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bioRxiv2017

Reduced transmission of Mycobacterium africanum compared to Mycobacterium tuberculosis in urban West Africa

BackgroundUnderstanding transmission dynamics is useful for tuberculosis (TB) control. We conducted a population-based molecular epidemiological study to understand TB transmission in Ghana.\n\nMethodsMycobacterium tuberculosis complex (MTBC) isolates obtained from prospectively-sampled pulmonary TB patients between July, 2012 and December, 2015 were confirmed as MTBC using IS6110 PCR. MTBC lineages were identified by large sequence polymorphism and single nucleotide polymorphism assays and further characterized using spoligotyping and standard 15-loci MIRU-VNTR typing. We used the n-1 method to estimate recent TB transmission and identified associated risk factors using logistic regression analysis.\n\nFindingsOut of 2,309 MTBC isolates, we identified 1,082 (46{middle dot}9%) single cases with 1,227 (53{middle dot}1%) isolates belonging to one of 276 clustered cases (clustering range; 2-35). Recent TB transmission rate was estimated to be 41{middle dot}2%. While we see no significant difference in the recent transmission rates between lineages of Mycobacterium africanum (lineage-5 (31{middle dot}8%); lineage-6 (24{middle dot}7%), p=0{middle dot}118), we found that lineage-4 belonging to the M. tuberculosis transmitted significantly higher (44{middle dot}9%, p<0{middle dot}001). Finally, apart from age being significantly associated with recent TB transmission (p=0{middle dot}007), we additionally identified a significant departure in the male/female ratio among very large clustered cases compared to the general TB patient population (3:1 vs. 2:1, p=0{middle dot}022).\n\nInterpretationsOur findings indicate high recent TB transmission suggesting occurrences of unsuspected outbreaks. The observed reduced transmission rate of M. africanum suggests other factor(s) may be responsible for its continuous presence in West Africa.\n\nFundingWellcome Trust Intermediate Fellowship Grant 097134/Z/11/Z to Dorothy Yeboah-Manu.

epidemiology↗

bioRxiv2017

Pathogen Population Structure Can Explain Hospital Outbreaks

ObjectiveTo analyze Hospital Acquired Infection (HAI) outbreaks using microbial population biology dynamics in order to understand outbreaks as a biological system.\n\nDesignComputational modeling study.\n\nMethodsThe majority of HAI transmission models describe dynamics on the level of the host rather than on the level of the pathogens themselves. Accordingly, epidemiologists often cannot complete transmission chains without direct evidence of either host-host contact or large reservoir populations. Here, we propose an ecology-based model to explain the transmission of pathogens in hospitals. The model is based upon metapopulation biology, which describes a group of interacting localized populations and island biogeography, which provides a basis for how pathogens may be moving between locales. Computational simulation trials are used to assess the applicability of the model.\n\nResultsResults indicate that pathogens survive for extended periods without the need for large reservoirs by living in localized ephemeral populations while continuously transmitting pathogens to new seed populations. Computational simulations show small populations spending significant portions of time at sizes too small to be detected by most surveillance protocols. The number and type of these ephemeral populations enable the overall pathogen population to be sustained.\n\nConclusionsBy modeling hospital pathogens as a metapopulation, observations characteristic of hospital acquired infection outbreaks for which there has previously been no sufficient biological explanation, including how and why empirically successful interventions work, can now be accounted for using population dynamic hypotheses. Epidemiological links between temporally isolated outbreaks are explained via pathogen population dynamics and potential outbreak intervention targets are identified.

epidemiology↗

bioRxiv2017

Stochastic dynamics of an epidemics with recurrent spillovers from an endemic reservoir

