Ecological epidemiology articles within Nature Communications

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  • Article
    | Open Access

    Temperature and absolute humidity are associated with influenza activity, and recent data from Hong Kong have suggested ozone as an additional environmental driver. Here, the authors investigate the relationship between ozone and influenza transmission using surveillance data from the USA and find evidence for an inhibitory effect.

    • Fang Guo
    • , Pei Zhang
    •  & Linwei Tian

  • Article
    | Open Access

    Human encroachment into nature alters species communities and can lead to changes in disease dynamics. Here, Meyer et al. find that coronavirus prevalence increased in less diverse bat communities, which were dominated by susceptible host species.

    • Magdalena Meyer
    • , Dominik W. Melville
    •  & Simone Sommer

  • Article
    | Open Access

    Highly pathogenic avian influenza virus subtype H5 is an important pathogen of wild birds and poultry that has also caused infection in humans and other mammals. Here the authors use wild bird movement tracking data and virus genome sequences to quantify how seasonal bird migration facilitates global dispersal of the virus.

    • Qiqi Yang
    • , Ben Wang
    •  & Bryan Grenfell

  • Article
    | Open Access

    Monitoring antimicrobial resistance in food animals is challenging due to limited surveillance systems. Here, the authors combine data from point prevalence surveys in lower- and middle-income settings to map resistance to seven antimicrobials and predict which are likely to exceed key resistance thresholds.

    • Cheng Zhao
    • , Yu Wang
    •  & Thomas P. Van Boeckel

  • Article
    | Open Access

    Dengue virus circulation was unusually low in Brazil in 2015-2018 following the emergence of Zika virus, but subsequently resurged causing large outbreaks with a lower mean age of infection. Here, the authors use mathematical modelling to investigate the links between dengue dynamics and prior Zika infection.

    • Francesco Pinotti
    • , Marta Giovanetti
    •  & José Lourenço

  • Article
    | Open Access

    The SARS-CoV-2 Omicron lineage XBB/XBB.1.5 became the leading cause of new infections in the US in January 2023. Here, the authors use testing and hospitalisation data and show that this variant has increased ability to evade infection-derived immunity but enhanced vaccine sensitivity.

    • Joseph A. Lewnard
    • , Vennis Hong
    •  & Sara Y. Tartof

  • Article
    | Open Access

    Certain bats species have previously been identified as ancestral sources of coronaviruses that infect humans but there is limited data on the genomic diversity or zoonotic potential of viruses infecting bats in the UK. Here, the authors use deep sequencing and in vitro assays to characterise coronaviruses recovered from 48 bat faecal samples.

    • Cedric C. S. Tan
    • , Jahcub Trew
    •  & Vincent Savolainen

  • Article
    | Open Access

    The emerging fungal pathogen Bsal is a potential threat for amphibians. Here, the authors use data from dose-response experiments on 35 species to assess vulnerability of North American amphibians to Bsal and identify species and areas potentially at risk.

    • Matthew J. Gray
    • , Edward Davis Carter
    •  & Debra L. Miller

  • Article
    | Open Access

    Cooperative disease defense is part of group-level collective behavior. Here, the authors explore individual decisions, finding that garden ants increase grooming highly infectious individuals when they perceive a high pathogen load and suppress grooming after having been groomed by nestmates.

    • Barbara Casillas-Pérez
    • , Katarína Boďová
    •  & Sylvia Cremer

  • Article
    | Open Access

    Many rodent species are known as hosts of zoonotic pathogens, but the ecological conditions that trigger spillover are not well-understood. Here, the authors show that population fluctuations and association with human-dominated habitats explain the zoonotic reservoir status of rodents globally.

    • Frauke Ecke
    • , Barbara A. Han
    •  & Richard S. Ostfeld

  • Article
    | Open Access

    The ecological and evolutionary impacts of disease vary in spatially structured populations. Here, the authors study ~4000 populations of Plantago lanceolata and find that resistance evolution depends on both disease history and population structure, with isolated populations more susceptible to fungal disease.

    • Layla Höckerstedt
    • , Elina Numminen
    •  & Anna-Liisa Laine

  • Article
    | Open Access

    Coronaviruses may spill over from bats to humans. This study uses epidemiological data, species distribution models, and probabilistic risk assessment to map overlap among people and SARSr-CoV bat hosts and estimate how many people are infected with bat-origin SARSr-CoVs in Southeast Asia annually.

    • Cecilia A. Sánchez
    • , Hongying Li
    •  & Peter Daszak

  • Article
    | Open Access

    Estimating the effectiveness of malaria vector control interventions has typically relied on resource-intensive cluster randomised trials. Here, the authors estimate changes in malaria prevalence using entomological data from experimental hut trials, which may provide an alternative route to approval of interventions in some situations.

    • Ellie Sherrard-Smith
    • , Corine Ngufor
    •  & Thomas S. Churcher

  • Article
    | Open Access

    Alien species invasions are thought to be important to zoonotic diseases through the introduction of both existing and novel pathogens to invaded ranges. Using data from 795 established alien animals and 10,473 zoonosis events worldwide, this study examines the role of alien zoonotic hosts on zoonosis emergences after accounting for climate, propagule pressure, global change and sampling bias.

