The role of time-varying viral shedding in modelling environmental surveillance for public health: revisiting the 2013 poliovirus outbreak in Israel.

Environmental pathogen surveillance is a sensitive tool that can detect early-stage outbreaks, and it is being used to track poliovirus and other pathogens. However, interpretation of longitudinal environmental surveillance signals is difficult because the relationship between infection incidence and viral load in wastewater depends on time-varying shedding intensity. We developed a mathematical model of time-varying poliovirus shedding intensity consistent with expert opinion across a range of immunization states.

Effect of Population Partitioning on the Probability of Silent Circulation of Poliovirus.

Polio can circulate unobserved in regions that are challenging to monitor. To assess the probability of silent circulation, simulation models can be used to understand transmission dynamics when detection is unreliable. Model assumptions, however, impact the estimated probability of silent circulation.

A runtime alterable epidemic model with genetic drift, waning immunity and vaccinations.

We present methods for building a Java Runtime-Alterable-Model Platform (RAMP) of complex dynamical systems. We illustrate our methods by building a multivariant SEIR (epidemic) RAMP. Underlying our RAMP is an individual-based model that includes adaptive contact rates, pathogen genetic drift, waning and cross-immunity.

Modeling the population effects of escape mutations in SARS-CoV-2 to guide vaccination strategies.

SARS-Cov-2 escape mutations (EM) have been detected and are spreading. Vaccines may need adjustment to respond to these or future mutations. We designed a population level model integrating both waning immunity and EM.

Evaluating the probability of silent circulation of polio in small populations using the silent circulation statistic.

As polio-endemic countries move towards elimination, infrequent first infections and incomplete surveillance make it difficult to determine when the virus has been eliminated from the population. Eichner and Dietz [, 143, 8 (1996)] proposed a model to estimate the probability of silent polio circulation depending upon when the last paralytic case was detected. Using the same kind of stochastic model they did, we additionally model waning polio immunity in the context of isolated, small, and unvaccinated populations.

Corrigendum to "Silent circulation of poliovirus in small populations" [Infectious Disease Modeling 2 (2017) 431-440].

[This corrects the article DOI: 10.1016/j.idm.

Silent circulation of poliovirus in small populations.

Background: Small populations that have been isolated by conflict make vaccination and surveillance difficult, threatening polio eradication. Silent circulation is caused by asymptomatic infections. It is currently not clear whether the dynamics of waning immunity also influence the risk of silent circulation in the absence of vaccination.

Asymmetric transfer efficiencies between fomites and fingers: Impact on model parameterization.

Background: Healthcare-associated infections (HAIs) affect millions of patients every year. Pathogen transmission via fomites and healthcare workers (HCWs) contribute to the persistence of HAIs in hospitals. A critical parameter needed to assess risk of environmental transmission is the pathogen transfer efficiency between fomites and fingers.

Models and analyses to understand threats to polio eradication.

To achieve complete polio eradication, the live oral poliovirus vaccine (OPV) currently used must be phased out after the end of wild poliovirus transmission. However, poorly understood threats may arise when OPV use is stopped. To counter these threats, better models than those currently available are needed.

Fomite-fingerpad transfer efficiency (pick-up and deposit) of Acinetobacter baumannii-with and without a latex glove.

Background: Acinetobacter baumannii is a significant health care-associated pathogen because it is easily transmitted via fomites, extremely difficult to eradicate from the environment, and highly drug resistant. Understanding the environmentally mediated transmission dynamics of A baumannii is critical for more effective infection control. However, transfer efficiency of pathogen pick-up and deposit remains poorly understood.

Strong influence of behavioral dynamics on the ability of testing and treating HIV to stop transmission.

Choosing between strategies to control HIV transmission with antivirals requires understanding both the dynamics affecting those strategies' effectiveness and what causes those dynamics. Alternating episodes of high and low contact rates (episodic risk) interact with increased transmission probabilities during early infection to strongly influence HIV transmission dynamics. To elucidate the mechanics of this interaction and how these alter the effectiveness of universal test and treat (UT8T) strategies, we formulated a model of UT8T effects.

The dynamics of methicillin-resistant Staphylococcus aureus exposure in a hospital model and the potential for environmental intervention.

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of healthcare-associated infections. An important control strategy is hand hygiene; however, non-compliance has been a major problem in healthcare settings. Furthermore, modeling studies have suggested that the law of diminishing return applies to hand hygiene.

HIV-1 transmission during early infection in men who have sex with men: a phylodynamic analysis.

Background: Conventional epidemiological surveillance of infectious diseases is focused on characterization of incident infections and estimation of the number of prevalent infections. Advances in methods for the analysis of the population-level genetic variation of viruses can potentially provide information about donors, not just recipients, of infection. Genetic sequences from many viruses are increasingly abundant, especially HIV, which is routinely sequenced for surveillance of drug resistance mutations.

Episodic HIV Risk Behavior Can Greatly Amplify HIV Prevalence and the Fraction of Transmissions from Acute HIV Infection.

