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| Open AccessMitigation of SARS-CoV-2 transmission at a large public university
Safely opening university campuses has been a major challenge during the COVID-19 pandemic. Here, the authors describe a program of public health measures employed at a university in the United States which, combined with other non-pharmaceutical interventions, allowed the university to stay open in fall 2020 with limited evidence of transmission.
- Diana Rose E. Ranoa
- , Robin L. Holland
- & Martin D. Burke
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Article
| Open AccessDisease-economy trade-offs under alternative epidemic control strategies
Pandemic control policy requires balancing economic and disease outcomes. This study develops a joint modeling approach that allows both aspects to be considered simultaneously and shows that targeted isolation is superior economically and can achieve similar disease outcomes to voluntary isolation or blanket lockdowns.
- Thomas Ash
- , Antonio M. Bento
- & Ana I. Bento
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| Open AccessCross-sectional seroprevalence surveys of SARS-CoV-2 antibodies in children in Germany, June 2020 to May 2021
Children are less likely to be infected with SARS-CoV-2 and develop less severe disease than adults, which makes estimation of infection rates challenging. Here, the authors conduct seroprevalence surveys of children in Germany, describe changes in prevalence over time, and identify risk factors for infection.
- Anna-Lisa Sorg
- , Leon Bergfeld
- & Horst Schroten
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Article
| Open AccessUntangling the changing impact of non-pharmaceutical interventions and vaccination on European COVID-19 trajectories
Non-pharmaceutical interventions (NPIs) and COVID-19 vaccination have been implemented concurrently, making their relative effects difficult to measure. Here, the authors show that effects of NPIs reduced as vaccine coverage increased, but that NPIs could still be important in the context of more transmissible variants.
- Yong Ge
- , Wen-Bin Zhang
- & Shengjie Lai
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| Open AccessWhole genome sequencing reveals hidden transmission of carbapenemase-producing Enterobacterales
Carbapenemase-producing Enterobacterales cause healthcare-associated infections but modes of transmission are not well understood. Here, the authors find evidence of transmission without direct patient contact, indicating presence of undetected environmental reservoirs, whilst half of the transmission events are likely due to plasmid-mediated transmission.
- Kalisvar Marimuthu
- , Indumathi Venkatachalam
- & Oon Tek Ng
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| Open AccessA framework for reconstructing SARS-CoV-2 transmission dynamics using excess mortality data
Testing capacity continues to limit detection of COVID-19 infections and impacts reliability of mortality estimates. Here, the authors develop a statistical model to estimate COVID-19 attributable deaths using all-cause mortality data from Iran and estimate that around half of these deaths have been reported.
- Mahan Ghafari
- , Oliver J. Watson
- & Aris Katzourakis
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Article
| Open AccessNon-selective distribution of infectious disease prevention may outperform risk-based targeting
Pre-exposure prophylaxis (PrEP) is an effective HIV prevention measure but identifying those most at risk to target for treatment is challenging. Here, the authors demonstrate that non-selective PrEP distribution outperforms targeted strategies when use is not consistent, and/or prevalence of untreated HIV is high.
- Benjamin Steinegger
- , Iacopo Iacopini
- & Eugenio Valdano
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Article
| Open AccessWireless implantable optical probe for continuous monitoring of oxygen saturation in flaps and organ grafts
Although continuous monitoring of tissue oxygenation is critically important after tissue/organ graft procedures, current technologies have key limitations. Here, the authors develop a miniaturized, minimally invasive, self-anchoring optical probe and demonstrate continuous monitoring of oxygenation in porcine flap and organ models.
- Hexia Guo
- , Wubin Bai
- & John A. Rogers
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Article
| Open AccessA lncRNA signature associated with tumor immune heterogeneity predicts distant metastasis in locoregionally advanced nasopharyngeal carcinoma
Long noncoding RNAs (lncRNAs) can be used for the development of prognostic signatures to predict tumour metastasis. Here the authors identify an immune-associated nine-lncRNA signature for predicting metastasis in a multicentre cohort of locoregionally advanced nasopharyngeal cancer patients.
