Epidemiology articles within Nature Communications

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  • Article
    | Open Access

    Estimates of COVID-19-related mortality are limited by incomplete testing. Here, the authors perform counterfactual analyses and estimate that there were 59,000–62,000 deaths from COVID-19 in Italy until 9th September 2020, approximately 1.5 times higher than official statistics.

    • Chirag Modi
    • , Vanessa Böhm
    •  & Uroš Seljak

  • Article
    | Open Access

    Whole genome sequencing is increasingly being adopted for Shigella sonnei outbreak investigation and surveillance, but there is no global classification standard. Here, the authors develop and validate a genomic framework implemented using open-source software, and demonstrate its application using surveillance data.

    • Jane Hawkey
    • , Kalani Paranagama
    •  & Kathryn E. Holt

  • Article
    | Open Access

    Indoor residual spraying (IRS) of insecticide is one of the primary malaria vector control initiatives, but implementation is limited. Here, the authors show that discontinuation of IRS in Uganda was associated with increased malaria incidence, and introduction of IRS was associated with decreased incidence.

    • Jane F. Namuganga
    • , Adrienne Epstein
    •  & Isabel Rodriguez-Barraquer

  • Article
    | Open Access

    Diarrhoea is a major cause of morbidity and mortality in China. Here, the authors present results from a large sentinel surveillance scheme from 217 hospitals in all 31 provinces in mainland China, including ~150,000 patients with acute diarrhoea and covering years 2009-2018.

    • Li-Ping Wang
    • , Shi-Xia Zhou
    •  & Jun Wang

  • Article
    | Open Access

    Sleep dysregulation has been linked to dementia, but it is unknown whether sleep duration earlier in life is associated with dementia risk. Here, the authors show higher dementia risk associated with short sleep duration (six hours or less) in a longitudinal study of middle and older age adults.

    • Séverine Sabia
    • , Aurore Fayosse
    •  & Archana Singh-Manoux

  • Article
    | Open Access

    Hydroxychloroquine and chloroquine have been investigated as a potential treatment for Covid-19 in several clinical trials. Here the authors report a meta-analysis of published and unpublished trials, and show that treatment with hydroxychloroquine for patients with Covid-19 was associated with increased mortality, and there was no benefit from chloroquine.

    • Cathrine Axfors
    • , Andreas M. Schmitt
    •  & Lars G. Hemkens

  • Article
    | Open Access

    Clarithromycin is a macrolide antibiotic widely used for eradication of Helicobacter pylori infection. Here, Kocsmár et al. study clarithromycin resistance and previous macrolide consumption in 4,744 H. pylori-infected patients, shedding light into the sources of primary resistant cases and the role played by prior consumption of macrolides for non-eradication purposes.

    • Éva Kocsmár
    • , György Miklós Buzás
    •  & Gábor Lotz

  • Article
    | Open Access

    Estimating the effects of non-pharmaceutical interventions for COVID-19 is challenging, partly due to variations in testing. Here, the authors use viral sequence data as an alternative means of inferring intervention effects, and show that delays in implementation resulted in more severe epidemics.

    • Manon Ragonnet-Cronin
    • , Olivia Boyd
    •  & Erik Volz

  • Article
    | Open Access

    Large fissure eruptions can cause air pollution events when the volcanic plume returns to the same area after the initial advisory has been lifted. Here, the authors show that these events had a significant impact on health care usage in Iceland, and the impact was exacerbated when advisories were not issued successfully.

    • Hanne Krage Carlsen
    • , Evgenia Ilyinskaya
    •  & Thorolfur Gudnason

  • Article
    | Open Access

    Population-based studies of SARS-CoV-2 seroprevalence are needed to understand levels of immunity and antibody dynamics. Here, the authors show that the seroprevalence in Bonn, Germany was low (<1%) following the first epidemic wave, and that neutralising antibodies waned within a few months.

    • N. Ahmad Aziz
    • , Victor M. Corman
    •  & Monique M. B. Breteler

  • Article
    | Open Access

    Our understanding of the immune response to SARS-CoV-2 infection is still incomplete. Here, the authors find that IL-33, produced during immune recall potentially by CD14+ monocytes, correlates with CD4+ T cell activation, anti-SARS-CoV-2 antibody titer, and disease severity in a cohort of convalescent individuals professionally exposed to the virus.

    • Michal A. Stanczak
    • , David E. Sanin
    •  & Erika L. Pearce

  • Article
    | Open Access

    Serological detection of antibodies against SARS-CoV-2 can help establish rates of seroconversion. Here the authors develop a red cell agglutination test to detect antibodies against the receptor binding domain for distribution free of charge to qualified research groups.

