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

The counterintuitive implications of superspreading diseases

The superspreading that characterized SARS and now COVID-19 can be rapidly quantified; however, its implications for outbreak control were never well understood. Recent studies point to its profound impact on outbreak dynamics and prospects for effective control of a future Disease X. These insights necessitate research into the mechanisms, impact and different modes of superspreading more widely.
- Bjarke Frost Nielsen
- Kim Sneppen
- Lone Simonsen
CommentOpen Access31 Oct 2023 Nature Communications
Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty

The US COVID-19 Scenario Modeling Hub produced medium to long term projections based on different epidemic scenarios. In this study, the authors evaluate 14 rounds of projections by comparing them to the epidemic trajectories that occurred, and discuss lessons learned for future similar projects.
- Emily Howerton
- Lucie Contamin
- Justin Lessler
ArticleOpen Access20 Nov 2023 Nature Communications
Circadian disturbances and frailty risk in older adults

The relationship between circadian function and frailty is not well understood. Here, the authors show that disturbances in circadian rest-activity rhythms were associated with an elevated frailty risk and faster progress of frailty in older adults.
- Ruixue Cai
- Lei Gao
- Peng Li
ArticleOpen Access16 Nov 2023 Nature Communications
Impact of COVID-19 on mortality in coastal Kenya: a longitudinal open cohort study

SARS-CoV-2-associated mortality estimates for sub-Saharan Africa are uncertain due to lack of comprehensive surveillance systems. Here, the authors analyse data from a detailed surveillance system in Kilifi, Kenya and find that excess mortality rates were relatively low, except for older adults.
- M. Otiende
- A. Nyaguara
- J. A. G. Scott
ArticleOpen Access28 Oct 2023 Nature Communications
Using drivers and transmission pathways to identify SARS-like coronavirus spillover risk hotspots

Identification of areas with risk factors for spillover of viruses from animals to humans could assist with early detection of emerging infectious diseases. In this study, the authors characterise potential risks for spillover of SARS-like viruses from bats to humans and identify geographical regions in which multiple risk factors cluster together.
- Renata L. Muylaert
- David A. Wilkinson
- David T. S. Hayman
ArticleOpen Access27 Oct 2023 Nature Communications
Individual level analysis of digital proximity tracing for COVID-19 in Belgium highlights major bottlenecks

Digital proximity tracing apps were widely used during the COVID-19 pandemic but have not been thoroughly evaluated. Here, the authors use data from students in Leuven, Belgium and estimate that apps notified only ~4% exposed contacts, had a 1–2 day delay for notification, and identified fewer infected contacts than manual contact tracing.
- Caspar Geenen
- Joren Raymenants
- Emmanuel André
ArticleOpen Access23 Oct 2023 Nature Communications
Viral kinetics of sequential SARS-CoV-2 infections

In this study, the authors compare the viral kinetics of first and second SARS-CoV-2 infections using data from an occupational surveillance scheme in the National Basketball League. They find that second infections tend to have a faster clearance time, and that clearance times in first and second infections were positively correlated.
- Stephen M. Kissler
- James A. Hay
- Yonatan H. Grad
ArticleOpen Access5 Oct 2023 Nature Communications
Global burden of disease due to rifampicin-resistant tuberculosis: a mathematical modeling analysis

Rifampicin-resistant tuberculosis (RR-TB) requires longer, more toxic therapy than rifampicin-sensitive disease and is associated with a higher occurrence of long-term sequelae. In this mathematical modeling study, the authors estimate that incident RR-TB in 2020 will be responsible for ~6.9 million disability-adjusted life years; 44% due to post-tuberculosis sequelae.
- Nicolas A. Menzies
- Brian W. Allwood
- Ted Cohen
ArticleOpen Access4 Oct 2023 Nature Communications
Predictors of the post-COVID condition following mild SARS-CoV-2 infection

In this study, the authors investigate the incidence and risk factors for post-COVID condition among people who had a mild initial SARS-CoV-2 infection in Norway. They use national linked registry data including ~215,000 individuals with a positive SARS-CoV-2 test who were not hospitalised and followed them up for 180 days after infection.
- B-A. Reme
- J. Gjesvik
- K. Magnusson
ArticleOpen Access20 Sep 2023 Nature Communications
Zoonotic malaria requires new policy approaches to malaria elimination

