Focus 26 January 2021

Public health

Protecting and improving public health requires multidisciplinary research into the determinants of health and disease, and large-scale solutions. Here we showcase work across these areas, including epidemiology, health policy, mathematical modelling, electronic health records research, and Registered Reports.

Featured articles

Drivers of SARS-CoV-2 testing behaviour: a modelling study using nationwide testing data in England

SARS-CoV-2 testing rates have varied during the pandemic but the drivers of changes in testing behaviour are unclear. Here, the authors link national testing data from England to indicators of epidemic trends to describe how testing varies according to level of virus transmission, disease susceptibility/severity, public health measures, and risk perception.
- Younjung Kim
- Christl A. Donnelly
- Pierre Nouvellet
ArticleOpen Access14 Apr 2023 Nature Communications
The impact of introduction of the 10-valent pneumococcal conjugate vaccine on pneumococcal carriage in Nigeria

Nigeria has the highest incidence of pneumococcal disease in Africa and introduced the 10-valent pneumococcal vaccine for infants between 2014 and 2016. Here, the authors conduct repeated cross-sectional surveys to analyse the impact of the vaccination campaign on pneumococcal carriage and serotype distribution.
- Aishatu L. Adamu
- J. Ojal
- Ifedayo M. O. Adetifa
ArticleOpen Access9 May 2023 Nature Communications
Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas

The Amazonas region has been the most heavily affected by COVID-19 in Brazil. In this study, the authors conduct phylodynamic analyses to assess SARS-CoV-2 lineage replacement dynamics in the region and infer the impact of population immunity on the spread and severity of the Delta and Omicron variants.
- Ighor Arantes
- Gonzalo Bello
- Felipe Gomes Naveca
ArticleOpen Access11 Apr 2023 Nature Communications
Effectiveness of BNT162b2 after extending the primary series dosing interval in children and adolescents aged 5–17

Extending the interval between doses of mRNA Covid-19 vaccines has been linked with a reduced risk of myocarditis in children and adolescents, but impacts on vaccine effectiveness are not known. Here, the authors perform a nested case-control study using data from Hong Kong and find evidence of reduced risk of infection following a longer dosing interval.
- Francisco Tsz Tsun Lai
- Min Fan
- Esther Wai Yin Chan
ArticleOpen Access3 Apr 2023 Nature Communications
Transmission modeling to infer tuberculosis incidence prevalence and mortality in settings with generalized HIV epidemics

Accurately estimating the burden of tuberculosis is challenging due to incomplete registration systems and the relationship with HIV. Here, the authors develop a Bayesian modelling strategy accounting for these factors that estimates age- and country-specific annual risks of infection and the proportion resulting from recent infection.
- Peter J. Dodd
- Debebe Shaweno
- Helen Ayles
ArticleOpen Access24 Mar 2023 Nature Communications
Risk of death following COVID-19 vaccination or positive SARS-CoV-2 test in young people in England

Rare but serious cardiac disease side effects have been linked to COVID-19 vaccinations, especially in young people. Here, the authors find very little evidence of an association between vaccination and mortality, except for in females after a non mRNA vaccine, but show an increased risk of death following COVID-19 infection
- Vahé Nafilyan
- Charlotte R. Bermingham
- James C. Doidge
ArticleOpen Access27 Mar 2023 Nature Communications
Long-term measles antibody profiles following different vaccine schedules in China, a longitudinal study

The timing of measles vaccination in infants affects the risk of infection in young children and the duration of protection provided. Here, the authors investigate optimal vaccination timing by characterising antibody kinetics following different vaccine schedules in two cohorts of children in southern China.
- Qianli Wang
- Wei Wang
- Hongjie Yu
ArticleOpen Access29 Mar 2023 Nature Communications
Non-falciparum malaria infection and IgG seroprevalence among children under 15 years in Nigeria, 2018

Nigeria has a high burden of malaria which mostly results from Plasmodium falciparum infection, but other species are also endemic. Here, the authors estimate the prevalence of active infection and previous exposure to P malariae, P ovale, and P vivax in children in Nigeria in 2018 and determine risk factors.
- Camelia Herman
- Colleen M. Leonard
- Eric Rogier
ArticleOpen Access13 Mar 2023 Nature Communications
Maternal SARS-CoV-2 vaccination and infant protection against SARS-CoV-2 during the first six months of life

This study investigates the impact of maternal COVID-19 vaccination during pregnancy on infant infection during the first six months of life. Using data from California, USA, the authors find that protection against infection during the period of Delta dominance was high, but that it declined during the Omicron period.
- Ousseny Zerbo
- G. Thomas Ray
- Nicola P. Klein
ArticleOpen Access28 Feb 2023 Nature Communications
Epidemiological impacts of the NHS COVID-19 app in England and Wales throughout its first year