Most emerging human infectious diseases have an animal origin. Yet, while zoonotic diseases originate from a primary reservoir, most theoretical studies have principally focused on single-host processes, either exclusively humans or exclusively animals, without considering the importance of animal to human transmission for understanding the dynamics of emerging infectious diseases. Here we aim to investigate the importance of spillover transmission for explaining the number and the size of outbreaks. We propose a simple stochastic Susceptible-Infected-Recovered model with a recurrent infection of an incidental host from a reservoir (e.g. humans by a zoonotic species), considering two modes of transmission, (1) animal-to-human and (2) human-to-human. The model assumes that (i) epidemiological processes are faster than other processes such as demographics or pathogen evolution and (ii) that an epidemic occurs until there are no susceptible individuals left. The results show that during an epidemic, even when the pathogens are barely contagious, multiple outbreaks are observed due to spillover transmission. Overall, the findings demonstrate that the only consideration of direct transmission between individuals is not sufficient to explain the dynamics of zoonotic pathogens in an incidental host.

epidemiology↗

bioRxiv2017

Bayesian estimation of MSM population size in Côte d’Ivoire

Cote dIvoire has one of the largest HIV epidemics in West Africa with around half million people living with HIV. Key populations like gay men and other men who have sex with men (MSM) are often disproportionately burdened with HIV due to specific acquisition and transmission risks. Quantifying the MSM population sizes at subnational level is critical to improving the HIV prevention interventions. While survey-based direct estimates of MSM numbers are available at a few urban centers in C{circumflex}ote dIvoire, no data on MSM population size exists at other areas without any community infrastructure to facilitate sufficient access to the MSM community. We use this limited data in a Bayesian regression setup to produce first empirically calculated estimates of the numbers of MSM in all areas of C{circumflex}ote dIvoire prioritized in the HIV response. Our hierarchical model imputes missing covariates using geospatial information and allows for proper uncertainty quantification leading to meaningful confidence bounds for the predicted MSM population size estimates. The intended impact of this process is to increase uptake and use of high quality, comprehensive epidemiologic and interventional data in program planning. These estimates will help design future surveys and support the planning of the scale and content of HIV prevention and treatment programs for MSM in C{circumflex}ote dIvoire.

epidemiology↗

bioRxiv2017

The elephant in the room- Universal coverage for Costly treatments in an upper middle income country

BackgroundUpper middle income countries have made substantial progress towards universal health coverage. We investigated whether the coverage extended to diseases that incur catastrophic health spending, the contribution of pooled financing and the factors driving it in Malaysia.\n\nMethodsWe adapted the WHO definition of catastrophic health spending to define costly treatment as one that cost, at prevailing market price, more than 10% of the median annual household income in Malaysia. Coverage is defined as the proportion of patients in a year who were in need of a treatment and who received it. Data to estimate coverage and financing were extracted from the published and grey literature, as well as secondary data sources available on disease epidemiology and healthcare in Malaysia.\n\nResultsWe found coverage varies from universal for dialysis, cataract surgery, medicines for organ transplant and CML, to practically none for HCV, stroke, psoriasis and epilepsy surgery. Coverage of targeted therapies for solid cancers, knee replacement surgery, anti-TNF for arthritis and coagulation factors for haemophilia were poor while iron chelation for thalassemia, coronary revacularization, epoetin and anti-retrovirals were barely adequate. Coverage correlates negatively (r=-0.82) with health benefits foregone, and is entirely driven by the contribution of pooled financing (r=0.99 p<0.0001). The relative effectiveness of a treatment, its budget impact, media coverage and political influence of the disease area have little influence on financing. Only effectiveness of the leadership representing the therapy area is influential; an increase in one point on the leadership effectiveness scale is associated with 30% increase in the contribution of pooled financing.\n\nConclusionCoverage for catastrophically costly treatments is uneven and inequitable in Malaysia, despite most of these are affordable. Decisions on coverage are driven by political-economic consideration.

epidemiology↗

bioRxiv2017

The Basic Reproductive Number for Disease Systems with Multiple Coupled Heterogeneities

