scholarly journals Reconstructing contact network structure and cross-immunity patterns from multiple infection histories

2021 ◽  
Vol 17 (9) ◽  
pp. e1009375
Author(s):  
Christian Selinger ◽  
Samuel Alizon
Keyword(s):  
Infectious Diseases ◽  
Multiple Infection ◽  
Contact Network ◽  
Multiple Infections ◽  
Similarity Metrics ◽  
Summary Statistics ◽  
Transmission Networks ◽  
Contact Patterns ◽  
Network Properties ◽  
Cross Immunity

Interactions within a population shape the spread of infectious diseases but contact patterns between individuals are difficult to access. We hypothesised that key properties of these patterns can be inferred from multiple infection data in longitudinal follow-ups. We developed a simulator for epidemics with multiple infections on networks and analysed the resulting individual infection time series by introducing similarity metrics between hosts based on their multiple infection histories. We find that, depending on infection multiplicity and network sampling, multiple infection summary statistics can recover network properties such as degree distribution. Furthermore, we show that by mining simulation outputs for multiple infection patterns, one can detect immunological interference between pathogens (i.e. the fact that past infections in a host condition future probability of infection). The combination of individual-based simulations and analysis of multiple infection histories opens promising perspectives to infer and validate transmission networks and immunological interference for infectious diseases from longitudinal cohort data.

scholarly journals Using multiple infection history to infer contact network structure

2019 ◽  
Author(s):  
Christian Selinger ◽  
Samuel Alizon
Keyword(s):  
Infectious Diseases ◽  
Disease Transmission ◽  
Multiple Infection ◽  
Contact Network ◽  
Multiple Infections ◽  
Human Populations ◽  
Gillespie Algorithm ◽  
Epidemiological Modeling ◽  
Contact Patterns ◽  
Recent Developments

The structure of host interactions within a population shapes the spread of infectious diseases but contact patterns between hosts are difficult to access. We hypothesised that key properties of these patterns can be inferred by using multiple infections data from individual longitudinal follow-ups. To show this, we simulated multiple infections on a contact network in an unbiased way by implementing a non-Markovian extension of the Gillespie algorithm for a community of parasites spreading on this network. We then analysed the resulting individual infection time series in an original way by introducing the concept of ‘infection barcodes’ to represent the infection history in each host. We find that, depending on infection multiplicity and immunity assumptions, knowledge about the barcode topology makes it possible to recover key properties of the network topology and even of individual nodes. The combination of individual-based simulations and barcode analysis of infection histories opens promising perspectives for the study of infectious disease transmission networks.Significance StatementThe way hosts interact with each other is known to shape epidemics spread. However, these interactions are difficult to infer, especially in human populations. Using recent developments in stochastic epidemiological modeling and barcode theory, we show that the diversity of infections each host has undergone over time contains key information about contact network between hosts. This means that longitudinal follow-ups of some individuals in a population can tell us how hosts are in contact with each other. It can also inform us on how connected a particular individual is. This opens new possibilities regarding the use of genetic diversity of infectious diseases in epidemiology.

scholarly journals Predictors of free-roaming domestic dogs' contact network centrality and their relevance for rabies control

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Charlotte Warembourg ◽  
Guillaume Fournié ◽  
Mahamat Fayiz Abakar ◽  
Danilo Alvarez ◽  
Monica Berger-González ◽  
...  
Keyword(s):  
Disease Transmission ◽  
Small World ◽  
Domestic Dogs ◽  
Contact Network ◽  
Potential Contribution ◽  
Dog Ownership ◽  
Contact Patterns ◽  
Rabies Control ◽  
The Social ◽  
Study Sites

