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Carmen Lía Murall

Carmen Lía Murall
French National Centre for Scientific Research (CNRS), Montpellier

PhD

About

55
Publications
4,018
Reads
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269
Citations
Additional affiliations
January 2009 - August 2013
University of Guelph
Position
  • PhD Student
Education
September 2000 - June 2005
University of Toronto
Field of study
  • Ecology and Evolutionary Biology

Publications

Publications (55)
Preprint
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a generalist virus, infecting and evolving in numerous mammals, including captive and companion animals, free-ranging wildlife, and humans. Transmission among non-human species poses considerable risk for the establishment of SARS-CoV-2 reservoirs, makes eradication difficult, and prov...
Article
Full-text available
The genome of the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the pathogen that causes coronavirus disease 2019 (COVID-19), has been sequenced at an unprecedented scale leading to a tremendous amount of viral genome sequencing data. To assist in tracing infection pathways and design preventive strategies, a deep understanding of t...
Preprint
Full-text available
Menstrual cups are gaining in popularity worldwide as a more environmentally sustainable and affordable alternative to disposable personal hygiene products. However, there is currently a lack of scientific literature regarding their safety and potential effects on women’s health. We analysed biological, demographic, and behavioural data in a cohort...
Article
Full-text available
Background Québec was the Canadian province most impacted by COVID-19, with 401,462 cases as of September 24th, 2021, and 11,347 deaths due mostly to a very severe first pandemic wave. In April 2020, we assembled the Coronavirus Sequencing in Québec (CoVSeQ) consortium to sequence SARS-CoV-2 genomes in Québec to track viral introduction events and...
Preprint
Full-text available
The genome of the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the pathogen that causes coronavirus disease 2019 (COVID-19), has been sequenced at an unprecedented scale, leading to a tremendous amount of viral genome sequencing data. To understand the evolution of this virus in humans, and to assist in tracing infection pathways a...
Article
Full-text available
Human papillomaviruses (HPVs) are oncogenic viruses causing most cervical cancers. Highly prevalent in young, sexually active women, only a minority of HPV infections persist. To better characterize the immuno-modulatory impact of early HPV infections, we measured changes in a panel of 20 cytokines in cervicovaginal samples collected from young wom...
Article
Objective To characterize SARS-CoV-2 transmission following a COVID-19 outbreak in an emergency childcare centre (ECCC) in April 2020 in Quebec, Canada.Methods The study population consisted of all the children and employees who attended the ECCC as well as household contacts of the confirmed COVID-19 cases. Of the 120 individuals in the study, fiv...
Preprint
Full-text available
Using genomic epidemiology, we investigated the arrival of SARS-CoV-2 to Québec, the Canadian province most impacted by COVID-19, with >280,000 positive cases and >10,000 deaths in a population of 8.5 million as of March 1st, 2021. We report 2,921 high-quality SARS-CoV-2 genomes in the context of >12,000 publicly available genomes sampled globally...
Preprint
Full-text available
Human papillomaviruses (HPVs) are the most oncogenic viruses known to human, causing nearly all cervical cancers worldwide. Highly prevalent in young, sexually active women, most HPV infections are cleared within 3 years, and only a minority of those infections persist and lead to cancer later in life. To better characterize the immuno-modulatory i...
Preprint
Background: Following an outbreak in April 2020 in Quebec, Canada, an investigation was carried out to characterize SARS-CoV-2 transmission within an Emergency Childcare Centre (ECCC) setting.Methods: The study population consisted of all the children and employees who attended the ECCC as well as household contacts of the confirmed COVID-19 cases....
Article
Full-text available
Microbes are embedded in complex communities where they engage in a wide array of intra- and inter-specific interactions. The extent to which these interactions drive or impede microbiome diversity is not well understood. Historically, two contrasting hypotheses have been suggested to explain how species interactions could influence diversity. 'Eco...
Article
Understanding genital infections by Human papillomaviruses (HPVs) remains a major public health issue, especially in countries where vaccine uptake is low. We investigate HPV prevalence and antibody status in 150 women (ages 18 to 25) in Montpellier, France. At inclusion and one month later, cervical swabs, blood samples and questionnaires (for dem...
Preprint
Background. Understanding genital infections by Human papillomaviruses (HPVs) remains a major public health issue, especially in countries where vaccine uptake is low. Methods. We investigate HPV prevalence and antibody status in 150 women (ages 18 to 25) in Montpellier, France. At inclusion and one month later, cervical swabs, blood samples and qu...
Article
Full-text available
Parasite genetic diversity can provide information on disease transmission dynamics but most mathematical and statistical frameworks ignore the exact combinations of genotypes in infections. We introduce and validate a new method that combines explicit epidemiological modelling of coinfections and regression-Approximate Bayesian Computing (ABC) to...
Article
Full-text available
Introduction Human papillomaviruses (HPVs) are responsible for one-third of all cancers caused by infections. Most HPV studies focus on chronic infections and cancers, and we know little about the early stages of the infection. Our main objective is to better understand the course and natural history of cervical HPV infections in healthy, unvaccin...
Article
Most human oncogenic viruses share several characteristics, such as being DNA viruses, having long (co)evolutionary histories with their hosts and causing either latent or chronic infections. They can reach high prevalences while causing relatively low case mortality, which makes them quite fit according to virulence evolution theory. After analysi...
Article
Full-text available
Infections of stratified epithelia contribute to a large group of common diseases, such as dermatological conditions and sexually transmitted diseases. To investigate how epithelial structure affects infection dynamics, we develop a general ecology-inspired model for stratified epithelia. Our model allows us to simulate infections, explore new hypo...
Data
Effect of re-seeding on wart-associated HPV infection kinetics. a. Infection with baseline parameters. b. Here infection rate of basal cells β decays to zero with time (with decay rate b = 0.05). No wart-like manifestation of the infection is possible. (EPS)
Data
Chlamydia dynamics. a. Time series of uninfected cells (Ud and Up) and the infected cells of the same layers (Id and Ip). Infection with baseline parameters. (EPS)
Data
Supporting information. Supplementary methods and results. (PDF)
Data
Non-stratified HPV infection model schematic. A population of target cells, T, becomes infected by interacting with free virions, V at a rate β. Infected cells, I, self-proliferate, ρa, due to HPV infection. Infected cells die naturally, μ, and release the virions they contain with a burst size of θ. Free virions are cleared by mucus, ζ, and infect...
Data
Supporting code. Mathematica file that generates figures for non-stratified model. (NB)
Data
Supporting code. R file that uses 3 csv data files for model fits. (R)
Data
Effect of parameter variations on the kinetics of HR-HPV infection. a. Infection with baseline parameters. b. and c. HR-HPV gives wart-like infections with either higher HPV-driven proliferation, (3x αb) or higher burst size (1 order of magnitude higher), thus demonstrating that HR-HPVs need to keep both of these parameters down in order to have fl...