- Ye-Lin Liang
- , Yuan Zhang
- & Na Liu
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Article
| Open AccessCombining rapid antigen testing and syndromic surveillance improves community-based COVID-19 detection in a low-income country
Rapid antigen tests and syndromic surveillance for identification of COVID-19 cases are limited by low sensitivity and specificity, respectively. Here, the authors use data from Bangladesh and show that combining the two methods improves diagnostic accuracy in a range of epidemiological scenarios.
- Fergus J. Chadwick
- , Jessica Clark
- & Ayesha Sania
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| Open AccessSeeking patterns of antibiotic resistance in ATLAS, an open, raw MIC database with patient metadata
Pathogens are typically classified as ‘antibiotic-resistant’ for clinical purposes based on cut-off values of minimum inhibitory concentrations (MICs). In this study, the authors explore quantitative values of MICs using the global ‘ATLAS’ database of pathogen-antibiotic pairs, describe trends in resistance, and compare results to other antibiotic resistance surveillance data.
- Pablo Catalán
- , Emily Wood
- & Robert E. Beardmore
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Article
| Open AccessOff-season RSV epidemics in Australia after easing of COVID-19 restrictions
Non-pharmaceutical interventions for COVID-19 also reduced incidence of respiratory pathogens such as respiratory syncytial virus (RSV). Here, the authors report the resurgence of RSV in Australia following lifting of some of the restrictions and describe reduction in genetic diversity in circulating clades.
- John-Sebastian Eden
- , Chisha Sikazwe
- & Tyna Tran
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| Open AccessElimination of human rabies in Goa, India through an integrated One Health approach
Dog vaccination is an effective rabies prevention measure, but widespread vaccination campaigns are challenging in settings like India with large free-roaming dog populations. Here, the authors describe a One Health campaign in Goa state which led to a large reduction of cases in dogs and elimination in humans.
- A. D. Gibson
- , G. Yale
- & R. J. Mellanby
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Article
| Open AccessLarge-scale GWAS of food liking reveals genetic determinants and genetic correlations with distinct neurophysiological traits
Genetic determinants of food consumption and food liking are likely to be distinct, although it has not been well studied. Here, the authors identify genetic variants associated with food-liking, finding that different food-liking traits correlate with different brain areas and other food consumption traits.
- Sebastian May-Wilson
- , Nana Matoba
- & Nicola Pirastu
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Article
| Open AccessIntelligent wireless theranostic contact lens for electrical sensing and regulation of intraocular pressure
Towards intelligent treatment for glaucoma, here authors demonstrate integrated wireless theranostic contact lenses for in situ electrical sensing of intraocular pressure and on demand anti-glaucoma drug delivery.
- Cheng Yang
- , Qianni Wu
- & Xi Xie
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Comment
| Open AccessA broader perspective on the economics of malaria prevention and the potential impact of SARS-CoV-2
Economic evaluations of public health interventions to prevent malaria should consider the adoption of wider perspectives and the inclusion of non-health impacts, particularly economic development outcomes, such as education. This is especially relevant in malaria elimination settings and in the context of the current SARS-CoV-2 pandemic.
- Elisa Sicuri
- , Francesco Ramponi
- & Francisco Saúte
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| Open AccessHeterologous immunization with inactivated vaccine followed by mRNA-booster elicits strong immunity against SARS-CoV-2 Omicron variant
Emerging SARS-CoV-2 variants of concern (VOCs) raises concerns regarding vaccine efficacy. Here, the authors evaluate the neutralizing antibody, and cellular response elicited following inactivated vaccine immunization, and mRNA booster, against the Omicron variant.
- Fanglei Zuo
- , Hassan Abolhassani
- & Qiang Pan-Hammarström
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| Open AccessPrecisely translating computed tomography diagnosis accuracy into therapeutic intervention by a carbon-iodine conjugated polymer
Poly(diiododiacetylene)—PIDA—contains iodine atoms, which are commonly found in computed tomography contrast agents. Here, the authors find that PIDA can function as a contrast agent and can also be used as a visual marker to delineate tumour margins.
- Mingming Yin
- , Xiaoming Liu
- & Liang Luo
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| Open AccessSystematic review and meta-analysis of the effectiveness and perinatal outcomes of COVID-19 vaccination in pregnancy
Pregnant women have been disproportionately under-vaccinated against COVID-19, partly because they were excluded from initial trials. This systematic review and meta-analysis supports efficacy of vaccination in pregnancy, and finds no evidence of adverse maternal or perinatal outcomes.