    • Alain Townsend
    • , Pramila Rijal
    •  & Etienne Joly

  • Article
    | Open Access

    Many countries have closed schools as part of their COVID-19 response. Here, the authors model SARS-CoV-2 transmission on a network of schools and households in England, and find that risk of transmission between schools is lower if primary schools are open than if secondary schools are open.

    • James D. Munday
    • , Katharine Sherratt
    •  & Sebastian Funk

  • Article
    | Open Access

    COVID-19 has caused many healthcare systems to become overwhelmed, potentially impacting patient care. Here, the authors show that COVID-19-related in-hospital mortality rates in Israel increased in periods of moderate or high hospital load, independent of patient characteristics.

    • Hagai Rossman
    • , Tomer Meir
    •  & Malka Gorfine

  • Article
    | Open Access

    Contact tracing for a timely isolation of potentially infected individuals can be provided manually or via digital applications. Mancastroppa et al. show that in the combination of both procedures the manual tracing is dominant and allows for better detection of infection super-spreaders.

    • Marco Mancastroppa
    • , Claudio Castellano
    •  & Raffaella Burioni

  • Article
    | Open Access

    Digital contact tracing is increasingly considered as one of the tools to control infectious disease outbreaks, in particular the COVID-19 epidemic. Here, the authors present a modeling framework informed by empirical high-resolution contact data to analyze the impact of digital contact tracing apps.

    • G. Cencetti
    • , G. Santin
    •  & B. Lepri

  • Article
    | Open Access

    Malaria transmission-blocking vaccines are in development, but roll-out strategies have not been assessed. Here, the authors show that transmission-blocking activity is likely to be higher in the field than in laboratory conditions, and that school-aged children are an important group to target.

    • Joseph D. Challenger
    • , Daniela Olivera Mesa
    •  & Thomas S. Churcher

  • Article
    | Open Access

    Recent toxicological studies suggest that wildfire particulate matter may be more toxic than equal doses of ambient PM2.5. Here, the authors show that even for similar exposure levels, PM2.5 from wildfires is considerably more dangerous for respiratory health at the population level.

    • Rosana Aguilera
    • , Thomas Corringham
    •  & Tarik Benmarhnia

  • Article
    | Open Access

    Here, the authors determine seroprevalence of antibodies to SARS-CoV-2 in healthy blood donors in the cities of Wuhan, Shenzhen, and Shijiazhuang in China between January and April 2020. The age- and sex-standardized SARS-CoV-2 seroprevalence among 18–60 year-old adults is, with 2.66%, the highest in Wuhan.

    • Le Chang
    • , Wangheng Hou
    •  & Lunan Wang

  • Article
    | Open Access

    One of the primary tools that researchers use to predict risk is the case-control study. Here, the authors identify a flaw, temporal bias, that is specific to and uniquely associated with these studies that occurs when the study period is not representative of the data that clinicians have during the diagnostic process, undermining the validity of predictions.

    • William Yuan
    • , Brett K. Beaulieu-Jones
    •  & Isaac S. Kohane

  • Article
    | Open Access

    Social distancing policies aiming to reduce COVID-19 transmission have been reflected in reductions in human mobility. Here, the authors show that reduced mobility is correlated with decreased transmission, but that this relationship weakened over time as social distancing measures were relaxed.

    • Pierre Nouvellet
    • , Sangeeta Bhatia
    •  & Christl A. Donnelly

  • Article
    | Open Access

    The role of children in the spread of COVID-19 is not fully understood, and the circumstances under which schools should be opened are therefore debated. Here, the authors demonstrate protocols by which schools in France can be safely opened without overwhelming the healthcare system.

    • Laura Di Domenico
    • , Giulia Pullano
    •  & Vittoria Colizza

  • Article
    | Open Access

    New Zealand has been relatively successful in controlling COVID-19 due to implementation of strict non-pharmaceutical interventions. Here, the authors demonstrate a striking decline in reports of influenza and other non-influenza respiratory pathogens over winter months in which the interventions have been in place.

    • Q. Sue Huang
    • , Tim Wood
    •  & Richard J. Webby

  • Article
    | Open Access

    Dexamethasone has been shown to have survival benefits for critically ill patients hospitalised with COVID-19 in the UK. Here, the authors estimated the number of lives that could be saved through a UK and global roll out of the drug and demonstrate that it is a cost-effective option.

    • Ricardo Águas
    • , Adam Mahdi
    •  & Mesulame Namedre

  • Article
    | Open Access

    Asymptomatic malaria infections contribute to transmission. Here, Sumner et al. infer participant-to-mosquito transmission by sampling naturally-fed mosquitoes from households in Western Kenya and find that asymptomatic infections more than double the odds of transmission to a mosquito compared to symptomatic infections.

