Carolin Vegvari

Imperial College London | Imperial · Department of Infectious Disease Epidemiology

Acute viral infections pose many practical challenges for the accurate assessment of the impact of novel therapies on viral growth and decay. Using the example of influenza A, we illustrate how the measurement of infection-related quantities that determine the dynamics of viral load within the human host, can inform investigators on the course and...

Background: About 90% of drugs fail in clinical development. The question is whether trials fail because of insufficient efficacy of the new treatment, or rather because of poor trial design that is unable to detect the true efficacy. The variance of the measured endpoints is a major, largely underestimated source of uncertainty in clinical trial...

Alzheimer's disease (AD) is a progressive and fatal neurodegenerative disease, with no effective treatment or cure. A gold standard therapy would be treatment to slow or halt disease progression; however, knowledge of causation in the early stages of AD is very limited. In order to determine effective endpoints for possible therapies, a number of q...

Mathematical models have provided important insights into acute viral dynamics within individual patients. In this paper, we study the simplest target cell-limited models to investigate the within-host dynamics of influenza A virus infection in humans. Despite the biological simplicity of the models, we show how these can be used to understand the...

Introduction: In lower tuberculosis (TB) incidence countries (<100 cases/100,000/year), screening and preventive treatment (PT) for latent TB infection (LTBI) among people living with HIV (PLWH) is often recommended, yet guidelines advising which groups to prioritise for screening can be contradictory and implementation patchy. Evidence of LTBI scr...

The early termination of the Accelerating the Sustainable Control and Elimination of Neglected Tropical Diseases (Ascend) programme by the UK government in June 2021 was a bitter blow to countries in East and West Africa where no alternative source of funding existed. Here we assess the potential impact the cuts may have had if alternative funding...

Background In line with movement restrictions and physical distancing essential for the control of the COVID-19 pandemic, WHO recommended postponement of all neglected tropical disease (NTD) control activities that involve community-based surveys, active case finding, and mass drug administration in April, 2020. Following revised guidance later in...

Background Klebsiella pneumoniae is a World Health Organization high-priority antibiotic-resistant pathogen. However, little is known about Klebsiella lineages circulating in Nigeria. Methods We performed whole-genome sequencing (WGS) of 141 Klebsiella isolated between 2016 and 2018 from clinical specimens at 3 antimicrobial-resistance (AMR) senti...

In this Supplement, we detail outputs of the National Institute for Health Research Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance project, covering practical implementation of whole-genome sequencing across our consortium, which consists of laboratories in Colombia, India, Nigeria, and the Philippines.

Performing whole genome sequencing (WGS) for the surveillance of antimicrobial resistance offers the ability to determine not only the antimicrobials to which rates of resistance are increasing, but also the evolutionary mechanisms and transmission routes responsible for the increase at local, national, and global scales. To derive WGS-based output...

Antimicrobial resistance (AMR) is considered a global threat, and novel drug discovery needs to be complemented with systematic and standardized epidemiological surveillance. Surveillance data are currently generated using phenotypic characterization. However, due to poor scalability, this approach does little for true epidemiological investigation...

Background Klebsiella pneumoniae is a critically important pathogen in the Philippines. Isolates are commonly resistant to at least 2 classes of antibiotics, yet mechanisms and spread of its resistance are not well studied. Methods A retrospective sequencing survey was performed on carbapenem-, extended spectrum beta-lactam-, and cephalosporin-res...

Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an emerging public health problem. This study explores the specifics of CRKP epidemiology in Colombia based on whole genome sequencing (WGS) of the National Reference Laboratory at Instituto Nacional de Salud (INS)’s 2013–2017 sample collection. Methods A total of 425 CRKP isolates fr...

Advanced genomics and sequencing technologies are increasingly becoming critical for global health applications such as pathogen and antimicrobial resistance (AMR) surveillance. Limited resources challenge capacity development in low- and middle-income countries (LMICs), with few countries having genomics facilities and adequately trained staff. Tr...

A review of the epidemiology of SARS-CoV-2 conducted in August 2021

Since the beginning of the COVID-19 pandemic, the reproduction number [Formula: see text] has become a popular epidemiological metric used to communicate the state of the epidemic. At its most basic, [Formula: see text] is defined as the average number of secondary infections caused by one primary infected individual. [Formula: see text] seems conv...

The design and evaluation of control programmes for soil-transmitted helminths (STHs) is based on surveillance data recording measurements of egg counts in the stool of infected individuals which underpin estimates of the prevalence and average intensity of infection. There is considerable uncertainty around these measurements and their interpretat...

Abstract Background Soil-transmitted helminths (STHs) are a major cause of poor health in low- and middle-income countries. In particular, hookworm is known to cause anaemia in children and women of reproductive age (WRA). One goal of the World Health Organization’s (WHO) 2030 roadmap for neglected tropical diseases is to reduce STH-related morbidi...

The life cycle of parasitic organisms that are the cause of much morbidity in humans often depend on reservoirs of infection for transmission into their hosts. Understanding the daily, monthly and yearly movement patterns of individuals between reservoirs is therefore of great importance to implementers of control policies seeking to eliminate vari...

Introduction: In lower tuberculosis (TB) incidence countries (<100 cases/100,000/year), screening and preventive treatment (PT) for latent TB infection (LTBI) among people living with HIV (PLWH) is often recommended, yet guidelines advising which groups to prioritise for screening can be contradictory and implementation patchy. Evidence of LTBI scr...