- Smriti Prasad
- , Erkan Kalafat
- & Asma Khalil
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| Open AccessGenetic diversity of SARS-CoV-2 infections in Ghana from 2020-2021
In this genomic epidemiology study from Ghana, the authors sequence ~1,000 SARS-CoV-2 whole genomes from March 2020 to September 2021. They describe changes in the predominant circulating lineages over time and infer how variants of concern were likely introduced into the country.
- Collins M. Morang’a
- , Joyce M. Ngoi
- & Gordon A. Awandare
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| Open AccessUsing sero-epidemiology to monitor disparities in vaccination and infection with SARS-CoV-2
Continued monitoring of SARS-CoV-2 at the population level is important for identifying at-risk groups. Here the authors analyse data from a serological surveillance platform in San Francisco and find considerable variation in infection and vaccination history by race/ethnicity and socioeconomic status.
- Isobel Routledge
- , Saki Takahashi
- & Isabel Rodríguez-Barraquer
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| Open AccessComparative effectiveness over time of the mRNA-1273 (Moderna) vaccine and the BNT162b2 (Pfizer-BioNTech) vaccine
In this retrospective cohort study, Islam et al. estimate the effectiveness of two mRNA-based COVID-19 vaccines in over 3.5 million fully vaccinated individuals and find no differences in vaccine effectiveness for protection against hospitalization, ICU admission, or death/hospice transfer.
- Nazmul Islam
- , Natalie E. Sheils
- & Kenneth Cohen
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| Open AccessTrends and associated factors for Covid-19 hospitalisation and fatality risk in 2.3 million adults in England
In this retrospective cohort study, the authors investigate the risk of hospitalisation and death for all adults in England who tested positive for COVID-19 from October 2020–April 2021. They find that the risk of hospitalisation and death varied substantially over time after taking into account individual risk factors.
- T. Beaney
- , A. L. Neves
- & J. Clarke
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| Open AccessComparing COVID-19-related hospitalization rates among individuals with infection-induced and vaccine-induced immunity in Israel
The relative degree of immunity to SARS-CoV-2 provided by combinations of natural infection, vaccination, and booster doses is unknown. Here, the authors show that infection-induced immunity provides more protection against COVID-19-related hospitalization than non-recent vaccine immunity, but less than booster vaccination.
- Jacob G. Waxman
- , Maya Makov-Assif
- & Noam Barda
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Article
| Open AccessEconomic shocks predict increases in child wasting prevalence
Economic shocks may lead to food insecurity and therefore acute child malnutrition (wasting). Here, the authors use data from Demographic Health Surveys to estimate impacts of past economic shocks on wasting and project possible effects of shocks related to the COVID-19 pandemic.
- Derek D. Headey
- & Marie T. Ruel
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Article
| Open AccessA fully automatic AI system for tooth and alveolar bone segmentation from cone-beam CT images
Accurate delineation of individual teeth and alveolar bones from dental cone-beam CT images is an essential step in digital dentistry for precision dental healthcare. Here, the authors present a deep learning system for efficient, precise, and fully automatic segmentation of real-patient CBCT images presenting highly variable appearances.
- Zhiming Cui
- , Yu Fang
- & Dinggang Shen
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Article
| Open AccessCommunication-efficient federated learning via knowledge distillation
This work presents a communication-efficient federated learning method that saves a major fraction of communication cost. It reveals the advantage of reciprocal learning in machine knowledge transfer and the evolutional low-rank properties of deep model updates.
- Chuhan Wu
- , Fangzhao Wu
- & Xing Xie
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Article
| Open AccessNon-metallic T2-MRI agents based on conjugated polymers
The toxicity of heavy metals for MRI contrast agents is an issue. Here, the authors report on the development of conjugated polymers nanoparticles based on paramagnetic polypyrrole to generate T2 MRI contrast effects by changing the interactions between polarons and water protons.
- Qinrui Lin
- , Yuhong Yang
- & Zhengzhong Shao
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Comment
| Open AccessAnalysing the relationship between the fields of thermo- and electrocatalysis taking hydrogen peroxide as a case study
Research in thermo- and electrocatalysis have often preceded in isolation, even for similar reactions. Here, the authors compare current trends in both fields and elaborate on the commonalities and differences with a specific focus on the production of hydrogen peroxide.
