptibility in data from cohort studies of rotavirus infection among children in Mexico City, Mexico, and Vellore, India, and evaluated how these factors may have contributed to differences in estimates of naturally-acquired immune protection between the studies. We found that more children were at \"high risk\" of acquiring rotavirus infection, and of experiencing gastroenteritis when infected, in Vellore versus Mexico City. The probability of belonging to this high-risk stratum was associated with recognized risk factors such as lower socioeconomic status, lower birth weight, and risk of diarrhea due to other causes. We also found the risk for rotavirus infections to cause symptoms declined with age, and was independent of acquired immunity. Together, these findings can account for estimates of lower protective efficacy of acquired immunity against rotavirus gastroenteritis in high-incidence settings, which mirrors estimates of reduced effectiveness of live oral rotavirus vaccines in low- and middle-income countries.

epidemiology↗

bioRxiv2018

10 Year Epidemiologic data of Parkinson`s Disease: A Nationwide Population-based Retrospective Cohort of South Korea

ObjectivesThe aims of this study were to determine the prevalence, incidence, and P/I ratio of Parkinsons disease (PD) in South Korea and to present basic epidemiological information on PD patients for making effective health policies.\n\nMethodsWe used National Health Insurance Service-National Sample Cohort (KNHIS-NSC) data to analyze the prevalence, incidence, and P/I ratio of PD from 2003 to 2013 and then followed up using the NHID in 2008 to obtain the hazard ratio (HR) of death in PD itself and other comorbidities from 2008 to 2013.\n\nResultsThe prevalence and incidence of PD increased rapidly from 72.9 and 32.8 in 2003 to 213.4 and 58.0 in 2013, and the P/I ratio increased from 2.22 in 2003 to 3.62 in 2013. The prevalence, incidence, and P/I ratio of PD were all higher in women than in men. The hazard ratio for death was significantly higher in PD patients (15.36) compared to subjects without the disease. Stroke was the most frequent cause of death in the PD patient population followed by cancer and pneumonia.\n\nConclusionThe prevalence, incidence, and P/I ratio of PD rapidly increased as the years progressed. This indirectly proves that the health insurance system in Korea is efficient and has allowed patients with PD to access medical facilities more easily. However, a newer public healthy strategy should be established for patients with PD because PD itself has a high HR for death, and patients with PD have a high mortality rate when stroke and pneumonia are also involved.\n\nDisclosureAll authors have reported no biomedical interests and potential conflicts of interests.

epidemiology↗

bioRxiv2018

Modeling Uncertainty in Grapevine Powdery Mildew Epidemiology Using Fuzzy Logic

Powdery mildew is the most important disease of grapevines worldwide. Despite the potential for rapid spread by the causal pathogen, grape powdery mildew has been effectively managed using fungicide applications applied based on a calendar schedule or modeled disease risk index. Various epidemiological models for predicting disease development or risk have helped to improve disease management. The Gubler-Thomas (GT) risk index is a popular disease risk model used by many growers in the western U.S. We modified the GT risk index using fuzzy logic to address both biological and mechanical uncertainty in the pathosystem. The spraying schedule suggested by the fuzzy-modified GT risk index was tested in eight site-years. Overall, the fuzzy-modified risk index maintained comparable levels of disease control as both the original model and a calendar based treatment, and had significantly less disease than the untreated control. The fungicide use efficiency of the fuzzy-modified GT risk index suggests that the updated risk index was significantly more efficient with fungicide applications than both the calendar and original GT risk index.

epidemiology↗

bioRxiv2018

Surveillance of CKD epidemiology in the US -- a joint analysis of NHANES and KEEP

Chronic Kidney Disease (CKD), is highly prevalent in the United States. Epidemiological systems for surveillance of CKD rely on data that are based solely on the NHANES survey, which does not include many patients with the most severe and less frequent forms of CKD. We investigated the feasibility of estimating CKD prevalence from the large-scale community disease detection Kidney Early Evaluation and Program (KEEP, n = 127,149). We adopted methodologies from the field of web surveys to address the self-selection bias inherent in KEEP. Primary outcomes studied were CKD Stage 3-5 (estimated glomerular filtration rate [eGFR] <60 mL/min/1.73m2, and CKD Stage 4-5 (eGFR <30 mL/min/1.73m2). The unweighted prevalence of Stage 4-5 CKD was higher in KEEP (1.00%, 95%CI: 0.94-1.05%) than in NHANES (0.51%, 95% CI: 0.43-0.59%). Application of a selection model with IPW of variables related to demographics, recruitment and socio-economic factors resulted in estimates similar to NHANES (0.55%, 95% CI: 0.50-0.60%). Weighted prevalence of Stages 3-5 CKD in KEEP was 6.45% (95% CI: 5.70 7.28%) compared to 6.73% (95% CI: 6.30-7.19%) for NHANES. Application of methodologies that address the self-selection bias in the KEEP program may allow the use of this large, geographically diverse dataset for CKD surveillance.

epidemiology↗