SEARCH · Search bioRxiv

Results for “Epidemiology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 307 records · Page 17Linked to original sources

bioRxiv2018

Molecular typing and macrolide resistance analyses of Treponema pallidumin heterosexuals and men who have sex with men communities in Japan, 2017.

In recent years, syphilis notifications have increased dramatically in Japan. We performed molecular typing and analyzed macrolide resistance of Treponema pallidum samples collected from four clinics and a hospital in Tokyo and Osaka prefectures in 2017.\n\nMacrolide resistant strain type 14d/f was found significantly more in heterosexual syphilis cases compared with those strains identified in men who have sex with men (MSM) syphilis cases. The proportion of 14d/f among heterosexuals was 79% (31/39) compared to 37% (7/19) among MSM [OR, 6.6 (95% CI, 1.7 to 26.7); P=0.002]. 83% (50/60) of the strains were identified as macrolide resistant with an A2058G mutation at the 23S rRNA gene. 90% (35/39) of the heterosexual strains were macrolide resistant, relative to 58% (11/19) of MSM strains; the odds of having the resistant mutation was considerably higher in heterosexuals compared with MSM [OR, 6.4 (95% CI, 1.3 to 33.5); P=0.02]. Heterosexual females and males showed similar distributions, and the results remained the same when restricted to men.\n\nThe strain type distribution and frequency of macrolide resistance differed substantially between heterosexual and MSM syphilis samples, suggesting distinct epidemiologic profiles for the two communities and insight into syphilis transmission dynamics in Japan.

epidemiology↗

bioRxiv2018

Rethinking the efficacy of acellular pertussis vaccines for primary immunization

BackgroundThe US has experienced a nationwide resurgence of pertussis since the mid-1970s, despite high vaccine coverage. Short-lived immunity induced by Diphtheria-Tetanus-acellular Pertussis (DTaP) vaccines in young children is widely believed to be responsible for this growing burden. However, the duration of protection conferred by DTaP vaccines remains incompletely quantified.\n\nMethods and FindingsWe employed a rigorously validated, age-structured model of pertussis transmission to explore a range of hypotheses regarding the degree of waning DTaP-derived immunity. For every hypothesis, we calculated the vaccine effectiveness and the relative increase in the odds of acquiring pertussis (or odds ratio) in children aged 5 to 9 years. We then assessed the simulated DTaP vaccine traits that best reproduced the empirical values of odds ratios from recent US epidemiological studies. We found a marked association between the degree of waning immunity, the vaccine effectiveness, and the odds ratio. Unexpectedly, the odds ratio was positively associated with the vaccine effectiveness, as a consequence of non-linear, age-assortative dynamics. Based on the empirical odds ratios, we estimated that vaccine effectiveness exceeded 75% and that more than 65% of children remained immune to pertussis 5 years after the last DTaP dose.\n\nConclusionsOur results show that temporal trends in the odds of acquiring pertussis are a seriously flawed measure of the durability of vaccine-induced protection. They further demonstrate that DTaP vaccines confer imperfect, but long-lived protection. We argue that control strategies should be based upon the best available estimates of vaccine properties and the age-structure of the transmission network.

epidemiology↗

bioRxiv2018

Causal effects of lifetime smoking on risk for depression and schizophrenia: Evidence from a Mendelian randomisation study