- Guilherme V. Fortunato
- , Enrico Pizzutilo
- & Marc Ledendecker
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Article
| Open AccessProtection following BNT162b2 booster in adolescents substantially exceeds that of a fresh 2-dose vaccine
This study compares SARS-CoV-2 infection rates following a recent second or third dose of the BNT162b2 (Pfizer/BioNTech) vaccine. They use data from Israel for 12–14 year olds (second dose) and 16–18 year olds (third dose), and find a 3.7-fold higher risk in the second-dose group.
- Ofra Amir
- , Yair Goldberg
- & Ron Milo
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| Open AccessPersistent COVID-19 symptoms in a community study of 606,434 people in England
This study characterises Long COVID using data from the REACT-2 community-based study in England. It estimates that 38% (in autumn/winter 2020/21) and 22% (in spring 2021) of people reported at least one symptom 12 weeks after symptom onset; identifies risk factors for persistent symptoms; and finds evidence of symptom clustering.
- Matthew Whitaker
- , Joshua Elliott
- & Paul Elliott
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Article
| Open AccessTherapeutic homology-independent targeted integration in retina and liver
Limits of AAV-mediated gene therapy include targeting dominant mutations and inducing long-term transgene expression. Here, the authors show that AAV-HITI results in efficient allele-independent integration of a donor DNA in both retina and liver providing therapeutic benefit in mouse models of either a genetic form of blindness or a lysosomal storage disease, respectively.
- Patrizia Tornabene
- , Rita Ferla
- & Alberto Auricchio
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Article
| Open AccessUsing high-resolution contact networks to evaluate SARS-CoV-2 transmission and control in large-scale multi-day events
Here, the authors simulate COVID-19 outbreaks on an empirical contact network derived from digital contact data collected on cruise ships. They model impacts of different control measures and find that combinations of measures, particularly vaccination and rapid antigen testing, are important for mitigating outbreaks.
- Rachael Pung
- , Josh A. Firth
- & Adam J. Kucharski
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Article
| Open AccessCarbonized paramagnetic complexes of Mn (II) as contrast agents for precise magnetic resonance imaging of sub-millimeter-sized orthotopic tumors
Improving the imaging of cancer may enhance the treatment of patients, Here, the authors develop a Mn(II) based nanoparticle contrast agent for MRI imaging and show that the nanoparticles can cross the brain barrier and image glioma cells.
- Ruixue Qin
- , Shi Li
- & Hongmin Chen
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Article
| Open AccessAccurate auto-labeling of chest X-ray images based on quantitative similarity to an explainable AI model
Here the authors develop a method for accurate auto-labelling of CXR images from large public datasets based on quantitative probability-of similarity to an explainable AI model. The labels can be used to fine-tune the original model through iterative re-training.
- Doyun Kim
- , Joowon Chung
- & Synho Do
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| Open AccessHigh failure rate of ChAdOx1-nCoV19 immunization against asymptomatic infection in healthcare workers during a Delta variant surge
The authors study a cohort of healthcare workers in India who received two doses of the ChAdOx-1-nCoV19 vaccine during the Delta wave. Using serological data, they infer that 25% of the cohort were infected within 60 days of vaccination, although there were no severe infections leading to hospitalisations.
- Rajat Ujjainiya
- , Akansha Tyagi
- & Shantanu Sengupta
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Article
| Open AccessDigital plasmonic nanobubble detection for rapid and ultrasensitive virus diagnostics
Digital immunoassays are powerful platforms but are complex and require multiple steps to perform. Here the authors show that digital plasmonic nanobubble detection allows rapid and ultrasensitive diagnostics via a one-step homogeneous immunoassay.
- Yaning Liu
- , Haihang Ye
- & Zhenpeng Qin
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Article
| Open AccessAutomated multilabel diagnosis on electrocardiographic images and signals
The application of artificial intelligence for automated diagnosis of electrocardiograms can improve care in remote settings but is limited by the reliance on infrequently available signal-based data. Here, the authors report the development of a multi-label automated diagnosis model for electrocardiographic images.
- Veer Sangha
- , Bobak J. Mortazavi
- & Rohan Khera
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Article
| Open AccessComparative effectiveness and safety of homologous two-dose ChAdOx1 versus heterologous vaccination with ChAdOx1 and BNT162b2
Different homologous and heterologous vaccination regimens have been used for COVID-19. Here the authors show in a cohort analysis from Catalonia that heterologous vaccination with ChAdOx1 followed by BNT162b2 has better vaccine effectiveness than two doses of ChAdOx1.
