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)
​

​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!

We organize together with Sony Lab in Paris the first edition of the Scientific Evolutionary Writing Workshop (SEW #1).


All scientific research involves attempts to resolve a mystery overcome an obstacle or solve a problem. This makes them stories with narrative potential. But most scientific papers lack basic story-telling mechanisms. This workshop will explore story-telling techniques and how they can be used in scientific papers while maintaining the scientific rigour required for the world’s top journals. Participants will be challenged to embark in an evolutionary process of their creations to rewrite and refine their texts till to a point in which “texts can only be worsened”.

​Teachers: Mark Buchanan and Justin Mullins
When: January 30-31, 2019
Where: Institut des Systemes Complexes, Paris
Sponsors: Sony CSL, INSERM, ANR, ISC
Organizers: Vittorio Loreto, Vittoria Colizza
More info: sew-workshop.org/

We published 3 papers this summer, approaching very different epidemic contexts (bovine brucellosis, varicella, influenza) with different methods.

​
With the first paper we were able to explain the persistence of bovine brucellosis in southern Italy, that is a matter of great concern for animal health and welfare, trade and commerce and economic reasons. Based on a network approach coupled with detailed cattle trade movements and outbreak data, we found that more efficient biosecurity measures in the north and limited compliance to trade regulations for epidemic control in the south are key factors explaining the diverse success of Italian regions in eradicating brucellosis.


We were also able to identify for the first time illegal trade behavior from data!

The study was a collaboration with the IZS - Italian Agency for Animal Health (Teramo, Italy). 








Network-based assessment of the vulnerability of Italian regions to bovine brucellosis
A Darbon, E Valdano, C Poletto, A Giovannini, L Savini, L Candeloro, V Colizza
Preventive Veterinary Medicine 158, 25 (2018)



The second paper highlighted the role of changes in children contacts in daycare over time, also due to higher attendance, in the dynamics of varicella transmission in France. We used an agent-based model with data-driven contacts obtained from a large scale survey conducted in France. This study was a collaboration with the lab of Stefano Merler at Fondazione Bruno Kessler (Trento, Italy). 

In the third paper we analyzed 30 influenza seasons in France to characterize their season-by-season variability both in the start of the epidemic and in the time of the epidemic peak. We introduced a clustering approach to assess the deviations from typical spreading patterns and identified groups of seasons whose behavior largely deviates from the features of a typical season well-known in the literature. This study was a collaboration with Reseau Sentinelles, the disease surveillance team in France.

​​Shifting patterns of seasonal influenza epidemics
P Coletti, C Poletto, C Turbelin, T Blanchon, V Colizza
Scientific Reports 8, 12786 (2018)
​

A couple of months have passed since NetSci 2018... and much more time since our last post - the organization of NetSci strongly impacted the lab's agenda!

NetSci has been an amazing experience and a terrific event!
​791 participants... new record - very proud. 

Have a look at some photos:

​Influenzanet was cited in a recent Nature Outlook issue on the future of medicine, addressing specifically "Infection forecasts powered by big data". Have a look!