BackgroundSmoking prevalence is higher amongst individuals with schizophrenia and depression compared to the general population. Mendelian randomisation (MR) can examine whether this association is causal using genetic variants identified in genome-wide association studies (GWAS).\n\nMethodsWe conducted a GWAS of lifetime smoking behaviour (capturing smoking duration, heaviness and cessation) in a sample of 462,690 individuals from the UK Biobank, and validated the findings via two-sample MR analyses of positive control outcomes (e.g., lung cancer). Having established the validity of our instrument, we used bi-directional two-sample Mendelian randomisation to explore its effects on schizophrenia and depression.\n\nOutcomesThere was strong evidence to suggest smoking is a causal risk factor for both schizophrenia (OR = 2.27, 95% CI = 1.67 - 3.08, P < 0.001) and depression (OR = 1.99, 95% CI = 1.71 - 2.32, P < 0.001). We also found some evidence that genetic risk for both schizophrenia and depression cause increased lifetime smoking ({beta} = 0.022, 95% CI = 0.005 - 0.038, P = 0.009; {beta}= 0.091, 95% CI = 0.027 - 0.155, P = 0.005).\n\nInterpretationThese findings suggest that the association between smoking, schizophrenia and depression is due, at least in part, to a causal effect of smoking, providing further evidence for the detrimental consequences of smoking for mental health.\n\nFundingThis work was supported by the Medical Research Council Integrative Epidemiology Unit, the NIHR Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust and the University of Bristol.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe association between smoking and mental health (especially schizophrenia and depression) is often assumed to be the result of self-medication (for example, to alleviate symptoms). However, more recent evidence has suggested that smoking might also be a risk factor for schizophrenia and depression. This alternative direction of effect is supported by meta-analyses and previous prospective observational evidence using related individuals to control for genetic and environmental confounding. However, observational evidence cannot completely account for confounding or the possibility of reverse causation. One way to get around these problems is Mendelian randomisation (MR). Previous MR studies of smoking and mental health have not shown an effect of smoking on depression and are inconclusive for the effects of smoking on schizophrenia. However, these studies have only looked at individual aspects of smoking behaviour and some studies required stratifying participants into smokers and non-smokers, reducing power.\n\nAdded value of this studyWe have developed a novel genetic instrument for lifetime smoking exposure which can be used within a two-sample MR framework, using publicly-available GWAS summary statistics. We were therefore able to test the bi-directional association between smoking with schizophrenia and depression to see if the effects are causal. We found strong evidence to suggest that smoking is a causal risk factor for both schizophrenia and depression. There was some evidence to suggest that risk of schizophrenia and depression increases lifetime smoking (consistent with the self-medication hypothesis) but the effects were stronger for depression than schizophrenia.\n\nImplications of all the available evidenceThis study was the first to demonstrate evidence for an effect of lifetime smoking exposure on risk of schizophrenia and depression within a causal inference framework. This emphasises the detrimental public health consequences of smoking, not just for physical health, but also to mental illness.

epidemiology↗

bioRxiv2018

Magnitude of road traffic accident related injuries and fatalities in Ethiopia

BackgroundIn many developing countries there is paucity of evidence regarding the epidemiology of road traffic accidents (RTAs). The study determines the rates of injuries and fatalities associated with RTAs in Ethiopia based on the data of a recent national survey.\n\nMethodsThe study is based on the secondary data of the Ethiopian Demographic and Health Survey conducted in 2016. The survey collected information about occurrence injuries and accidents including RTAs in the past 12 months among 75,271 members of 16,650 households. Households were selected from nine regions and two city administrations of Ethiopia using stratified cluster sampling procedure.\n\nResultsOf the 75,271 household members enumerated, 123 encountered RTAs in the reference period and rate of RTA-related injury was 163 (95% confidence interval (CI): 136-195) per 100,000 population. Of the 123 causalities, 28 were fatal, making the fatality rate 37 (95% CI: 25-54) per 100,000 population. The RTA-related injuries and fatalities per 100,000 motor vehicles were estimated as 21,681 (95% CI: 18,090-25,938) and 4,922 (95% CI: 3325-7183), respectively. Next to accidental falls, RTAs were the second most common form of accidents and injuries accounting for 22.8% of all such incidents. RTAs contributed to 43.8% of all fatalities secondary to accidents and injuries. Among RTA causalities, 21.9% were drivers, 35.0% were passenger vehicle occupants and 36.0% were vulnerable road users including: motorcyclists (21.0%), pedestrians (12.1%) and cyclists (2.9%). Approximately half (47.1%) of the causalities were between 15-29 years of age and 15.3% were either minors younger than 15 years or seniors older than 64 years of age. Nearly two-thirds (65.0%) of the victims were males.\n\nConclusionRTA-related causalities are extremely high in Ethiopia. Male young adults and vulnerable road users are at increased risk of RTAs. There is a urgent need for bringing road safety to the countrys public health agenda.

