Intuitively, sampling is likely to be more efficient for prevalence estimation, if the cases (or positives) have a relatively higher representation in the sample than in the population. In case the virus is transmitted via personal contacts, contact tracing of the observed cases (but not noncases), to be referred to as \emph{adaptive network tracing}, can generate a higher yield of cases than random sampling from the population. The efficacy of relevant designs for cross-sectional and change estimation is investigated. The availability of these designs allows one unite tracing for combating the epidemic and sampling for estimating the prevalence in a single endeavour.
While probabilistic projection methods for projecting life expectancy exist, few account for covariates related to life expectancy. Generalized HIV/AIDS epidemics have a large, immediate negative impact on the life expectancy in a country, but this impact can be mitigated by widespread use of antiretroviral therapy (ART). Thus projection methods for countries with generalized HIV/AIDS epidemics could be improved by accounting for HIV prevalence, the future course of the epidemic and coverage of ART. We propose a method for making probabilistic projections of life expectancy to 2100 for all cou…
This study proposes a nonhomogeneous birth--death model which captures the dynamics of a directly transmitted infectious disease. Our model accounts for an important aspect of observed epidemic data in which only symptomatic infecteds are observed. The nonhomogeneous birth--death process depends on survival distributions of reproduction and removal, which jointly yield an estimate of the effective reproduction number $R(t)$ as a function of epidemic time. We employ the Burr distribution family for the survival functions and, as special cases, proportional rate and accelerated event-time models…
Ending the HIV/AIDS pandemic is among the Sustainable Development Goals for the next decade. In order to overcome the gap between the need for care and the available resources, better understanding of HIV epidemics is needed to guide policy decisions, especially for key populations that are at higher risk for HIV infection. Accurate HIV epidemic estimates for key populations have been difficult to obtain because their HIV surveillance data is very limited. In this paper, we propose a so-called joint spatial conditional auto-regressive model for estimating HIV prevalence rates among key populat…
Multi-parameter evidence synthesis (MPES) is receiving growing attention from the epidemiological community as a coherent and flexible analytical framework to accommodate a disparate body of evidence available to inform disease incidence and prevalence estimation. MPES is the statistical methodology adopted by the Health Protection Agency in the UK for its annual national assessment of the HIV epidemic, and is acknowledged by the World Health Organization and UNAIDS as a valuable technique for the estimation of adult HIV prevalence from surveillance data. This paper describes the results of ut…
This paper offers a qualitative insight into the convergence of Bayesian parameter inference in a setup which mimics the modeling of the spread of a disease with associated disease measurements. Specifically, we are interested in the Bayesian model's convergence with increasing amounts of data under measurement limitations. Depending on how weakly informative the disease measurements are, we offer a kind of `best case' as well as a `worst case' analysis where, in the former case, we assume that the prevalence is directly accessible, while in the latter that only a binary signal corresponding t…
The spread of COVID-19 makes it essential to investigate its prevalence. In such investigation research, as far as we know, the widely-used sampling methods didn't use the information sufficiently about the numbers of the previously diagnosed cases, which provides a priori information about the true numbers of infections. This motivates us to develop a new, two-stage sampling method in this paper, which utilises the information about the distributions of both population and diagnosed cases, to investigate the prevalence more efficiently. The global likelihood sampling, a robust and efficient s…
Large-scale testing is considered key to assess the state of the current COVID-19 pandemic. Yet, the link between the reported case numbers and the true state of the pandemic remains elusive. We develop mathematical models based on competing hypotheses regarding this link, thereby providing different prevalence estimates based on case numbers, and validate them by predicting SARS-CoV-2-attributed death rate trajectories. Assuming that individuals were tested based solely on a predefined risk of being infectious implies the absolute case numbers reflect the prevalence, but turned out to be a po…
The pandemic linked to COVID-19 infection represents an unprecedented clinical and healthcare challenge for many medical researchers attempting to prevent its worldwide spread. This pandemic also represents a major challenge for statisticians involved in quantifying the phenomenon and in offering timely tools for the monitoring and surveillance of critical pandemic parameters. In a recent paper, Alleva et al. (2020) proposed a two-stage sample design to build a continuous-time surveillance system designed to correctly quantify the number of infected people through an indirect sampling mechanis…
Respondent-driven sampling (RDS) is frequently used when sampling hard-to-reach and/or stigmatized communities. RDS utilizes a peer-driven recruitment mechanism where sampled individuals pass on participation coupons to at most $c$ of their acquaintances in the community ($c=3$ being a common choice), who then in turn pass on to their acquaintances if they choose to participate, and so on. This process of distributing coupons is shown to behave like a new Reed-Frost type network epidemic model, in which becoming infected corresponds to receiving a coupon. The difference from existing network e…
