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| Open AccessReservoir displacement by an invasive rodent reduces Lassa virus zoonotic spillover risk
Mastomys natalensis is a rodent species native to West Africa that is the primary reservoir host for Lassa virus. Here, the authors investigate whether the invasive rodent Rattus rattus decreases M. natalensis density and could therefore indirectly decrease zoonotic transmission of Lassa virus to humans.
- Evan A. Eskew
- , Brian H. Bird
- & Scott L. Nuismer
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Article
| Open AccessFine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
Here, the authors perform large trans-ancestry fine-mapping analyses identifying large numbers of association signals and putative target genes for colorectal cancer risk, advancing our understanding of the genetic and biological basis of this cancer.
- Zhishan Chen
- , Xingyi Guo
- & Wei Zheng
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Article
| Open AccessThe airborne transmission of viruses causes tight transmission bottlenecks
Genomic analyses have indicated that a small number of virus particles usually found new infections. Here, the authors use a mathematical model to show that this small transmission bottleneck is a result of the physical processes of airborne virus emission, diffusion, and inhalation.
- Patrick Sinclair
- , Lei Zhao
- & Christopher J. R. Illingworth
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Article
| Open AccessTravel surveillance uncovers dengue virus dynamics and introductions in the Caribbean
Dengue is a major public health concern in the Americas, and the Caribbean can be a source for reintroduction and spread. Here, the authors use travel surveillance data and genomic epidemiology to reconstruct Dengue epidemic dynamics in the Caribbean from 2009-2022.
- Emma Taylor-Salmon
- , Verity Hill
- & Nathan D. Grubaugh
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Article
| Open AccessAmbient carbon dioxide concentration correlates with SARS-CoV-2 aerostability and infection risk
Carbon dioxide concentration has previously been used as a proxy for overall ventilation efficiency to indirectly estimate the risk of indoor SARS-CoV-2 transmission. Here, authors investigate whether the concentration of carbon dioxide also has a direct mechanistic role in improving transmission efficiency.
- Allen Haddrell
- , Henry Oswin
- & Jonathan P. Reid
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Article
| Open AccessOverlapping Streptococcus pyogenes and Streptococcus dysgalactiae subspecies equisimilis household transmission and mobile genetic element exchange
Streptococcus dysgalactiae subsp. equisimilis is closely related to Streptococcus pyogenes and colonises the same sites in humans. This study examines cross-species transmission interactions and genetic exchange in a high disease burden setting.
- Ouli Xie
- , Cameron Zachreson
- & Steven Y. C. Tong
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Article
| Open AccessLong-term monitoring of SARS-CoV-2 seroprevalence and variants in Ethiopia provides prediction for immunity and cross-immunity
Detailed data on SARS-CoV-2 dynamics in Africa remain limited. Here, the authors use longitudinal serology and SARS-CoV-2 sequencing data from Ethiopia between August 2020 and July 2022 to characterise circulating variants, identify infection pathways, and explore cross-immunity properties.
- Simon Merkt
- , Solomon Ali
- & Andreas Wieser
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Article
| Open AccessEstimating the effects of temperature on transmission of the human malaria parasite, Plasmodium falciparum
Malaria transmission is affected by temperature but this relationship is not well characterised. Here, the authors experimentally determine the effect of temperature on parasite development in the mosquito and model how it impacts malaria transmission in Kenya under current and future climate scenarios.
- Eunho Suh
- , Isaac J. Stopard
- & Matthew B. Thomas
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Article
| Open AccessDeviations in RSV epidemiological patterns and population structures in the United States following the COVID-19 pandemic
Non-pharmaceutical interventions for COVID-19 also impacted the transmission of other viruses including respiratory syncytial virus (RSV). Here the authors describe the changing epidemiology, clinical severity, and genetic diversity of RSV in Chicago, Illinois, from July 2010 to April 2023.
- Estefany Rios-Guzman
- , Lacy M. Simons
- & Judd F. Hultquist
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Article
| Open AccessPerinatal outcomes after admission with COVID-19 in pregnancy: a UK national cohort study
The impacts of maternal SARS-CoV-2 infection on newborns are not well understood. Here, the authors perform a national cohort study using data on births in the UK from March 2020—March 2022 and find that moderate to severe maternal COVID-19 was associated with adverse perinatal outcomes.