In mathematical epidemiology, a well-known formula describes the impact of heterogeneity on the basic reproductive number, R0, for situations in which transmission is separable and for which there is one source of variation in susceptibility and one source of variation in infectiousness. This formula is written in terms of the magnitudes of the heterogeneities, as quantified by their coefficients of variation, and the correlation between them. A natural question to ask is whether analogous results apply when there are multiple sources of variation in susceptibility and/or infectiousness. In this paper we demonstrate that with three or more coupled heterogeneities, R0 under separable transmission depends on details of the distribution of the heterogeneities in a way that is not seen in the well-known simpler situation. We provide explicit formulae for the cases of multivariate normal and multivariate log-normal distributions, showing that R0 can again be expressed in terms of the magnitudes of the heterogeneities and the pairwise correlations between them. The formulae, however, differ between the two multivariate distributions, demonstrating that no formula of this type applies generally when there are three or more coupled heterogeneities. We see that the results of the formulae are approximately equal when heterogeneities are relatively small and show that an earlier result in the literature (Koella, 1991) should be viewed in this light. We provide numerical illustrations of our results and discuss a setting in which coupled heterogeneities are likely to have a major impact on the value of R0. We also describe a rather surprising result: in a system with three heterogeneities, R0 can exhibit non-monotonic behavior with increasing levels of heterogeneity, in marked contrast to the familiar two heterogeneity setting in which R0 either increases or decreases with increasing heterogeneity.

epidemiology↗

bioRxiv2017

Latent TB infection in foreign-born communities: import vs. transmission in the Netherlands derived through mathematical modelling

While tuberculosis represents a significant disease burden worldwide, low-incidence countries strive to reach the WHO target of elimination by 2025. Screening for TB in immigrants is an important component of the strategy to reduce the TB burden in low-incidence settings. An important option is the screening and preventive treatment of latent tuberculosis infection (LTBI). Whether this policy is worthwhile depends on the extent of transmission within the country, and introduction of new cases through import. Mathematical transmission models of tuberculosis have been used to identify key parameters in the epidemiology of TB and estimate transmission rates. An important application has also been to investigate the consequences of policy scenarios.\n\nHere, we formulate a mathematical model for TB transmission within the Netherlands to estimate the size of the pool of latent infections, and to determine the share of importation -either through immigration or travel- versus transmission within the Netherlands. We take into account importation of infections due to immigration, and travel to the country of origin, focusing on the three ethnicities most represented among TB cases, excluding those overrepresented in asylum seekers: Moroccans, Turkish and Indonesians. We fit a system of ordinary differential equations to the data from the Netherlands Tuberculosis Registry on (extra-)pulmonary TB cases from 1995-2013.\n\nWe find that for all three foreign-born communities, immigration is the most important source of LTBI, but the extent of within-country transmission is much lower (about half) for the Turkish and Indonesian communities than for the Moroccan. This would imply that contact investigation would have a greater yield in the latter community than in the former. Travel remains a minor factor contributing LTBI, suggesting that targeting returning travelers might be less effective at preventing LTBI than immigrants upon entry in the country.

epidemiology↗

bioRxiv2017

Antiretroviral treatment, prevention of transmission, and modeling the HIV epidemic: why the ART efficacy, coverage, and effectiveness parameters matter

IntroductionHIV remains a major public health threat with over 75 million deaths, 2 million annual infections and over 1 million HIV-associated TB cases a year. Population-based studies suggest a marked decline in incidence, prevalence and deaths, mostly likely due to treatment expansion, in countries in East and Southern Africa. This calls into question the ART efficacy, effectiveness and coverage parameters used by many modelers to project HIV incidence and prevalence.\n\nMethodsFor 2015 and 2016 we reviewed global and national mathematical modeling studies regarding ART impact (with or without other HIV prevention interventions) and/or 90-90-90 on either new HIV infections or investment or both. We reviewed these HIV epidemiologic and costing models for their structure and parameterization around ART; we directly compared two models to illustrate differences in outcome.\n\nResultsThe nine models published in 2015 or 2016 included parameters for ART effectiveness ranging from 20% to 86% for ART effectiveness. Model 1 limits eligibility for ART initiation to 80% coverage of people living with HIV and with a CD4+ cell count below 350 cells/L, 70% retention, and ART reduces transmission by 80%, with a derived ART effectiveness of 20%. Model 2 assumes 90-90-90 by 2020 (i.e., 73% viral suppression of estimated PLHIV), ART reduces transmission by 96% in those on ART and virally suppressed, and by 88% in those on ART but not virally suppressed with a derived effectiveness of 86% and consequent decline towards ending AIDS and HIV elimination. ART parameter selection and assumptions dominate and low ART effectiveness translates into lower impact.\n\nDiscussionUsing more realistic parameters for ART effectiveness suggests that through expanding access and supporting sustainable viral suppression it will be possible to significantly reduce transmission and eliminate HIV in many settings.

