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| Open AccessOptimising genomic approaches for identifying vancomycin-resistant Enterococcus faecium transmission in healthcare settings
Vancomycin-resistant Enterococcus faecium is an important healthcare-associated pathogen and genomic analyses could inform targeted interventions. Here, the authors optimise an analysis pipeline for identification of putative transmission events using core genome multilocus sequence type clustering and split kmer analysis.
- Charlie Higgs
- , Norelle L. Sherry
- & Benjamin P. Howden
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Article
| Open AccessRegional excess mortality during the 2020 COVID-19 pandemic in five European countries
In this study, the authors estimate excess mortality at the regional level for five European countries (England, Greece, Italy, Spain, and Switzerland) in 2020. They identify the regions and time periods with highest excess mortality and show how these patterns evolved through different pandemic waves.
- Garyfallos Konstantinoudis
- , Michela Cameletti
- & Marta Blangiardo
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| Open AccessViral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant
The SARS-CoV-2 Delta variant has spread rapidly worldwide. Here, the authors characterise a single chain of transmission of Delta in China, and find evidence that it is more infectious and replicates faster during early infection compared to early pandemic lineages.
- Baisheng Li
- , Aiping Deng
- & Jing Lu
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Article
| Open AccessMultimorbidity and adverse events of special interest associated with Covid-19 vaccines in Hong Kong
Adverse events resulting from COVID-19 vaccination are a public health concern and it is not known whether pre-existing conditions may impose an increased risk. Here, using electronic health records from Hong Kong, the authors show that adverse events are rare for all groups, and there is no evidence of risk modification due to multimorbidity.
- Francisco Tsz Tsun Lai
- , Lei Huang
- & Ian Chi Kei Wong
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| Open AccessLarge-scale diet tracking data reveal disparate associations between food environment and diet
Studying diets is challenging, typically restricted to small sample sizes, single locations, and non-uniform design across studies. Here, the authors leverage food entry data of a popular diet tracking app to observe diet health and weight status, studying the associations of fast food and grocery access, income and education with diet health outcomes.
- Tim Althoff
- , Hamed Nilforoshan
- & Jure Leskovec
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| Open AccessDistinct kinetics of antibodies to 111 Plasmodium falciparum proteins identifies markers of recent malaria exposure
Serological markers of recent Plasmodium falciparum infection could be useful to estimate incidence. Here, the authors identify a combination of five serological markers to detect exposure to infection within the previous three months with >80% sensitivity and specificity.
- Victor Yman
- , James Tuju
- & Anna Färnert
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Article
| Open AccessModel-based evaluation of alternative reactive class closure strategies against COVID-19
Reactive school class closures have been widely implemented to mitigate COVID-19 outbreaks. Here, the authors show that, compared to symptom-prompted PCR testing, screening for cases in schools with antigen tests leads to greater reductions in infection rates in both students and the wider community.
- Quan-Hui Liu
- , Juanjuan Zhang
- & Marco Ajelli
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| Open AccessPopulation homogeneity for the antibody response to COVID-19 BNT162b2/Comirnaty vaccine is only reached after the second dose across all adult age ranges
Here, in a longitudinal cohort of 1245 hospital care workers and 146 nursing home residents, the authors find that a large inter-individual variation in anti-spike antibody levels after one dose of BNT162b2mRNA vaccine is partially explained by age, sex, previous exposure, and treatments, while the 2nd dose is required to reach sero-conversion at the population level.
- João Faro-Viana
- , Marie-Louise Bergman
- & Jocelyne Demengeot
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Article
| Open AccessEstimating the strength of selection for new SARS-CoV-2 variants
Identifying new SARS-CoV-2 genetic variants of concern is important to inform public health strategies, but distinguishing those causing a significant threat is challenging. Here, the authors develop and evaluate two models for assessing the strength of selection for new variants.
- Christiaan H. van Dorp
- , Emma E. Goldberg
- & Ethan O. Romero-Severson
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Article
| Open AccessIncreased transmissibility of SARS-CoV-2 lineage B.1.1.7 by age and viral load
Establishing the relative transmissibility of emerging variants of SARS-CoV-2 is key for pandemic management. Here, the authors use full-population administrative data from Denmark linked to PCR test results and estimate that the Alpha variant was ~60% higher than other strains circulating in early 2021.