WHO guidelines for classification of malaria elimination in a country require that the risk of human infection from zoonotic, as well as nonzoonotic, malaria parasites is negligible. In this Comment, the authors discuss the implications of this policy for countries, such as Malaysia, with no recent reported nonzoonotic cases but ongoing zoonotic transmission.
- Kimberly M. Fornace
- Chris J. Drakeley
- Kamruddin Ahmed
CommentOpen Access16 Sep 2023 Nature Communications
Breastfeeding and impact on childhood hospital admissions: a nationwide birth cohort in South Korea

Benefits of breastfeeding are well established, but a comprehensive study about its impacts on hospitalizations is lacking. Here, the authors use Korean nationwide birth cohort data (n = 1,608,540) and find that breastfeeding for at least 6 months was associated with a lower risk for subsequent hospital admissions.
- Jeong-Seon Lee
- Jae Il Shin
- Dong Keon Yon
ArticleOpen Access20 Sep 2023 Nature Communications
Food inflation and child undernutrition in low and middle income countries

The 21st Century has witnessed a series of global food crises, though little is known about how rising food prices affect child nutrition. The authors show that increases in the real price of food elevate the risk of a child being wasted, which in turn poses a serious risk for their survival.
- Derek Headey
- Marie Ruel
ArticleOpen Access16 Sep 2023 Nature Communications
Quantifying the causal impact of biological risk factors on healthcare costs

Understanding the causal impact that risk factors have on healthcare cost is critical to evaluate healthcare interventions. Here, authors show that waist circumference, body mass index, and blood pressure have robust causal impact on healthcare cost.
- Jiwoo Lee
- Sakari Jukarainen
- Andrea Ganna
ArticleOpen Access13 Sep 2023 Nature Communications
Gabapentinoid consumption in 65 countries and regions from 2008 to 2018: a longitudinal trend study

With their misuse potential, there is a need to understand the global consumption of gabapentinoids. Here, authors show a + 17.20% worldwide average annual increase in consumption of gabapentinoids from 2008 to 2018.
- Adrienne Y. L. Chan
- Andrew S. C. Yuen
- Kenneth K. C. Man
ArticleOpen Access17 Aug 2023 Nature Communications
Highly pathogenic avian influenza A (H5N1) in marine mammals and seabirds in Peru

Highly pathogenic avian influenza (HPAI) A/H5N1 has recently emerged in the Americas and has been implicated in mass die-off events of pelicans and sea lions. Here, the authors report sampling and characterisation of HPAI A/H5N1 genomes from five marine mammal and seabird species in Peru.
- Mariana Leguia
- Alejandra Garcia-Glaessner
- Jesus Lescano
ArticleOpen Access7 Sep 2023 Nature Communications
Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer

White-tailed deer are an important reservoir of SARS-CoV-2 in the USA and continued monitoring of the virus in deer populations is needed. In this genomic epidemiology study from Ohio, the authors show that the virus has been introduced multiple times to deer from humans, and that it has evolved faster in deer.
- Dillon S. McBride
- Sofya K. Garushyants
- Andrew S. Bowman
ArticleOpen Access28 Aug 2023 Nature Communications
Evidence of leaky protection following COVID-19 vaccination and SARS-CoV-2 infection in an incarcerated population

Measuring an individual’s level of exposure to COVID-19 is challenging, and it is therefore unclear whether high exposure may impact immunity. Here, the authors investigate this question using data from a correctional facility in Connecticut, USA, by comparing rates of infection in people who share cells, cellblocks, and with no known exposure.
- Margaret L. Lind
- Murilo Dorion
- Albert I. Ko
ArticleOpen Access19 Aug 2023 Nature Communications
Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19

The serial interval (time between symptom onset in an infector and infectee) is usually estimated from contact tracing data, but this is not always available. Here, the authors develop a method for estimation of serial intervals using whole genome sequencing data and apply it data from clusters of SARS-CoV-2 in Victoria, Australia.
- Jessica E. Stockdale
- Kurnia Susvitasari
- Caroline Colijn
ArticleOpen Access10 Aug 2023 Nature Communications
Estimating long-term vaccine effectiveness against SARS-CoV-2 variants: a model-based approach

