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Article ; Online: Epidemic Management via Imperfect Testing: A Multi-criterial Perspective.

Palma, Giuseppe / Caprioli, Damiano / Mari, Lorenzo

2023 Volume 85, Issue 7, Page(s) 66

Abstract: Diagnostic testing may represent a key component in response to an ongoing epidemic, especially if coupled with containment measures, such as mandatory self-isolation, aimed to prevent infectious individuals from furthering onward transmission while ... ...

Abstract	Diagnostic testing may represent a key component in response to an ongoing epidemic, especially if coupled with containment measures, such as mandatory self-isolation, aimed to prevent infectious individuals from furthering onward transmission while allowing non-infected individuals to go about their lives. However, by its own nature as an imperfect binary classifier, testing can produce false negative or false positive results. Both types of misclassification are problematic: while the former may exacerbate the spread of disease, the latter may result in unnecessary isolation mandates and socioeconomic burden. As clearly shown by the COVID-19 pandemic, achieving adequate protection for both people and society is a crucial, yet highly challenging task that needs to be addressed in managing large-scale epidemic transmission. To explore the trade-offs imposed by diagnostic testing and mandatory isolation as tools for epidemic containment, here we present an extension of the classical Susceptible-Infected-Recovered model that accounts for an additional stratification of the population based on the results of diagnostic testing. We show that, under suitable epidemiological conditions, a careful assessment of testing and isolation protocols can contribute to epidemic containment, even in the presence of false negative/positive results. Also, using a multi-criterial framework, we identify simple, yet Pareto-efficient testing and isolation scenarios that can minimize case count, isolation time, or seek a trade-off solution for these often contrasting epidemic management objectives.
MeSH term(s)	Humans ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/prevention & control ; SARS-CoV-2 ; Pandemics/prevention & control ; Models, Biological ; Mathematical Concepts
Language	English
Publishing date	2023-06-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	184905-0
ISSN	1522-9602 ; 0007-4985 ; 0092-8240
ISSN (online)	1522-9602
ISSN	0007-4985 ; 0092-8240
DOI	10.1007/s11538-023-01172-1
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Article ; Online: Helminth ecological requirements shape the impact of climate change on the hazard of infection.

Vanalli, Chiara / Mari, Lorenzo / Casagrandi, Renato / Gatto, Marino / Cattadori, Isabella M

Ecology letters

2024 Volume 27, Issue 2, Page(s) e14386

Abstract: Outbreaks and spread of infectious diseases are often associated with seasonality and environmental changes, including global warming. Free-living stages of soil-transmitted helminths are highly susceptible to climatic drivers; however, how multiple ... ...

Abstract	Outbreaks and spread of infectious diseases are often associated with seasonality and environmental changes, including global warming. Free-living stages of soil-transmitted helminths are highly susceptible to climatic drivers; however, how multiple climatic variables affect helminth species, and the long-term consequences of these interactions, is poorly understood. We used experiments on nine trichostrongylid species of herbivores to develop a temperature- and humidity-dependent model of infection hazard, which was then implemented at the European scale under climate change scenarios. Intestinal and stomach helminths exhibited contrasting climatic responses, with the former group strongly affected by temperature while the latter primarily impacted by humidity. Among the demographic traits, larval survival heavily modulated the infection hazard. According to the specific climatic responses of the two groups, climate change is expected to generate differences in the seasonal and spatial shifts of the infection hazard and group co-circulation. In the future, an intensification of these trends could create new opportunities for species range expansion and co-occurrence at European central-northern latitudes.
MeSH term(s)	Animals ; Climate Change ; Helminths ; Global Warming ; Larva
Language	English
Publishing date	2024-02-25
Publishing country	England
Document type	Journal Article
ZDB-ID	1441608-6
ISSN	1461-0248 ; 1461-023X
ISSN (online)	1461-0248
ISSN	1461-023X
DOI	10.1111/ele.14386
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Article ; Online: Symptomatic Narcolepsy/Cataplexy in a Dog with Brainstem Meningoencephalitis of Unknown Origin.

Mari, Lorenzo / Shea, Anita

Journal of the American Animal Hospital Association

2020 Volume 56, Issue 2, Page(s) e56201

MeSH term(s)	Animals ; Brain Stem/pathology ; Cataplexy/etiology ; Cataplexy/veterinary ; Dog Diseases/pathology ; Dogs ; Female ; Immunosuppressive Agents/therapeutic use ; Meningoencephalitis/complications ; Meningoencephalitis/veterinary ; Narcolepsy/etiology ; Narcolepsy/veterinary
Chemical Substances	Immunosuppressive Agents
Language	English
Publishing date	2020-01-21
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	410383-x
ISSN	1547-3317 ; 1062-8266 ; 0587-2871
ISSN (online)	1547-3317
ISSN	1062-8266 ; 0587-2871
DOI	10.5326/JAAHA-MS-6892
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Article ; Online: The Haiti cholera epidemic: from surveillance to action.