- Frederik Plesner Lyngse
- , Kåre Mølbak
- & Carsten Thure Kirkeby
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| Open AccessMeta-analyses identify DNA methylation associated with kidney function and damage
Many genetic loci have been identified to be associated with kidney disease, but the molecular mechanisms are not well understood. Here, the authors perform epigenome-wide association studies on kidney function measures to identify epigenetic marks and pathways involved in kidney function.
- Pascal Schlosser
- , Adrienne Tin
- & Alexander Teumer
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Article
| Open AccessEpigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus
Serum urate concentration can be studied in large datasets to find genetic and epigenetic loci that may be related to cardiometabolic traits. Here the authors identify and replicate 100 urate-associated CpGs, which provide insights into urate GWAS loci and shared CpGs of urate and cardiometabolic traits.
- Adrienne Tin
- , Pascal Schlosser
- & Anna Köttgen
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Article
| Open AccessChanges in notifiable infectious disease incidence in China during the COVID-19 pandemic
Non-pharmaceutical interventions implemented to mitigate COVID-19 transmission are likely to have impacted spread of other infectious diseases. Here, the authors investigate changes in the incidence of 31 notifiable infectious diseases using surveillance data from China.
- Meng-Jie Geng
- , Hai-Yang Zhang
- & Wei Liu
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| Open AccessSARS-CoV-2 transmission across age groups in France and implications for control
In this study, Tran Kiem et al. examine the contribution of different age groups to COVID-19 transmission. Using data from the French epidemic in summer 2020, they report that while individuals aged 80 years and older are more at risk, pandemic control in the absence of vaccines required measures targeted at all age groups.
- Cécile Tran Kiem
- , Paolo Bosetti
- & Simon Cauchemez
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| Open AccessAdaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands
SARS-CoV-2 was detected in mink farms in the Netherlands in the first wave of the pandemic with evidence of human-to-mink and mink-to-human transmission. Here, the authors investigate this outbreak using phylodynamic analysis and show that personnel links and spatial proximity are predictors of transmission between farms.
- Lu Lu
- , Reina S. Sikkema
- & Marion P. G. Koopmans
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Article
| Open AccessAge-seroprevalence curves for the multi-strain structure of influenza A virus
Multi-strain pathogens, such as influenza, present challenges for interpretation of seroprevalence data as estimates may vary by strain. Here, the authors develop a method for estimating age-specific seroprevalence based on principal components analysis and apply it to influenza data from Vietnam.
- Dao Nguyen Vinh
- , Nguyen Thi Duy Nhat
- & Maciej F. Boni
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| Open AccessModel-based assessment of Chikungunya and O’nyong-nyong virus circulation in Mali in a serological cross-reactivity context
O’nyong nyong and Chikungunya virus are arboviruses present in Africa but their prevalence is unknown, partly due to high antibody cross-reactivity with one another. Here, the authors develop a statistical model that accounts for cross-reactivity to characterise circulation of both viruses from seroprevalence surveys.
- Nathanaël Hozé
- , Issa Diarra
- & Simon Cauchemez
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Article
| Open AccessAssociations between patterns in comorbid diagnostic trajectories of individuals with schizophrenia and etiological factors
Schizophrenia is a complex disorder where individuals experience different symptoms and outcomes that can be captured by patterns in other diagnoses. Here the authors use computational approaches to summarize these patterns and suggest they are associated with genetic and environmental exposure.
- Morten Dybdahl Krebs
- , Gonçalo Espregueira Themudo
- & Wesley K. Thompson
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| Open AccessBurdens of post-acute sequelae of COVID-19 by severity of acute infection, demographics and health status
Post-acute sequelae of COVID-19 (PASC, or ‘Long COVID’) has caused concern but the burden and risk factors are not well understood. Here, the authors use US electronic health record data and estimate an overall burden of PASC of ~7% at six months, with variation by severity of acute infection, baseline health status and demographics.