epidemiology↗

bioRxiv2017

Efficacy of Aedes aegypti control by indoor Ultra Low Volume (ULV) insecticide spraying in Iquitos, Peru

BackgroundAedes aegypti is a primary vector of dengue, chikungunya, Zika, and urban yellow fever viruses. Indoor, ultra low volume (ULV) space spraying with pyrethroid insecticides is the main approach used for Ae. aegypti emergency control in many countries. Given the widespread use of this method, the lack of large-scale experiments or detailed evaluations of municipal spray programs is problematic.\n\nMethodology/Principal FindingsTwo experimental evaluations of non-residual, indoor ULV pyrethroid spraying were conducted in Iquitos, Peru. In each, a central sprayed sector was surrounded by an unsprayed buffer sector. In 2013, spray and buffer sectors included 398 and 765 houses, respectively. Spraying reduced the mean number of adults captured per house by ~83 percent relative to the pre-spray baseline survey. In the 2014 experiment, sprayed and buffer sectors included 1,117 and 1,049 houses, respectively. Here, the sprayed sectors number of adults per house was reduced ~64 percent relative to baseline. Parity surveys in the sprayed sector during the 2014 spray period indicated an increase in the proportion of very young females. We also evaluated impacts of a 2014 citywide spray program by the local Ministry of Health, which reduced adult populations by ~60 percent. In all cases, adult densities returned to near-baseline levels within one month.\n\nConclusions/SignificanceOur results demonstrate that densities of adult Ae. aegypti can be reduced by experimental and municipal spraying programs. The finding that adult densities return to approximately pre-spray densities in less than a month is similar to results from previous, smaller scale experiments. Our results demonstrate that ULV spraying is best viewed as having a short-term entomological effect. The epidemiological impact of ULV spraying will need evaluation in future trials that measure capacity of insecticide spraying to reduce disease transmission.

epidemiology↗

bioRxiv2018

Malaria during pregnancy and newborns outcome in an unstable transmission area in Brazil: a population-based record linkage study

BackgroundMalaria during pregnancy is one of the major causes of mortality in tropical regions, causing maternal anemia, intrauterine growth retardation, preterm birth, and low birth weight (LBW). The integration of the information systems is crucial to assess the dimension of gestational malaria in a wide and useful way, to improve decision making and maternal-child health.\n\nMethods and FindingsAn observational population-based study acquired information retrospectively from all live births that occurred between 2006 and 2014 in Cruzeiro do Sul (Acre, Brazil). Social and clinical data of the mother and newborn was extracted from the Information System of Live Births. Malaria episodes information was obtained from the Brazilian Epidemiological Surveillance Information System Malaria. A deterministic record linkage was performed to assess malaria impact on pregnancy. The studied population presented a malaria incidence of 8.9%, of which 63.9% infected by Plasmodium (P.) vivax. Reduction of newborns birth weight at term (small for gestational age (SGA) and LBW) has been found associated with P. vivax infection during pregnancy (SGA - OR 1.24, 95% CI 1.02-1.52, p=0.035; term LBW - OR 1.39, 95% CI 1.03-1.88, p=0.033). Additionally, P. falciparum infection during pregnancy has been found to be associated with preterm births (OR 1.54, 95% CI 1.09-2.18, p=0.016), which is related with late preterm births (OR 1.59, 95% CI 1.11-2.27, p=0.011).\n\nConclusionsDespite the decrease of malaria cases during the evaluated period, we present evidence of the deleterious effects of gestational malaria in a low transmission area in the Amazonian region. Regardless of Plasmodium species, malaria during pregnancy poses a risk for newborns birth weight reduction, highlighting the impact that P. vivax has on the fetus.\n\nFundingSao Paulo Research Foundation - FAPESP/Brazil.