- Hilde Marie Engjom
- , Rema Ramakrishnan
- & Marian Knight
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Article
| Open AccessEpidemiological, clinical, and genomic landscape of coccidioidomycosis in northeastern Brazil
Coccidioidomycosis, a WHO-listed mycosis, is neglected in South America. Analysis of 292 cases in Brazil, often tied to armadillo hunting, unveils unique disease patterns, environmental factors and pathogen genetics causing the disease.
- Kelsen Dantas Eulálio
- , Daniel R. Kollath
- & Marcus de Melo Teixeira
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Article
| Open AccessThe recent rapid expansion of multidrug resistant Ural lineage Mycobacterium tuberculosis in Moldova
Chitwood et al. report on the rapid expansion of a Ural-lineage multidrug resistant strain of Mycobacterium tuberculosis in Moldova. This strain has an estimated reproduction number more than two times greater than otherwise similar drug susceptible strains.
- Melanie H. Chitwood
- , Caroline Colijn
- & Benjamin Sobkowiak
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Article
| Open AccessOrigin and dispersal history of Hepatitis B virus in Eastern Eurasia
Hepatitis B virus is an ancient human pathogen that dates back more than 10,000 years. Here, the authors investigate the evolutionary history of the virus in Eastern Eurasia by sequencing 34 genomes dating from approximately 400–5,000 years ago and comparing them with other contemporary sequences.
- Bing Sun
- , Aida Andrades Valtueña
- & Yinqiu Cui
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Article
| Open AccessConcomitant medication, comorbidity and survival in patients with breast cancer
Preliminary epidemiological evidence suggests that some non-cancer medications may affect breast cancer risk, recurrence, and survival. In this study, the authors utilized a nationwide database of breast cancer patients to estimate the association between frequently used drugs taken prior to diagnosis and breast cancer prognosis. And they identified 16 drugs associated with breast cancer outcomes.
- Elise Dumas
- , Beatriz Grandal Rejo
- & Anne-Sophie Hamy
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Article
| Open AccessMaternal hybrid immunity and risk of infant COVID-19 hospitalizations: national case-control study in Israel
Maternal anti-SARS-CoV-2 antibodies can provide protection against severe COVID-19 in infants, but the relative protection conferred by maternal infection, vaccination, and hybrid immunity is unknown. Here, the authors use data from Israel and show that infants born to mothers with hybrid immunity had lowest rates of COVID-19 hospitalisation.
- Joshua Guedalia
- , Michal Lipschuetz
- & Ofer Beharier
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Article
| Open AccessIncident allergic diseases in post-COVID-19 condition: multinational cohort studies from South Korea, Japan and the UK
SARS-CoV-2 infection has been linked to various persistent or new-onset health consequences, including disruption of the immune system. Here, the authors investigate the risk of new-onset allergic diseases following SARS-CoV-2 infection using data from South Korea, Japan, and the UK.
- Jiyeon Oh
- , Myeongcheol Lee
- & Dong Keon Yon
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Perspective
| Open AccessEcological countermeasures to prevent pathogen spillover and subsequent pandemics
In this Perspective, the authors discuss the importance of preventing zoonotic spillover to prevent pandemics. They highlight mechanisms by which environmental changes can enable spillover, identify ecological interventions for spillover prevention and suggest policy frameworks through which interventions can be implemented.
- Raina K. Plowright
- , Aliyu N. Ahmed
- & Annika T. H. Keeley
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Article
| Open AccessPredictive evolutionary modelling for influenza virus by site-based dynamics of mutations
Seasonal influenza vaccine effectiveness depends on including virus strains in the vaccine that closely match those circulating in the upcoming season. In this study, the authors develop a computational model of influenza virus evolution to predict future circulating strains and therefore support vaccine strain selection.