- Yan Xie
- , Benjamin Bowe
- & Ziyad Al-Aly
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| Open AccessA novel SARS-CoV-2 related coronavirus in bats from Cambodia
In this study, Delaune et al., isolate and characterise a SARS-CoV-2-related coronavirus from two bats sampled in Cambodia. Their findings suggest that the geographic distribution of SARS-CoV-2-related viruses is wider than previously reported.
- Deborah Delaune
- , Vibol Hul
- & Veasna Duong
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| Open AccessEstimating disease prevalence in large datasets using genetic risk scores
Estimating disease prevalence in biobanks is prone to error, especially for self-reported traits. Here, the authors propose a method to estimate the prevalence of a disease within a cohort based on genetic risk scores.
- Benjamin D. Evans
- , Piotr Słowiński
- & Nicholas J. Thomas
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| Open AccessAssociation between serum retinol and overall and cause-specific mortality in a 30-year prospective cohort study
Vitamin A, of which retinol is the major form in the circulation, is a determinant of human health but whether vitamin A status is associated with mortality is not well understood. Here the authors report that in a prospective observational analysis of 29 104 men, higher serum retinol associates with lower risk of overall and cause-specific mortality.
- Jiaqi Huang
- , Stephanie J. Weinstein
- & Demetrius Albanes
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| Open AccessCorrelation of SARS-CoV-2-breakthrough infections to time-from-vaccine
The duration of effectiveness of SARS-CoV-2 vaccination is not yet known. Here, the authors present preliminary evidence of BNT162b2 vaccine waning across all age groups above 16, with a higher incidence of infection in people who received their second dose early in 2021 compared to later in the year.
- Barak Mizrahi
- , Roni Lotan
- & Tal Patalon
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| Open AccessHigher intake of whole grains and dietary fiber are associated with lower risk of liver cancer and chronic liver disease mortality
Higher intake of dietary fiber and whole grains are associated with reduced risk of various diseases including some cancers. Here, the authors estimate reductions in liver cancer of 22% and 31% and chronic liver disease mortality of 56% and 63% associated with increased whole grain and dietary fiber intake, respectively.
- Xing Liu
- , Wanshui Yang
- & Xuehong Zhang
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| Open AccessPotential global impacts of alternative dosing regimen and rollout options for the ChAdOx1 nCoV-19 vaccine
The ChAdOx1 nCoV-19 vaccine requires two doses, but under limited supply single dose regimens have also been considered. Here, the authors show using static transmission modelling that under certain conditions it is optimal to more expediently administer a single dose to a larger proportion of the population.
- Ricardo Aguas
- , Anouska Bharath
- & Rima Shretta
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| Open AccessUsing secondary cases to characterize the severity of an emerging or re-emerging infection
Estimates of the severity of emerging infections did not consider the case ascertainment method, but secondary cases identified by contact tracing of index cases may be more reliable as they are less susceptible to ascertainment bias. Here, the authors perform a systematic review to quantify these differences and model their impacts for COVID-19.
- Tim K. Tsang
- , Can Wang
- & Benjamin J. Cowling
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Article
| Open AccessUnderstanding how Victoria, Australia gained control of its second COVID-19 wave
The state of Victoria, Australia experienced a substantial second wave of COVID-19 but brought it under control with strict non-pharmaceutical interventions. Here, the authors model the second wave in Victoria to estimate the impacts of the different interventions.
- James M. Trauer
- , Michael J. Lydeamore
- & Romain Ragonnet
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| Open AccessClinical outcomes and cost-effectiveness of COVID-19 vaccination in South Africa
Cost, supply and logistics present challenges to COVID-19 vaccine rollout in low and middle income countries. Here, the authors model vaccination programmes in South Africa and demonstrate the importance of the pace of vaccine rollout, with even moderately efficacious vaccines likely to be cost-effective.
- Krishna P. Reddy
- , Kieran P. Fitzmaurice
- & Mark J. Siedner
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| Open AccessAnti-spike antibody response to natural SARS-CoV-2 infection in the general population
Most people who are infected with SARS-CoV-2 seroconvert within a few weeks, but the determinants and duration of the antibody response are not known. Here, the authors characterise these features of the immune response using data from a large representative community sample of the UK population.