epidemiology↗

bioRxiv2018

Assessment of Menstrual Health Status and Evolution through Mobile Apps for Fertility Awareness

For most women of reproductive age, assessing menstrual health and fertility typically involves regular visits to a gynecologist or another clinician. While these evaluations provide critical information on an individuals reproductive health status, they typically rely on memory-based self-reports, and the results are rarely, if ever, assessed at the population level. In recent years, mobile apps for menstrual tracking have become very popular, allowing us to evaluate the reliability and tracking frequency of millions of self-observations, thereby providing an unparalleled view, both in detail and scale, on menstrual health and its evolution for large populations. In particular, we were interested in exploring the tracking behavior of the app users and their overall observation patterns in an effort to understand if they were consistent with previous small-scale medical studies. We also investigated whether their precision allowed the detection and estimation of ovulation timing, which is critical for reproductive and menstrual health. Retrospective self-observation data were acquired from two mobile apps dedicated to the application of the sympto-thermal fertility awareness method, resulting in a dataset of more than 30 million days of observations from over 2.7 million cycles. The analysis of the data showed that up to 40% of the cycles in which users were seeking pregnancy had recordings every single day. With a modeling approach using Hidden Markov Models to describe the collected data and estimate ovulation timing, it was found that follicular phases average duration and range were larger than previously reported, with only 24% of ovulations occurring at days 14 to 15, while the luteal phase duration and range were in line with previous reports, although short luteal phases (10 days or less) were more frequently observed (in up to 20% of cycles). The digital epidemiology approach presented here can help to lead to a better understanding of menstrual health and its connection to womens health overall, which has historically been severely understudied.

epidemiology↗

bioRxiv2018

The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria

Individual malaria infections can carry multiple strains of Plasmodium falciparum with varying levels of relatedness. Yet, how local epidemiology affects the properties of such mixed infections remains unclear. Here, we develop an enhanced method for strain deconvolution from genome sequencing data, which estimates the number of strains, their proportions, identity-by-descent (IBD) profiles and individual haplotypes. Applying it to the Pf3k data set, we find that the rate of mixed infection varies from 29% to 63% across countries and that 51% of mixed infections involve more than two strains. Further-more, we estimate that 47% of symptomatic dual infections contain sibling strains likely to have been co-transmitted from a single mosquito, and find evidence of mixed infections propagated over successive infection cycles. Finally, leveraging data from the Malaria Atlas Project, we find that prevalence correlates within Africa, but not Asia, with both the rate of mixed infection and the level of IBD.

epidemiology↗

bioRxiv2018

Correlates of cannabinoid concentrations, real-world driving, and driving-related skills

Research on the relationship between cannabis use and safe driving has produced mixed results. Most studies have focused exclusively on the presence or concentration of delta-9-tetrahydrocannabinol (THC), the primary psychoactive ingredient in the drug. However, cannabis is a complex substance, and both toxicological research and user experience suggests that some cannabis strains--often those with at least moderate levels of cannabidiol (CBD)-- produce a different, more sedating \"high\" than cannabis strains with no or low levels of CBD. We hypothesize that the sedating properties of some high-CBD cannabis strains has potential to impair driving and driving-related skills above and beyond the effects of THC intoxication. Three studies--one instrumented vehicle driving study and two laboratory-style epidemiological studies--examined real driving and computerized task performance as a function THC and CBD concentrations (and their interactions). In all three studies, higher CBD levels predicted greater impairment. There was relatively little evidence of impairment when CBD was zero, even at high THC levels. The results suggest that THC concentrations alone are not sufficient to predict impairment due to cannabis use. Results are interpreted in the context of drug tolerance.

