Detecting within-host interactions from genotype combination prevalence data

AbstractParasite 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. Using genital infections by different types of Human Papillomaviruses (HPVs) as a test case, we show that, if sufficiently strong, within-host parasite interactions can be detected from epidemiological data and that this detection is robust even in the face of host heterogeneity in behaviour. These results suggest that the combination of mathematical modelling and sophisticated inference techniques is promising to extract additional epidemiological information from existing datasets.

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Genetic diversity and evolution of hepatitis C virus – 15 years on

Journal of General Virology ◽

10.1099/vir.0.80401-0 ◽

2004 ◽

Vol 85 (11) ◽

pp. 3173-3188 ◽

Cited By ~ 564

Author(s):

Peter Simmonds

Keyword(s):

Genetic Diversity ◽

Hepatitis C Virus ◽

Hepatitis C ◽

Human Liver ◽

Large Population ◽

Sequence Divergence ◽

Selection Pressures ◽

Host Interactions ◽

Persistent Viruses ◽

The Face

In the 15 years since the discovery of hepatitis C virus (HCV), much has been learned about its role as a major causative agent of human liver disease and its ability to persist in the face of host-cell defences and the immune system. This review describes what is known about the diversity of HCV, the current classification of HCV genotypes within the family Flaviviridae and how this genetic diversity contributes to its pathogenesis. On one hand, diversification of HCV has been constrained by its intimate adaptation to its host. Despite the >30 % nucleotide sequence divergence between genotypes, HCV variants nevertheless remain remarkably similar in their transmission dynamics, persistence and disease development. Nowhere is this more evident than in the evolutionary conservation of numerous evasion methods to counteract the cell's innate antiviral defence pathways; this series of highly complex virus–host interactions may represent key components in establishing its ‘ecological niche’ in the human liver. On the other hand, the mutability and large population size of HCV enables it to respond very rapidly to new selection pressures, manifested by immune-driven changes in T- and B-cell epitopes that are encountered on transmission between individuals with different antigen-recognition repertoires. If human immunodeficiency virus type 1 is a precedent, future therapies that target virus protease or polymerase enzymes may also select very rapidly for antiviral-resistant mutants. These contrasting aspects of conservatism and adaptability provide a fascinating paradigm in which to explore the complex selection pressures that underlie the evolution of HCV and other persistent viruses.

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European Strategic Autonomy: The Test Case of Iran

ERIS – European Review of International Studies ◽

10.1163/21967415-08030009 ◽

2021 ◽

Vol 8 (3) ◽

pp. 443-477

Author(s):

Sascha Lohmann

Keyword(s):

United States ◽

The United States ◽

Test Case ◽

The European Union ◽

Policy Makers ◽

Special Purpose Vehicle ◽

The Face ◽

Global Peace ◽

Security Actor ◽

Strategic Autonomy

Abstract The ideal of the European Union (EU) as a global peace and security actor is increasingly clashing with the reality of a multipolar world defined by militarised conflict, and a loosening of the formerly close trans-Atlantic relationship with the United States. European policy-makers have identified strategic autonomy as a possible remedy in the face of a growing number of internal and external security threats. This paper adds to the conceptualisation of strategic autonomy by contextualising its current usage and political genealogy. Empirically, European strategic autonomy is examined concerning the efforts to preserve the Iranian nuclear deal after the Trump administration had ceased US participation in May 2018. In particular, the paper assesses the European response to counter the re-imposed unilateral United States (US) sanctions against European individuals and entities by updating the so-called blocking regulation, and setting up a special purpose vehicle (spv) for facilitating trade with Iran. The results show that the European struggle toward achieving strategic autonomy has largely failed, but that it holds valuable lessons to approximate this ideal in the future.