    • Kelsey M. Sumner
    • , Elizabeth Freedman
    •  & Steve M. Taylor

  • Article
    | Open Access

    REACT-2 is a large-scale community study of SARS-CoV-2 seroprevalence in England. Here, the authors estimate that 6% of adults in England had been infected by mid-July 2020, with health and long-term care workers and those of Black or South Asian ethnicity disproportionately affected.

    • Helen Ward
    • , Christina Atchison
    •  & Paul Elliott

  • Article
    | Open Access

    Understanding if lasting immune responses can be induced by SARS-CoV-2 infection is important for controlling the COVID-19 pandemic. Here, the authors show, in a cohort of 25 patients, that IgG and T cell responses, as well as neutralising antibody, are still detectable against various SARS-CoV-2 proteins 3 months post-symptom onset, while IgM levels largely wane at this time.

    • Xiao-Lin Jiang
    • , Guo-Lin Wang
    •  & Mai-Juan Ma

  • Article
    | Open Access

    Spread of SARS-CoV-2 in the early phase of the pandemic has been driven by high population susceptibility, but virus sensitivity to climate may play a role in future outbreaks. Here, the authors simulate SARS-CoV-2 dynamics in winter assuming climate dependence is similar to an endemic coronavirus strain.

    • Rachel E. Baker
    • , Wenchang Yang
    •  & Bryan T. Grenfell

  • Article
    | Open Access

    Establishing the natural history of COVID-19 requires longitudinal data from population-based cohorts. Here, the authors use linked primary care, testing, and hospital data to describe the disease in ~100,000 individuals with a COVID-19 diagnosis among a population of ~5.5 million in Catalonia, Spain.

    • Edward Burn
    • , Cristian Tebé
    •  & Talita Duarte-Salles

  • Article
    | Open Access

    Incidence of COVID-19 has been high in parts of South America including Brazil, and information on effective intervention strategies is needed. Here, the authors use mathematical modelling to show that reductions in social distancing should be made gradually to avoid a severe second peak of cases.

    • Osmar Pinto Neto
    • , Deanna M. Kennedy
    •  & Renato Amaro Zângaro

  • Article
    | Open Access

    Test, trace, and isolate programmes are central to COVID-19 control. Here, Viola Priesemann and colleagues evaluate how to allocate scarce resources to keep numbers low, and find that if case numbers exceed test, trace and isolate capacity, there will be a self-accelerating spread.

    • Sebastian Contreras
    • , Jonas Dehning
    •  & Viola Priesemann

  • Article
    | Open Access

    The growing need for realism in addressing complex public health questions calls for accurate models of the human contact patterns that govern disease transmission. Here, the authors generate effective population-level contact matrices by using highly detailed macro (census) and micro (survey) data on key socio-demographic features.

    • Dina Mistry
    • , Maria Litvinova
    •  & Alessandro Vespignani

  • Article
    | Open Access

    Sparse testing early in the SARS-CoV-2 pandemic hinders estimation of the dates and origins of initial case importations. Here, the authors show that the main source of cases imported from China shifted from Wuhan to other Chinese cities by mid-February, especially for African locations.

    • Tigist F. Menkir
    • , Taylor Chin
    •  & Rene Niehus

  • Article
    | Open Access

    Low-resource settings can face additional challenges in managing the COVID-19 pandemic. Here, the authors use mathematical modelling to investigate transmission in the state of Bahia, Brazil, and quantify control measures needed to prevent the hospital system becoming overwhelmed.

    • Juliane F. Oliveira
    • , Daniel C. P. Jorge
    •  & Roberto F. S. Andrade

  • Article
    | Open Access

    Contact tracing is critical to controlling COVID-19, but most protocols only “forward-trace” to notify people who were recently exposed. Using a stochastic branching-process model, the authors show that “bidirectional” tracing to identify infector individuals and their other infectees robustly improves outbreak control.

    • William J. Bradshaw
    • , Ethan C. Alley
    •  & Kevin M. Esvelt

  • Article
    | Open Access

    Anecdotal reports suggest potential severity and outcome differences between sexes following infection by SARS-CoV-2. Here, the authors perform meta-analyses of more than 3 million cases collected from global public data to demonstrate that male patients with COVID-19 are 3 times more likely to require intensive care, and have ~40% higher death rate.

    • Hannah Peckham
    • , Nina M. de Gruijter
    •  & Claire T. Deakin

  • Article
    | Open Access

    Although many COVID-19 cases are mild, most information about symptoms is derived from hospitalized patients. Here, the authors link self-reported symptom surveys to primary care data to describe the longitudinal dynamics of COVID-19 in non-hospitalized individuals.

    • Barak Mizrahi
    • , Smadar Shilo
    •  & Eran Segal

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