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| Open AccessChildhood body size directly increases type 1 diabetes risk based on a lifecourse Mendelian randomization approach
The rise in type 1 diabetes is thought to be related to increased childhood obesity, but this relationship is not well understood. In this study, the authors utilize Mendelian randomization to separate the direct and indirect effects of childhood body size on risk of type 1 diabetes and 7 other immune-associated disease outcomes.
- Tom G. Richardson
- , Daniel J. M. Crouch
- & George Davey Smith
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Article
| 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 AccessApp-based COVID-19 syndromic surveillance and prediction of hospital admissions in COVID Symptom Study Sweden
The app-based COVID Symptom Study was launched in Sweden in April 2020 to contribute to real-time COVID-19 surveillance using daily symptom reports from study participants. Here, the authors show how syndromic surveillance can be used to estimate regional COVID-19 prevalence and to predict later COVID-19 hospital admissions.
- Beatrice Kennedy
- , Hugo Fitipaldi
- & Tove Fall
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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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Article
| Open AccessA polygenic risk score for nasopharyngeal carcinoma shows potential for risk stratification and personalized screening
Polygenic Risk Scores (PRS) show promise for facilitating cancer risk stratification. Here, the authors performed a large genome-wide association study and develop a PRS for nasopharyngeal carcinoma, which could improve risk stratification and personalized screening.
- Yong-Qiao He
- , Tong-Min Wang
- & Wei-Hua Jia
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Article
| 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 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 AccessEmergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage
The SARS-CoV-2 PANGO lineage C.1.2 has been under monitoring by global health authorities as it has spread worldwide. Here, Bhiman and colleagues characterise the emergence of the lineage, and its neutralisation sensitivity using data from vaccinees and previously infected individuals.
- Cathrine Scheepers
- , Josie Everatt
- & Jinal N. Bhiman
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Article
| Open AccessCourse of post COVID-19 disease symptoms over time in the ComPaRe long COVID prospective e-cohort
Long-term complications and persistent symptoms occur following COVID-19, but the nature and duration of the long-term symptoms are not fully characterised. Here the authors report the evolution of post COVID-19 symptoms using a validated self-reported questionnaire assessing 53 symptoms over time in the ComPaRe long COVID prospective e-cohort.
- Viet-Thi Tran
- , Raphaël Porcher
- & Philippe Ravaud
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Article
| Open AccessIdentification of host–pathogen-disease relationships using a scalable multiplex serology platform in UK Biobank
Here, the authors design a multiplex serology platform to quantitatively measure antibodies against 20 infectious agents in UK Biobank participants and confirm associations of antibody responses with sociodemographic characteristics, HLA genetic variants, and disease outcomes.
- Alexander J. Mentzer
- , Nicole Brenner
- & Tim Waterboer
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Article
| 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 AccessSerum proteomics links suppression of tumor immunity to ancestry and lethal prostate cancer
Ancestry-related differences in immunobiology may explain the health disparities observed in prostate cancer patients, with men of African origin bearing the highest prostate cancer burden. By measuring immune-related proteins in serum samples, here the authors report that systemic cytokines linked to suppression of tumor immunity are upregulated in men of African ancestry and associated with reduced survival.
- Tsion Zewdu Minas
- , Julián Candia
- & Stefan Ambs
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Article
| Open AccessHuman seasonal influenza under COVID-19 and the potential consequences of influenza lineage elimination
COVID-19 control measures have suppressed circulation of other infections including influenza. Here, the authors analyse WHO global influenza sequence and case report data and describe changes in the phylogenetic and geographic distribution of influenza lineages during the COVID-19 pandemic.
- Vijaykrishna Dhanasekaran
- , Sheena Sullivan
- & Ian G. Barr
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| 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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| 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 AccessComparative effectiveness of the BNT162b2 and ChAdOx1 vaccines against Covid-19 in people over 50
Several vaccines have been approved for Covid-19 and effectiveness data could guide public health decisions on vaccine usage. Here, the authors compare effectiveness of BNT162b2 and ChAdOx1 vaccines in people over 50 in the UK and find that BNT162b2 confers lower risk of infection and hospitalization.