The NHS COVID-19 digital contact tracing app was designed to notify people of potential exposure to SARS-CoV-2. Here, the authors summarise the uptake and engagement with the app in its first year, and estimate its epidemiological impact in terms of numbers of cases, hospitalisations, and deaths averted.
- Michelle Kendall
- Daphne Tsallis
- Christophe Fraser
ArticleOpen Access22 Feb 2023 Nature Communications
Optimal age targeting for pneumococcal vaccination in older adults; a modelling study

Vaccination against invasive pneumococcal disease is recommended for older adults but the optimal age group to target has not been determined and may vary by epidemiological setting. Here, the authors use statistical modelling to estimate the optimal ages for vaccination in Brazil, England, Malawi, and South Africa.
- Deus Thindwa
- Samuel Clifford
- Stefan Flasche
ArticleOpen Access16 Feb 2023 Nature Communications
A scoping review of the impacts of COVID-19 physical distancing measures on vulnerable population groups

Physical distancing measures introduced to control the spread of COVID-19 had socio-economic trade-offs that may have particularly impacted vulnerable population groups. Here, the authors perform a scoping review and summarise the impacts on different vulnerable groups described in 265 studies.
- Lili Li
- Araz Taeihagh
- Si Ying Tan
ArticleOpen Access3 Feb 2023 Nature Communications
Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa

Emergence of the Omicron BA.1/2 SARS-CoV-2 subvariants led to a wave of infection South Africa. Here, the authors use serological data from a prospective household study to characterise infection rates in the context of diverse immune histories following vaccination and exposure to different variants.
- Kaiyuan Sun
- Stefano Tempia
- the PHIRST-C group
ArticleOpen Access16 Jan 2023 Nature Communications
Impact of the Euro 2020 championship on the spread of COVID-19

In this Bayesian inference study, the authors aim to quantify the impact of the men’s 2020 UEFA Euro Football Championship on COVID-19 spread in twelve participating countries. They estimate that 0.84 million cases and 1,700 deaths were attributable to the championship, with most impacts in England and Scotland.
- Jonas Dehning
- Sebastian B. Mohr
- Viola Priesemann
ArticleOpen Access18 Jan 2023 Nature Communications
Effectiveness of ChAdOx1-S COVID-19 booster vaccination against the Omicron and Delta variants in England

Vaccine effectiveness of a ChAdOx1-S booster was estimated in a test-negative case-control study in England. Protection was found to be moderate against mild disease but remained high and comparable to that of an mRNA booster against hospitalisation with Omicron.
- Freja Cordelia Møller Kirsebom
- Nick Andrews
- Jamie Lopez Bernal
ArticleOpen Access12 Dec 2022 Nature Communications
A population-based serological study of post-COVID syndrome prevalence and risk factors in children and adolescents

The post-acute impacts of COVID-19 in children and adolescents are not well understood. In this population-based study in Geneva, the authors find evidence of COVID-19-related symptom persistence beyond 12 weeks in adolescents, and identify chronic conditions and lower socioeconomic status as risk factors.
- Roxane Dumont
- Viviane Richard
- Idris Guessous
ArticleOpen Access29 Nov 2022 Nature Communications
Disparate impacts on online information access during the Covid-19 pandemic

The COVID-19 pandemic has stimulated an important changes in online information access. Here, the authors analyse everyday web search interactions across 25,150 US ZIP codes revealing significant differences in how digital informational resources are mobilized by different communities.
- Jina Suh
- Eric Horvitz
- Tim Althoff
ArticleOpen Access19 Nov 2022 Nature Communications
Global disparities in SARS-CoV-2 genomic surveillance

In this study, the authors provide a global overview of SARS-CoV-2 genome sequencing, and estimate the proportion of cases sequenced and time to genome upload. They identify disparities and highlight the need to strengthen surveillance in lower and middle income countries.
- Anderson F. Brito
- Elizaveta Semenova
- Nuno R. Faria
ArticleOpen Access16 Nov 2022 Nature Communications
Variant-specific symptoms of COVID-19 in a study of 1,542,510 adults in England

In this study, the authors assess changing symptom profiles associated with different SARS-CoV-2 variants from May 2020 to March 2022 in England. Using data from the REACT-1 study, they find that Omicron infection is more often associated with cold and influenza-like symptoms, and less with loss of taste and smell.
- Matthew Whitaker
- Joshua Elliott
- Paul Elliott
ArticleOpen Access11 Nov 2022 Nature Communications
Contact tracing reveals community transmission of COVID-19 in New York City

In this study, the authors analyse contact tracing records for ~650,000 suspected or confirmed COVID-19 cases in New York City during the second epidemic wave. They reconstruct transmission networks and find that vaccination and zone-based control policies likely contributed to control of the epidemic.
- Sen Pei
- Sasikiran Kandula
- Jeffrey Shaman
ArticleOpen Access23 Oct 2022 Nature Communications
Global mortality of snakebite envenoming between 1990 and 2019

Snakebite envenoming is a leading cause of mortality among neglected tropical diseases. Here, the authors analyze a global data repository and estimate that snakebite envenoming caused over 63,000 deaths in 2019, primarily concentrated in South Asia and Sub-Saharan Africa.
- GBD 2019 Snakebite Envenomation Collaborators
ArticleOpen Access25 Oct 2022 Nature Communications
Impact of antigen test target failure and testing strategies on the transmission of SARS-CoV-2 variants