epidemiology↗

bioRxiv2018

A simulation study on the relative role of age groups under differing pertussis transmission scenarios

Pertussis has resurged in many countries where it was once regarded as under control, with the recent outbreaks showing a shift in incidence towards teens and older individuals. Here, using an age-stratified transmission model, we tested two potential causes for underlying changes in pertussis transmission dynamics. We did so assuming hypothesized mechanisms supporting present-day pertussis epidemiology: (I) improved diagnostics, (II) acellular vaccines leading to asymptomatic transmission (III) both. We used the relative risks and odds ratio methods to examine the impact of these differing assumptions on signatures of relative roles of key age groups through time, allowing us to explore those age cohorts that disproportionately account for transmission. Our findings show that for epidemics after the vaccine switch, a scenario with increased adult reporting and no asymptomatic transmission reflect a loss of signal, where no age group appears to be key. While scenarios with asymptomatic transmission, reflect a population where children (1-10 years old) are still disproportionally at risk. These results demonstrate that understanding the underlying transmission mechanisms in a population are paramount for vaccination policies in attaining herd immunity and eventually eradication.

epidemiology↗

bioRxiv2018

Design principles for TB vaccines’ clinical trials based on spreading dynamics

Tuberculosis (TB) is one of the most complex diseases from the perspective of mathematical epidemiology. Individuals recently infected with the bacillus Mycobacterium tuberculosis can either develop TB directly in a matter of several weeks, or enter into an asymptomatic latent TB infection state (LTBI) that only occasionally derives into active disease, sometimes even decades after the infection event. The possible interruptions that a vaccine might provoke on these two mechanisms are indistinguishable in phase II clinical trials. In this work, we present a new methodology that allows differentiating vaccines that slow down the progression to disease from vaccines that prevent it. By introducing a stochastic framework for simulating synthetic clinical trials based on transmission models, we show how the method proposed here contributes both to reduce uncertainty in vaccine characterization and impact forecasts as well as to assist the design of clinical trials, improving their probabilities of success.

epidemiology↗

bioRxiv2018

Temporal evolution of immunity distributions in a population with waning and boosting

We investigate the temporal evolution of the distribution of immunities in a population, which is determined by various epidemiological, immunological and demographical phenomena: after a disease outbreak, recovered individuals constitute a large immune population, however their immunity is waning in the long term and they may become susceptible again. Meanwhile, their immunity can be boosted by repeated exposure to the pathogen, which is linked to the density of infected individuals present in the population. This prolongs the length of their immunity.\n\nWe consider a mathematical model formulated as a coupled system of ordinary and partial differential equations, that connects all these processes, and systematically compare a number of boosting assumptions proposed in the literature, showing that different boosting mechanisms lead to very different stationary distributions of the immunity at the endemic steady state. In the situation of periodic disease outbreaks, the waveforms of immunity distributions are studied and visualized. Our results show that there is a possibility to infer the boosting mechanism from the population level immune-dynamics.\n\nAMS Classification92D30, 34K60, 34K34, 37M05

epidemiology↗

bioRxiv2018

Onset, Time to Recurrence, and Recurrence Risk Factors of Myocardial Infarction and Ischemic Stroke: 10-Year Nationwide one-Million Population Database