AbstractFree roaming domestic dogs (FRDD) are the main vectors for rabies transmission to humans worldwide. To eradicate rabies from a dog population, current recommendations focus on random vaccination with at least 70% coverage. Studies suggest that targeting high-risk subpopulations could reduce the required vaccination coverage, and increase the likelihood of success of elimination campaigns. The centrality of a dog in a contact network can be used as a measure of its potential contribution to disease transmission. Our objectives were to investigate social networks of FRDD in eleven study sites in Chad, Guatemala, Indonesia and Uganda, and to identify characteristics of dogs, and their owners, associated with their centrality in the networks. In all study sites, networks had small-world properties and right-skewed degree distributions, suggesting that vaccinating highly connected dogs would be more effective than random vaccination. Dogs were more connected in rural than urban settings, and the likelihood of contacts was negatively correlated with the distance between dogs’ households. While heterogeneity in dog's connectedness was observed in all networks, factors predicting centrality and likelihood of contacts varied across networks and countries. We therefore hypothesize that the investigated dog and owner characteristics resulted in different contact patterns depending on the social, cultural and economic context. We suggest to invest into understanding of the sociocultural structures impacting dog ownership and thus driving dog ecology, a requirement to assess the potential of targeted vaccination in dog populations.

scholarly journals What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae ?

2009 ◽  
Vol 7 (47) ◽  
pp. 905-919 ◽  
Author(s):  
Caroline Colijn ◽  
Ted Cohen ◽  
Christophe Fraser ◽  
William Hanage ◽  
Edward Goldstein ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Infectious Diseases ◽  
Multiple Infection ◽  
Drug Resistant ◽  
Host Interactions ◽  
Resistant Strains ◽  
Neutral Models ◽  
Drug Resistant Strains ◽  
And Control

The rise of antimicrobial resistance in many pathogens presents a major challenge to the treatment and control of infectious diseases. Furthermore, the observation that drug-resistant strains have risen to substantial prevalence but have not replaced drug-susceptible strains despite continuing (and even growing) selective pressure by antimicrobial use presents an important problem for those who study the dynamics of infectious diseases. While simple competition models predict the exclusion of one strain in favour of whichever is ‘fitter’, or has a higher reproduction number, we argue that in the case of Streptococcus pneumoniae there has been persistent coexistence of drug-sensitive and drug-resistant strains, with neither approaching 100 per cent prevalence. We have previously proposed that models seeking to understand the origins of coexistence should not incorporate implicit mechanisms that build in stable coexistence ‘for free’. Here, we construct a series of such ‘structurally neutral’ models that incorporate various features of bacterial spread and host heterogeneity that have been proposed as mechanisms that may promote coexistence. We ask to what extent coexistence is a typical outcome in each. We find that while coexistence is possible in each of the models we consider, it is relatively rare, with two exceptions: (i) allowing simultaneous dual transmission of sensitive and resistant strains lets coexistence become a typical outcome, as does (ii) modelling each strain as competing more strongly with itself than with the other strain, i.e. self-immunity greater than cross-immunity. We conclude that while treatment and contact heterogeneity can promote coexistence to some extent, the in-host interactions between strains, particularly the interplay between coinfection, multiple infection and immunity, play a crucial role in the long-term population dynamics of pathogens with drug resistance.

scholarly journals Using network properties to predict disease dynamics on human contact networks

2011 ◽  
Vol 278 (1724) ◽  
pp. 3544-3550 ◽  
Author(s):  
Gregory M. Ames ◽  
Dylan B. George ◽  
Christian P. Hampson ◽  
Andrew R. Kanarek ◽  
Cayla D. McBee ◽  
...  
Keyword(s):  
Degree Distribution ◽  
Stochastic Simulations ◽  
Disease Spread ◽  
Contact Structures ◽  
Contact Network ◽  
Contact Networks ◽  
Human Contact ◽  
Differential Equation Models ◽  
Network Properties ◽  
Intermediate Density

Recent studies have increasingly turned to graph theory to model more realistic contact structures that characterize disease spread. Because of the computational demands of these methods, many researchers have sought to use measures of network structure to modify analytically tractable differential equation models. Several of these studies have focused on the degree distribution of the contact network as the basis for their modifications. We show that although degree distribution is sufficient to predict disease behaviour on very sparse or very dense human contact networks, for intermediate density networks we must include information on clustering and path length to accurately predict disease behaviour. Using these three metrics, we were able to explain more than 98 per cent of the variation in endemic disease levels in our stochastic simulations.

