Epidemiology articles within Nature Communications

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  • Article
    | Open Access

    This study investigates the effectiveness of COVID-19 vaccine boosters following a primary series of CoronaVac vaccination. Using data from Brazil during the Omicron wave, the authors show that boosters provided protection against severe disease, with higher effectiveness from a BNT162b2 than CoronaVac booster.

    • Otavio T. Ranzani
    • , Matt D. T. Hitchings
    •  & Julio Croda

  • Article
    | Open Access

    Increasing reliance on antigen tests for SARS-CoV-2 screening may risk selection for variants not detected by these tests. Here, the authors identify a variant of this type circulating in Italy, estimate the potential impact of failure to detect the variant, and model testing strategies to mitigate the risk.

    • Claudia Del Vecchio
    • , Bethan Cracknell Daniels
    •  & Andrea Crisanti

  • Article
    | Open Access

    South Africa experienced a resurgence in COVID-19 in 2022 driven by Omicron subvariants BA.4 and BA.5. Here, the authors investigate the severity of infections caused by these subvariants, and find no difference in the risk of severe outcomes when compared to Omicron BA.1, whilst all Omicron subvariants were less severe than Delta.

    • Nicole Wolter
    • , Waasila Jassat
    •  & Cheryl Cohen

  • Article
    | Open Access

    In this study the authors investigate household transmission of SARS-CoV-2 in Norway. They find that the secondary attack rate was higher for Omicron than Delta, but that among three-dose vaccinated contacts the secondary attack rate was lower for both variants compared to contacts with two doses.

    • Neda Jalali
    • , Hilde K. Brustad
    •  & Birgitte Freiesleben de Blasio

  • Article
    | Open Access

    Iceland has used four different SARS-CoV-2 vaccines in various combinations. Here, the authors describe differences in the immune responses elicited by different initial/booster vaccine combinations, and then use population-level data to assess the effects of booster doses against Delta and Omicron infection.

    • Gudmundur L. Norddahl
    • , Pall Melsted
    •  & Kari Stefansson

  • Article
    | Open Access

    SARS-CoV-2 genome sequencing data can be used to infer epidemiological parameters, but the impact of the strategy used to select samples on these estimates is rarely considered. Here, the authors produce estimates using different sampling strategies and compare results to those based on case reporting data.

    • Rhys P. D. Inward
    • , Kris V. Parag
    •  & Nuno R. Faria

  • Article
    | Open Access

    In this study, the authors compare the transmission dynamics of the Delta and Omicron SARS-CoV-2 variants using household data from Denmark. They find that Omicron has a higher secondary attack rate, and that the odds of infection with Omicron was higher than with Delta, particularly for vaccinated individuals.

    • Frederik Plesner Lyngse
    • , Laust Hvas Mortensen
    •  & Carsten Thure Kirkeby

  • Article
    | Open Access

    In this study, the authors develop a method for estimation of SARS-CoV-2 community transmission rates based on a sentinel population of people seeking outpatient testing with recent symptom onset. This method has fewer operational delays than methods based on hospital data, and may be subject to fewer biases.

    • Reese Richardson
    • , Emile Jorgensen
    •  & Jaline Gerardin

  • Article
    | Open Access

    Antiviral treatments for SARS-CoV-2 infection are only beneficial when used early in infection, so early case detection is important. Here, the authors assess the frequency of testing needed to achieve population-level benefits and demonstrate the importance of high coverage and short delays from test to treatment.

    • Tigist F. Menkir
    •  & Christl A. Donnelly

  • Article
    | Open Access

    Frailty is associated with an increased risk for negative health outcomes in older populations, and being able to predict frailty could facilitate prevention measures. By performing an epigenome-wide screen, the authors derived a DNA methylation based measure for frailty which can predict both prevalence and longer-term incidence of frailty.

    • Xiangwei Li
    • , Thomas Delerue
    •  & Hermann Brenner

  • Article
    | Open Access

    This study presents results from a SARS-CoV-2 genomic surveillance study at a university campus in which ~2,000 samples were sequenced over five months. The authors document the replacement of Delta with Omicron as the dominant variant, and describe clinical characteristics and transmission dynamics.