A review of what is still uncertain about the epidemiology of SARS-CoV-2

Background On 1 April 2020, the WHO recommended an interruption of all activities for the control of neglected tropical diseases, including soil-transmitted helminths (STH), in response to the COVID-19 pandemic. This paper investigates the impact of this disruption on the progress towards the WHO 2030 target for STH. Methods We used two stochastic...

Where people acquire infection depends on many factors, including changes over time induced by social distancing measures (non-pharmaceutical interventions (NPIs)) in place at any point in time, prevailing compliance patterns to such measures, variation between geographical locations, and confounding variables such as age, gender, and cultural diff...

Mass vaccination to create herd immunity to Covid-19 (SARS-CoV-2)

Background On the 1 st of April 2020, the World Health Organization (WHO) recommended an interruption of all neglected tropical disease control programmes, including soil-transmitted helminths (STH), in response to the COVID-19 pandemic. This paper investigates the impact of this disruption on the achieved progress towards the WHO 2030 target for S...

Background The first cases of extensively drug resistant gonorrhoea were recorded in the United Kingdom in 2018. There is a public health need for strategies on how to deploy existing and novel antibiotics to minimise the risk of resistance development. As rapid point-of-care tests (POCTs) to predict susceptibility are coming to clinical use, coupl...

Due to the COVID-19 pandemic, many key neglected tropical disease (NTD) activities have been postponed. This hindrance comes at a time when the NTDs are progressing towards their ambitious goals for 2030. Mathematical modelling on several NTDs, namely gambiense sleeping sickness, lymphatic filariasis, onchocerciasis, schistosomiasis, soil-transmitt...

Background: Soil-transmitted helminths (STHs) are a major cause of poor health in low- and middle-income countries. In particular, hookworm is known to cause anaemia in children and women of reproductive age (WRA). One goal of the World Health Organization’s (WHO) 2030 roadmap for neglected tropical diseases is to reduce STH-related morbidity in WR...

Background: Soil-transmitted helminths (STHs) are a major cause of poor health in low- and middle-income countries. In particular, hookworm is known to cause anaemia in children and women of reproductive age (WRA). One goal of the World Health Organization’s (WHO) 2030 roadmap for neglected tropical diseases is to reduce STH-related morbidity in WR...

Background: Soil-transmitted helminths (STHs) are a major cause of poor health in low- and middle-income countries. In particular, hookworm is known to cause anaemia in children and women of reproductive age (WRA). One goal of the World Health Organization’s (WHO) 2030 roadmap for neglected tropical diseases is to reduce STH-related morbidity in WR...

This paper examines how estimates of the reproduction number R and the epidemic growth rate r are made, what data are used in their estimation, the models on which the estimation methods are based, what other data sources and epidemiological parameters could be employed to assess the effectiveness of social distancing measures (‘lockdown’) and to e...

The life cycle of parasitic organisms that are the cause of much morbidity in humans often depend on reservoirs of infection for transmission into their hosts. Understanding the daily, monthly and yearly movement patterns of individuals between reservoirs is therefore of great importance to implementers of control policies seeking to eliminate vari...

Starting and stopping preventive chemotherapy (PC) for soil-transmitted helminthiasis is typically based on the prevalence of infection as measured by Kato-Katz (KK) fecal smears. Kato-Katz-based egg counts can vary highly over repeated stool samples and smears. Consequentially, the sensitivity of KK-based surveys depends on the number of stool sam...

Building on past research, we here develop an analytic framework for describing the dynamics of the transmission of soil-transmitted helminth (STH) parasitic infections near the transmission breakpoint and equilibria of endemic infection and disease extinction, while allowing for perturbations in the infectious reservoir of the parasite within a de...

Background: Soil-transmitted helminth (STH) infections affect predominantly socio-economically disadvantaged populations in sub-Saharan Africa, East Asia and the Americas. Previous mathematical modelling studies have evaluated optimal intervention strategies to break STH transmission in clusters of villages. These studies assumed that villages are...

Background: The current World Health Organization (WHO) target for the three major soil-transmitted helminth (STH) infections is to reduce prevalence of moderate-to-heavy infections to below 1% by 2020. In terms of monitoring and evaluation (M&E), the current WHO guidelines for control of STHs recommend evaluation of infection levels in school-age...

Building on past research, we here develop an analytic framework for describing the dynamics of the transmission of Soil-Transmitted Helminth (STH) parasitic infections near the transmission breakpoint and equilibria of endemic infection and disease extinction, while allowing for perturbations in the infectious reservoir of the parasite within a de...

The current World Health Organization strategy to address soil-transmitted helminth (STH) infections in children is based on morbidity control through routine deworming of school and pre-school aged children. However, given that transmission continues to occur as a result of persistent reservoirs of infection in untreated individuals (including adu...

Markov Chain Monte Carlo (MCMC) parameter estimation. Description of the parameter estimation procedure. (DOCX)

Analytical expressions of infection-related quantities for acute viral infections. (DOCX)

Coefficients of variation of infection-related quantities. (DOCX)

Model of acute viral infections with terms representing treatment. (DOCX)

Median estimates of model parameters and 95% credible intervals. (DOCX)

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Clinical Trial Simulator code files. S3 does not contain any information that would allow the identification of human subjects. (ZIP)

The evolution of cumulative adaptive culture has received widespread interest in recent years, especially the factors promoting its occurrence. Current evolutionary models suggest that an increase in population size may lead to an increase in cultural complexity via a higher rate of cultural transmission and innovation. However, relatively little a...

Competition for resources can be considered a major driving force for social and cultural change in human societies. Here, we suggest two directly observable measures of competition at the individual and group levels: 1) the percentage of individuals within a group that do not meet their resource requirements and 2) the percentage of groups within...