epidemiology↗

bioRxiv2018

Mortality attributable to seasonal influenza in Greece, 2013-2017: variation by type and age, and a possible harvesting effect

BACKGROUNDEstimating the contribution of influenza to excess mortality in the population presents substantial methodological challenges. We combined environmental, epidemiological and laboratory surveillance data to estimate influenza-attributable mortality in Greece, over four seasons (2013-2014 to 2017-2018), specifically addressing the lag dimension and the confounding effect of temperature.\n\nMETHODSAssociations of influenza type-specific incidence proxies and of daily mean temperature with mortality were estimated with a distributed-lag non-linear model with 30 days of maximum lag, separately for each age group. Total and weekly deaths attributable to influenza and cold temperatures were calculated.\n\nRESULTSOverall influenza-attributable mortality was 23.6 deaths per 100,000 population (95%CI: 17.8, 29.2), and varied greatly between seasons, by influenza type and by age group, with the vast majority occurring in persons 65 years or older. Most deaths were attributable to A/H3N2, followed by type B influenza. During periods of A/H1N1 circulation, weekly attributable mortality to this subtype among older people increased rapidly in the first half, but then fell to zero and even negative, suggesting a mortality displacement (harvesting) effect. Mortality attributable to non-optimum temperatures was much higher than that attributable to influenza.\n\nCONCLUSIONSStudies of influenza-attributable mortality need to take distributed-lag effects into account, stratify by age group and adjust for circulating influenza types and daily mean temperatures, in order to produce reliable estimates. Our approach is useful and readily applicable in the context of influenza surveillance.

epidemiology↗

bioRxiv2018

Individual and temporal variation in pathogen load predicts long-term impacts of an emerging infectious disease

Emerging infectious diseases increasingly threaten wildlife populations. Most studies focus on managing short-term epidemic properties, such as controlling early outbreaks. Predicting long-term endemic characteristics with limited retrospective data is more challenging. We used individual-based modelling informed by individual variation in pathogen load and transmissibility to predict long-term impacts of a lethal, transmissible cancer on Tasmanian devil (Sarcophilus harrisii) populations. For this, we employed Approximate Bayesian Computation to identify model scenarios that best matched known epidemiological and demographic system properties derived from ten years of data after disease emergence, enabling us to forecast future system dynamics. We show that the dramatic devil population declines observed thus far are likely attributable to transient dynamics. Only 21% of matching scenarios led to devil extinction within 100 years following devil facial tumour disease (DFTD) introduction, whereas DFTD faded out in 57% of simulations. In the remaining 22% of simulations, disease and host coexisted for at least 100 years, usually with long-period oscillations. Our findings show that pathogen extirpation or host-pathogen coexistence are much more likely than the DFTD-induced devil extinction, with crucial management ramifications. Accounting for individual-level disease progression and the long-term outcome of devil-DFTD interactions at the population-level, our findings suggest that immediate management interventions are unlikely to be necessary to ensure the persistence of Tasmanian devil populations. This is because strong population declines of devils after disease emergence do not necessarily translate into long-term population declines at equilibria. Our modelling approach is widely applicable to other host-pathogen systems to predict disease impact beyond transient dynamics.