- Junqing Xie
- , Shuo Feng
- & Dani Prieto-Alhambra
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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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| Open AccessThe indirect effect of mRNA-based COVID-19 vaccination on healthcare workers’ unvaccinated household members
COVID-19 vaccines are effective in preventing disease, but the extent of protection against transmission is unclear. Here, the authors use data from a cohort of healthcare workers in Finland and show that vaccination is associated with reduced infection in their unvaccinated adult household contacts.
- Jussipekka Salo
- , Milla Hägg
- & Lauri Sääksvuori
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| Open AccessWaning of SARS-CoV-2 booster viral-load reduction effectiveness
The BNT162b2 COVID-19 vaccine has been shown to reduce viral load of breakthrough infections (BTIs). Here, analyzing viral loads of BTIs post third vaccine shot, Levine-Tiefenbrun et al. show waning of the booster’s effectiveness in reducing infectiousness within months, mirroring the rate and magnitude of decline observed post the second shot.
- Matan Levine-Tiefenbrun
- , Idan Yelin
- & Roy Kishony
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Article
| Open AccessHomotypic protection against influenza in a pediatric cohort in Managua, Nicaragua
Here Wraith et al. report homotypic protection from repeated influenza infection in a prospective pediatric cohort in Nicaragua followed for 9 years. This protection is observed across multiple seasons, subtypes, and lineages and is consistent for older and younger children.
- Steph Wraith
- , Angel Balmaseda
- & Aubree Gordon
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Article
| Open AccessIncorporating temporal distribution of population-level viral load enables real-time estimation of COVID-19 transmission
The time-varying effective reproductive number (Rt) is useful for monitoring transmission of infections such as COVID-19, but reporting delays impact case count-based estimation methods. Here, the authors demonstrate and validate a method for estimation of Rt based on viral load data from Hong Kong that does not require accurate daily counts.
- Yun Lin
- , Bingyi Yang
- & Benjamin J. Cowling
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Article
| Open AccessAntibody escape and global spread of SARS-CoV-2 lineage A.27
The A.27 SARS-CoV-2 lineage spread globally in 2021 but did not become dominant. Here, the authors show that A.27 shares some mutations in the spike gene that are present in variants of concern, but lacks the D614G mutation, indicating independent evolution of immune escape properties.
- Tamara Kaleta
- , Lisa Kern
- & Jonas Fuchs
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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
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| Open AccessEffect of biannual azithromycin distribution on antibody responses to malaria, bacterial, and protozoan pathogens in Niger
In a randomized placebo-controlled trial in rural Niger, biannual azithromycin distribution to children 1-59 months reduced all-cause mortality. Based on serology, Arzika et al. here report a reduction of Campylobacter infection, supporting one mechanism for the intervention’s impact on mortality.
- Ahmed M. Arzika
- , Ramatou Maliki
- & Benjamin F. Arnold
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Article
| Open AccessPopulation antibody responses following COVID-19 vaccination in 212,102 individuals
The authors present results from the REACT-2 study, a series of cross-sectional community surveys during the SARS-CoV-2 pandemic in England. They measure antibodies by self-administered lateral flow tests and describe antibody positivity by time since vaccination, age, sex, co-morbidities, infection history, and vaccine type.
- Helen Ward
- , Matthew Whitaker
- & Graham S. Cooke
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Article
| Open AccessMark-release-recapture experiment in Burkina Faso demonstrates reduced fitness and dispersal of genetically-modified sterile malaria mosquitoes
Release of genetically-modified sterile mosquitoes is a potential method of malaria control but has yet to be tested in the field. Here, the authors perform a mark-release-recapture experiment and show that genetically-modified mosquitoes have reduced survival and dispersal compared to wild-types.
- Franck Adama Yao
- , Abdoul-Azize Millogo
- & Abdoulaye Diabaté
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Article
| Open AccessGenomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong
Hong Kong has used an elimination strategy to control SARS-CoV-2 with stringent measures including traveller quarantine. Here, the authors show that the majority of community-acquired cases until January 2021 resulted from three importations, and that increased transmission followed prolonged periods of restrictions, likely due to adherence fatigue.
- Haogao Gu
- , Ruopeng Xie
- & Leo L. M. Poon
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| Open AccessGenomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
In this study, Aggarwal and colleagues perform prospective sequencing of SARS-CoV-2 isolates derived from asymptomatic student screening and symptomatic testing of students and staff at the University of Cambridge. They identify important factors that contributed to within university transmission and onward spread into the wider community.
