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Article ; Online: A Municipality-Based Approach Using Commuting Census Data to Characterize the Vulnerability to Influenza-Like Epidemic

Lara Savini / Luca Candeloro / Paolo Calistri / Annamaria Conte

Microorganisms, Vol 8, Iss 911, p

The COVID-19 Application in Italy

2020 Volume 911

Abstract: In February 2020, Italy became the epicenter for COVID-19 in Europe, and at the beginning of March, the Italian Government put in place emergency measures to restrict population movement. Aim of our analysis is to provide a better understanding of the ... ...

Abstract	In February 2020, Italy became the epicenter for COVID-19 in Europe, and at the beginning of March, the Italian Government put in place emergency measures to restrict population movement. Aim of our analysis is to provide a better understanding of the epidemiological context of COVID-19 in Italy, using commuting data at a high spatial resolution, characterizing the territory in terms of vulnerability. We used a Susceptible–Infectious stochastic model and we estimated a municipality-specific infection contact rate () to capture the susceptibility to the disease. We identified in Lombardy, Veneto and Emilia Romagna regions (52% of all Italian cases) significant clusters of high , due to the simultaneous presence of connections between municipalities and high population density. Local simulated spreading in regions, with different levels of infection observed, showed different disease geographical patterns due to different values and commuting systems. In addition, we produced a vulnerability map (in the Abruzzi region as an example) by simulating the epidemic considering each municipality as a seed. The result shows the highest vulnerability values in areas with commercial hubs, close to the highest populated cities and the most industrial area. Our results highlight how human mobility can affect the epidemic, identifying particular situations in which the health authorities can promptly intervene to control the disease spread.
Keywords	COVID-19 ; commuting census data ; municipality-specific infection contact rate ; vulnerability ; infectious disease modeling ; Biology (General) ; QH301-705.5 ; covid19
Subject code	910
Language	English
Publishing date	2020-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A New Weighted Degree Centrality Measure

Luca Candeloro / Lara Savini / Annamaria Conte

PLoS ONE, Vol 11, Iss 11, p e

The Application in an Animal Disease Epidemic.

2016 Volume 0165781

Abstract: In recent years researchers have investigated a growing number of weighted heterogeneous networks, where connections are not merely binary entities, but are proportional to the intensity or capacity of the connections among the various elements. ... ...

Abstract	In recent years researchers have investigated a growing number of weighted heterogeneous networks, where connections are not merely binary entities, but are proportional to the intensity or capacity of the connections among the various elements. Different degree centrality measures have been proposed for this kind of networks. In this work we propose weighted degree and strength centrality measures (WDC and WSC). Using a reducing factor we correct classical centrality measures (CD) to account for tie weights distribution. The bigger the departure from equal weights distribution, the greater the reduction. These measures are applied to a real network of Italian livestock movements as an example. A simulation model has been developed to predict disease spread into Italian regions according to animal movements and animal population density. Model's results, expressed as infected regions and number of times a region gets infected, were related to weighted and classical degree centrality measures. WDC and WSC were shown to be more efficient in predicting node's risk and vulnerability. The proposed measures and their application in an animal network could be used to support surveillance and infection control strategy plans.
Keywords	Medicine ; R ; Science ; Q
Subject code	001
Language	English
Publishing date	2016-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Disease persistence on temporal contact networks accounting for heterogeneous infectious periods

Alexandre Darbon / Davide Colombi / Eugenio Valdano / Lara Savini / Armando Giovannini / Vittoria Colizza

Royal Society Open Science, Vol 6, Iss

2019 Volume 1

Abstract: The infectious period of a transmissible disease is a key factor for disease spread and persistence. Epidemic models on networks typically assume an identical average infectious period for all individuals, thus allowing an analytical treatment. This ... ...