epidemiology↗

bioRxiv2018

Pharmacovigilance or patient safety: analysis from a patient safety program

Purposedrugs are the common point of pharmacovigilance and patient safety programs. Despite using a common language, the same epidemiological method and legislation that requires the operation of the two programs, there does not seem to be a clear relationship between them.\n\nMethodologyobservational descriptive cross sectional study of the reports database from an institutional patient safety program. Medication errors were classified according to the document The Conceptual Framework for the International Classification for Patient Safety (ICPS) WHO 2009. Adverse Reactions (ADR) were classified according to Uppsala Monitoring Center.\n\nResultsthe omission of drugs or doses was the most frequent error with 42.8% followed by ADRs (20.9%). No harm incidents corresponded to 61.2% and the remaining 38.8% was represented in near missincidents and no harm incidents. There were included 41 ADR and 15 therapeutic failures corresponding to a point-prevalence of 57 ADR/10,000 patients-year and 28.6% (56/196) of reports related to drugs. Phlebitis is the most frequently reported with 23, 7% followed by hypersensitivity reactions with 18.4% and excessive neuromuscular blockade with 13.1%.\n\nConclusionsconsidering time, level of care and number of bed, ADR prevalence seem low. A very important proportion of reports corresponding to near miss incidents or no harm incidents is not taken into account by the security managers, losing a valuable risk management opportunity in the patient safety programs.

epidemiology↗

bioRxiv2018

Mycoplasma genitalium incidence, persistence, concordance between partners and progression: systematic review and meta-analysis

BackgroundMycoplasma genitalium is increasingly seen as an emerging sexually transmitted pathogen, and has been likened to Chlamydia trachomatis, but its natural history is poorly understood. The objectives of this systematic review were to determine M. genitalium incidence, persistence, concordance between sexual partners, and the risk of pelvic inflammatory disease (PID).\n\nMethodsWe searched Medline, EMBASE, LILACS, IndMed and African Index Medicus from 1 January 1981 until 17 March 2018. Two independent researchers screened studies for inclusion and extracted data. We examined results in forest plots, assessed heterogeneity and conducted meta-analysis where appropriate. Risk of bias was assessed for all studies.\n\nResultsWe screened 4634 records and included 17 studies; five (4100 women) reported on incidence, five (636 women) on persistence, 10 (1346 women and men) on concordance and three (5139 women) on PID. Incidence in women in two very highly developed countries was 1.07 per 100 person-years (95% CI, 0.61 to 1.53, I2 0%). Median persistence of M. genitalium was estimated from one to three months in four studies but 15 months in one study. In ten studies measuring M. genitalium infection status in couples, 39-50% of male or female sexual partners of infected participants also had M. genitalium detected. In prospective studies, the incidence of PID was higher in women with M. genitalium than those without (RR 1.68, 95% CI 0.59 to 2.77, I2 0%, 2 studies).\n\nDiscussionBased on findings from this and our linked review of prevalence, concordant M. genitalium might be less common than for C. trachomatis and the age distributions of the infections differ. The synthesised data about prevalence, incidence and persistence of M. genitalium infection are inconsistent. Taken together with evidence about antimicrobial resistance in the two infections, M. genitalium is not the new chlamydia.\n\nRegistration NumbersPROSPERO: CRD42015020420, CRD42015020405\n\nKEY MESSAGESO_LIThere are calls for widespread screening for Mycoplasma genitalium, but the natural history of this emerging sexually transmitted pathogen is poorly understood.\nC_LIO_LIM. genitalium incidence was 1.07 (95% confidence intervals, CI 0.61 to 1.53) per 100-person years in women in highly developed countries, 39-50% of infected individuals had a heterosexual partner with M. genitalium and the risk ratio for pelvic inflammatory disease was 1.68 (95% CI 0.59 to 2.77).\nC_LIO_LIThe duration of untreated M. genitalium infection is probably longer than persistent detection of M. genitalium, as measured in most cohort studies, in which inadvertent treatment cannot be ruled out.\nC_LIO_LIThe results of this systematic review and other evidence sources show important differences in the epidemiology and dynamics of M. genitalium and Chlamydia trachomatis infection.\nC_LI

epidemiology↗

bioRxiv2018

Disease persistence on temporal contact networks accounting for heterogeneous infectious periods