    • Lin Zhang
    • , Jason Rohr
    •  & Xuan Liu

  • Article
    | Open Access

    Population density can influence the dynamics of emerging infections, but the specific effects at a local (within-city) level are not well understood. Here, the authors investigate the influence of population density on dynamics of dengue outbreaks in Rio de Janeiro and propose that this variable holds the key to how space should be aggregated.

    • Victoria Romeo-Aznar
    • , Laís Picinini Freitas
    •  & Mercedes Pascual

  • Article
    | Open Access

    Release of genetically-modified sterile mosquitoes is a potential method of malaria control but has yet to be tested in the field. Here, the authors perform a mark-release-recapture experiment and show that genetically-modified mosquitoes have reduced survival and dispersal compared to wild-types.

    • Franck Adama Yao
    • , Abdoul-Azize Millogo
    •  & Abdoulaye Diabaté

  • Article
    | Open Access

    Amid climate and land use changes, it is important to identify and monitor hotspots of animal activity where disease transmission can occur. Using experimental and observational methods in an East African savannah, this study shows water sources increase the concentration of faecal-oral parasites in the environment and that this effect is amplified in drier areas and following periods of low rainfall.

    • Georgia Titcomb
    • , John Naisikie Mantas
    •  & Hillary Young

  • Article
    | Open Access

    The skin disease chytridiomycosis is linked to global amphibian declines but effective mitigation measures require improved understanding of the mechanisms underpinning the disease ecology. This study identifies key mediators of interactions between the fungal pathogen and amphibian skin, providing a marker of host colonization that can predict susceptibility between amphibian species.

    • Yu Wang
    • , Elin Verbrugghe
    •  & An Martel

  • Article
    | Open Access

    Lassa Fever is a rodent-borne viral haemorrhagic fever that is a public health problem in West Africa. Here, the authors develop a spatiotemporal model of the socioecological drivers of disease using surveillance data from Nigeria, and find evidence of climate sensitivity.

    • David W. Redding
    • , Rory Gibb
    •  & Chikwe Ihekweazu

  • Article
    | Open Access

    Climate change is expected to have major impacts on forest tree diseases. Here the authors analyse long-term data of white pine blister rust in the southern Sierra Nevada, finding evidence of climate change-driven disease range expansion that was mediated by spatially varying host-pathogen-drought interactions.

    • Joan Dudney
    • , Claire E. Willing
    •  & John J. Battles

  • Article
    | Open Access

    Schistosomiasis control strategies rely on mass drug administration (MDA) using praziquantel. Here, Berger et al. perform whole-genome sequencing of larvae from infected children across Ugandan regions with differing MDA histories. They find extensive gene flow with limited positive selection suggesting minimal change post MDA.

    • Duncan J. Berger
    • , Thomas Crellen
    •  & James A. Cotton

  • Article
    | Open Access

    This study combines ethnobotanical and epidemiological data to understand how social networks of seed exchange influence the genetic structure of the African cassava mosaic virus in Gabon. Results reveal contrasted patterns of viral diversity in patrilineal and matrilineal communities, consistent with cultural differences in modes of seed exchange.

    • Marc Delêtre
    • , Jean-Michel Lett
    •  & Charles Spillane

  • Article
    | Open Access

    A more comprehensive map of viral host ranges can help identify and mitigate zoonotic and animal-disease risks. A divide-and-conquer approach which separates viral, mammalian and network features predicts over 20,000 unknown associations between known viruses and susceptible mammalian species.

    • Maya Wardeh
    • , Marcus S. C. Blagrove
    •  & Matthew Baylis

  • Article
    | Open Access

    The role of meteorological factors in SARS-COV-2 transmission is not well understood. Here, the authors use county-level data from the United States to the end of 2020 and find evidence of a moderate association between increased transmissibility and cold, dry weather and low ultraviolet radiation.

    • Yiqun Ma
    • , Sen Pei
    •  & Kai Chen

  • Article
    | Open Access

    Several prognostic indices are available to predict the long-term fate of emerging infectious diseases and the effect of their containment measures, including a variety of reproduction numbers. Here, the authors introduce the epidemicity index, a complementary index to evaluate the potential for transient increases of SARS-Cov-2 epidemics.

    • Lorenzo Mari
    • , Renato Casagrandi
    •  & Marino Gatto

  • Article
    | Open Access

    Indoor residual spraying (IRS) of insecticide is one of the primary malaria vector control initiatives, but implementation is limited. Here, the authors show that discontinuation of IRS in Uganda was associated with increased malaria incidence, and introduction of IRS was associated with decreased incidence.

    • Jane F. Namuganga
    • , Adrienne Epstein
    •  & Isabel Rodriguez-Barraquer

  • Article
    | Open Access

    There are stable relationships between diet and microbiome in humans and lab animals. A study on African buffalo finds that diet influences microbiome variation and enterotype formation. Three pathogens may associate with microbiome depending on host diet, suggesting nutrition impacts relationships between gut microbiome and host health.