- Eduardo Hermosilla
- , Ermengol Coma
- & Daniel Prieto-Alhambra
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Article
| Open AccessReconstructing antibody dynamics to estimate the risk of influenza virus infection
Serological classification of influenza infection has classically been based on a four-fold or higher increase in antibody levels, but this approach may not be optimal. Here, the authors develop a Bayesian model to improve identification of infections in serological samples by accounting for individual antibody dynamics.
- Tim K. Tsang
- , Ranawaka A. P. M. Perera
- & Simon Cauchemez
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Article
| Open AccessSpelling interface using intracortical signals in a completely locked-in patient enabled via auditory neurofeedback training
The authors record neural firing rates in a patient with ALS in completely locked-in state and show that the patient can modulate neural firing rates based on auditory feedback to select letters to form words and phrases to communicate his needs and experiences.
- Ujwal Chaudhary
- , Ioannis Vlachos
- & Niels Birbaumer
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Article
| Open AccessIdentifying regions for enhanced control of gambiense sleeping sickness in the Democratic Republic of Congo
Gambiense human African trypanosomiasis (sleeping sickness or gHAT) has been targeted for elimination of transmission by 2030. Here, the authors project impacts of gHAT interventions in the Democratic Republic of the Congo and derive a priority list of health zones requiring enhanced control to achieve this target.
- Ching-I Huang
- , Ronald E. Crump
- & Kat S. Rock
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Article
| Open AccessAgent-based modelling of reactive vaccination of workplaces and schools against COVID-19
The authors use an agent-based model to investigate the potential of reactive vaccination strategies for COVID-19 outbreak mitigation. They find that distributing vaccines in schools and workplaces where cases are detected is more impactful than non-reactive strategies in a wide range of epidemic scenarios.
- Benjamin Faucher
- , Rania Assab
- & Chiara Poletto
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Article
| Open AccessIn vivo three-dimensional multispectral photoacoustic imaging of dual enzyme-driven cyclic cascade reaction for tumor catalytic therapy
Photoacoustic imaging can be used to monitor chemical reaction in cells and tissues. Here, the authors develop a Pd based nanozyme conjugated with glucose oxidase that can induce the change of photoacoustic signals during the catalytic cascade process, the system can also be used to treat tumor-bearing mice.
- Shan Lei
- , Jing Zhang
- & Peng Huang
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| Open AccessActive label cleaning for improved dataset quality under resource constraints
High quality labels are important for model performance, evaluation and selection in medical imaging. As manual labelling is time-consuming and costly, the authors explore and benchmark various resource-effective methods for improving dataset quality.
- Mélanie Bernhardt
- , Daniel C. Castro
- & Ozan Oktay
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Article
| Open AccessPopulation-scale dietary interests during the COVID-19 pandemic
The SARS-CoV-2 virus has altered people’s lives around the world, not only through the disease it causes, but also through unprecedented restrictions. Here the authors document population-wide shifts in dietary interests in 18 countries in 2020, as revealed through time series of Google search volumes.
- Kristina Gligorić
- , Arnaud Chiolero
- & Robert West
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Article
| Open AccessCost-effectiveness of sleeping sickness elimination campaigns in five settings of the Democratic Republic of Congo
Gambiense human African trypanosomiasis has been targeted for elimination of transmission by 2030. Here, the authors assess the cost-effectiveness of elimination strategies in the Democratic Republic of the Congo and find that those which lead to elimination of transmission might also be considered cost-effective by conventional thresholds.
- Marina Antillon
- , Ching-I Huang
- & Fabrizio Tediosi
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Article
| Open AccessGenomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission
Post-international travel quarantine has been widely implemented to mitigate SARS-CoV-2 transmission, but the impacts of such policies are unclear. Here, the authors used linked genomic and contact tracing data to assess the impacts of a 14-day quarantine on return to England in summer 2020.
- Dinesh Aggarwal
- , Andrew J. Page
- & Ewan M. Harrison
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Article
| Open AccessFine-scale heterogeneity in population density predicts wave dynamics in dengue epidemics
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