Evaluation of the effectiveness of COVID-19 vaccines is increasingly challenging due to high levels of exposure to infection and vaccination. Here, the authors use a model-based approach incorporating these factors and estimate that using a variant-matched rather than ancestral booster could prevent nearly twice as many hospitalisations and deaths over one year.
- Alexandra B. Hogan
- Patrick Doohan
- Azra C. Ghani
ArticleOpen Access19 Jul 2023 Nature Communications
Preventing antimalarial drug resistance with triple artemisinin-based combination therapies

Triple artemisinin-based combination therapies have shown high efficacy for treatment of malaria in preliminary studies. Here, the authors use mathematical modelling to assess whether these therapies could also delay the emergence and spread of antimalarial drug resistance when compared against frontline therapies.
- Tran Dang Nguyen
- Bo Gao
- Ricardo Aguas
ArticleOpen Access29 Jul 2023 Nature Communications
Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England

The COVID-19 pandemic has been characterised by periods of dominance of different SARS-CoV-2 variants. In this mathematical modelling study, the authors investigate the epidemiological properties of successive variants in England until early 2022 and quantify the impacts of control measures.
- Pablo N. Perez-Guzman
- Edward Knock
- Marc Baguelin
ArticleOpen Access17 Jul 2023 Nature Communications
The role of vaccination and public awareness in forecasts of Mpox incidence in the United Kingdom

An outbreak of Mpox in the UK began in May 2022 and peaked in July. In this modelling study, the authors show that the decline in cases was likely due to behavioural changes among high-risk populations, whilst vaccination could prevent a rebound.
- Samuel P. C. Brand
- Massimo Cavallaro
- Matt J. Keeling
ArticleOpen Access11 Jul 2023 Nature Communications
Natural history of long-COVID in a nationwide, population cohort study

The long-term natural history of long-COVID is not well understood. In this population-based cohort study from Scotland, the authors describe symptom prevalence and health-related quality of life up to 18 months after a positive SARS-CoV-2 test and compare with matched test-negative controls.
- Claire E. Hastie
- David J. Lowe
- Jill P. Pell
ArticleOpen Access13 Jun 2023 Nature Communications
Multiplexed ddPCR-amplicon sequencing reveals isolated Plasmodium falciparum populations amenable to local elimination in Zanzibar, Tanzania

Sequencing malaria parasites from low density infections in small amounts of dried blood is important for large-scale genomic surveillance. Here, the authors develop and validate a highly multiplexed droplet digital PCR-based amplicon deep sequencing assay and apply it to data from Zanzibar, Tanzania.
- Aurel Holzschuh
- Anita Lerch
- Cristian Koepfli
ArticleOpen Access22 Jun 2023 Nature Communications
Bias assessment of a test-negative design study of COVID-19 vaccine effectiveness used in national policymaking

Test-negative case control studies have been widely used to estimate COVID-19 vaccine effectiveness, but the accuracy of estimates may be impacted by bias and unmeasured confounding. Here, the authors investigate the these impacts by collecting additional data from individuals included in the first UK COVID-19 test negative study.
- Sophie Graham
- Elise Tessier
- Helen I. McDonald
ArticleOpen Access6 Jul 2023 Nature Communications
No evidence of sustained nonzoonotic Plasmodium knowlesi transmission in Malaysia from modelling malaria case data

Plasmodium knowlesi is a zoonotic malaria parasite that can infect humans, but whether human-mosquito-human transmission occurs is not known. Here, the authors use data from Malaysia and show, through mathematical modelling, that sustained non-zoonotic transmission is unlikely to be occurring in this setting.
- Kimberly M. Fornace
- Hillary M. Topazian
- Chris Drakeley
ArticleOpen Access1 Jun 2023 Nature Communications
Estimating the impact of COVID-19 vaccine inequities: a modeling study

Global COVID-19 vaccine distribution has been inequitable. In this mathematical modelling study, the authors estimate the proportion of deaths that could have been averted in twenty low- and lower-middle-income countries if vaccines had been more widely available early in the pandemic.
- Nicolò Gozzi
- Matteo Chinazzi
- Alessandro Vespignani
ArticleOpen Access6 Jun 2023 Nature Communications
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

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