Starting December 2019, cases of pneumonia of unknown etiology were reported in the city of Wuhan, in China. The infective pathogen was later identified to be a novel coronavirus, called 2019-nCoV. Here we report an analysis on the risk of importation estimated for Europe. 

​THE REPORT IS AVAILABLE HERE.
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We have a new preprint on the study of healthcare-associated infections:

Reorganization of nurse scheduling reduces the risk of healthcare associated infections
E Valdano, C Poletto, PY Boelle, V Colizza

​We use time-referenced contact data measured by Sociopatterns sensors at a short-stay geriatric ward of a hospital in Lyon. After studying the activity pattern of nurses, we propose a proof-of-concept modeling study for hospital infection control based on the reorganization of care in a hospital ward through changes in the schedule of work shifts of nurses.



The reorganized schedule maintains full staff capacity at any given time, preserves all time-referenced contacts recorded in the dataset without affecting quality standards of medical services, and respects basic occupational constraints (weekly workload, length of a work shift).

This study is done within the framework of the SPHINX project. 

We are entering into Fall with a whole bunch of news - Summer has been super busy with the sabbatical months of Prof. Shweta Bansal and her lab at EPIcx, the visit of collaborators from the University of La Havana (Cuba), and 5 Master students. 

In random order:

2 new papers. Over summer we published 2 new papers on the digital surveillance cohort Grippenet.fr. 
Man flu or woman flu? We analyzed 6 full influenza season with Grippenet.fr data to recover commonly known risk factors for an ILI episode and discover new ones. We found that women are at higher risk of contracting the infection, even after discounting for household composition and contacts with children. An addition to the interesting debate about man vs. woman flu, we'll look further into this problem integrating the database of GP surveillance. 
Factors associated with influenza-like-illness: a crowdsourced cohort study from 2012/13 to 2017/18
C Guerrisi, M Ecollan, C Souty, L Rossignol, C Turbelin, M Debin, T Goronflot, P-Y Boëlle, T Hanslik, V Colizza, T Blanchon
BMC Public Health 19, 879 (2019)

​From recommended to mandatory vaccination. On January 1st, 2018, France changed its policy for vaccinations against childhood diseases, changing 8 recommended vaccines into mandatory. We asked Grippenet.fr population about their opinion on this change of policy. 2/3 of the French population were in favor with the measure, though 60% found it to be authoritarian. A nice editorial on how vaccination policies are currently evolving in Europe accompanied the article. 
Population perception of mandatory childhood vaccination programme before its implementation, France, 2017
P Mathieu, A Gautier, J Raude, T Goronflot, T Launay, M Debin, C Guerrisi, C Turbelin, T Hanslik, C Jestin, V Colizza, T Blanchon, L Rossignol
Eurosurveillance 24(25):pii=1900053 (2019)


1 student ends, 1 student starts. Caroline Guerrisi will soon finish her PhD, with a defense planned for November 20 to discuss her work on digital surveillance in France. Here's her thesis. Laura Di Domenico, currently finishing her Master between the University of Trento, Dept of Mathematics, and INSERM, will enroll the PhD School of Public Health next November to work on the CDR4EBOLA project.  


4 new grants. We got 4 new grants selected over summer, these have been amazing months. More details here, new cycle at EPIcx soon to start, massive hiring ahead!


EPIcx freshens up. We took advantage of these months of great events to update and freshen up the lab website to reflect the evolution of the lab. You will see some changes.

• The research direction on multistrain epidemics is becoming a full-body spin-off led by Chiara Poletto, deserving a novel digital space - follow Chiara for updates.
• We added a novel line of research on the use of mobile phone data to assess the epidemic risk. This is something we've already been working on in the past (e.g. here and here) and that we're now pursuing in the context of developing countries. It is in collaboration with Orange, UCLA, INRIA, University of La Havana. 
• A larger space will soon be dedicated to global animal health. It will cover a large-scale study on European livestock industry we are conducting in collaboration with 14 partners in Europe. We also collaborate on livestock industries in Brazil, Uruguay. 
• Zoonoses will be the link between our work and the work of Raphaelle Metras who will join INSERM and our team in November, yay!

Networks2021. This is the very first Joint Sunbelt and NetSci Conference, hosted by IUNI in Washington, DC, in July 2021. Vittoria Colizza is member of the Steering Committee. It is going to be a unique and exciting event - the biggest network conference ever?!