Data
Non-stratified HPV model. A. Time series of i. low cell proliferation driven by HPV infection (wart-associated-HPV-like), ρa = 0.7 and θ = 106, and ii. high cell proliferation by HPV infection (HR-HPV-like), ρa = 1.4 and θ = 104. Cell accumulation and duration are the opposite of what is seen in real infections, i.e. HR-HPV infections should accumu...
Preprint
Full-text available
Most human oncogenic viruses share several characteristics, such as being DNA viruses, having long (co)evolutionary histories with their hosts and causing either latent or chronic infections. They can reach high prevalences while causing relatively low case mortality, which makes them quite fit according to virulence evolution theory. After analysi...
Preprint
Parasite genetic diversity can provide information on disease transmission dynamics but most methods ignore the exact combinations of genotypes in infections. We introduce and validate a new method that combines explicit epidemiological modelling of coinfections and regression Approximate Bayesian Computing (ABC) to detect within-host interactions....
Preprint
Full-text available
Infections of stratified epithelia collectively represent a large burden on global health. Experimental models provide a means to understand how the cell dynamics themselves influence the outcomes of these infections. Mathematical approaches are needed to improve quantification and theoretical advancement of these complex systems. Here, we develop...
Article
Full-text available
Most infections by human papillomaviruses (HPVs) are `acute’, that is non-persistent. Yet, for HPVs, as for many other oncoviruses, there is a striking gap between our detailed understanding of chronic infections and our limited data on the early stages of infection. Here we argue that studying HPV acute infections is necessary and timely. Focusing...
Preprint
Full-text available
Most infections by human papillomaviruses (HPVs) are ‘acute’, that is non-persistent. Yet, for HPVs, as for many other oncoviruses, there is a striking gap between our detailed understanding of chronic infections and our limited data on the early stages of infection. Here we argue that studying HPV acute infections is necessary and timely. Focusing...
Preprint
Full-text available
Chronic infection by oncogenic Human papillomaviruses (HPVs) leads to cancers. Public health interventions, such as cancer screening and mass vaccination, radically change the ecological conditions encountered by circulating viruses. It is currently unclear how HPVs communities may respond to these environmental changes, because little is known abo...
Chapter
The study of biological invasions of ecological systems has much to offer research on within–host (WH) systems, particularly for understanding infections and developing therapies using biological agents. Thanks to the ground-work established in other fields, such as community ecology and evolutionary biology, and to modern methods of measurement an...
Article
Full-text available
Background Sexual transmission of Ebola virus disease (EVD) 6 months after onset of symptoms has been recently documented, and Ebola virus RNA has been detected in semen of survivors up to 9 months after onset of symptoms. As countries affected by the 2013–2015 epidemic in West Africa, by far the largest to date, are declared free of Ebola virus di...
Article
Full-text available
Background: Sexual transmission of Ebola virus disease (EVD) 6 months after onset of symptoms has been recently documented, and Ebola virus RNA has been detected in semen of survivors up to 9 months after onset of symptoms. As countries affected by the 2013-2015 epidemic in West Africa, by far the largest to date, are declared free of Ebola virus...
Preprint
Full-text available
Sexual transmission of Ebola virus disease (EVD) 6 months after onset of symptoms has been recently documented, and Ebola virus RNA has been detected in semen of survivors up to 9 months after onset of symptoms. As countries affected by the 2013-2015 epidemic in West Africa, by far the largest to date, are declared free of Ebola virus disease (EVD)...
Article
Full-text available
The human papillomavirus (HPV) vaccines hold great promise for preventing several cancers caused by HPV infections. Yet little attention has been given to whether HPV could respond evolutionarily to the new selection pressures imposed on it by the novel immunity response created by the vaccine. Here, we present and theoretically validate a mechanis...
Article
Full-text available
Measuring epidemic parameters early in an outbreak is essential to inform control efforts. Using the viral genome sequence and collection date from 74 infections in the 2014 Ebola virus outbreak in Sierra Leone, we estimate key epidemiological parameters such as infectious period duration (approximately 71 hours) and date of the first case in Sierr...
Conference Paper
There is currently little evidence to close the question of whether the type-specific HPV vaccines will cause increased prevalence of non-targeted, oncogenic types, a scenario known as ‘type replacement’. The abundance of hypotheses in the literature about how HPV types interact (facilitation, immune-mediated competition and independence) illustrat...
Article
Innovative sequencing techniques now allow the routine access of whole genomes of pathogens, generating vast amounts of data. Phylogenetic trees are a common method for synthesizing this information. Unfortunately, these trees are often seen only as a visual support to guide researchers, thus neglecting the value of employing phylogenetic technique...
Article
The controversy over whether vaccine-targeted HPV types will be replaced by other oncogenic, non-vaccine-targeted types remains unresolved. This is in part because little is known about the ecology of HPV types. Patient data has been interpreted to suggest independence or facilitative interactions between types and therefore replacement is believed...
Article
Full-text available
The dynamics of in-host infections are central to predicting the progression of natural infections and the effectiveness of drugs or vaccines, however, they are not well understood. Here, we apply food web theory to in-host disease networks of the human body that are structured similarly to food web models that treat both predation and competition...
Data
Full-text available
Conditions for Coexistence inside a Host. (PDF)
Data
Phase-plane cases. A: Competitive exclusion. (i and ii) The black dots represent the equilibrium solution of each subsystem (i.e. where X, Yi, Z can exist together). The winner is determined by invasion criteria, such that if the isocline of strain i is above the equilibrium of the subsystem with strain j, then strain i can invade but strain j cann...
Data
The reproduction and decay trade-off in HPV with matching phase-planes. No coexistence. Plots (i) and (iii) represent the phase-planes before and after the bifurcation, respectively, and plot (ii) is at the bifurcation. Parameter estimates. HPV: λ = 36000 cells•day−1 [49], d = 0.048 day−1 [50], β1 = β1 = 0.0067 day−1 [51], k1 = 100 virions•cell−1•d...
Data
The reproduction and lytic effect trade-off in HPV allows for coexistence. Plots (i) and (v) are before and after the bifurcations, (ii) and (iv) are at the bifurcations, and (iii) is stable coexistence. Parameter estimates. HPV: λ = 36000 cells•day−1 [49], d = 0.048 day−1 [50], β1 = β1 = 0.0067 day−1 [51], k1 = 100 virions•cell−1•day−1 , k2 = 50 v...
Data
Full-text available
Using modules to understand community dynamics. (PDF)
Conference Paper
Background/Question/Methods Untangling the ecological interactions happening inside hosts is critical for predicting the progression of natural infections and the effectiveness of drugs or vaccines. Though attempts to view microbial infections inside hosts as ecological communities exist, most human infectious disease researchers do not investiga...