The United Nations (UN) issued official probabilistic population projections for all countries to 2100 in July 2015. This was done by simulating future levels of total fertility and life expectancy from Bayesian hierarchical models, and combining the results using a standard cohort-component projection method. The 40 countries with generalized HIV/AIDS epidemics were treated differently from others, in that the projections used the highly multistate Spectrum/EPP model, a complex 15-compartment model that was designed for short-term projections of quantities relevant to policy for the epidemic.…
An increasing amount of geo-referenced mobile phone data enables the identification of behavioral patterns, habits and movements of people. With this data, we can extract the knowledge potentially useful for many applications including the one tackled in this study - understanding spatial variation of epidemics. We explored the datasets collected by a cell phone service provider and linked them to spatial HIV prevalence rates estimated from publicly available surveys. For that purpose, 224 features were extracted from mobility and connectivity traces and related to the level of HIV epidemic in…
Imperial College London（帝国理工学院）；King’s College London（伦敦国王学院）；The Royal Brompton & Harefield NHS Foundation Trust（皇家布朗普顿与哈菲尔德国民保健服务基金会信托）；University College London（伦敦大学学院）
Datasets are rarely a realistic approximation of the target population. Say, prevalence is misrepresented, image quality is above clinical standards, etc. This mismatch is known as sampling bias. Sampling biases are a major hindrance for machine learning models. They cause significant gaps between model performance in the lab and in the real world. Our work is a solution to prevalence bias. Prevalence bias is the discrepancy between the prevalence of a pathology and its sampling rate in the training dataset, introduced upon collecting data or due to the practioner rebalancing the training batc…
For many diseases, logistic and other constraints often render large incidence studies difficult, if not impossible, to carry out. This becomes a drawback, particularly when a new incidence study is needed each time the disease incidence rate is investigated in a different population. However, by carrying out a prevalent cohort study with follow-up it is possible to estimate the incidence rate if it is constant. In this paper we derive the maximum likelihood estimator (MLE) of the overall incidence rate, $λ$, as well as age-specific incidence rates, by exploiting the well known epidemiologic r…
Measuring the prevalence of active SARS-CoV-2 infections in the general population is difficult because tests are conducted on a small and non-random segment of the population. However, people admitted to the hospital for non-COVID reasons are tested at very high rates, even though they do not appear to be at elevated risk of infection. This sub-population may provide valuable evidence on prevalence in the general population. We estimate upper and lower bounds on the prevalence of the virus in the general population and the population of non-COVID hospital patients under weak assumptions on wh…
People who inject drugs are an important population to study in order to reduce transmission of blood-borne illnesses including HIV and Hepatitis. In this paper we estimate the HIV and Hepatitis C prevalence among people who inject drugs, as well as the proportion of people who inject drugs who are female in Mauritius. Respondent driven sampling (RDS), a widely adopted link-tracing sampling design used to collect samples from hard-to-reach human populations, was used to collect this sample. The random walk approximation underlying many common RDS estimators assumes that each social relation (e…
Given the urgent informational needs connected with the diffusion of infection with regard to the COVID-19 pandemic, in this paper, we propose a sampling design for building a continuous-time surveillance system. Compared with other observational strategies, the proposed method has three important elements of strength and originality: (i) it aims to provide a snapshot of the phenomenon at a single moment in time, and it is designed to be a continuous survey that is repeated in several waves over time, taking different target variables during different stages of the development of the epidemic …
We describe Epilocal, a simple R program designed to automatically download the most recent data on reported infected SARS-CoV-2 cases for all Italian provinces and regions, and to provide a simple descriptive analysis. For each province the cumulative number of reported infected cases is available each day. In addition, the current numbers of hospitalized patients (separately for intensive care or not) and the cumulative number of deceased individuals are available at the region level. The data are analyzed through Poisson generalized linear models with logarithmic link function and polynomia…
Estimating the prevalence of a disease is necessary for evaluating and mitigating risks of its transmission within or between populations. Estimates that consider how prevalence changes with time provide more information about these risks but are difficult to obtain due to the necessary sampling intensity and commensurate testing costs. We propose pooling and jointly testing multiple samples to reduce testing costs and use a novel nonparametric, hierarchical Bayesian model to infer population prevalence from the pooled test results. This approach is shown to reduce uncertainty compared to indi…