    • Ana A. Weil
    • , Kyle G. Luiten
    •  & Helen Y. Chu

  • Article
    | Open Access

    Analyses of real-world evidence from digital clinical practice data provide important insights for healthcare decision makers. Here, authors test reproducibility of 150 peer-reviewed studies, reporting strong reproducibility, which could be further improved through more complete reporting in future original studies

    • Shirley V. Wang
    • , Sushama Kattinakere Sreedhara
    •  & Deborah Zarin

  • Comment
    | Open Access

    In the current monkeypox outbreak, vaccination and treatment of pregnant women are recommended only if the benefits outweigh risks, but the extremely sparse data available limit evidence-based recommendations. We must facilitate a unified consensus approach to rapidly collect robust data. Two years into the COVID-19 pandemic, monkeypox has emerged as yet another challenge to the mother-fetus dyad, potentially placing both at risk, if exposed.

    • Asma Khalil
    • , Athina Samara
    •  & Shamez Ladhani

  • Article
    | Open Access

    Globally it is recognised that Indigenous populations should be able to access the benefits of genomics and precision medicine. Here, authors show that there are disparities in access to clinical genetic health services for Aboriginal and/or Torres Strait Islander people in Australia.

    • Joanne Luke
    • , Philippa Dalach
    •  & Margaret Kelaher

  • Article
    | Open Access

    The ’Roadmap’ for relaxation of COVID-19 restrictions in England in 2021 was informed by mathematical modelling. Here, the authors perform a retrospective assessment of the accuracy of modelling predictions and identify the main sources of uncertainty that led to observed values deviating from projections.

    • Matt J. Keeling
    • , Louise Dyson
    •  & Samuel Moore

  • Article
    | Open Access

    This mathematical modelling study projects the dynamics of SARS-CoV-2 in England until the end of 2022 assuming that the Omicron BA.2 sublineage remains dominant. They show that booster vaccination was highly effective in mitigating severe outcomes and that future dynamics will depend greatly on assumptions about waning immunity.

    • Rosanna C. Barnard
    • , Nicholas G. Davies
    •  & W. John Edmunds

  • Article
    | Open Access

    Here the authors provide data from a sub-cohort of the Virus Watch study (19,556 adults) who completed at-home capillary blood sampling on a monthly basis and describe an association between anti-spike antibody levels and risk of SARS-CoV-2 infection.

    • Robert W. Aldridge
    • , Alexei Yavlinsky
    •  & Andrew Hayward

  • Article
    | Open Access

    This study investigates trends in mortality and length of stay for people hospitalised with COVID-19 in England until September 2021. It shows that risks were higher for unvaccinated people and those with multiple comorbidities, and that busier hospitals had higher mortality rates at the start of the pandemic but this effect lessened over time.

    • Peter D. Kirwan
    • , Andre Charlett
    •  & Anne M. Presanis

  • Article
    | Open Access

    Here, Simpson et al. analyze data from 3.6 million COVID-19 vaccine second doses (ChAdOx1 and BNT162b2) in Scotland for risk of thrombocytopenic, thromboembolic and hemorrhagic events. Borderline increased risks of immune thrombocytopenic purpura and cerebral venous sinus thrombosis were found for the ChAdOx1 vaccine. These events were rare and usually short-lived.

    • Colin R. Simpson
    • , Steven Kerr
    •  & Aziz Sheikh

  • Article
    | Open Access

    The dynamics of SARS-CoV-2 transmission in the Middle East have been relatively under-studied. Here, the authors integrate genomic and travel data and show that introductions to the region were initially driven by intercontinental air travel, after which regional land travel became a more important driver.

    • Edyth Parker
    • , Catelyn Anderson
    •  & Issa Abu-Dayyeh

  • Article
    | Open Access

    There is limited evidence of the effectiveness of the CoronaVac vaccine for children against the Omicron SARS-CoV-2 variant. Here, the authors use data from Brazil for children aged 6–11 years and estimate effectiveness of 40% against infection and 59% against severe disease at least two weeks after the second dose.

    • Pilar T. V. Florentino
    • , Flávia J. O. Alves
    •  & Enny S. Paixão

  • Article
    | Open Access

    Backward contact tracing aims to identify individuals who were infected by the same person as infected an index case, and has been shown to be effective in modelling studies of SARS-COV-2. Here, the authors present empirical data of the effectiveness of backward contact tracing from a program amongst university students in Belgium.

    • Joren Raymenants
    • , Caspar Geenen
    •  & Emmanuel Andre

  • Article
    | Open Access

    The protection of COVID-19 vaccines against emerging variants needs to be monitored. Here, the authors use community testing data from the Netherlands and find that protection against infection by Omicron subvariants BA.1 and 2 is low and that booster vaccines considerably but temporarily increase protection.