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Food Safety and Employee Health Implications of COVID-19

Journal of Food Protection ◽

10.4315/jfp-21-201 ◽

2021 ◽

Author(s):

Aljosa Trmcic ◽

Elizabeth Demmings ◽

Kalmia Kniel ◽

Martin Wiedmann ◽

Samuel David Alcaine

Keyword(s):

Food Safety ◽

Food Supply ◽

Food Industry ◽

Food Packaging ◽

Control Strategies ◽

Epidemiological Data ◽

Control Culture ◽

Safety Risks ◽

The Face ◽

Effective Program

The COVID-19 pandemic has greatly impacted the US food supply and consumer behavior. Food production and processing are being disrupted as illnesses, proactive quarantines, and government-mandated movement restrictions cause labor shortages. In this environment, the food industry has been required to adopt new, additional practices to minimize the risk of COVID-19 cases and outbreaks among its workforce. Successfully overcoming these challenges requires a comprehensive approach that addresses COVID-19 transmission both within and outside the facility; possible interventions include strategies to (i) vaccinate employees, (ii) assure that employees practice social distancing, (iii) assure that employees wear face coverings, (iv) screen employees for COVID-19 (v) assure that employees practice frequent handwashing and avoid touching their faces, (vi) clean frequently touched surfaces, and (vii) assure proper ventilation. Compliance with these control strategies needs to be verified and an overall “COVID-19 control culture” needs to be established to facilitate an effective program. Despite some public misperceptions about SARS-CoV-2 presence on foods or food packaging representing a public health risk, it is important to note that both the virus’ biology and epidemiological data clearly support a negligible risk of COVID-19 transmission through food and food packing. However, COVID-19 pandemic related supply chain and workforce disruptions, as well as the shift in resources to protect food industry employees from COVID-19 may increase the actual food safety risks. The goal of this paper is to review the COVID-19 mitigation practices adopted by the food industry, and the potential impact of these practices and COVID-19 related disruptions on the industry’s food safety mission. A review of these impacts is necessary to ensure that the food industry is prepared to maintain a safe and nutritious food supply in the face of future global disruptions.

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Machine learning approaches to calibrate individual-based infectious disease models

10.1101/2021.01.27.21250484 ◽

2021 ◽

Author(s):

Theresa Reiker ◽

Monica Golumbeanu ◽

Andrew Shattock ◽

Lydia Burgert ◽

Thomas A. Smith ◽

...

Keyword(s):

Machine Learning ◽

Disease Transmission ◽

Goodness Of Fit ◽

Epidemiological Data ◽

Bayesian Optimization ◽

Model Complexity ◽

Learning Approaches ◽

Dimensional Parameter ◽

Novel Approach ◽

Transmission Models

AbstractIndividual-based models have become important tools in the global battle against infectious diseases, yet model complexity can make calibration to biological and epidemiological data challenging. We propose a novel approach to calibrate disease transmission models via a Bayesian optimization framework employing machine learning emulator functions to guide a global search over a multi-objective landscape. We demonstrate our approach by application to an established individual-based model of malaria, optimizing over a high-dimensional parameter space with respect to a portfolio of multiple fitting objectives built from datasets capturing the natural history of malaria transmission and disease progression. Outperforming other calibration methodologies, the new approach quickly reaches an improved final goodness of fit. Per-objective parameter importance and sensitivity diagnostics provided by our approach offer epidemiological insights and enhance trust in predictions through greater interpretability.One Sentence SummaryWe propose a novel, fast, machine learning-based approach to calibrate disease transmission models that outperforms other methodologies

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Estimation of age-stratified contact rates during the COVID-19 pandemic using a novel inference algorithm

10.1101/2022.01.12.22269157 ◽

2022 ◽

Author(s):

Christopher M Pooley ◽

Andrea B Doeschl-Wilson ◽

Glenn Marion

Keyword(s):

Hospital Admissions ◽

Epidemiological Data ◽

Joint Analysis ◽

Model Parameters ◽

Inference Algorithm ◽

Public Response ◽

Contact Rates ◽

Reproduction Numbers ◽

Public Data ◽

Approximate Bayesian

Well parameterised epidemiological models including accurate representation of contacts, are fundamental to controlling epidemics. However, age-stratified contacts are typically estimated from pre-pandemic/peace-time surveys, even though interventions and public response likely alter contacts. Here we fit age-stratified models, including re-estimation of relative contact rates between age-classes, to public data describing the 2020-21 COVID-19 outbreak in England. This data includes age-stratified population size, cases, deaths, hospital admissions, and results from the Coronavirus Infection Survey (almost 9000 observations in all). Fitting stochastic compartmental models to such detailed data is extremely challenging, especially considering the large number of model parameters being estimated (over 150). An efficient new inference algorithm ABC-MBP combining existing Approximate Bayesian Computation (ABC) methodology with model-based proposals (MBP) is applied. Modified contact rates are inferred alongside time-varying reproduction numbers that quantify changes in overall transmission due to pandemic response, and age-stratified proportions of asymptomatic cases, hospitalisation rates and deaths. These inferences are robust to a range of assumptions including the values of parameters that cannot be estimated from available data. ABC-MBP is shown to enable reliable joint analysis of complex epidemiological data yielding consistent parametrisation of dynamic transmission models that can inform data-driven public health policy and interventions.