Abstract	The infectious period of a transmissible disease is a key factor for disease spread and persistence. Epidemic models on networks typically assume an identical average infectious period for all individuals, thus allowing an analytical treatment. This simplifying assumption is, however, often unrealistic, as hosts may have different infectious periods, due, for instance, to individual host–pathogen interactions or inhomogeneous access to treatment. While previous work accounted for this heterogeneity in static networks, a full theoretical understanding of the interplay of varying infectious periods and time-evolving contacts is still missing. Here, we consider a susceptible-infectious-susceptible epidemic on a temporal network with host-specific average infectious periods, and develop an analytical framework to estimate the epidemic threshold, i.e. the critical transmissibility for disease spread in the host population. Integrating contact data for transmission with outbreak data and epidemiological estimates, we apply our framework to three real-world case studies exploring different epidemic contexts—the persistence of bovine tuberculosis in southern Italy, the spread of nosocomial infections in a hospital, and the diffusion of pandemic influenza in a school. We find that the homogeneous parametrization may cause important biases in the assessment of the epidemic risk of the host population. Our approach is also able to identify groups of hosts mostly responsible for disease diffusion who may be targeted for prevention and control, aiding public health interventions.
Keywords	susceptible-infectious-susceptible model ; epidemic spread ; temporal network ; epidemic threshold ; mathematical modelling ; Science ; Q
Subject code	612
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	The Royal Society
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Network-based assessment of the vulnerability of Italian regions to bovine brucellosis

Darbon, Alexandre / Armando Giovannini / Chiara Poletto / Eugenio Valdano / Lara Savini / Luca Candeloro / Vittoria Colizza

Preventive veterinary medicine. 2018 Oct. 01, v. 158

2018

Abstract: The endemic circulation of bovine brucellosis in cattle herds has a markedly negative impact on economy, due to decreased fertility, increased abortion rates, reduced milk and meat production. It also poses a direct threat to human health. In Italy, ... ...

Abstract	The endemic circulation of bovine brucellosis in cattle herds has a markedly negative impact on economy, due to decreased fertility, increased abortion rates, reduced milk and meat production. It also poses a direct threat to human health. In Italy, despite the long lasting efforts and the considerable economic investment, complete eradication of this disease still eludes the southern regions, as opposed to the northern regions that are disease-free. Here we introduced a novel quantitative network-based approach able to fully exploit the highly resolved databases of cattle trade movements and outbreak reports to yield estimates of the vulnerability of a cattle market to brucellosis. Tested on the affected regions, the introduced vulnerability indicator was shown to be accurate in predicting the number of bovine brucellosis outbreaks (Spearman r= 0.82, p= 0.04), thus confirming the suitability of our tool for epidemic risk assessment. We evaluated the dependence of regional vulnerability to brucellosis on a set of factors including premises spatial distribution, trading patterns, farming practices, herd market value, compliance to outbreak regulations, and exploring different epidemiological conditions. Animal trade movements were identified as a major route for brucellosis spread between farms (r=0.85, p<10-5 between vulnerability and number of inbound movements), with an additional potential risk attributed to the use of shared pastures (r=0.4, p=0.04). By comparing the vulnerability of disease-free regions in the north to affected regions in the south, we found that more intense trade and higher market value of the cattle sector in the north (r=0.56, p=0.01) likely inducing more efficient biosafety measures, together with poor compliance to trade restrictions following outbreaks in the south were key factors explaining the diverse success in eradicating brucellosis. Our modeling scheme is both synthetic and effective in gauging regional vulnerability to brucellosis persistence. Its general formulation makes it adaptable to other diseases and host species, providing a useful tool for veterinary epidemiology and policy assessment.
Keywords	biosafety ; bovine brucellosis ; cattle ; compliance ; databases ; economic investment ; epidemiology ; farming systems ; herds ; hosts ; human health ; issues and policy ; market value ; markets ; meat production ; milk ; models ; pastures ; prediction ; risk ; risk assessment ; trade ; Italy
Language	English
Dates of publication	2018-1001
Size	p. 25-34.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	43399-8
ISSN	1873-1716 ; 0167-5877
ISSN (online)	1873-1716
ISSN	0167-5877
DOI	10.1016/j.prevetmed.2018.07.004
Database	NAL-Catalogue (AGRICOLA)

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Article: Farm productive contexts and the dynamics of bovine viral diarrhea (BVD) transmission

Iotti, Bryan / Armando Giovannini / Eugenio Valdano / Lara Savini / Luca Candeloro / Mario Giacobini / Sergio Rosati / Vittoria Colizza

Preventive veterinary medicine. 2019 Apr. 01, v. 165

2019

Abstract: Bovine viral diarrhea (BVD) is a viral disease that affects cattle and that is endemic to many European countries. It has a markedly negative impact on the economy, through reduced milk production, abortions, and a shorter lifespan of the infected ... ...