- Jia Wei
- , Philippa C. Matthews
- & Chris Cunningham
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| Open AccessThe impact of the timely birth dose vaccine on the global elimination of hepatitis B
The timely hepatitis B birth dose vaccination is recommended for all new-borns by the WHO, but coverage is inconsistent. Here, the authors model the impact of scaling-up coverage in 110 low and middle income countries and assess how it may be affected by delays for example caused by the COVID-19 pandemic.
- Margaret J. de Villiers
- , Shevanthi Nayagam
- & Timothy B. Hallett
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| Open AccessEffectiveness of ChAdOx1 vaccine in older adults during SARS-CoV-2 Gamma variant circulation in São Paulo
Here, the authors investigate the effectiveness of the Oxford-AstraZeneca (ChAdOx1) vaccine during extensive Gamma variant SARS-CoV-2 circulation in São Paulo state, Brazil, and find that a two-dose regime is more effective than one dose against mild to severe Covid-19 outcomes in older adults.
- Matt D. T. Hitchings
- , Otavio T. Ranzani
- & Julio Croda
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| Open AccessQuantifying previous SARS-CoV-2 infection through mixture modelling of antibody levels
The proportion of a population that has previously been infected by a pathogen is typically estimated using antibody thresholds adjusted for sensitivity and specificity. Here, the authors present a model-based alternative to threshold methods which accounts for antibody waning and other sources of spectrum bias.
- C. Bottomley
- , M. Otiende
- & J. A. G. Scott
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| Open AccessRapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020
The true number of infections from SARS-Cov-2 is unknown and believed to exceed the reported numbers by several fold. National testing policies, in particular, can strongly affect the proportion of undetected cases. Here, the authors propose a method that reconstructs incidence profiles within minutes, solely from publicly available, time-stamped viral genomes.
- Maureen Rebecca Smith
- , Maria Trofimova
- & Max von Kleist
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| Open AccessA cross-sectional analysis of meteorological factors and SARS-CoV-2 transmission in 409 cities across 26 countries
Possible effects of weather conditions on COVID-19 transmission are debated. Here, the authors analyse data from early in the pandemic and show that although temperature and humidity had small effects on transmission, they were far out-weighed by the effects of non-pharmaceutical interventions.
- Francesco Sera
- , Ben Armstrong
- & Rachel Lowe
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| Open AccessNationwide rollout reveals efficacy of epidemic control through digital contact tracing
The effectiveness of digital contact tracing for COVID-19 control remains uncertain. Here, the authors use data from the Smittestopp app, used in Norway in spring 2020, and estimate that 80% of nearby devices were detected by the app, and at least 11% of close contacts were not visible to manual contact tracing.
- Ahmed Elmokashfi
- , Joakim Sundnes
- & Olav Lysne
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| Open AccessSARS-CoV-2 antibody seroprevalence and associated risk factors in an urban district in Cameroon
Many African countries have reported relatively low numbers of COVID-19 cases but the true scale of the epidemic is unclear. Here, the authors conduct a population-based survey in a province of Cameroon and estimate 29% seroprevlance, >300 fold higher than the nationwide attack rate implied by case counts.
- Kene Nwosu
- , Joseph Fokam
- & Laura Ciaffi
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| Open AccessUnderstanding the effectiveness of government interventions against the resurgence of COVID-19 in Europe
European governments control resurging waves of COVID-19 using nonpharmaceutical interventions. Here, the authors estimate the effectiveness of 17 interventions in Europe’s second wave, and analyse differences to the first wave as well as implications for the future of the pandemic.
- Mrinank Sharma
- , Sören Mindermann
- & Jan Markus Brauner
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Article
| Open AccessGeographical drivers and climate-linked dynamics of Lassa fever in Nigeria
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
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Article
| Open AccessPossible future waves of SARS-CoV-2 infection generated by variants of concern with a range of characteristics
Understanding the potential impacts of new variants of SARS-CoV-2 is important for pandemic planning. Here, the authors develop a model incorporating hypothetical new variants with varying transmissibility and immune evasion properties, and use it to project possible future epidemic waves in the UK.
- Louise Dyson
- , Edward M. Hill
- & Matt J. Keeling
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Article
| Open AccessGenomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity
Genomic surveillance of SARS-CoV-2 can inform regional transmission dynamics and inform public health interventions. Here, the authors sequence ~200 samples from Rwanda, identify shifts in predominating strains from May 2020 to February 2021, and infer geographic origins.