Mari, Lorenzo

Pathogens and global health

2014 Volume 108, Issue 1, Page(s) 3

MeSH term(s)	Cholera/epidemiology ; Cholera/mortality ; Female ; Humans ; Male
Language	English
Publishing date	2014-02-17
Publishing country	England
Document type	Journal Article ; Comment
ZDB-ID	2625162-0
ISSN	2047-7732 ; 2047-7724
ISSN (online)	2047-7732
ISSN	2047-7724
DOI	10.1179/2047772413Z.000000000169
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Article ; Online: Data-driven analysis of amino acid change dynamics timely reveals SARS-CoV-2 variant emergence.

Bernasconi, Anna / Mari, Lorenzo / Casagrandi, Renato / Ceri, Stefano

Scientific reports

2021 Volume 11, Issue 1, Page(s) 21068

Abstract: Since its emergence in late 2019, the diffusion of SARS-CoV-2 is associated with the evolution of its viral genome. The co-occurrence of specific amino acid changes, collectively named 'virus variant', requires scrutiny (as variants may hugely impact the ...

Abstract	Since its emergence in late 2019, the diffusion of SARS-CoV-2 is associated with the evolution of its viral genome. The co-occurrence of specific amino acid changes, collectively named 'virus variant', requires scrutiny (as variants may hugely impact the agent's transmission, pathogenesis, or antigenicity); variant evolution is studied using phylogenetics. Yet, never has this problem been tackled by digging into data with ad hoc analysis techniques. Here we show that the emergence of variants can in fact be traced through data-driven methods, further capitalizing on the value of large collections of SARS-CoV-2 sequences. For all countries with sufficient data, we compute weekly counts of amino acid changes, unveil time-varying clusters of changes with similar-rapidly growing-dynamics, and then follow their evolution. Our method succeeds in timely associating clusters to variants of interest/concern, provided their change composition is well characterized. This allows us to detect variants' emergence, rise, peak, and eventual decline under competitive pressure of another variant. Our early warning system, exclusively relying on deposited sequences, shows the power of big data in this context, and concurs to calling for the wide spreading of public SARS-CoV-2 genome sequencing for improved surveillance and control of the COVID-19 pandemic.
MeSH term(s)	Amino Acids/metabolism ; COVID-19/prevention & control ; COVID-19/therapy ; COVID-19/virology ; Cluster Analysis ; Computational Biology/methods ; Data Mining ; Europe/epidemiology ; Genome, Viral ; Humans ; Japan/epidemiology ; Phylogeny ; SARS-CoV-2/genetics ; Time Factors ; United States/epidemiology
Chemical Substances	Amino Acids
Language	English
Publishing date	2021-10-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-00496-z
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Article ; Online: The dynamics of microplastics and associated contaminants: Data-driven Lagrangian and Eulerian modelling approaches in the Mediterranean Sea.

Guerrini, Federica / Mari, Lorenzo / Casagrandi, Renato

The Science of the total environment

2021 Volume 777, Page(s) 145944

Abstract: Plastic pollution is widespread in the global oceans, but at the same time several other types of hydrophobic pollutants contaminate the marine environment. As more and more evidence highlights, microplastics and polluting chemicals are intertwined via ... ...

Abstract	Plastic pollution is widespread in the global oceans, but at the same time several other types of hydrophobic pollutants contaminate the marine environment. As more and more evidence highlights, microplastics and polluting chemicals are intertwined via adsorption/desorption processes. A thorough assessment of their total impact on marine ecosystems thus requires that these two kinds of pollution are not considered separately. Here we compare the outcomes of two complementary, data-driven modelling approaches for microplastic dispersal and for Plastic-Related Organic Pollutants (PROPs) in the marine environment. Focusing on the Mediterranean Sea, we simulate two years of Lagrangian particle tracking to map microplastic dispersion from the most impacting sources of pollution (i.e. coastal areas, the watersheds of major rivers, and fishing activities). Our particle sources are data-informed by national census data, hydrological regimes, and vessel tracking data to account for spatial and temporal variability of mismanaged plastic waste generation. These particle-based simulations are complemented with a simulation of the dynamics of primary pollutants in the sea, obtained via an advection-diffusion Eulerian model. While providing further understanding of the spatiotemporal distribution of microplastics and the dynamics of PROPs at a Mediterranean-wide scale, our results call for the development of novel integrated modelling approaches aimed at coupling the dynamics of microplastics with the chemical exchanges occurring through them, thus promoting a holistic description of marine plastic pollution.
Language	English
Publishing date	2021-02-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2021.145944
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Article ; Online: Modeling the contribution of antibody attack rates to single and dual helminth infections in a natural system.