The infectious period of a transmissible disease is a key factor for disease spread and persistence. Epidemic models on networks typically assume an identical average infectious period for all individuals, thus allowing an analytical treatment. This simplifying assumption is however often unrealistic, as hosts may have different infectious periods, due, for instance, to individual host-pathogen interactions or inhomogeneous access to treatment. While previous work accounted for this heterogeneity in static networks, a full theoretical understanding of the interplay of varying infectious periods and time-evolving contacts is still missing. Here we consider an SIS epidemic on a temporal network with host-specific average infectious periods, and develop an analytical framework to estimate the epidemic threshold, i.e. the critical transmissibility for disease spread in the host population. Integrating contact data for transmission with outbreak data and epidemiological estimates, we apply our framework to three real-world case studies exploring different epidemic contexts - the persistence of bovine tuberculosis in southern Italy, the spread of nosocomial infections in a hospital, and the diffusion of pandemic influenza in a school. We find that the homogeneous parameterization may cause important biases in the assessment of the epidemic risk of the host population. Our approach is also able to identify groups of hosts mostly responsible for disease diffusion who may be targeted for prevention and control, aiding public health interventions.

epidemiology↗

bioRxiv2018

General aspects of visceral leishmaniasis with or without HIV co-infection in Northeast Brazil

BackgroundThe case of visceral leishmaniasis (VL) and human immunodeficiency virus (HIV) co-infection was reported in Spain first in 1985, and coincidence of these diseases has also been confirmed in more than 35 countries.\n\nMethodologyWe performed a comparative study in the states reference hospital for infectious/parasitic diseases, which treats adults with HIV/acquired immune deficiency syndrome (AIDS), between January 2007 and July 2017. The data obtained using this protocol were analyzed using SPSS.\n\nPrincipal findingsIn total, 163 patients were evaluated in this study, including 126 patients with coincident VL/HIV and 37 patients with VL alone. Both groups consisted primarily of male patients. The most commonly affected age group was 30-39 years (p < 0.001). Fever (p < 0.001) and hair loss (p = 0.007), which were more common in patients with VL alone, were more common. On hemogram, segmented neutrophils (p < 0.0001) were found to be more in the VL/HIV group than in the VL alone group. Additionally, AST and ALT levels differed between the groups (p < 0.001). On average, HIV was diagnosed 2.6 years before VL (p < 0.001). VL relapse was observed only in the co-infection group (36.5% of cases). Fever ({beta} = +0.17; p = 0.032) in the first VL/HIV episode was identified as a risk factor for relapse (R2 = 0.18). The death rate of co-infected patients was 11.1%.\n\nConclusion/SignificanceVL/HIV was prevalent among young adults, whereas the median patient age was higher in the VL group. The classic symptomatology of VL was more common in patients not co-infected with HIV, but attention is needed regarding the presence of fever in the first episode of VL as a risk factor for relapse in co-infected patients. No cases of VL relapse occurred in patients without HIV.\n\nAUTHOR SUMMARYVisceral Leishmaniasis (VL) and HIV have maintained increasing rates of populational occurrence in the Northeast region of Brazil, with advancing in rural areas and VL advancing in urban areas. This dynamic explains the increase of co-infection from 0.7% in 2001 to 8.5% in 2012. The state of Maranhao presents a large number of cases in the Northeast Brazil, a region with the majority of patients with this co-infection. The severity presented by these patients, in the observation of frequent relapses and high lethality, is presented in this study, which contributes to epidemiological, clinical, laboratorial, and evolutionary knowledge, trying to demonstrate these in the statistical data. Therefore, it should be pointed out that young adult patients with HIV/AIDS who present with any cytopenia, with or without hepatosplenomegaly and accompanied by fever or not, must be investigated for VL.