Abstract	Bovine viral diarrhea (BVD) is a viral disease that affects cattle and that is endemic to many European countries. It has a markedly negative impact on the economy, through reduced milk production, abortions, and a shorter lifespan of the infected animals. Cows becoming infected during gestation may give birth to Persistently Infected (PI) calves, which remain highly infective throughout their life, due to the lack of immune response to the virus. As a result, they are the key driver of the persistence of the disease both at herd scale, and at the national level. In the latter case, the trade-driven movements of PIs, or gestating cows carrying PIs, are responsible for the spatial dispersion of BVD. Past modeling approaches to BVD transmission have either focused on within-herd or between-herd transmission. A comprehensive portrayal, however, targeting both the generation of PIs within a herd, and their displacement throughout the country due to trade transactions, is still missing. We overcome this by designing a multiscale metapopulation model of the spatial transmission of BVD, accounting for both within-herd infection dynamics, and its spatial dispersion. We focus on Italy, a country where BVD is endemic and seroprevalence is very high. By integrating simple within-herd dynamics of PI generation, and the highly-resolved cattle movement dataset available, our model requires minimal arbitrary assumptions on its parameterization. We use our model to study the role of the different productive contexts of the Italian market, and test possible intervention strategies aimed at prevalence reduction. We find that dairy farms are the main drivers of BVD persistence in Italy, and any control strategy targeting these farms would lead to significantly higher prevalence reduction, with respect to targeting other production compartments. Our multiscale metapopulation model is a simple yet effective tool for studying BVD dispersion and persistence at country level, and is a good instrument for testing targeted strategies aimed at the containment or elimination of this disease. Furthermore, it can readily be applied to any national market for which cattle movement data is available.
Keywords	bovine viral diarrhea ; calves ; cows ; dairy farming ; data collection ; farms ; herds ; immune response ; longevity ; markets ; milk production ; models ; pregnancy ; seroprevalence ; trade ; viruses ; Italy
Language	English
Dates of publication	2019-0401
Size	p. 23-33.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	43399-8
ISSN	1873-1716 ; 0167-5877
ISSN (online)	1873-1716
ISSN	0167-5877
DOI	10.1016/j.prevetmed.2019.02.001
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A Web Geographic Information System to share data and explorative analysis tools

Lara Savini / Susanna Tora / Alessio Di Lorenzo / Daniela Cioci / Federica Monaco / Andrea Polci / Massimiliano Orsini / Paolo Calistri / Annamaria Conte

PLoS ONE, Vol 13, Iss 6, p e

The application to West Nile disease in the Mediterranean basin.

2018 Volume 0196429

Abstract: BACKGROUND:In the last decades an increasing number of West Nile Disease cases was observed in equines and humans in the Mediterranean basin and surveillance systems are set up in numerous countries to manage and control the disease. The collection, ... ...