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How host phenology impacts multi-season epidemic cycles

10.1101/2021.06.07.447391 ◽

2021 ◽

Author(s):

Hannelore MacDonald ◽

Dustin Brisson

Keyword(s):

Mathematical Model ◽

Population Dynamics ◽

Population Cycles ◽

Seasonal Activity ◽

Host Interactions ◽

Host Phenology ◽

Demographic Impact ◽

Host Parasite ◽

Parasite Populations ◽

Parasite Dynamics

Parasite-host interactions can result in periodic population dynamics when parasites over-exploit host populations. The timing of host seasonal activity, or host phenology, determines the frequency and demographic impact of parasite-host interactions which may govern if the parasite can sufficiently over-exploit their hosts to drive population cycles. We describe a mathematical model of a monocyclic, obligate-killer parasite system with seasonal host activity to investigate the consequences of host phenology on host-parasite dynamics. The results suggest that parasites can reach the densities necessary to destabilize host dynamics and drive cycling in only some phenological scenarios, such as environments with short seasons and synchronous host emergence. Further, only parasite lineages that are sufficiently adapted to phenological scenarios with short seasons and synchronous host emergence can achieve the densities necessary to over-exploit hosts and produce population cycles. Host-parasite cycles can also generate an eco-evolutionary feedback that slows parasite adaptation to the phenological environment as rare advantageous phenotypes are driven to extinction when introduced in phases of the cycle where host populations are small and parasite populations are large. The results demonstrate that seasonal environments can drive population cycling in a restricted set of phenological patterns and provides further evidence that the rate of adaptive evolution depends on underlying ecological dynamics.

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The effects of seasonality on host–bat fly ecological networks in a temperate mountain cave

Parasitology ◽

10.1017/s0031182016002390 ◽

2016 ◽

Vol 144 (5) ◽

pp. 692-697 ◽

Cited By ~ 9

Author(s):

KARINA D. RIVERA-GARCÍA ◽

CÉSAR A. SANDOVAL-RUIZ ◽

ROMEO A. SALDAÑA-VÁZQUEZ ◽

JORGE E. SCHONDUBE

Keyword(s):

Species Composition ◽

Host Species ◽

Rainy Season ◽

Ecological Networks ◽

Host Interactions ◽

Bat Flies ◽

Bat Fly ◽

Low Prevalence ◽

Host Parasite

SUMMARYChanges in the specialization of parasite–host interactions will be influenced by variations in host species composition. We evaluated this hypothesis by comparing the composition of bats and bat flies within a roost cave over one annual. Five bat and five bat fly species occupied the cave over the course of the study. Bat species composition was 40% different in the rainy season compared with the dry–cold and dry–warm seasons. Despite the incorporation of three new bat species into the cave during the rainy season, bat fly species composition was not affected by seasonality, since the bats that arrived in the rainy season only contributed one new bat fly species at a low prevalence. Bat–bat fly ecological networks were less specialized in the rainy season compared with the dry–cold and dry–warm seasons because of the increase of host overlap among bat fly species during this season. This study suggests that seasonality promote: (1) differences in host species composition, and (2) a reduction in the specialization of host–parasite ecological networks.