Localization, length and reproduction in single- and multiple-worm infections of Echinostoma revolutum (Trematoda) in the chick

Parasitology ◽  
1981 ◽  
Vol 82 (1) ◽  
pp. 49-53 ◽  
Author(s):  
B. Fried ◽  
D. S. Alenick
Keyword(s):  
Localization Length ◽  
Domestic Chick ◽  
Multiple Infection ◽  
Multiple Infections ◽  
Echinostoma Revolutum ◽  
Length Measurements ◽  
Cross Fertilization

SUMMARYMono-metacercarial infections of Echinostoma revolutum in the domestic chick yielded 14- or 15-day-old worms that produced viable eggs, indicating that this species can self-fertilize under conditions which preclude cross-fertilization. In multiple infection studies, chicks were fed either 5 or 10 cysts and each infected chick contained 2–7 worms at necropsy 14 or 15 days later. Worms from multiple infections were mainly paired or clustered and they tended to locate more posteriorly in the intestine than single worms. Length measurements of single and multiple worms were similar. Both the number of eggs and the percentage of hatched eggs were considerably greater in multiple than in single infections.

Prevalence of Rhabdias africanus and other Endoparasites of Sclerophrys regularis (Anura: Bufonidae) From Ogoni Land, Nigeria

2020 ◽  
Vol 41 (2) ◽  
Author(s):  
C.C Amuzie ◽  
T.M Marcus ◽  
J.F Espínola-Novelo
Keyword(s):  
Niger Delta ◽  
The Other ◽  
Multiple Infection ◽  
Multiple Infections ◽  
Helminth Parasites ◽  
Niger Delta Region ◽  
High Prevalence ◽  
Low Prevalence ◽  
Keywords Lung ◽  
Cosmocerca Ornata

Sclerophrys regularis specimens from Ogoni, Nigeria, were investigated for the prevalence of the lung nematodes, Rhabdiasafricanus. Hosts were collected from two locations, Zor Sogho, Bori and Kaani 1, Khana. High prevalence of R. africanusinfection was observed, 69% in Bori and 100% in Khana. Other helminth parasites recovered from the hosts includedacanthocephalan cystacanths, pentastomids (Raillietiella sp.), trematodes (Diplodiscus fischthalicus and Mesocoeliummonodi) and nematodes (ascaridida larvae, Amplicaecum africanum, Cosmocerca ornata, Oswaldocruzia hoepplii). Coinfectionof C. ornata and R. africanus was very common in both locations, and multiple infection was more prevalent thansingle infection. This is the second report of Diplodiscus fischthalicus from a bufonid in Nigeria, with both occurring in thehumid Niger Delta region, however in low prevalence and intensity. The other parasites have been reported by previousauthors. Research into the environmental factors that enhance transmission of Rhabdias africanus should be investigated. Keywords: Lung nematode parasite, bufonids, co-infection, multiple infections, amphibians, Ogoni

scholarly journals The effects of social structure and sex-biased transmission on macroparasite infection

Parasitology ◽  
2008 ◽  
Vol 135 (13) ◽  
pp. 1561-1569 ◽  
Author(s):  
S. E. PERKINS ◽  
M. F. FERRARI ◽  
P. J. HUDSON
Keyword(s):  
Social Structure ◽  
Network Models ◽  
Male Mice ◽  
Heligmosomoides Polygyrus ◽  
Transmission Networks ◽  
Male Bias ◽  
Contact Patterns ◽  
Dynamics And Control ◽  
Models Of Disease ◽  
And Control

