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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
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Article
| Open AccessDeterminants of epidemic size and the impacts of lulls in seasonal influenza virus circulation
Seasonal influenza levels were unusually low when non-pharmaceutical interventions for COVID-19 were in place. Here, the authors analyse serological and epidemiological evidence for the hypothesis that such lulls in influenza transmission lead to reduced immunity and therefore larger epidemics in subsequent seasons.
- Simon P. J. de Jong
- , Zandra C. Felix Garza
- & Colin A. Russell
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Article
| Open AccessA Machine Learning-Driven Virtual Biopsy System For Kidney Transplant Patients
Despite being recommended, day-zero biopsies are often not performed, due to the cost and time. Here, the authors show that machine learning and donor’s basic parameters can predict the biopsy, offering a reliable virtual estimation of the day-zero biopsy findings.
- Daniel Yoo
- , Gillian Divard
- & Alexandre Loupy
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Article
| Open AccessLarge scale plasma proteomics identifies novel proteins and protein networks associated with heart failure development
The pathobiology of heart failure (HF) is incompletely understood. The authors identify 37 circulating proteins and 5 protein modules associated with HF risk, with several demonstrating causal effects on HF, risk factors, or cardiac dysfunction by Mendelian randomization analysis.
- Amil M. Shah
- , Peder L. Myhre
- & Bing Yu
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Article
| Open AccessSystematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples
SARS-CoV-2 coinfections may lead to recombination events which could be important in the emergence of new variants. Here, the authors develop an automated bioinformatics pipeline to identify coinfections in genomic data and test it on >2 million publicly available raw read data sets collected globally.
- Orsolya Anna Pipek
- , Anna Medgyes-Horváth
- & István Csabai
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Article
| Open AccessConvergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China
Bacteria in the same environment can share genetic material but the extent to which this influences development of antimicrobial resistance is unclear. Here, the authors investigate the evidence for co-evolution of antimicrobial resistance in bacteria found coexisting in animals and the environment in chicken farms and slaughterhouses in China.
- Michelle Baker
- , Xibin Zhang
- & Tania Dottorini
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Article
| Open AccessRedirecting antibody responses from egg-adapted epitopes following repeat vaccination with recombinant or cell culture-based versus egg-based influenza vaccines
Here the authors report an exploratory analysis of a clinical trial that tested different influenza virus vaccination platforms. The results show that multiple seasons of recombinant or cell-based influenza vaccinations may be needed to redirect antibody responses away from immune memory to egg-adapted epitopes and refocus on epitopes on the circulating viruses.
- Feng Liu
- , F. Liaini Gross
- & Min Z. Levine
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Article
| Open AccessIncidence and transmission of respiratory syncytial virus in urban and rural South Africa, 2017-2018
Respiratory syncytial virus (RSV) causes a high burden of disease in children, particularly in lower- and middle-income countries. In this prospective household-based observational cohort study in South Africa, the authors estimate the incidence of RSV and identify risk factors for transmission.
- Cheryl Cohen
- , Jackie Kleynhans
- & Stefano Tempia
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Article
| Open AccessQuantitatively assessing early detection strategies for mitigating COVID-19 and future pandemics
Monitoring samples from hospital patients, wastewater, or air travel may enable early detection of pathogens. Here, the authors assess how these surveillance systems could have impacted detection of COVID-19 and their potential benefits for detection of other emerging pathogens.
- Andrew Bo Liu
- , Daniel Lee
- & Michael Springer
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Article
| Open AccessOptimal timing of nirmatrelvir/ritonavir treatment after COVID-19 symptom onset or diagnosis: target trial emulation
Nirmatrelvir/ritonavir can reduce COVID-19 severity when initiated within five days of symptom onset but the optimal timing within this window is unknown. Here, the authors emulate a randomised trial using electronic health records from Hong Kong and find evidence for a benefit of early treatment initiation.
- Carlos K. H. Wong
- , Jonathan J. Lau
- & Joseph T. Wu
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Article
| Open AccessDietary circadian rhythms and cardiovascular disease risk in the prospective NutriNet-Santé cohort
The relation between daily meal and fasting timing with cardiovascular disease incidence remains unclear. Here, authors show that a later daily meal timing is associated with increased cardiovascular disease risk, especially in women. This study suggests that adopting earlier daily eating patterns may be beneficial for cardiovascular prevention.