Time to celebrate, summer 2019 has been particularly generous and we've been awarded 4 grants, yay! Here they are:
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funded by INSERM, INRIA, in collaboration with Orange. 
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funded by Sorbonne Universite, Programme Emergence, in collaboration with UCLA.
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funded by ANR (French National Funding Agency for Research), in collaboration with CNRS, ENS-Lyon.
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funded by EC - H2020 - this is a huge Consortium with 25 partners.
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We published a new paper about the impact of host contact structure on the ecology of multiple strains

Host contact dynamics shapes richness and dominance of pathogen strains
F Pinotti, E Fleury, D Guillemot, P-Y Böelle, C Poletto, PLoS Computational Biology

We considered a population of individuals interacting  through a time varying network. New individuals and strains continuously enter and leave the system. We explored different scenarios in terms of host contact structure and characterised the resulting pathogen ecosystem through ecological indicators. We found that contact heterogeneities reduce strain richness, i.e. the number of co-circulating strains, favouring the dominance of few strains. Our results have far-reaching consequences for multi-strain pathogens such as Staphylococcus aureus, suggesting that contact structure is an important driver of strain diversity.

Our article has been featured on the top of the journal home! 

Deadline is Friday, April 12 2019. Full info here: 

https://www.findaphd.com/phds/project/modelling-behavioural-changes-induced-by-infectious-disease-via-physical-activity-trackers/?p107523

​Don't miss this amazing opportunity!

A call is open for a PhD position at the University of Exeter, UK, with Prof. Ronaldo Menezes on Modeling epidemic spreading in cattle herds. This is a joint collaboration with Vittoria Colizza (EPIcx lab) and Dr. Christiane Rocha (Federal University of Lavras, Brazil). 

Deadline is Friday, March 15, 2019.
Full info here: 
https://www.findaphd.com/phds/project/modelling-epidemic-spreading-in-cattle-herds-computer-science-phd-funded/?p107128
http://www.exeter.ac.uk/studying/funding/award/?id=3471

Don't miss it!

We published a paper on bovine viral diarrhea (BVD), a disease affecting cattle that is endemic in many regions in Europe, with a marked impact on the economy. 

It is characterized by a rather complex transmission dynamics that led previous work to focus exclusively on within-herd scale. 

In our work we introduced a metapopulation model at the national level considering within-farm transmission dynamics at the animal level and cattle trade between farms as a driver for spatial dissemination. We focused on Italy, a country where BVD is endemic and seroprevalence is very high. We found 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.

Farm productive contexts and the dynamics of bovine viral diarrhea (BVD) transmission​
B Iotti, E Valdano, L Savini, L Candeloro, A Giovannini, S Rosati, V Colizza, M Giacobini
Preventive Veterinary Medicine (2019) https://doi.org/10.1016/j.prevetmed.2019.02.001

The paper is part of our research activity on livestock diseases that we are currently expanding, see also these other news on bovine brucellosis and bovine tuberculosis. 

A great start for this new year. In this first month we published two papers. The first article extends the infection propagator approach to compute the epidemic threshold of a disease epidemic spreading on a temporal network of contacts between hosts, once each infected host is characterized by a distinct average infectious period. We applied our approach to:

• bovine tuberculosis in a southern region of Italy
• MRSA infection in a hospital setting
• pandemic influenza in a school​

​Disease persistence on temporal contact networks accounting for heterogeneous infectious periods
A Darbon , D Colombi , E Valdano , L Savini , A Giovannini, V Colizza
Royal Society Open Science 6, 181404 (2019)

The second article identifies the mechanisms for lyssavirus persistence in European bats. Based on population and migratory data of bats in colonies in the East of Spain, and on serological samples, we find that migration and cross-species mixing are fundamental to allow the virus to circulate and persist in the two bat species under study. In addition, our model predicts that bats survive the infection and gain temporary immunity against the virus. ​Our approach have important implications for other zoonoses of public health concern where long-range migration and habitat sharing may play an important role.

​Mechanisms for lyssavirus persistence in non-synanthropic bats in Europe: insights from a modeling study
D Colombi, J Serra-Cobo, R Métras, A Apolloni, C Poletto, M López-Roig, H Bourhy, V Colizza
Scientific Reports 9, 537 (2019)
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​And before January reaches its end, we have an important and fundamentally new event! It is the Scientific Evolutionary Writing Workshop, organized together with Sony Lab in Paris. Looking forward to learning on improving our writing till they can only get worse!