Epidemiology articles within Nature Communications

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  • Article
    | Open Access

    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

  • Article
    | Open Access

    Reopening of universities to students following COVID-19 restrictions risks increased transmission due to high numbers of social contacts and the potential for asymptomatic transmission. Here, the authors use a mathematical model with social contact data to estimate the impacts of reopening a typical non-campus based university in the UK.

    • Ellen Brooks-Pollock
    • , Hannah Christensen
    •  & Leon Danon

  • Article
    | Open Access

    SARS-CoV-2 was first detected in Kenya in March 2020 and there was evidence of local transmission in the following months. Here, the authors characterise the early stages of the epidemic in coastal Kenya using phylogenetics and find evidence of multiple strain importations from international points of entry.

    • George Githinji
    • , Zaydah R. de Laurent
    •  & Charles N. Agoti

  • Article
    | Open Access

    West and colleagues develop the Variant Database software tool for examination of changing Spike mutations in SARS-CoV-2 genomes. The authors use this to detect emerging lineages of SARS-CoV-2 in New York and report the rapid spread of the B.1.526 lineage in the city.

    • Anthony P. West Jr.
    • , Joel O. Wertheim
    •  & Pamela J. Bjorkman

  • Article
    | Open Access

    Detailed information on SARS-CoV-2 infection rates in Latin America by occupation, socioeconomic group and geographic area are rarely available. Here, the authors provide these estimates for in Bogota, Colombia using data from a sentinel surveillance scheme, and find that over half the population had been infected by March 2021.

    • Rachid Laajaj
    • , Camilo De Los Rios
    •  & Duncan Webb

  • Article
    | Open Access

    In the context of limited supply, strategies for optimising allocation of COVID-19 vaccines are needed. Here, the authors explore time-varying strategies that adapt to the epidemiological situation and simultaneously optimise for multiple objectives including reducing numbers of infections, hospitalisations, and deaths.

    • Shasha Han
    • , Jun Cai
    •  & Hongjie Yu

  • Article
    | Open Access

    Diet and food intake have been associated with a risk of developing different types of cancer but individual nutritional epidemiology studies are prone to inherent bias. Here, the authors perform an umbrella review of meta-analyses of observational studies and show the level of evidence for associating food and nutrients to cancer risk.

    • Nikos Papadimitriou
    • , Georgios Markozannes
    •  & Konstantinos K. Tsilidis

  • Article
    | Open Access

    Vo’, Italy, is a unique setting for studying SARS-CoV-2 antibody dynamics because mass testing was conducted there early in the pandemic. Here, the authors perform two follow-up serological surveys and estimate seroprevalence, the extent of within-household transmission, and the impact of contact tracing.

    • Ilaria Dorigatti
    • , Enrico Lavezzo
    •  & Andrea Crisanti

  • Article
    | Open Access

    Plasmodium vivax generally accounts for a low proportion of malaria cases in Africa, but population-level data on the distribution of infections is limited. Here, the authors use data from the Democratic Republic of the Congo and show that the prevalence is low (~3%) and diffusely spread.

    • Nicholas F. Brazeau
    • , Cedar L. Mitchell
    •  & Jonathan J. Juliano

  • Article
    | Open Access

    Sex and gender have been associated with differences in SARS-CoV-2 incidence and clinical outcomes and therefore warrant consideration in study designs. Here, the authors assess registered and published clinical COVID-19 studies and find that sex-disaggregated analyses are infrequently presented or planned.

    • Emer Brady
    • , Mathias Wullum Nielsen
    •  & Sabine Oertelt-Prigione

  • Article
    | Open Access

    Release of freshwater into the oceans as a result of ice sheet melting could impact the distribution of climate-sensitive diseases. Here, the authors show that a rapid ice sheet melting in Greenland could cause an emergence of malaria in Southern Africa whilst transmission risks in West Africa may decline.

    • Alizée Chemison
    • , Gilles Ramstein
    •  & Cyril Caminade

  • Article
    | Open Access

    Resistance of Neisseria gonorrhoeae to extended spectrum cephalosporins is an increasing concern. Here, the authors conduct whole genome sequencing of isolates from the United States and find that most resistant isolates were associated with a persistent circulating lineage.

    • Jesse C. Thomas IV
    • , Sandeep J. Joseph
    •  & Zach Perry

  • Article
    | Open Access

    Selection of COVID-19 mitigation measures requires balancing health outcomes with economic impacts. Here, the authors derive a system to set triggers for increasing mitigation measures to preserve healthcare capacity, and describe how it has been used to support public health decision making in Austin, Texas.

    • Haoxiang Yang
    • , Özge Sürer
    •  & Lauren Ancel Meyers

  • Article
    | Open Access

    COVID-19-related mortality in England shows geographical variation but the reasons for this are not well understood. This study estimated excess mortality in the first wave of the pandemic and found associations with higher density of care homes, overcrowding, and economic deprivation, but not with population density or air pollution.

    • Bethan Davies
    • , Brandon L. Parkes
    •  & Paul Elliott

  • Article
    | Open Access

    Estimating the effectiveness of COVID-19 control measures requires large prospective data including symptoms and personal risk factors. Here, the authors used data from smartphone-based application and found that individual face mask use was associated with a 64% reduced risk of COVID-19 symptoms.

    • Sohee Kwon
    • , Amit D. Joshi
    •  & Andrew T. Chan

  • Article
    | Open Access

    A central problem in the COVID-19 pandemic is that there is not enough testing to prevent infectious spread of SARS-CoV-2, causing surges and lockdowns with human and economic toll. Here, the authors evaluate an alternative strategy based on the monitoring of olfactory dysfunction with a mathematical model.