- Jingzhi Lou
- , Weiwen Liang
- & Maggie Haitian Wang
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Article
| Open AccessElevated blood remnant cholesterol and triglycerides are causally related to the risks of cardiometabolic multimorbidity
Dysmetabolism of triglyceride-rich lipoproteins is considered a shared risk factor for cardiometabolic diseases, but their associations with cardiometabolic multimorbidity have not been fully understood. Here, the authors show that elevated levels of remnant cholesterol and triglycerides were observationally and genetically associated with a higher risk of cardiometabolic multimorbidity.
- Yimin Zhao
- , Zhenhuang Zhuang
- & Tao Huang
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Article
| Open AccessGenomic malaria surveillance of antenatal care users detects reduced transmission following elimination interventions in Mozambique
Routine sampling of pregnant women at first antenatal care (ANC) visits could be used for malaria surveillance. Here, the authors compare the genetic structure of Plasmodium falciparum parasite populations between samples from first ANC users and children from the community in Mozambique, and show that it can inform about changes in transmission beyond epidemiological data.
- Nanna Brokhattingen
- , Glória Matambisso
- & Alfredo Mayor
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Article
| Open AccessUptake of COVID-19 vaccinations amongst 3,433,483 children and young people: meta-analysis of UK prospective cohorts
COVID-19 vaccination has been recommended for children and young people (aged 5–17) in the UK since 2021/2022. In this study, the authors use linked health and administrative data to estimate vaccine uptake in this age group and show that age and adult household vaccination status are associated with uptake.
- Sarah J. Aldridge
- , Utkarsh Agrawal
- & Rhiannon K. Owen
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Article
| Open AccessThe decline of the 2022 Italian mpox epidemic: Role of behavior changes and control strategies
Mpox cases in Italy rapidly declined following a peak in summer 2022. Here, the authors investigate potential reasons for the decline in cases using an individual-based model of a sexual contact network of men who have sex with men.
- Giorgio Guzzetta
- , Valentina Marziano
- & Stefano Merler
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Article
| Open AccessImpact of vaccination on the association of COVID-19 with cardiovascular diseases: An OpenSAFELY cohort study
SARS-CoV-2 infection is associated with an increased risk of arterial and venous thrombotic events. Here, the authors investigate the degree to which this association is modified by virus variant and vaccination using electronic health record data for ~18 million adults in England.
- Genevieve I. Cezard
- , Rachel E. Denholm
- & Venexia Walker
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Article
| Open AccessUnderstanding the infection severity and epidemiological characteristics of mpox in the UK
Mpox cases without known travel links to endemic countries began to be detected in the UK in mid-2022. In this study, the authors characterise the severity of mpox cases in the UK and estimate the overall infection hospitalisation risk at ~4%.
- Thomas Ward
- , Christopher E. Overton
- & Martyn Fyles
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Article
| Open AccessDrivers and impact of the early silent invasion of SARS-CoV-2 Alpha
The SARS-CoV-2 Alpha variant of concern emerged in the UK in late 2020 but spread internationally before it was detected. Here, the authors reconstruct the dynamics of dissemination of this variant out of the UK by combining extent of genomic sequencing, travel volume, and local epidemic dynamics in a Bayesian model.
- Benjamin Faucher
- , Chiara E. Sabbatini
- & Chiara Poletto
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Article
| Open AccessDeep learning model for personalized prediction of positive MRSA culture using time-series electronic health records
Identification of patients at high risk of methicillin-resistant Staphylococcus aureus (MRSA) infection could improve treatment outcomes by optimising antimicrobial therapy. Here the authors develop a deep learning model that uses electronic health record data from the United States to predict MRSA culture positivity.
- Masayuki Nigo
- , Laila Rasmy
- & Degui Zhi
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Article
| Open AccessComparing frequency of booster vaccination to prevent severe COVID-19 by risk group in the United States
The optimal frequency of COVID-19 booster vaccination is unclear. Here, the authors use a microsimulation model to assess the impact of different vaccine schedules on severe disease and show that regular boosters have large benefits for older and immunocompromised individuals but less so for younger age groups.
- Hailey J. Park
- , Gregg S. Gonsalves
- & Nathan C. Lo
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Article
| Open AccessInequalities in healthcare use during the COVID-19 pandemic
An indirect impact of the COVID-19 pandemic was a decline in healthcare utilisation for other conditions. Here, the authors quantify this decline in the Netherlands and show that impacts were greater for individuals with lower household income, females, older people, and those with a migrant background.