- Yvan Butera
- , Enatha Mukantwari
- & Nadine Rujeni
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Article
| Open AccessAnalyses of child cardiometabolic phenotype following assisted reproductive technologies using a pragmatic trial emulation approach
Huang and colleagues used machine-learning estimators to analyse a broad range of parameters in a prospective cohort consisting ART and spontaneously conceived children. Small differences in stature and growth could not be explained by parental or perinatal environment factors, nor differences in fetal DNA methylation. No strong differences in metabolic parameters were seen.
- Jonathan Yinhao Huang
- , Shirong Cai
- & Shiao-Yng Chan
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Article
| Open AccessSARS-CoV-2 mucosal antibody development and persistence and their relation to viral load and COVID-19 symptoms
There has been limited research on the role of the mucosal immune response to SARS-CoV-2 infection. Here, the authors perform a prospective observational household study and find that mucosal antibody responses are associated with decreased viral load and faster resolution of systemic symptoms.
- Janeri Fröberg
- , Joshua Gillard
- & Dimitri A. Diavatopoulos
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Article
| Open AccessDevelopment of a model-inference system for estimating epidemiological characteristics of SARS-CoV-2 variants of concern
Quantification of the transmissibility and immune escape properties of SARS-CoV-2 variants is necessary to support pandemic planning. Here, the authors develop a model inference system to estimate these properties using incidence and mortality data for three variants of concern.
- Wan Yang
- & Jeffrey Shaman
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Article
| Open AccessModelling the persistence and control of Rift Valley fever virus in a spatially heterogeneous landscape
Rift Valley fever is a zoonotic haemorrhagic fever with complex transmission dynamics influenced by environmental variables and animal movements. Here, the authors develop a metapopulation model incorporating these factors and use it to identify the main drivers of transmission in the Comoros archipelago.
- Warren S. D. Tennant
- , Eric Cardinale
- & Raphaëlle Métras
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Article
| Open AccessContact tracing is an imperfect tool for controlling COVID-19 transmission and relies on population adherence
Evaluations of the UK’s contact tracing programme have shown that it has had limited impact on COVID-19 control. Here, the authors show that with high levels of reporting and adherence, contact tracing could reduce transmission, but it should not be used as the sole control measure.
- Emma L. Davis
- , Tim C. D. Lucas
- & Petra Klepac
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Article
| Open AccessA pre-registered short-term forecasting study of COVID-19 in Germany and Poland during the second wave
Forecasting models have been used extensively to inform decision making during the COVID-19 pandemic. In this preregistered and prospective study, the authors evaluated 14 short-term models for Germany and Poland, finding considerable heterogeneity in predictions and highlighting the benefits of combined forecasts.
- J. Bracher
- , D. Wolffram
- & Frost Tianjian Xu
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Article
| Open AccessGlobal spread of Salmonella Enteritidis via centralized sourcing and international trade of poultry breeding stocks
Salmonella enterica serotype Enteritidis is a pathogen of poultry that can cause outbreaks in humans. Here the authors use genomic and trade data to investigate a pandemic in the 1980s, finding evidence that international trade of breeding stocks led to global spread of the pathogen.
- Shaoting Li
- , Yingshu He
- & Xiangyu Deng
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Article
| Open AccessThe risk of indoor sports and culture events for the transmission of COVID-19
Mass gathering events represent a risk for transmission of SARS-CoV-2. Here, the authors describe an experimental indoor test event in which individual contacts were measured and use aerosol and epidemiological modelling to evaluate transmission risks of different types of restrictions in the arena.
- Stefan Moritz
- , Cornelia Gottschick
- & Rafael Mikolajczyk
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Article
| Open AccessEtiological and epidemiological features of acute respiratory infections in China
China operates a national surveillance program for acute respiratory infections and sampled over 200,000 patients between 2009–2019. Here, the authors present results from this program and describe patterns by age, pathogen type, presence of pneumonia, and season.
- Zhong-Jie Li
- , Hai-Yang Zhang
- & Jun Wang