    • Daniel B. Larremore
    • , Derek Toomre
    •  & Roy Parker

  • Article
    | Open Access

    Despite the consensus that mass vaccination against SARS-CoV-2 will ultimately end the pandemic, it is not clear when and which control measures can be relaxed during the rollout of vaccination programmes. Here, the authors investigate relaxation scenarios using an age-structured transmission model that has been fitted to data for Portugal.

    • João Viana
    • , Christiaan H. van Dorp
    •  & Ganna Rozhnova

  • Article
    | Open Access

    The concentration of SARS-CoV-2 changes during an individual’s infection, and mutations accumulate as viruses are transmitted between people. Here, the authors use data from Iceland to demonstrate how this information can be exploited at the population-level to determine the phase of the epidemic.

    • Hakon Jonsson
    • , Olafur T. Magnusson
    •  & Kari Stefansson

  • Article
    | Open Access

    The role of meteorological factors in SARS-COV-2 transmission is not well understood. Here, the authors use county-level data from the United States to the end of 2020 and find evidence of a moderate association between increased transmissibility and cold, dry weather and low ultraviolet radiation.

    • Yiqun Ma
    • , Sen Pei
    •  & Kai Chen

  • Article
    | Open Access

    Disentangling the impacts of non-pharmaceutical interventions on COVID-19 transmission is challenging as they have been used in different combinations across time and space. This study shows that, early in the epidemic, school/daycare closures and stopping nursing home visits were associated with the biggest reduction in transmission in the United States.

    • Bingyi Yang
    • , Angkana T. Huang
    •  & Derek A. T. Cummings

  • Article
    | Open Access

    Population-based surveys are the gold standard for estimating seroprevalence but are expensive and often only capture a small geographic area or window of time. This study describes a new platform, SCALE-IT, for serosurveillance based on algorithmic sampling of electronic health records, and uses it to estimate the seroprevalence of SARS-CoV-2 in San Francisco.

    • Isobel Routledge
    • , Adrienne Epstein
    •  & Isabel Rodriguez-Barraquer

  • Article
    | Open Access

    Many job sectors classified as ‘essential’ have continued operating with limited restrictions during the COVID-19 pandemic, potentially placing workers at higher risk of infection. Here, the authors show that seropositivity rates in workers vary widely across and between job sectors in Geneva, Switzerland.

    • Silvia Stringhini
    • , María-Eugenia Zaballa
    •  & Idris Guessous

  • Article
    | Open Access

    Matthew M. Hernandez and Ana S. Gonzalez-Reiche and colleagues report evidence of SARSCoV-2 infections in respiratory pathogen-negative nasopharyngeal specimens collected in New York, which date back to over one month before the first officially documented case in the state. The findings provide insights in to the origins of the virus in New York.

    • Matthew M. Hernandez
    • , Ana S. Gonzalez-Reiche
    •  & Emilia Mia Sordillo

  • Article
    | Open Access

    Non-pharmaceutical interventions (NPIs) implemented to interrupt COVID-19 transmission may also impact the spread of other infectious diseases. Here, the authors estimate that influenza activity in China and the United States reduced by up to 80% when NPIs were in place in the 2019–2020 season.

    • Luzhao Feng
    • , Ting Zhang
    •  & George F. Gao

  • Article
    | Open Access

    Open fires can increase heavy exposure to hazardous particulate matters, and thus harm human health, particularly among the vulnerable individuals, such as pregnant women. Here, the authors show an association between maternal exposure to fire smoke and increased risk of pregnancy loss in South Asia.

    • Tao Xue
    • , Guannan Geng
    •  & Tong Zhu

  • Article
    | Open Access

    The percentage of national populations infected during the first stages of the COVID-19 pandemic are unclear owing to limited early testing. Here the authors provide a nation-wide prevalence study of SARS-CoV-2 antibodies in France from the first wave of COVID-19 in 2020, including stratification based on age, sex and region.

    • Stéphane Le Vu
    • , Gabrielle Jones
    •  & Harold Noel

  • Article
    | Open Access

    Initial COVID-19 containment in the United States focused on limiting mobility, including school and workplace closures, with enormous societal and economic costs. Here, the authors demonstrate the feasibility of a test-trace-quarantine strategy using an agent-based model and detailed data on the Seattle region.

    • Cliff C. Kerr
    • , Dina Mistry
    •  & Daniel J. Klein

  • Article
    | Open Access

    Influenza forecasting in the United States is challenging and consequential, with the ability to improve the public health response. Here the authors show the performance of the multiscale flu forecasting model, Dante, that won the CDC’s 2018/19 national, regional and state flu forecasting challenges.

    • Dave Osthus
    •  & Kelly R. Moran

  • Article
    | Open Access

    Generics contribute to increased availability of antibiotics, benefiting healthcare systems but potentially leading to increased consumption with implications for antibiotic stewardship and resistance. Here, the authors found no consistent changes in prescribing patterns of the 13 antibiotics that entered the US market as generics from 2000–2012.

    • Cecilia Kållberg
    • , Jemma Hudson
    •  & Ramanan Laxminarayan

  • Article
    | Open Access

    Whole genome sequencing data are increasingly becoming routinely available but generating actionable insights is challenging. Here, the authors describe Pathogenwatch, a web tool for genomic surveillance of S. Typhi, and demonstrate its use for antimicrobial resistance assignment and strain risk assessment.

    • Silvia Argimón
    • , Corin A. Yeats
    •  & David M. Aanensen

  • Article
    | Open Access

    Higher vitamin D is associated with improved pregnancy and live birth rates, but its potential role in the human offspring sex ratio in unknown. Here, the authors show that the levels of vitamin D at preconception are positively associated with male live birth, particularly among women presenting inflammatory markers.

    • Alexandra C. Purdue-Smithe
    • , Keewan Kim
    •  & Sunni L. Mumford

  • 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

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