Abstract	BACKGROUND:In the last decades an increasing number of West Nile Disease cases was observed in equines and humans in the Mediterranean basin and surveillance systems are set up in numerous countries to manage and control the disease. The collection, storage and distribution of information on the spread of the disease becomes important for a shared intervention and control strategy. To this end, a Web Geographic Information System has been developed and disease data, climatic and environmental remote sensed data, full genome sequences of selected isolated strains are made available. This paper describes the Disease Monitoring Dashboard (DMD) web system application, the tools available for the preliminary analysis on climatic and environmental factors and the other interactive tools for epidemiological analysis. METHODS:WNV occurrence data are collected from multiple official and unofficial sources. Whole genome sequences and metadata of WNV strains are retrieved from public databases or generated in the framework of the Italian surveillance activities. Climatic and environmental data are provided by NASA website. The Geographical Information System is composed by Oracle 10g Database and ESRI ArcGIS Server 10.03; the web mapping client application is developed with the ArcGIS API for Javascript and Phylocanvas library to facilitate and optimize the mash-up approach. ESRI ArcSDE 10.1 has been used to store spatial data. RESULTS:The DMD application is accessible through a generic web browser at https://netmed.izs.it/networkMediterraneo/. The system collects data through on-line forms and automated procedures and visualizes data as interactive graphs, maps and tables. The spatial and temporal dynamic visualization of disease events is managed by a time slider that returns results on both map and epidemiological curve. Climatic and environmental data can be associated to cases through python procedures and downloaded as Excel files. CONCLUSIONS:The system compiles multiple datasets through user-friendly web tools; it ...
Keywords	Medicine ; R ; Science ; Q
Subject code	302
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A New Information System for the Management of Non-Epidemic Veterinary Emergencies

Luigi Possenti / Lara Savini / Annamaria Conte / Nicola D'Alterio / Maria Luisa Danzetta / Alessio Di Lorenzo / Maria Nardoia / Paolo Migliaccio / Susanna Tora / Paolo Dalla Villa

Animals, Vol 10, Iss 983, p

2020 Volume 983

Abstract: The Italian National Veterinary Services, public health professionals, and policy makers are asked to participate at different levels in the decision-making process for the management of non-epidemic emergencies. A decision support system offering the ... ...

Abstract	The Italian National Veterinary Services, public health professionals, and policy makers are asked to participate at different levels in the decision-making process for the management of non-epidemic emergencies. A decision support system offering the different administrative and operational emergency management levels with a spatial and decisional tool to be used in the case of natural disasters is still missing at the national level. Within this context, the Italian General Directorate for Animal Health of the Ministry of Health funded a research project for the implementation of a new Veterinary Information System for Non-Epidemic Emergencies (SIVENE), an innovative real-time decision support tool for emergency response in a disaster management scenario. SIVENE was developed according to a multi-layer architecture with four integrated components: the database layer, which was implemented by an RDBMS Oracle 11 g; the ReST service layer, which was created using J2EE, Spring, and MyBatis technologies; the web application (business framework and user interface), which was developed in Angular4 framework using TypeScript language; and the web Geographic Information Systems (GIS), which was realized through the implementation of a geodatabase in Oracle RDBMS 11 g. This system allows us to build up and dynamically create a set of dedicated checklists to be used in the field when gathering the information needed for the management of non-epidemic emergencies; employ the application on mobile devices, such as tablets and smartphones; and use the web GIS to manage and visualize data of veterinary interest and territorial maps of risk and damage.
Keywords	non-epidemic emergencies ; veterinary emergencies ; web GIS ; information system ; web application ; livestock ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
Language	English
Publishing date	2020-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Rift Valley fever transmission dynamics described by compartmental models

Danzetta, Maria Luisa / Francesca Sauro / Lara Savini / Paolo Calistri / Rossana Bruno

Preventive veterinary medicine. 2016 Nov. 01, v. 134

2016

Abstract: Rift Valley fever (RVF) is one of the most important zoonotic Transboundary Animal Diseases able to cross international borders and cause devastating effect on animal health and food security. Climate changes and the presence of competent vectors in the ... ...