    • Claire E. Couch
    • , Keaton Stagaman
    •  & Anna E. Jolles

  • Article
    | Open Access

    The effect of climate change on highland malaria transmission remains unclear because of increasing and decreasing trends. Here, Rodó et al. analyze malaria case data and climate data for the Ethiopian highlands from 1968 to 2008 and find that changes in temperature and associated climate variability facilitated the effect of interventions at the beginning of the 21st century.

    • Xavier Rodó
    • , Pamela P. Martinez
    •  & Mercedes Pascual

  • Article
    | Open Access

    The effects of climate on vector-borne disease systems are highly context-dependent. Here, the authors incorporate laboratory-measured physiological traits of the mosquito Aedes aegypti into climate-driven mechanistic models to predict number, timing, and duration of outbreaks in Ecuador and Kenya.

    • Jamie M. Caldwell
    • , A. Desiree LaBeaud
    •  & Erin A. Mordecai

  • Article
    | Open Access

    Ticks are an important vector of disease in China, posing threats to humans, livestock and wild animals. Here, Zhao et al. compile a database of the distributions of the 124 tick species known in China and 103 tick-borne pathogens and predict the additional suitable habitats for the predominant vector species.

    • Guo-Ping Zhao
    • , Yi-Xing Wang
    •  & Li-Qun Fang

  • Article
    | Open Access

    Homologous recombination between co-infecting coronaviruses can produce novel pathogens. Here, Wardeh et al. develop a machine learning approach to predict associations between mammals and multiple coronaviruses and hence estimate the potential for generation of novel coronaviruses by recombination.

    • Maya Wardeh
    • , Matthew Baylis
    •  & Marcus S. C. Blagrove

  • Article
    | Open Access

    Spread of SARS-CoV-2 in the early phase of the pandemic has been driven by high population susceptibility, but virus sensitivity to climate may play a role in future outbreaks. Here, the authors simulate SARS-CoV-2 dynamics in winter assuming climate dependence is similar to an endemic coronavirus strain.

    • Rachel E. Baker
    • , Wenchang Yang
    •  & Bryan T. Grenfell

  • Article
    | Open Access

    Here, Griffiths et al. show infection of 80–100% of sampled vampire bats in Peru with a newly discovered betaherpesvirus (DrBHV) that exhibits specificity within neotropical bats and evidence for superinfection. These data suggest that DrBHV could be a candidate for virally vectored vaccines that spread autonomously through a bat population.

    • Megan E. Griffiths
    • , Laura M. Bergner
    •  & Daniel G. Streicker

  • Comment
    | Open Access

    Early studies of weather, seasonality, and environmental influences on COVID-19 have yielded inconsistent and confusing results. To provide policy-makers and the public with meaningful and actionable environmentally-informed COVID-19 risk estimates, the research community must meet robust methodological and communication standards.

    • Benjamin F. Zaitchik
    • , Neville Sweijd
    •  & Xavier Rodó

  • Article
    | Open Access

    Classical epidemiological approaches have been limited in their ability to formally test hypotheses. Here, Dellicour et al. illustrate how phylodynamic and phylogeographic analyses can be leveraged for hypothesis testing in molecular epidemiology using West Nile virus in North America as an example.

    • Simon Dellicour
    • , Sebastian Lequime
    •  & Philippe Lemey

  • Article
    | Open Access

    The factors that determine whether pathogens co-occur in a host are poorly understood, especially for plant viruses. Here the authors conduct field experiments with the plant Plantago lanceolata and its viruses, showing that viral co-occurrences are driven predominantly by environmental context and host genotype rather than viral interactions.

    • Suvi Sallinen
    • , Anna Norberg
    •  & Anna-Liisa Laine

  • Article
    | Open Access

    The pathogen Batrachochytrium dendrobatidis (BD) associated with widespread amphibian declines is present in Europe but has not consistently caused disease-induced declines in that region. Here, the authors suggest that an endemic strain of BD with low virulence may protect the hosts upon co-infection with more virulent strains.

    • Mark S. Greener
    • , Elin Verbrugghe
    •  & An Martel

  • Article
    | Open Access

    Spatiotemporal sampling gaps in existing pathogen genomic data limits their use in understanding epidemiological patterns. Here, the authors apply a phylogeographic approach with SARS-CoV-2 genomes to accurately reproduce pathogen spread by accounting for spatial biases and travel history of the individual.

    • Philippe Lemey
    • , Samuel L. Hong
    •  & Marc A. Suchard

  • Perspective
    | Open Access

    In this Perspective, the authors review the different applications for mobile phone data to support COVID-19 pandemic response, the relevance of these applications for infectious disease transmission and control, and potential sources and implications of selection bias in mobile phone data.

    • Kyra H. Grantz
    • , Hannah R. Meredith
    •  & Amy Wesolowski

  • Article
    | Open Access

    Rarely are the outcomes of mathematical (probability) models of wildlife disease detection used to inform policy or management changes. Here the authors develop a proactive hunting surveillance program that shortened the time required to establish freedom from chronic wasting disease at the population level in reindeer.

    • Atle Mysterud
    • , Petter Hopp
    •  & Hildegunn Viljugrein

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