Background and PurposeWe aimed to determine the differences in the pathophysiology of myocardial infarction (MI) and ischemic stroke (IS) and present their basic epidemiologic data for public health policy.\n\nMethodsWe included patients with a history of admission with diagnostic codes of MI and IS in the National Health Information Database (NHID) of the National Health Insurance Service (NHIS) Sample Cohort 2002-2013. We investigated the time to primary and secondary events, difference in incidence based on sex, time interval for the secondary event following the primary event in MI and IS, and the relative risk of recurrent events compared with that of primary events.\n\nResultsThe mean age of onset of IS was significantly higher than that of MI (65.67{+/-}12.25 vs. 60.4{+/-}13.07 years; P<0.05). The mean period from primary IS to secondary IS was significantly shorter than that from primary IS to secondary MI (2.09{+/-}2.80 vs. 5.35{+/-}2.90 years; P=0.016). The mean period from primary MI to secondary MI was significantly shorter than that from primary MI to secondary IS (2.30{+/-}2.75 vs. 5.16{+/-}3.26 years; P<0.001). The incidence of IS in men was significantly higher than that in women. The relative risk of recurrent IS and MI was greater than that of the primary event. In patients younger than 70 years, the incidence of MI was higher than that of IS, while in those above 70 years it was lower (P<0.05).\n\nConclusionsThe age at onset, time to recurrence, sex, and relative risks are significantly different between ischemic stroke and myocardial infarction, suggesting that the underlying pathophysiologic mechanisms might be different between the two.

epidemiology↗

bioRxiv2018

A systematic review of Hepatitis B virus (HBV) drug and vaccine escape mutations in Africa: a call for urgent action

International sustainable development goals for the elimination of viral hepatitis as a public health problem by 2030 highlight the pressing need to optimize strategies for prevention, diagnosis and treatment. Selected or transmitted resistance associated mutations (RAMs) and vaccine escape mutations (VEMs) in hepatitis B virus (HBV) may reduce the success of existing treatment and prevention strategies. These issues are particularly pertinent for many settings in Africa where there is high HBV prevalence and co-endemic HIV infection, but lack of robust epidemiological data and limited education, diagnostics and clinical care. The prevalence, distribution and impact of RAMs and VEMs in these populations are neglected in the current literature. We therefore set out to assimilate data for sub-Saharan Africa through a systematic literature review and analysis of published sequence data, and present these in an on-line database (https://livedataoxford.shinyapps.io/1510659619-3Xkoe2NKkKJ7Drg/). The majority of the data were from HIV/HBV coinfected cohorts. The commonest RAM was rtM204I/V, either alone or in combination with compensatory mutations, and identified in both reportedly treatment-naive and treatment-experienced adults. We also identified the suite of mutations rtM204V/I + rtL180M + rtV173L, that has been associated with vaccine escape, in over 1/3 of cohorts. Although tenofovir has a high genetic barrier to resistance, it is of concern that emerging data suggest polymorphisms that may be associated with resistance, although the precise clinical impact of these is unknown. Overall, there is an urgent need for improved diagnostic screening, enhanced laboratory assessment of HBV before and during therapy, and sustained roll out of tenofovir in preference to lamivudine alone. Further data are needed in order to inform population and individual approaches to HBV diagnosis, monitoring and therapy in these highly vulnerable settings.\n\nAuthors summaryThe Global Hepatitis Health Sector Strategy is aiming for the elimination of viral hepatitis as a public health threat by 2030. However, mutations associated with drug resistance and vaccine escape may reduce the success of existing treatment and prevention strategies. In the current literature, the prevalence, distribution and impact of hepatitis B virus (HBV) mutations in many settings in Africa are neglected, despite the high prevalence of HBV and co-endemic HIV infection. This systematic review describes the frequency, prevalence and co-occurrence of mutations associated with HBV drug resistance and vaccine escape mutations in Africa. The findings suggest a high prevalence of these mutations in some populations in sub-Saharan Africa. Scarce resources have contributed to the lack of HBV diagnostic screening, inconsistent supply of drugs, and poor access to clinical monitoring, all of which contribute to drug and vaccine resistance. Sustainable long-term investment is required to expand consistent drug and vaccine supply, to provide screening to diagnose infection and to detect drug resistance, and to provide appropriate targeted clinical monitoring for treated patients.

epidemiology↗

bioRxiv2018

The national alert-response strategy against cholera in Haiti: a four-year assessment of its implementation