epidemiology↗

bioRxiv2018

Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission

Understanding which HIV-1 variants are most likely to be transmitted is important for vaccine design and predicting virus evolution. Since most infections are founded by single variants, it has been suggested that selection at transmission has a key role in governing which variants are transmitted. We show that the composition of the viral population within the donor at the time of transmission is also important. To support this argument, we developed a probabilistic model describing HIV-1 transmission in an untreated population, and parameterised the model using both within-host next generation sequencing data and population-level epidemiological data on heterosexual transmission. The most basic HIV-1 transmission models cannot explain simultaneously the low probability of transmission and the non-negligible proportion of infections founded by multiple variants. In our model, transmission can only occur when environmental conditions are appropriate (e.g. abrasions are present in the genital tract of the potential recipient), allowing these observations to be reconciled. As well as reproducing features of transmission in real populations, our model demonstrates that, contrary to expectation, there is not a simple link between the number of viral variants and the number of viral particles founding each new infection. These quantities depend on the timing of transmission, and infections can be founded with small numbers of variants yet large numbers of particles. Including selection, or a bias towards early transmission (e.g. due to treatment) acts to enhance this conclusion. In addition, we find that infections initiated by multiple variants are most likely to have derived from donors with intermediate set-point viral loads, and not from individuals with high set-point viral loads as might be expected. We therefore emphasise the importance of considering viral diversity in donors, and the timings of transmissions, when trying to discern the complex factors governing single or multiple variant transmission.

epidemiology↗

bioRxiv2018

Field evaluation of malachite green loop-mediated isothermal amplification as a malaria parasite detection tool in a health post in Roraima state, Brazil

Malaria is a debilitating parasitic disease that causes significant morbidity and mortality. Microscopic detection of parasites is currently the \"gold standard\" diagnostic. This technique is limited in its ability to detect low-density infections, is time consuming, and requires a highly trained microscopist. Malaria epidemiological surveillance studies especially aimed at the detection of low-density infection and asymptomatic cases will require more sensitive and user-friendly tools. We have shown previously that the molecular-based, colorimetric malachite green loop-mediated isothermal amplification (MG-LAMP) assay is a valuable tool for diagnosing malaria infection in a laboratory setting. In this study, we field evaluated this assay in a malaria diagnostic post in Roraima, Brazil. We prospectively collected 91 patient samples and performed microscopy, MG-LAMP, and real-time PCR (PET-PCR) to detect Plasmodium infection. Two independent readers were used to score the MG-LAMP tests to assess whether the sample was positive (blue/green) or negative (clear). There was 100% agreement between the two readers (Kappa=1). All tests detected 33 positive samples, but both the MG-LAMP and PET-PCR detected 6 and 7 more positive samples, respectively. The PET-PCR assay detected 6 mixed infections (defined as infection with both P. falciparum and P. vivax) while microscopy detected one and MG-LAMP detected two of these mixed infections. Microscopy did not detect any Plasmodium infection in 26 of the enrolled asymptomatic cases while MG-LAMP detected five and PET-PCR assay three positive cases. Overall, MG-LAMP provided a simpler and user-friendly molecular method for malaria diagnosis that is more sensitive than microscopy. Additionally, MG- LAMP has the capacity to test 38 samples per run (one hour), allowing for the screening of large number of samples which is appealing when large-scale studies are necessary e.g. in community surveillance studies. The current MG-LAMP assay was limited in its ability to detect mixed infection when compared to the PET-PCR, but otherwise proved to be a powerful tool for malaria parasite detection in the field and opens new perspectives in the implementation of surveillance studies in malaria elimination campaigns.

epidemiology↗

bioRxiv2018

Assessing the utility of minority variant composition in elucidating RSV transmission pathways

Reconstructing transmission pathways and defining the underlying determinants of virus diversity is critical for developing effective control measures. Whole genome consensus sequences represent the dominant virus subtype which does not provide sufficient information to resolve transmission events for rapidly spreading viruses with overlapping generations. We explored whether the within-host diversity of respiratory syncytial virus quantified from deep sequence data provides additional resolution to inform on who acquires infection from whom based on shared minor variants in samples that comprised epidemiological clusters and that shared similar genetic background. We report that RSV-A infections are characterized by low frequency diversity that occurs across the genome. Shared minor variant patterns alone, were insufficient to elucidate transmission chains within household members. However, they provided inference on potential transmission links where phylogenetic methods were uninformative of transmission when consensus sequences were identical. Interpretation of minor variant patterns was tractable only for small household outbreaks.