Vanalli, Chiara / Mari, Lorenzo / Casagrandi, Renato / Boag, Brian / Gatto, Marino / Cattadori, Isabella M

Mathematical biosciences

2023 Volume 360, Page(s) 109010

Abstract: Within-host models of infection can provide important insights into the processes that affect parasite spread and persistence in host populations. However, modeling can be limited by the availability of empirical data, a problem commonly encountered in ... ...

Abstract	Within-host models of infection can provide important insights into the processes that affect parasite spread and persistence in host populations. However, modeling can be limited by the availability of empirical data, a problem commonly encountered in natural systems. Here, we used six years of immune-infection observations of two gastrointestinal helminths (Trichostrongylus retortaeformis and Graphidium strigosum) from a population of European rabbits (Oryctolagus cuniculus) to develop an age-dependent, mathematical model that explicitly included species-specific and cross-reacting antibody (IgA and IgG) responses to each helminth in hosts with single or dual infections. Different models of single infection were formally compared to test alternative mechanisms of parasite regulation. The two models that best described single infections of each helminth species were then coupled through antibody cross-immunity to examine how the presence of one species could alter the host immune response to, and the within-host dynamics of, the other species. For both single infections, model selection suggested that either IgA or IgG responses could equally explain the observed parasite intensities by host age. However, the antibody attack rate and affinity level changed between the two helminths, it was stronger against T. retortaeformis than against G. strigosum and caused contrasting age-intensity profiles. When the two helminths coinfect the same host, we found variation of the species-specific antibody response to both species together with an asymmetric cross-immune response driven by IgG. Lower attack rate and affinity of antibodies in dual than single infections contributed to the significant increase of both helminth intensities. By combining mathematical modeling with immuno-infection data, our work provides a tractable model framework for disentangling some of the complexities generated by host-parasite and parasite-parasite interactions in natural systems.
MeSH term(s)	Animals ; Rabbits ; Incidence ; Helminths/physiology ; Immunoglobulin G ; Immunoglobulin A ; Host-Parasite Interactions
Chemical Substances	Immunoglobulin G ; Immunoglobulin A
Language	English
Publishing date	2023-04-23
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1126-5
ISSN	1879-3134 ; 0025-5564
ISSN (online)	1879-3134
ISSN	0025-5564
DOI	10.1016/j.mbs.2023.109010
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Article: The dynamics of microplastics and associated contaminants: Data-driven Lagrangian and Eulerian modelling approaches in the Mediterranean Sea

Guerrini, Federica / Mari, Lorenzo / Casagrandi, Renato

Science of the total environment. 2021 July 10, v. 777

2021

Abstract	Plastic pollution is widespread in the global oceans, but at the same time several other types of hydrophobic pollutants contaminate the marine environment. As more and more evidence highlights, microplastics and polluting chemicals are intertwined via adsorption/desorption processes. A thorough assessment of their total impact on marine ecosystems thus requires that these two kinds of pollution are not considered separately. Here we compare the outcomes of two complementary, data-driven modelling approaches for microplastic dispersal and for Plastic-Related Organic Pollutants (PROPs) in the marine environment. Focusing on the Mediterranean Sea, we simulate two years of Lagrangian particle tracking to map microplastic dispersion from the most impacting sources of pollution (i.e. coastal areas, the watersheds of major rivers, and fishing activities). Our particle sources are data-informed by national census data, hydrological regimes, and vessel tracking data to account for spatial and temporal variability of mismanaged plastic waste generation. These particle-based simulations are complemented with a simulation of the dynamics of primary pollutants in the sea, obtained via an advection-diffusion Eulerian model. While providing further understanding of the spatiotemporal distribution of microplastics and the dynamics of PROPs at a Mediterranean-wide scale, our results call for the development of novel integrated modelling approaches aimed at coupling the dynamics of microplastics with the chemical exchanges occurring through them, thus promoting a holistic description of marine plastic pollution.
Keywords	adsorption ; census data ; desorption ; hydrology ; hydrophobicity ; marine environment ; microplastics ; models ; pollution ; temporal variation ; Mediterranean Sea
Language	English
Dates of publication	2021-0710
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2021.145944
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Article ; Online: The enemy of my enemy is my friend: Immune‐mediated facilitation contributes to fitness of co‐infecting helminths

Dagostin, Francesca / Vanalli, Chiara / Boag, Brian / Casagrandi, Renato / Gatto, Marino / Mari, Lorenzo / Cattadori, Isabella M.