- Arun Frey
- , Andrea M. Tilstra
- & Mark D. Verhagen
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Article
| Open AccessDispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean
Genomic surveillance has been important for tracking the evolution and spread of SARS-CoV-2. Here, the authors analyse ~300,000 SARS-CoV-2 genomes from two years of sequencing in the Latin America and Caribbean regions and describe the emergence and spread of different lineages over time.
- Tiago Gräf
- , Alexander A. Martinez
- & Juliana Almeida Leite
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Article
| Open AccessPersistence in risk and effect of COVID-19 vaccination on long-term health consequences after SARS-CoV-2 infection
The long-term health consequences of COVID-19 infection are not fully understood. In this retrospective cohort study from Hong Kong, the authors describe changes in the risk of various clinical outcomes including all-cause mortality for one year following COVID-19 infection and how they vary by vaccination status.
- Ivan Chun Hang Lam
- , Ran Zhang
- & Eric Yuk Fai Wan
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Matters Arising
| Open AccessDaylight saving time and mortality—proceed with caution
- Elizabeth B. Klerman
- , Matthew D. Weaver
- & Karin G. Johnson
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Article
| Open AccessWASH interventions and child diarrhea at the interface of climate and socioeconomic position in Bangladesh
Household water, sanitation, and handwashing (WASH) interventions can reduce diarrhoea-related morbidity in young children. Here, the authors report findings from a pre-specified secondary analysis of a cluster-randomised trial assessing how WASH impacts vary by socioeconomic position and season.
- Pearl Anne Ante-Testard
- , Francois Rerolle
- & Benjamin F. Arnold
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Article
| Open AccessDemographic and Clinical Factors Associated With SARS-CoV-2 Spike 1 Antibody Response Among Vaccinated US Adults: the C4R Study
The antibody response to COVID-19 vaccines varies among individuals. Here the authors find that older age, male sex, smoking, higher BMI, vaccine type, and certain comorbidities are associated with lower anti-S1 antibody levels after COVID-19 vaccinations, indicating that certain groups might benefit from higher frequency or doses of vaccination.
- John S. Kim
- , Yifei Sun
- & Elizabeth C. Oelsner
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Article
| Open AccessLeisure engagement in older age is related to objective and subjective experiences of aging
The benefits of different leisure activities for different aspects of aging remain unclear. Here, authors show that performing physical or creative activities is associated with important aging metrics and could help to prevent age-related decline.
- Jessica K. Bone
- , Feifei Bu
- & Daisy Fancourt
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Article
| Open AccessAssessing emergence risk of double-resistant and triple-resistant genotypes of Plasmodium falciparum
Emergence of malaria parasites resistant to artemisinin has prompted the need for new drug regimens to ensure effective treatment. In this simulation study, the authors evaluate the risk of multidrug resistance under regimens with either concurrent or cyclic use of different first-line therapies.
- Eric Zhewen Li
- , Tran Dang Nguyen
- & Maciej F. Boni
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Article
| Open AccessGenomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli ST131 associated with bacteraemia in Wales
Escherichia coli ST131 is a globally dominant multidrug resistant clone associated with high rates of recurring urinary tract infections. In this genomic epidemiology study, the authors describe the evolution, population structure, and antimicrobial resistance in 142 E. coli ST131 samples from Wales, UK.
- Rhys T. White
- , Matthew J. Bull
- & Scott A. Beatson
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Article
| Open AccessIncome determines the impact of cash transfers on HIV/AIDS: cohort study of 22.7 million Brazilians
Brazil has operated a conditional cash transfer program to support families living in precarious conditions since 2004. Here, the authors use linked administrative and health data to investigate the impacts of the program on HIV/AIDS-related outcomes, demonstrating strong positive associations.
- Andréa F. Silva
- , Inês Dourado
- & Davide Rasella
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Article
| Open AccessComparative effectiveness of alternative intervals between first and second doses of the mRNA COVID-19 vaccines
The optimal timing between first and second mRNA COVID-19 vaccine doses has not been established. Here, the authors use electronic health record data from Georgia, USA in a target trial emulation study to estimate vaccine effectiveness against infection for different dose intervals.