epidemiology↗

bioRxiv2018

Estimating the burden of α-thalassaemia in Thailand using a comprehensive prevalence database for Southeast Asia

Severe forms of -thalassaemia, haemoglobin H disease and haemoglobin Barts hydrops fetalis, are an important public health concern in Southeast Asia. Yet information on the prevalence, genetic diversity and health burden of -thalassaemia in the region remains limited. We compiled a geodatabase of -thalassaemia prevalence and genetic diversity surveys and, using geostatistical modelling methods, generated the first continuous maps of -thalassaemia mutations in Thailand and sub-national estimates of the number of newborns with severe forms in 2020. We also summarised the current evidence-base for -thalassaemia prevalence and diversity for the region. We estimate that 3,595 (95% credible interval 1,717 - 6,199) newborns will be born with severe -thalassaemia in Thailand in 2020, which is considerably higher than previous estimates. Accurate, fine-scale epidemiological data are necessary to guide sustainable national and regional health policies for -thalassaemia control. Our maps and newborn estimates are an important first step towards this aim.\n\nFundingThis work was supported by European Unions Seventh Framework Programme (FP7//2007-2013)/European Research Council [268904 - DIVERSITY]

epidemiology↗

bioRxiv2018

Evaluation of management of snake bites in a teaching hospital in Northern Ghana- a retrospective descriptive study

BACKGROUNDSnakebite is a public health problem afflicting mainly rural farmers. We seek to examine the profile and management of snakebite cases presenting to the Tamale Teaching Hospital of Ghana over a 30-month period.\n\nMETHODSOne hundred and ninety-two cases of snakebites presenting to the Tamale Teaching Hospital over a 30-month period from January 2016 to June 2018 were retrospectively analyzed. Information about the clinical manifestation of the snakebites, treatment instituted as well as the outcome was extracted from patient folders for the analysis.\n\nRESULTSOut of the 192 cases of snakebite, 131 (68.2%) occurred in males. The mean age of the victims was 26.5 years. The major patterns of envenomation were coagulopathy (84.9%) and local swelling/pain (82.8%). The causative snake species was identified in only 11.5% of cases, all of which were vipers. Antivenom was administered in 94.8% of the victims and the average amount administered was 84.64 milliliters (approximately 8 vials). Reaction to antivenoms was observed in 13.5% of cases, comprising mostly minor reactions. Antibiotics were utilized in 99.5% of cases with more than half receiving more than one type of antibiotic. Steroids use was common (62%) whilst 22.9% received antifibrinolytics despite the absence of evidence supporting their use in snakebite.\n\nCONCLUSIONSnakebite is an occupational health hazard of mainly rural farmers. The unwarranted use of non-beneficial medications is still rife. In addition to ensuring the continuous availability of effective antivenoms, there is the need for the development and adherence to protocols that take into consideration the prevailing local conditions.\n\nAUTHOR SUMMARYSnakebite affects mainly rural farmers and is a disease of poverty. Unreliable epidemiological data in developing countries like Ghana makes ascertaining the true extent of snakebite difficult. We have examined the presentation and clinical management of snakebite cases presenting to the Tamale Teaching Hospital of Ghana which serves a mainly rural population. The Carpet Viper, which produces a syndrome of local swelling and bleeding, is implicated in most snakebites in this region. A variety of non-evidenced-based interventions are employed by medical personnel in managing snakebite victims underscoring the need to have written contextually appropriate protocols for snakebite management. Public education is also needed to minimize the delays in seeking healthcare following a snakebite whilst efforts at ensuring the continuous availability of effective antivenoms must be intensified.

epidemiology↗