SUMMARYMathematical models of disease dynamics tend to assume that individuals within a population mix at random and so transmission is random, and yet, in reality social structure creates heterogeneous contact patterns. We investigated the effect of heterogeneity in host contact patterns on potential macroparasite transmission by first quantifying the level of assortativity in a socially structured wild rodent population (Apodemus flavicollis) with respect to the directly-transmitted macroparasitic helminth, Heligmosomoides polygyrus. We found the population to be disassortatively mixed (i.e. male mice mixing with female mice more often than same sex mixing) at a constant level over time. The macroparasite H. polygyrus has previously been shown to exhibit male-biased transmission so we used a Susceptible-Infected (SI) mathematical model to simulate the effect of increasing strengths of male-biased transmission on the prevalence of the macroparasite using empirically-derived transmission networks. When transmission was equal between the sexes the model predicted macroparasite prevalence to be 73% and infection was male biased (82% of infection in the male mice). With a male-bias in transmission ten times that of the females, the expected macroparasite prevalence was 50% and was equally prevalent in both sexes, results that both most closely resembled empirical dynamics. As such, disassortative mixing alone did not produce macroparasite dynamics analogous to those from empirical observations; a strong male-bias in transmission was also required. We discuss the relevance of our results in the context of network models for transmission dynamics and control.

scholarly journals Impaired immune evasion in HIV through intracellular delays and multiple infection of cells

2012 ◽  
Vol 279 (1740) ◽  
pp. 3003-3010 ◽  
Author(s):  
Christian L. Althaus ◽  
Rob J. De Boer
Keyword(s):  
Life Cycle ◽  
Immune Escape ◽  
Multiple Infection ◽  
Multiple Infections ◽  
Wild Type ◽  
Hiv Dynamics ◽  
Rate Of Escape ◽  
Multiple Copies ◽  
Infected Cells ◽  
Eclipse Phase

With its high mutation rate, HIV is capable of escape from recognition, suppression and/or killing by CD8 + cytotoxic T lymphocytes (CTLs). The rate at which escape variants replace each other can give insights into the selective pressure imposed by single CTL clones. We investigate the effects of specific characteristics of the HIV life cycle on the dynamics of immune escape. First, it has been found that cells in HIV-infected patients can carry multiple copies of proviruses. To investigate how this process affects the emergence of immune escape, we develop a mathematical model of HIV dynamics with multiple infections of cells. Increasing the frequency of multiple-infected cells delays the appearance of immune escape variants, slows down the rate at which they replace the wild-type variant and can even prevent escape variants from taking over the quasi-species. Second, we study the effect of the intracellular eclipse phase on the rate of escape and show that escape rates are expected to be slower than previously anticipated. In summary, slow escape rates do not necessarily imply inefficient CTL-mediated killing of HIV-infected cells, but are at least partly a result of the specific characteristics of the viral life cycle.

scholarly journals Why multiple infections favour virulent parasites

2018 ◽  
Author(s):  
Mircea T. Sofonea ◽  
Samuel Alizon ◽  
Yannis Michalakis
Keyword(s):  
Dynamical Systems ◽  
Selection Bias ◽  
Selective Pressure ◽  
Growth Traits ◽  
Natural Host ◽  
Multiple Infection ◽  
Multiple Infections ◽  
Host Interactions ◽  
Host Growth ◽  
Host Mortality

AbstractIt is now a fact that several strains/species (hereafter types) of parasites circulate in natural host populations. Parasite polymorphism can even occur within the same host, where distinct parasite types can interact in various ways. This can affect their transmission and, therefore, their evolution. We still lack general predictions regarding the evolution, in such multiple infection contexts, of virulence – the infection-induced host mortality, essentially because its emanation from within-host growth was often ignored so far. Here, we explicitly investigate within-host interactions, within-host competition outcomes, epidemiological dynamics and evolutionary invasibility using a formalism as general as possible. Focusing on chronic dimorphic infections caused by horizontally-transmitted microparasites, we apply both dynamical systems and probabilistic approaches to this bottom-up sequence of dynamics to explore the evolutionary outcomes. We show that within-host growth traits are under strong selective pressure and when small mutations affect them, most of the surviving mutants are more virulent than their resident. We thus identify a robust and unavoidable selection bias towards higher virulence.

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