- Kayoko Shioda
- , Alexander Breskin
- & Elizabeth T. Rogawski McQuade
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Article
| Open AccessDisease clusters subsequent to anxiety and stress-related disorders and their genetic determinants
In this study, the authors found five disease clusters associated with a prior diagnosis of anxiety/stress-related disorders, and identified several underlying genetic components. These findings may aid mechanistic exploration and risk management for health decline among those patients.
- Xin Han
- , Qing Shen
- & Huan Song
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Article
| Open AccessContribution of climate change to the spatial expansion of West Nile virus in Europe
West Nile Virus is emerging as an important pathogen in Europe, likely driven by recent climate and land-use changes. Here, the authors estimate the extent of the climate change-driven impact by modelling the change in West Nile Virus ecological suitability across the continent in the absence of climate change.
- Diana Erazo
- , Luke Grant
- & Simon Dellicour
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Article
| Open AccessPredicting the risk and speed of drug resistance emerging in soil-transmitted helminths during preventive chemotherapy
Resistance to chemotherapy for soil-transmitted helminth infection has been detected in veterinary settings but not yet in human infections. Here, the authors investigate the risk of resistance in humans and how it may change as a result of scaling-up preventative deworming programs.
- Luc E. Coffeng
- , Wilma A. Stolk
- & Sake J. de Vlas
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Article
| Open AccessGeographic pair matching in large-scale cluster randomized trials
Geographic location can be a key determinant of human health outcomes. Here, the authors show that in large-scale trials, randomization that is pair matched by geography can lead to substantial improvements in statistical efficiency and enable insights into spatially varying intervention effects.
- Benjamin F. Arnold
- , Francois Rerolle
- & Jade Benjamin-Chung
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Article
| Open AccessRisk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population
The factors influencing risk of reinfection with SARS-CoV-2 are poorly understood. Here, the authors use data from the UK COVID-19 Infection Survey, a community based longitudinal study, to assess characteristics of ~45,000 reinfections compared to initial infections.
- Jia Wei
- , Nicole Stoesser
- & Chris Cunningham
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Article
| Open AccessMaternal pertussis immunization and the blunting of routine vaccine effectiveness: a meta-analysis and modeling study
Pertussis immunisation for pregnant women has been introduced to protect newborns, but immunological evidence suggests that this lessens subsequent infant immune response to vaccination. Here, the authors assess the epidemiological impacts of both consequences of maternal immunisation on infant infection.
- Michael Briga
- , Elizabeth Goult
- & Matthieu Domenech de Cellès
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Article
| Open AccessGlobal surveillance of antimicrobial resistance in food animals using priority drugs maps
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
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Article
| Open AccessRespiratory distress in SARS-CoV-2 exposed uninfected neonates followed in the COVID Outcomes in Mother-Infant Pairs (COMP) Study
Unusually high rates of respiratory distress were observed in infants following in utero exposure to SARS-CoV-2. Here the authors find, in a longitudinal cohort of infants born to persons infected with SARS-CoV-2 during pregnancy, that maternal vaccination is associated with a lower odds of infant respiratory distress.
- Olivia M. Man
- , Tamiris Azamor
- & Karin Nielsen-Saines
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Article
| Open AccessUsing big sequencing data to identify chronic SARS-Coronavirus-2 infections
Chronic SARS-CoV-2 infections have been hypothesised to be sources of new variants. Here, the authors use large-scale genome sequencing data to identify mutations predictive of chronic infections, which may therefore be relevant in future variants.
- Sheri Harari
- , Danielle Miller
- & Adi Stern
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Article
| Open AccessShifting patterns of dengue three years after Zika virus emergence in Brazil
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
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Article
| Open AccessMarkets as drivers of selection for highly virulent poultry pathogens
Live poultry markets in rural areas can be hotspots for transmission of pathogens, but the effects of markets on selection of viral virulence are not known. This study demonstrates through mathematical modelling that high turnover rate and persistence of viral particles can select for highly virulent pathogens in markets.
- Justin K. Sheen
- , Fidisoa Rasambainarivo
- & C. Jessica E. Metcalf