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Projects

Projects (2)
Project
There is a threat that evolutionary responses can render vaccines ineffective, as illustrated by the emergence of the increasingly virulent Marek Disease Virus strains in poultry following vaccination campaigns. Assessing the ‘evolution-proof’ nature of vaccines targeting human viruses is challenging because it requires an understanding of the epidemiology, the within-host ecology and the evolutionary potential of the virus. To date, most investigations into the spread of vaccine-resistant strains are theoretical and are rarely constrained by data. We propose a novel alliance between evolutionary ecology and clinical research to assess the risk of vaccines selecting for resistant or virulent strains. Human papillomaviruses (HPV) and their vaccines provide an ideal study system. However, the scope of the project is wider and encompasses other DNA viruses. The project is divided into three parts. In Part A, we will decipher HPV within-host dynamics in genital infections. By combining mathematical modelling and longitudinal patient data, we will be able to parameterise within-host models and compare them. In Part B, we will jointly analyse host, virus and genital microbiota diversity using a community ecology approach to understand the infectious process. These results will be integrated into evolutionary epidemiology models allowing for diverse infections. In Part C, we will estimate virus substitution rates and use the results from Parts 1 and 2 to develop a multilevel analysis of HPV evolution in response to vaccination. We will also tackle more general questions related to the evolution of the virulence of human oncoviruses. A major asset of the project is the collection of clinical data in order to address a major public health issue using ideas and methods from evolutionary ecology. This will set a new agenda for the study of human viral infections and establish a perennial leading research group in Europe.
Project
We develop within-host dynamics and epidemiological models to understand the role of life-history trade-offs on parasite evolution. We focus in particular on multiple infections, within-host evolution, tolerance and resistance.