- Anna Palomar-Cros
- , Valentina A. Andreeva
- & Bernard Srour
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Article
| Open AccessBinge-pattern alcohol consumption and genetic risk as determinants of alcohol-related liver disease
Deaths from alcohol-related liver disease have sharply increased following the Covid-19 pandemic. Here, the authors show that binge-pattern alcohol consumption, genetic factors and the presence of diabetes mellitus confer the greatest risk, allowing targeted interventions for high-risk individuals.
- Chengyi Ding
- , Linda Ng Fat
- & Gautam Mehta
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Article
| Open AccessEffects of accelerometer-based sedentary time and physical activity on DEXA-measured fat mass in 6059 children
Childhood obesity remains a global epidemic. Here, using objective measurements, the authors show that sedentary time increased from 6 h/day in childhood to 9 h/day in young adulthood, and was cumulatively associated with increased total and trunk fat mass. Both light or moderate-to-vigorous physical activity similarly partly reversed risk.
- Andrew O. Agbaje
- , Wei Perng
- & Tomi-Pekka Tuomainen
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Article
| Open AccessTemperature-related death burden of various neurodegenerative diseases under climate warming: a nationwide modelling study
Examining non-optimal temperatures’ influence on neurodegenerative diseases amid climate warming is vital for public health. Here, the authors project a notable net increase of death burden from neurodegenerative diseases after the mid-21st century.
- Peng Yin
- , Ya Gao
- & Haidong Kan
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Article
| Open AccessPhylogeny and molecular evolution of the first local monkeypox virus cluster in Guangdong Province, China
The first known local mpox outbreak in Guangdong Province, China occurred in June 2023. Here, the authors perform phylogenetic and molecular evolution analysis of ten mpox virus genome sequences from this outbreak, and place them in the context of other samples detected in surrounding regions.
- Jianhai Yu
- , Xin Zhang
- & Baisheng Li
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Article
| Open AccessInteractions between climate change, urban infrastructure and mobility are driving dengue emergence in Vietnam
The geographic distribution of dengue has been expanding in recent decades, and Vietnam is one of the most severely affected countries. In this study, the authors use Bayesian hierarchical modelling to investigate the socio-environmental and climatic drivers of dengue incidence in Vietnam and how they vary across the country.
- Rory Gibb
- , Felipe J. Colón-González
- & Rachel Lowe
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Article
| Open AccessHigh-throughput target trial emulation for Alzheimer’s disease drug repurposing with real-world data
Target trial emulation (TTE) simulates randomized controlled trials using real world data (RWD). Here, authors show the effectiveness of different TTE strategies to identify drug candidates that could be potentially repurposed to Alzheimer’s disease using two large scale RWD warehouses.
- Chengxi Zang
- , Hao Zhang
- & Fei Wang
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Article
| Open AccessEstimating the potential impact and diagnostic requirements for SARS-CoV-2 test-and-treat programs
Antivirals are now available for treating COVID-19 but must be used early in the course of infection to be effective. Here, the authors use mathematical modelling to assess the potential public health impacts of antiviral use considering different levels of testing and country sociodemographic characteristics.
- Alvin X. Han
- , Emma Hannay
- & Colin A. Russell
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Article
| Open AccessTrue prevalence of long-COVID in a nationwide, population cohort study
Determining the prevalence of Long COVID is challenging because many symptoms attributed to the syndrome could have other causes. Here, the authors estimate the prevalence of Long COVID in Scotland by comparing rates of symptoms reported by people with and without history of SARS-CoV-2 infection.
- Claire E. Hastie
- , David J. Lowe
- & Jill P. Pell
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Article
| Open AccessUtilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems
COVID-19 has impacted health systems unequally and widespread SARS-CoV-2 testing for community surveillance has been limited globally. This work in Malawi highlights how river and wastewater can be used to detect emerging SARS-CoV-2 waves, identify variants of concern, and provide an early warning system.
- Kayla G. Barnes
- , Joshua I. Levy
- & Nicholas Feasey
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Article
| Open AccessPersistent humoral immune response in youth throughout the COVID-19 pandemic: prospective school-based cohort study
Understanding the immune responses of school-aged children to SARS-CoV-2 is important for designing public health measures. Here, the authors report findings from cross-sectional and longitudinal anti-SARS-CoV-2 antibody measurements in a school-based study in Zurich, Switzerland, from 2020-2022.