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
ArticleOpen Access5 Oct 2022 Nature Communications
Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA

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
ArticleOpen Access22 Sep 2022 Nature Communications
Using multiple sampling strategies to estimate SARS-CoV-2 epidemiological parameters from genomic sequencing data

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
ArticleOpen Access23 Sep 2022 Nature Communications
Reproducibility of real-world evidence studies using clinical practice data to inform regulatory and coverage decisions

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
- REPEAT Initiative
ArticleOpen Access31 Aug 2022 Nature Communications
Investigating disparity in access to Australian clinical genetic health services for Aboriginal and Torres Strait Islander people

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
ArticleOpen Access24 Aug 2022 Nature Communications
Modelling the medium-term dynamics of SARS-CoV-2 transmission in England in the Omicron era

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
ArticleOpen Access19 Aug 2022 Nature Communications
Interrupted-time-series analysis of the immediate impact of COVID-19 mitigation measures on preterm birth in China

The broader impacts of COVID-19 mitigation measures may include changes in the incidence of preterm birth. Here, the authors use data from ~11.7 million pregnancies in China and find evidence of a small decline in preterm birth rates immediately following the implementation of COVID-19 mitigation measures.
- Yanxia Xie
- Yi Mu
- Jun Zhu
ArticleOpen Access3 Sep 2022 Nature Communications
Comparison of the 2021 COVID-19 roadmap projections against public health data in England

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
ArticleOpen Access22 Aug 2022 Nature Communications
Comparing the levelized cost of electric vehicle charging options in Europe

Charging costs are important for the diffusion of electric vehicles as required to decarbonize transport. Here, the authors show large variance of electrical vehicle charging costs across 30 European countries and charging options, suggesting different policy options to reduce charging costs.
- Lukas Lanz
- Bessie Noll
- Bjarne Steffen
ArticleOpen Access8 Sep 2022 Nature Communications
Trends in COVID-19 hospital outcomes in England before and after vaccine introduction, a cohort study

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
ArticleOpen Access17 Aug 2022 Nature Communications
Protection of COVID-19 vaccination and previous infection against Omicron BA.1, BA.2 and Delta SARS-CoV-2 infections

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
ArticleOpen Access12 Aug 2022 Nature Communications
SARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings

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
ArticleOpen Access11 Aug 2022 Nature Communications
The effect of COVID certificates on vaccine uptake, health outcomes, and the economy

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
ArticleOpen Access8 Jul 2022 Nature Communications
Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand

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
ArticleOpen Access12 Jul 2022 Nature Communications
An analysis of 45 large-scale wastewater sites in England to estimate SARS-CoV-2 community prevalence

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
ArticleOpen Access25 Jul 2022 Nature Communications
Long COVID burden and risk factors in 10 UK longitudinal studies and electronic health records

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
ArticleOpen Access28 Jun 2022 Nature Communications
Combining rapid antigen testing and syndromic surveillance improves community-based COVID-19 detection in a low-income country

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
ArticleOpen Access26 May 2022 Nature Communications
Non-selective distribution of infectious disease prevention may outperform risk-based targeting

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
ArticleOpen Access31 May 2022 Nature Communications
Disease-economy trade-offs under alternative epidemic control strategies

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
ArticleOpen Access9 Jun 2022 Nature Communications
Elimination of human rabies in Goa, India through an integrated One Health approach

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
ArticleOpen Access19 May 2022 Nature Communications
Off-season RSV epidemics in Australia after easing of COVID-19 restrictions

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
- the Australian RSV study group
ArticleOpen Access24 May 2022 Nature Communications
Seeking patterns of antibiotic resistance in ATLAS, an open, raw MIC database with patient metadata

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
ArticleOpen Access25 May 2022 Nature Communications
Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance

Here, using genomic approaches, Rockett et al. identify Omicron and Delta SARS-CoV-2 co-infections in two adults, highlighting the usefulness of genomic surveillance for the timely recognition of co-infections in situations when different variants of the virus are circulating in the community.
- Rebecca J. Rockett
- Jenny Draper
- Vitali Sintchenko
ArticleOpen Access18 May 2022 Nature Communications
Addressing the socioeconomic divide in computational modeling for infectious diseases

The COVID-19 pandemic has highlighted how structural social inequities fundamentally shape disease dynamics. Here, the authors provide a set of practical and methodological recommendations to address socioeconomic vulnerabilities in epidemic models.
- Michele Tizzoni
- Elaine O. Nsoesie
- Shweta Bansal
CommentOpen Access24 May 2022 Nature Communications
Comparing 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
ArticleOpen Access22 Apr 2022 Nature Communications
Economic shocks predict increases in child wasting prevalence

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
ArticleOpen Access20 Apr 2022 Nature Communications
App-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
ArticleOpen Access21 Apr 2022 Nature Communications

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