Abstract	Rift Valley fever (RVF) is one of the most important zoonotic Transboundary Animal Diseases able to cross international borders and cause devastating effect on animal health and food security. Climate changes and the presence of competent vectors in the most of the current RVF-free temperate countries strongly support the inclusion of RVF virus (RVFV) among the most significant emerging viral threats for public and animal health. The transmission of RVFV is driven by complex eco-climatic factors making the epidemiology of RVF infection difficult to study and to understand. Mathematical, statistical and spatial models are often used to explain the mechanisms underlying these biological processes, providing new and effective tools to plan measures for public health protection. In this paper we performed a systematic literature review on RVF published papers with the aim of identifying and describing the most recent papers developing compartmental models for the study of RVFV transmission dynamics.
Keywords	animal diseases ; animal health ; climate change ; epidemiology ; food security ; health foods ; health promotion ; models ; Rift Valley fever ; viruses
Language	English
Dates of publication	2016-1101
Size	p. 197-210.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	43399-8
ISSN	1873-1716 ; 0167-5877
ISSN (online)	1873-1716
ISSN	0167-5877
DOI	10.1016/j.prevetmed.2016.09.007
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Predicting epidemic risk from past temporal contact data.

Eugenio Valdano / Chiara Poletto / Armando Giovannini / Diana Palma / Lara Savini / Vittoria Colizza

PLoS Computational Biology, Vol 11, Iss 3, p e

2015 Volume 1004152

Abstract: Understanding how epidemics spread in a system is a crucial step to prevent and control outbreaks, with broad implications on the system's functioning, health, and associated costs. This can be achieved by identifying the elements at higher risk of ... ...

Abstract	Understanding how epidemics spread in a system is a crucial step to prevent and control outbreaks, with broad implications on the system's functioning, health, and associated costs. This can be achieved by identifying the elements at higher risk of infection and implementing targeted surveillance and control measures. One important ingredient to consider is the pattern of disease-transmission contacts among the elements, however lack of data or delays in providing updated records may hinder its use, especially for time-varying patterns. Here we explore to what extent it is possible to use past temporal data of a system's pattern of contacts to predict the risk of infection of its elements during an emerging outbreak, in absence of updated data. We focus on two real-world temporal systems; a livestock displacements trade network among animal holdings, and a network of sexual encounters in high-end prostitution. We define the node's loyalty as a local measure of its tendency to maintain contacts with the same elements over time, and uncover important non-trivial correlations with the node's epidemic risk. We show that a risk assessment analysis incorporating this knowledge and based on past structural and temporal pattern properties provides accurate predictions for both systems. Its generalizability is tested by introducing a theoretical model for generating synthetic temporal networks. High accuracy of our predictions is recovered across different settings, while the amount of possible predictions is system-specific. The proposed method can provide crucial information for the setup of targeted intervention strategies.
Keywords	Biology (General) ; QH301-705.5
Subject code	006
Language	English
Publishing date	2015-03-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Dynamical patterns of cattle trade movements.

Paolo Bajardi / Alain Barrat / Fabrizio Natale / Lara Savini / Vittoria Colizza

PLoS ONE, Vol 6, Iss 5, p e

2011 Volume 19869

Abstract: Despite their importance for the spread of zoonotic diseases, our understanding of the dynamical aspects characterizing the movements of farmed animal populations remains limited as these systems are traditionally studied as static objects and through ... ...

Abstract	Despite their importance for the spread of zoonotic diseases, our understanding of the dynamical aspects characterizing the movements of farmed animal populations remains limited as these systems are traditionally studied as static objects and through simplified approximations. By leveraging on the network science approach, here we are able for the first time to fully analyze the longitudinal dataset of Italian cattle movements that reports the mobility of individual animals among farms on a daily basis. The complexity and inter-relations between topology, function and dynamical nature of the system are characterized at different spatial and time resolutions, in order to uncover patterns and vulnerabilities fundamental for the definition of targeted prevention and control measures for zoonotic diseases. Results show how the stationarity of statistical distributions coexists with a strong and non-trivial evolutionary dynamics at the node and link levels, on all timescales. Traditional static views of the displacement network hide important patterns of structural changes affecting nodes' centrality and farms' spreading potential, thus limiting the efficiency of interventions based on partial longitudinal information. By fully taking into account the longitudinal dimension, we propose a novel definition of dynamical motifs that is able to uncover the presence of a temporal arrow describing the evolution of the system and the causality patterns of its displacements, shedding light on mechanisms that may play a crucial role in the definition of preventive actions.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2011-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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