Journal of Animal Ecology. 2023 Feb., v. 92, no. 2 p.477-491

2023

Abstract: The conceptual understanding of immune‐mediated interactions between parasites is rooted in the theory of community ecology. One of the limitations of this approach is that most of the theory and empirical evidence has focused on resource or immune‐ ... ...

Abstract	The conceptual understanding of immune‐mediated interactions between parasites is rooted in the theory of community ecology. One of the limitations of this approach is that most of the theory and empirical evidence has focused on resource or immune‐mediated competition between parasites and yet there is ample evidence of positive interactions that could be generated by immune‐mediated facilitation. We developed an immuno‐epidemiological model and applied it to long‐term data of two gastrointestinal helminths in two rabbit populations to investigate, through model testing, how immune‐mediated mechanisms of parasite regulation could explain the higher intensities of both helminths in rabbits with dual than single infections. The model framework was selected and calibrated on rabbit population A and then validated on the nearby rabbit population B to confirm the consistency of the findings and the generality of the mechanisms. Simulations suggested that the higher intensities in rabbits with dual infections could be explained by a weakened or low species‐specific IgA response and an asymmetric IgA cross‐reaction. Simulations also indicated that rabbits with dual infections shed more free‐living stages that survived for longer in the environment, implying greater transmission than stages from hosts with single infections. Temperature and humidity selectively affected the free‐living stages of the two helminths. These patterns were comparable in the two rabbit populations and support the hypothesis that immune‐mediated facilitation can contribute to greater parasite fitness and local persistence.
Keywords	animal ecology ; community ecology ; cross reaction ; gastrointestinal system ; helminths ; humidity ; mixed infection ; models ; rabbits ; temperature
Language	English
Dates of publication	2023-02
Size	p. 477-491.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	3024-7
ISSN	1365-2656 ; 0021-8790
ISSN (online)	1365-2656
ISSN	0021-8790
DOI	10.1111/1365-2656.13863
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Article ; Online: Epidemicity of cholera spread and the fate of infection control measures.

Trevisin, Cristiano / Lemaitre, Joseph C / Mari, Lorenzo / Pasetto, Damiano / Gatto, Marino / Rinaldo, Andrea

Journal of the Royal Society, Interface

2022 Volume 19, Issue 188, Page(s) 20210844

Abstract: The fate of ongoing infectious disease outbreaks is predicted through reproduction numbers, defining the long-term establishment of the infection, and epidemicity indices, tackling the reactivity of the infectious pool to new contagions. Prognostic ... ...

Abstract	The fate of ongoing infectious disease outbreaks is predicted through reproduction numbers, defining the long-term establishment of the infection, and epidemicity indices, tackling the reactivity of the infectious pool to new contagions. Prognostic metrics of unfolding outbreaks are of particular importance when designing adaptive emergency interventions facing real-time assimilation of epidemiological evidence. Our aim here is twofold. First, we propose a novel form of the epidemicity index for the characterization of cholera epidemics in spatial models of disease spread. Second, we examine in hindsight the survey of infections, treatments and containment measures carried out for the now extinct 2010-2019 Haiti cholera outbreak, to suggest that magnitude and timing of non-pharmaceutical and vaccination interventions imply epidemiological responses recapped by the evolution of epidemicity indices. Achieving negative epidemicity greatly accelerates fading of infections and thus proves a worthwhile target of containment measures. We also show that, in our model, effective reproduction numbers and epidemicity indices are explicitly related. Therefore, providing an upper bound to the effective reproduction number (significantly lower than the unit threshold) warrants negative epidemicity and, in turn, a rapidly fading outbreak preventing coalescence of sparse local sub-threshold flare-ups.
MeSH term(s)	Basic Reproduction Number ; Cholera/epidemiology ; Cholera/prevention & control ; Disease Outbreaks/prevention & control ; Epidemics ; Haiti/epidemiology ; Humans ; Infection Control
Language	English
Publishing date	2022-03-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2156283-0
ISSN	1742-5662 ; 1742-5689
ISSN (online)	1742-5662
ISSN	1742-5689
DOI	10.1098/rsif.2021.0844
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