    • Stijn P. Andeweg
    • , Brechje de Gier
    •  & Mirjam J. Knol

  • Article
    | Open Access

    Air surveillance offers a potential means of monitoring airborne pathogens without the need for individual sampling. Here, the authors perform continuous air sampling in 15 community settings in the US for 29 weeks and demonstrate its feasibility for routine detection of SARS-CoV-2 and other respiratory pathogens.

    • Mitchell D. Ramuta
    • , Christina M. Newman
    •  & Shelby L. O’Connor

  • Comment
    | Open Access

    We reflect on the extent to which the UK Events Research Programme adhered to four principles of design and evaluation in assessing risk of transmission from attending such mass events as football matches and festivals, and lessons learned.

    • Theresa M. Marteau
    • , Michael J. Parker
    •  & W. John Edmunds

  • Article
    | Open Access

    The level of immunity induced by infection with different SARS-CoV-2 Omicron sub-lineages against infection with other sub-lineages is not known. Here, the authors use data from Qatar and show that infection with BA.1 induces strong protection against infection with BA.2, and vice versa, for several weeks.

    • Hiam Chemaitelly
    • , Houssein H. Ayoub
    •  & Laith J. Abu-Raddad

  • Article
    | Open Access

    Clinical diagnosis of Treponema pallidum subspecies pallidum (TPA), the causative agent of syphilis, depends upon serological testing, which has reduced sensitivity for some stages of the disease. Accompanying methods to complement serological testing also have distinct limitations. In this work, authors develop an assay that combines PCR with CRISPR-LwCas13a, and demonstrate sensitivity and specificity on clinically confirmed syphilis samples.

    • Wentao Chen
    • , Hao Luo
    •  & Heping Zheng

  • Article
    | Open Access

    There is a broad range of research available on the relationship between food security and mental health. Here the authors carry out a systematic mapping of evidence on food security and nutrition related to mental health and identifies trends in themes, setting, and study design over the 20 year period studied.

    • Thalia M. Sparling
    • , Megan Deeney
    •  & Suneetha Kadiyala

  • Article
    | Open Access

    The REACT-1 study measures the community prevalence of SARS-CoV-2 in England through repeated cross-sectional surveys. Here, the authors present data from REACT-1 that document the increase in infection prevalence, particularly among children, associated with the Omicron variant in January 2022.

    • Paul Elliott
    • , Oliver Eales
    •  & Christl A. Donnelly

  • Article
    | Open Access

    REGEN-COV is a SARS-CoV-2 combined monoclonal antibody treatment which has been shown to be effective in randomised controlled trials. Here, the authors assess its real-world effectiveness using data from Israel during the Delta wave and find that it reduced the risk of hospitalisation, severe disease and death.

    • Samah Hayek
    • , Yatir Ben-shlomo
    •  & Alon Peretz

  • Article
    | Open Access

    The SARS-CoV-2 Omicron variant is associated with high rates of vaccine breakthrough infections, but the immunological basis for this is not well characterised. Here, the authors show that increased anti-Spike IgG antibody levels are associated with a reduced risk of infection with the Delta variant, but not with Omicron.

    • Nina Breinholt Stærke
    • , Joanne Reekie
    •  & Ole Schmeltz Søgaard

  • Article
    | Open Access

    This study presents data from the REACT-1 SARS-CoV-2 community sampling study in England from November 2021 to March 2022. They show that the Omicron variant peaked in January with a prevalence of ~7% and that the BA.2 sublineage had a 1.5x higher reproduction number compared to other Omicron sublineages.

    • Oliver Eales
    • , Leonardo de Oliveira Martins
    •  & Marc Chadeau-Hyam

  • Article
    | Open Access

    Wastewater surveillance could provide a means of monitoring SARS-CoV-2 prevalence that does not rely on testing individuals. Here, the authors report results from England’s national wastewater surveillance program, use it to estimate prevalence, and compare estimates with those from population-based prevalence surveys.

    • Mario Morvan
    • , Anna Lo Jacomo
    •  & Leon Danon

  • Article
    | Open Access

    The health impacts associated with SARS-CoV-2 infection are still not well understood. Here, the authors report findings from a survey of ~150,000 people in Denmark, and identify elevated risks associated with testing positive for SARS-CoV-2 for a range of acute and post-acute symptoms and new diagnoses.