A deterministic compartmental model was explored that relaxed the unrealistic assumption in most HIV transmission models that behaviors of individuals are constant over time. A simple model was formulated to better explain the effects observed. Individuals had a high and a low contact rate and went back and forth between them.

Acute-stage transmission of HIV: effect of volatile contact rates.

Background: The role of acute-stage transmission in sustaining HIV epidemics has been difficult to determine. This difficulty is exacerbated by a lack of theoretical understanding of how partnership dynamics and sexual behavior interact to affect acute-stage transmission. We propose that individual-level variation in rates of sexual contact is a key aspect of partnership dynamics that can greatly increase acute-stage HIV transmission.

Heterogeneity in Number and Type of Sexual Contacts in a Gay Urban Cohort.

HIV transmission models include heterogeneous individuals with different sexual behaviors including contact rates, mixing patterns, and sexual practices. However, heterogeneity can also exist within individuals over time. In this paper we analyze a two year prospective cohort of 882 gay men with observations at six month intervals focusing on heterogeneity both within and between individuals in sexual contact rates and sexual roles.

Successes and shortcomings of polio eradication: a transmission modeling analysis.

Polio eradication is on the cusp of success, with only a few regions still maintaining transmission. Improving our understanding of why some regions have been successful and others have not will help with both global eradication of polio and development of more effective vaccination strategies for other pathogens. To examine the past 25 years of eradication efforts, we constructed a transmission model for wild poliovirus that incorporates waning immunity (which affects both infection risk and transmissibility of any resulting infection), age-mediated vaccination rates, and transmission of oral polio vaccine.

Detectable signals of episodic risk effects on acute HIV transmission: strategies for analyzing transmission systems using genetic data.

Episodic high-risk sexual behavior is common and can have a profound effect on HIV transmission. In a model of HIV transmission among men who have sex with men (MSM), changing the frequency, duration and contact rates of high-risk episodes can take endemic prevalence from zero to 50% and more than double transmissions during acute HIV infection (AHI). Undirected test and treat could be inefficient in the presence of strong episodic risk effects.

Model analysis of fomite mediated influenza transmission.

Fomites involved in influenza transmission are either hand- or droplet-contaminated. We evaluated the interactions of fomite characteristics and human behaviors affecting these routes using an Environmental Infection Transmission System (EITS) model by comparing the basic reproduction numbers (R(0)) for different fomite mediated transmission pathways. Fomites classified as large versus small surface sizes (reflecting high versus low droplet contamination levels) and high versus low touching frequency have important differences.

Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection.

Phylogenies of highly genetically variable viruses such as HIV-1 are potentially informative of epidemiological dynamics. Several studies have demonstrated the presence of clusters of highly related HIV-1 sequences, particularly among recently HIV-infected individuals, which have been used to argue for a high transmission rate during acute infection. Using a large set of HIV-1 subtype B pol sequences collected from men who have sex with men, we demonstrate that virus from recent infections tend to be phylogenetically clustered at a greater rate than virus from patients with chronic infection ('excess clustering') and also tend to cluster with other recent HIV infections rather than chronic, established infections ('excess co-clustering'), consistent with previous reports.

HIV transmissions by stage in dynamic sexual partnerships.

Most models assessing relative transmissions during different progressive stages of human immunodeficiency virus (HIV) infection assume that infections are transmitted through instantaneous sexual contacts. In reality, however, HIV will often be transmitted through repeated sex acts during partnerships that form and dissolve at varying rates. We sought to understand how dynamic sexual partnerships would influence transmissions during different progression stages of HIV infection: primary HIV infection (PHI) and chronic stage.

Transmission clustering drives the onward spread of the HIV epidemic among men who have sex with men in Quebec.

Phylodynamic analysis and epidemiologic data identified 3 patterns of spread of primary human immunodeficiency virus type 1 infection (PHI) among men who have sex with men (2001-2009): 420 unique PHIs, 102 small clusters (2-4 PHIs per cluster, n = 280), and 46 large clusters (5-31 PHIs per cluster, n = 450). Large clusters disproportionately increased from 25.2% of PHIs in 2005 to 39.

A dynamic dose-response model to account for exposure patterns in risk assessment: a case study in inhalation anthrax.

The most commonly used dose-response models implicitly assume that accumulation of dose is a time-independent process where each pathogen has a fixed risk of initiating infection. Immune particle neutralization of pathogens, however, may create strong time dependence; i.e.

Informing optimal environmental influenza interventions: how the host, agent, and environment alter dominant routes of transmission.

Influenza can be transmitted through respirable (small airborne particles), inspirable (intermediate size), direct-droplet-spray, and contact modes. How these modes are affected by features of the virus strain (infectivity, survivability, transferability, or shedding profiles), host population (behavior, susceptibility, or shedding profiles), and environment (host density, surface area to volume ratios, or host movement patterns) have only recently come under investigation. A discrete-event, continuous-time, stochastic transmission model was constructed to analyze the environmental processes through which a virus passes from one person to another via different transmission modes, and explore which factors increase or decrease different modes of transmission.