Public health articles within Nature Communications

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  • 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

    As mass quarantines, absences due to sickness, or other shocks thin out patient-physician networks, the system might be pushed to a tipping point where it loses its ability to deliver care. Here, the authors propose a data-driven framework to quantify regional resilience to such shocks via an agent-based model.

    • Michaela Kaleta
    • , Jana Lasser
    •  & Peter Klimek

  • 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

    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

    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

    Dewald et al. combine a non-invasive sampling approach (Lolli-Test) with an RT qPCR-pool testing strategy to screen for SARS-CoV-2 infections in children and use the method for surveillance and infection control in > 4000 school and daycare settings.

    • Felix Dewald
    • , Isabelle Suárez
    •  & Florian Klein

  • 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

  • Article
    | Open Access

    In this retrospective study, authors show that relative protection against SARS-CoV-2 infection wanes from 53.4% one month after vaccination to 16.5% three months after vaccination, suggesting that there is a significant waning of mRNA vaccine effectiveness against infection with the Omicron variant.

    • Tal Patalon
    • , Yaki Saciuk
    •  & Sivan Gazit

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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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