- Alessia Raineri
- , Thomas Radtke
- & Susi Kriemler
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Article
| Open AccessEpidemiology, mortality, and health service use of local-level multimorbidity patterns in South Spain
Multimorbidity—the occurrence of chronic diseases together—represents a major challenge for healthcare systems. Here, the authors characterise multimorbidity patterns in a large dataset of patients residing in southern Spain and show the unequal distribution of multimorbidity patterns along different socioeconomic areas at the local level.
- Javier Alvarez-Galvez
- , Esther Ortega-Martin
- & Jesus Carretero-Bravo
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Article
| Open AccessAssessing the value of integrating national longitudinal shopping data into respiratory disease forecasting models
Novel indicators of infectious disease prevalence could improve real-time surveillance and support healthcare planning. Here, the authors show that sales data for non-prescription medications from a UK high street retailer can improve the accuracy of models forecasting mortality from respiratory infections.
- Elizabeth Dolan
- , James Goulding
- & Laila J. Tata
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Article
| Open AccessEvaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty
The US COVID-19 Scenario Modeling Hub produced medium to long term projections based on different epidemic scenarios. In this study, the authors evaluate 14 rounds of projections by comparing them to the epidemic trajectories that occurred, and discuss lessons learned for future similar projects.
- Emily Howerton
- , Lucie Contamin
- & Justin Lessler
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Article
| Open AccessThe burden of post-acute COVID-19 symptoms in a multinational network cohort analysis
Post-acute COVID-19 condition is difficult to quantify because it includes a range of symptoms that may have other causes. In this study, the authors use primary care data from England and Catalonia, Spain, to estimate the incidence of the condition and identify symptoms that occur more frequently following infection than in uninfected controls.
- Kristin Kostka
- , Elena Roel
- & Annika M. Jödicke
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Article
| Open AccessThe metabolic, virulence and antimicrobial resistance profiles of colonising Streptococcus pneumoniae shift after PCV13 introduction in urban Malawi
Pneumococcal vaccination has been shown to promote emergence of non-vaccine S. pneumoniae serotypes. Here, the authors use data from Malawi to investigate whether vaccine introduction also results in changes in metabolic, virulence, and antimicrobial resistance profiles of circulating strains.
- Uri Obolski
- , Todd D. Swarthout
- & Robert S. Heyderman
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Article
| Open AccessCircadian disturbances and frailty risk in older adults
The relationship between circadian function and frailty is not well understood. Here, the authors show that disturbances in circadian rest-activity rhythms were associated with an elevated frailty risk and faster progress of frailty in older adults.
- Ruixue Cai
- , Lei Gao
- & Peng Li
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Article
| Open AccessEvaluation of pragmatic oxygenation measurement as a proxy for Covid-19 severity
There is a need for an accurate measure of pulmonary oxygenation function that can be used as an intermediate endpoint in pragmatic clinical trials, to increase statistical power and efficiency. Here, the authors show that the S/F94, a modification of the S/F ratio, is a simple, meaningful and effective intermediate outcome measure.
- Maaike C. Swets
- , Steven Kerr
- & J. Kenneth Baillie
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Article
| Open AccessImpact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia
In this study, the authors develop a mathematical modelling framework to estimate the impacts of non-pharmaceutical interventions and vaccination on COVID-19 incidence. The model accounts for changes in SARS-CoV-2 variant and population immunity, and here they use it to investigate epidemic dynamics in French Polynesia.
- Lloyd A. C. Chapman
- , Maite Aubry
- & Adam J. Kucharski
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Article
| Open AccessMalaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal
Senegal has initiated a national sentinel surveillance program for malaria parasite genetics. Here, the authors report data from the first year of the program and use it to investigate local malaria incidence, patterns of transmission, and genetic loci under selection.
- Stephen F. Schaffner
- , Aida Badiane
- & Sarah K. Volkman
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Comment
| Open AccessThe counterintuitive implications of superspreading diseases
The superspreading that characterized SARS and now COVID-19 can be rapidly quantified; however, its implications for outbreak control were never well understood. Recent studies point to its profound impact on outbreak dynamics and prospects for effective control of a future Disease X. These insights necessitate research into the mechanisms, impact and different modes of superspreading more widely.
- Bjarke Frost Nielsen
- , Kim Sneppen
- & Lone Simonsen