- Dinesh Aggarwal
- , Ben Warne
- & Ian G. Goodfellow
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| Open AccessMultiple expansions of globally uncommon SARS-CoV-2 lineages in Nigeria
SARS-CoV-2 genomic surveillance has been important for informing pandemic responses but many regions remain under-sampled, limiting knowledge of circulating strains. Here, the authors sequence 378 isolates from Nigeria and identify two strains that appear to be important locally though globally uncommon.
- Egon A. Ozer
- , Lacy M. Simons
- & Ramon Lorenzo-Redondo
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| Open AccessCharacterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves
SARS-CoV-2 has resulted in multiple outbreaks in hospitals, but identifying transmission events is challenging. Here, the authors combine whole genome sequencing and epidemiological data from the first two waves of the pandemic at a UK hospital trust and characterise transmission chains.
- Benjamin B. Lindsey
- , Ch. Julián Villabona-Arenas
- & Thushan I. de Silva
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Article
| Open AccessA robust method for collider bias correction in conditional genome-wide association studies
Genetic associations can be biased by conditioning on a phenotype. This study presents ‘Slope-Hunter’, a method which uses model-based clustering to correct this bias, even in the presence of genetic correlation, assuming the class of SNPs affecting only the collider explains more variation in the collider than any other class of SNPs.
- Osama Mahmoud
- , Frank Dudbridge
- & Kate Tilling
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Article
| Open AccessA population-based cohort study of obesity, ethnicity and COVID-19 mortality in 12.6 million adults in England
Obesity is a known risk factor for severe COVID-19 disease. Here, the authors use linked Census, electronic health records, and mortality data for 12.6 million adults in England and show that the association between COVID-19 mortality and body mass index is stronger in ethnic minority groups.
- Thomas Yates
- , Annabel Summerfield
- & Vahé Nafilyan
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Article
| Open AccessCost-effectiveness of routine adolescent vaccination with an M72/AS01E-like tuberculosis vaccine in South Africa and India
The M72/AS01E tuberculosis vaccine has shown 50% efficacy in preventing pulmonary TB disease in infected 18–50 year olds. Here, the authors demonstrate that, in most scenarios modelled, vaccination of adolescents would also be cost effective in two high incidence settings, South Africa and India.
- Rebecca C. Harris
- , Matthew Quaife
- & Richard G. White
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Article
| Open AccessNationally representative SARS-CoV-2 antibody prevalence estimates after the first epidemic wave in Mexico
SARS-CoV-2 seroprevalence surveys provide estimates of the extent of prior infection in a population. In this nationally representative survey from Mexico, the authors estimate seroprevalence after the first epidemic wave at ~25%, with variation by region, age, socioeconomic status, and education level.
- Ana Basto-Abreu
- , Martha Carnalla
- & Andrés Sanchez-Pájaro
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Article
| Open AccessSelf-reported COVID-19 vaccine hesitancy and uptake among participants from different racial and ethnic groups in the United States and United Kingdom
The authors show differences in self-reported vaccine hesitancy and uptake among participants from different racial and ethnic groups in the United States and in the United Kingdom during the initial phase of the COVID-19 vaccine rollout.
- Long H. Nguyen
- , Amit D. Joshi
- & Andrew T. Chan
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Article
| Open AccessImpacts of rapid mass vaccination against SARS-CoV2 in an early variant of concern hotspot
Schwaz, Austria, experienced SARS-CoV-2 outbreaks caused by variants of concern in early 2021 and conducted a mass vaccination campaign in response, with 70% of the adult population vaccinated after 5 days. Here, the authors show that this campaign resulted in reduced infections and hospitalisations.
- Jörg Paetzold
- , Janine Kimpel
- & Hannes Winner
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Article
| Open AccessRelative infectiousness of SARS-CoV-2 vaccine breakthrough infections, reinfections, and primary infections
SARS-CoV-2 breakthrough infections in vaccinated individuals and reinfections in those with prior infection are a public health concern. Here, the authors show that viral loads of vaccine breakthrough infections and reinfections are generally lower than primary infections of unvaccinated individuals, potentially indicating lower infectiousness.
- Laith J. Abu-Raddad
- , Hiam Chemaitelly
- & Roberto Bertollini
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Article
| 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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Article
| 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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Article
| 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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Article
| 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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Article
| 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