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Strategic lockdown and blessing variation – potential success keys against COVID-19

Asian Journal of Medical Sciences ◽

10.3126/ajms.v11i4.28664 ◽

2020 ◽

Vol 11 (4) ◽

pp. 9-19

Author(s):

Koutilya Bhattacharjee ◽

Suvajit Saha ◽

Emili Banerjee ◽

Partha Ganguly

Keyword(s):

Statistical Modeling ◽

Disease Transmission ◽

Epidemiological Data ◽

Respiratory Illness ◽

Differential Rate ◽

Probable Number ◽

Variation Potential ◽

Functional Implications ◽

Potential Success ◽

Human Receptor

Background: COVID-19, a respiratory illness, has become a pandemic originating from the Wuhan city of China. Earlier, similar diseases like Severe Acute Respiratory Syndrome and Middle East Respiratory Syndrome had caused mass mortality in different parts of the globe. Therefore, a similar new disease was of great concern for the humankind. However, it is observed that COVID-19 has a differential rate disease prevalence and mortality among the countries. Aims and Objective: This disease has already affected 2.4 million people globally, leading to healthcare disasters, financial meltdowns due to worldwide lockdowns. Our objective was to evaluate the effect of lockdown in India and to characterize the functional implications of genetic variations of SARS-CoV-2 (the causative virus). Materials and Methods: Epidemiological data for COVID-19 was taken from WHO and other national or international bodies to evaluate the prevalence of the disease in different countries. A statistical modeling was done to estimate the probable number of COVID-19 affected persons with or without lockdown. Bioinformatic analyses were done to identify mutational variations of SARS-CoV-2 and their functional implications. Results: Statistical modeling predicted that number of COVID-19 case could be much higher without lockdown in countries. Countries with malaria and dengue prevalence are less affected by COVID-19. Bioinformatic analyses revealed presence of an Indian SARS-CoV-2 SP1 variant with lesser capability of human receptor binding. Conclusion: Lockdown and deliberate testing has played key important role in prevention of disease transmission. Indian variant of SARS-CoV-2 with less affinity towards human receptor may have a role for lesser virulence.

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Host-parasite relationships between Porichthys porosissimus (Pisces) and cestode larvae of the Scolex group

Helminthologia ◽

10.2478/s11687-009-0031-x ◽

2009 ◽

Vol 46 (3) ◽

pp. 162-167 ◽

Cited By ~ 2

Author(s):

S. Guagliardo ◽

D. Tanzola ◽

C. Schwerdt ◽

N. Galeano

Keyword(s):

Digestive Tract ◽

Condition Factor ◽

Infection Intensity ◽

Potential Effect ◽

The Body ◽

Epithelial Layer ◽

Pathological Features ◽

Host Interactions ◽

Parasite Intensity ◽

Host Parasite

AbstractLarvae of tetraphyllidean cestodes have been recorded in several species of marine teleosts. However, little is known on parasite-host interactions. In view of this, the present study aims at i) determining the localization sites of a larval type, belonging to the Scolex group, in the digestive tract mucose; ii) describing the anatomo-pathological features of the larval lesions produced; and iii) evaluating the potential effect of parasite intensity on the body condition of the host. Our findings reveal that parasitic charges were more intense in the second portion of the digestive tract. In the area of contact between the parasite and the epithelium a compressive atrophy of the cells was observed with a marked lowering and disappearance of the epithelial layer. The condition factor of the samples analyzed was significantly affected by infection intensity, thus revealing an adverse effect on the growth and physical condition of the host.

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Emmanuel Levinas and the Problem of Meaningless Suffering: the Holocaust as a Test Case

Horizons ◽

10.1017/s0360966900031534 ◽

1999 ◽

Vol 26 (1) ◽

pp. 73-84

Author(s):

Marie L. Baird

Keyword(s):

Emmanuel Levinas ◽

Human Life ◽

Christian Theology ◽

Test Case ◽

Christian Spirituality ◽

Johann Baptist Metz ◽

The Holocaust ◽

The Face ◽

The Subject ◽

The Individual

AbstractJohann Baptist Metz has exhorted Christian theologians to discard “system concepts” in favor of “subject concepts” in their theologizing. This revisioning of Christian theology recovers the primacy of the uniqueness and irreplaceability of the individual from totalizing doctrinal formulations and systems that function, for Metz, without reference to the subject. In short, a revisionist Christian theology in light of the Holocaust recovers the preeminence of the inviolability of individual human life.How can such a revisioning be accomplished in the realm of Christian spirituality? This article will utilize the thought of Emmanuel Levinas to assert the primacy of ethics as “first philosophy” replacing ontology, and by implication the ontological foundations undergirding Christian spirituality, with the ethical relation. Such a relation is the basis for a new Christian spirituality that posits the primacy of merciful and compasionate action in the face of conditions of life in extremity.

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