BackgroundA massive cholera epidemic struck Haiti on October 2010. As part of the national cholera elimination plan, the Haitian government, UNICEF and other international partners launched a nationwide alert-response strategy from July 2013. This strategy established a coordinated methodology to rapidly target cholera-affected communities with WaSH (water sanitation and hygiene) response interventions conducted by field mobile teams. An innovative red-orange-green alert system was established, based on routine surveillance data, to weekly monitor the epidemic.\n\nMethodology/Principal findingsWe used cholera consolidated surveillance databases, alert records and details of 31,306 response interventions notified by WaSH mobile teams to describe and assess the implementation of this approach between July 2013 and June 2017. Response to red and orange alerts was heterogeneous across the country, but significantly improved throughout the study period so that 75% of red and orange alerts were responded within the same epidemiological week during the 1st semester of 2017. Numbers of persons educated about cholera, houses decontaminated by chlorine spraying, households which received water chlorination tablets and water sources that were chlorinated during the same week as cholera alerts significantly increased. Alerts appeared to be an interesting and simple indicator to monitor the dynamic of the epidemic and assess the implementation of response activities.\n\nConclusions/SignificanceThe implementation of a nationwide alert-response strategy against cholera in Haiti was feasible albeit with certain obstacles. Its cost was less than USD 8 million per year. Continuing this strategy seems essential to eventually defeat cholera in Haiti while ambitious long-term water and sanitation projects are conducted in vulnerable areas. It constitutes a core element of the current national plan for cholera elimination of the Haitian Government.

epidemiology↗

bioRxiv2018

Considerations for the design of vaccine efficacy trials during public health emergencies

Public Health Emergencies (PHEs) provide a complex and challenging environment for vaccine evaluation. Under the R&D Blueprint Plan of Action, the World Health Organization (WHO) has convened a group of experts to agree on standard procedures to rapidly evaluate experimental vaccines during PHEs while maintaining the highest scientific and ethical standards. The Blueprint priority diseases, selected for their likelihood to cause PHEs and the lack of adequate medical countermeasures, were used to frame our methodological discussions. Here, we outline major vaccine study designs to be used in PHEs and summarize high-level recommendations for their use in this setting. We recognize that the epidemiology and transmission dynamics of the Blueprint priority diseases may be highly uncertain and that the unique characteristics of the vaccines and outbreak settings may affect our study design. To address these challenges, our group underscores the need for novel, flexible, and responsive trial designs. We conclude that assignment to study groups using randomization is a key principle underlying rigorous study design and should be utilized except in exceptional circumstances. Advance planning for vaccine trial designs is critical for rapid and effective response to a PHE and to advance knowledge to address and mitigate future PHEs.\n\nOne Sentence SummaryAs part of the WHO research and development Blueprint for action to prevent epidemics, we describe key considerations for the design and analysis of trials and studies to evaluate experimental vaccines during public health emergencies.

epidemiology↗

bioRxiv2018

Shifting patterns of seasonal influenza epidemics

Seasonal waves of influenza display a complex spatiotemporal pattern resulting from the interplay of biological, socio-demographic, and environmental factors. At country level many studies characterized the robust properties of annual epidemics, depicting a typical season. Here we analyzed season-by-season variability, introducing a clustering approach to assess the deviations from typical spreading patterns. The classification is performed on the similarity of temporal configurations of onset and peak times of regional epidemics, based on influenza-like-illness time-series in France from 1984 to 2014. We observed a larger variability in the onset compared to the peak. Two relevant classes of clusters emerge: groups of seasons sharing similar recurrent spreading patterns (clustered seasons) and single seasons displaying unique patterns (monoids). Recurrent patterns exhibit a more pronounced spatial signature than unique patterns. We assessed how seasons shift between these classes from onset to peak depending on epidemiological, environmental, and socio-demographic variables. We found that the spatial dynamics of influenza and its association with commuting, previously observed as a general property of French influenza epidemics, applies only to seasons exhibiting recurrent patterns. The proposed methodology is successful in providing new insights on influenza spread and can be applied to incidence time-series of different countries and different diseases.

epidemiology↗