    • Anna Irene Vedel Sørensen
    • , Lampros Spiliopoulos
    •  & Anders Hviid

  • Article
    | Open Access

    Primary CoronaVac vaccination followed by a BNT162b2 booster dose confers protection against some SARS-CoV-2 variants but its effectiveness against Omicron is unknown. Here, the authors show that this combination confers a high level of protection against severe outcomes for up to 120 days, with evidence of waning for those aged 80 or older.

    • Thiago Cerqueira-Silva
    • , Vinicius de Araujo Oliveira
    •  & Manoel Barral-Netto

  • Article
    | Open Access

    Aotearoa New Zealand pursued a COVID-19 elimination strategy until October 2021 when it moved to a suppression strategy. In this genomic surveillance study, the authors describe spread of the virus during the transition between these strategies, with evidence of substantial undetected community transmission.

    • Lauren Jelley
    • , Jordan Douglas
    •  & Jemma L. Geoghegan

  • Article
    | Open Access

    Here the authors estimate effectiveness of three COVID-19 vaccines in university students and find that 2-dose mRNA vaccines offer strong protection against general SARS-CoV-2 infection caused by delta, but protection substantially declines over 6 months. While previous infection protects against reinfection, vaccination substantially increases protection.

    • Lior Rennert
    • , Zichen Ma
    •  & Delphine Dean

  • Article
    | Open Access

    Many countries introduced COVID certificates that were required to access public venues. Here, the authors analyse data from France, Germany, and Italy, and estimate that these policies led to increased vaccine uptake of 6-13 percentage points with subsequent beneficial impacts on health and economic outcomes.

    • Miquel Oliu-Barton
    • , Bary S. R. Pradelski
    •  & Guntram B. Wolff

  • Article
    | Open Access

    The whipworm Trichuris trichiura is a soil-transmitted helminth that causes the neglected tropical disease trichuriasis in humans. Here, the authors produce whole genome sequences of modern and ancient samples from humans and non-human primates to characterise the genomic diversity and evolution of this pathogen.

    • Stephen R. Doyle
    • , Martin Jensen Søe
    •  & Christian Moliin Outzen Kapel

  • Article
    | Open Access

    Estimating the effectiveness of malaria vector control interventions has typically relied on resource-intensive cluster randomised trials. Here, the authors estimate changes in malaria prevalence using entomological data from experimental hut trials, which may provide an alternative route to approval of interventions in some situations.

    • Ellie Sherrard-Smith
    • , Corine Ngufor
    •  & Thomas S. Churcher

  • Article
    | Open Access

    COVID-19 vaccines may reduce the susceptibility of an individual to infection and/or the infectiousness of breakthrough infections. Here, the authors use data from Denmark and estimate that vaccine effectiveness was 61% for susceptibility and 31% for infectiousness during a period of Delta variant dominance.

    • Frederik Plesner Lyngse
    • , Kåre Mølbak
    •  & Carsten Thure Kirkeby

  • Article
    | Open Access

    The impact of prior infection on the immune response to COVID-19 vaccination has not been fully characterised. Here, the authors use data from ~100,000 adults in the UK and find that a single vaccine dose in those with prior infection produces a comparable or stronger response to two doses in those without infection.

    • Jia Wei
    • , Philippa C. Matthews
    •  & Chris Cunningham

  • Article
    | Open Access

    Current understanding of Long COVID is limited, in part, due to lack of evidence from population-representative studies. Here, the authors analyse data from ten UK population-based studies and electronic health records, and find wide variation in the frequency of Long COVID between studies but some consistent risk factors.

    • Ellen J. Thompson
    • , Dylan M. Williams
    •  & Claire J. Steves

  • Article
    | Open Access

    Infection with the SARS-CoV-2 Omicron variant appears to cause milder disease in the general population than infection with Delta. Here the authors use data from the US Department of Veterans Affairs and demonstrate that this also applies to infection in an at-risk population of older age and with more co-morbidities.

    • Florian B. Mayr
    • , Victor B. Talisa
    •  & Adeel A. Butt

  • Article
    | Open Access

    Hong Kong experienced a severe wave of SARS-CoV-2 in early 2022. Here, the authors use genomic and serosurveillance data and show that this wave was dominated by the Omicron BA.2 sublineage, and that low protective immunity, particularly in older age groups, contributed to its severity.

    • Lin-Lei Chen
    • , Syed Muhammad Umer Abdullah
    •  & Kelvin Kai-Wang To

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