Article
|
Open Access
Featured
-
-
Article
| Open AccessSerological responses and vaccine effectiveness for extended COVID-19 vaccine schedules in England
The UK extended the interval until the second COVID-19 vaccine dose up to 12 weeks. Here, the authors show in a cohort of 750 participants aged 50–89 years that the extended schedule results in higher antibody titers and estimate a higher vaccine effectiveness for the extended schedule.
- Gayatri Amirthalingam
- , Jamie Lopez Bernal
- & Mary E. Ramsay
-
Article
| Open AccessChanges in notifiable infectious disease incidence in China during the COVID-19 pandemic
Non-pharmaceutical interventions implemented to mitigate COVID-19 transmission are likely to have impacted spread of other infectious diseases. Here, the authors investigate changes in the incidence of 31 notifiable infectious diseases using surveillance data from China.
- Meng-Jie Geng
- , Hai-Yang Zhang
- & Wei Liu
-
Article
| Open AccessAdaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands
SARS-CoV-2 was detected in mink farms in the Netherlands in the first wave of the pandemic with evidence of human-to-mink and mink-to-human transmission. Here, the authors investigate this outbreak using phylodynamic analysis and show that personnel links and spatial proximity are predictors of transmission between farms.
- Lu Lu
- , Reina S. Sikkema
- & Marion P. G. Koopmans
-
Article
| Open AccessAge-seroprevalence curves for the multi-strain structure of influenza A virus
Multi-strain pathogens, such as influenza, present challenges for interpretation of seroprevalence data as estimates may vary by strain. Here, the authors develop a method for estimating age-specific seroprevalence based on principal components analysis and apply it to influenza data from Vietnam.
- Dao Nguyen Vinh
- , Nguyen Thi Duy Nhat
- & Maciej F. Boni
-
Article
| Open AccessBurdens of post-acute sequelae of COVID-19 by severity of acute infection, demographics and health status
Post-acute sequelae of COVID-19 (PASC, or ‘Long COVID’) has caused concern but the burden and risk factors are not well understood. Here, the authors use US electronic health record data and estimate an overall burden of PASC of ~7% at six months, with variation by severity of acute infection, baseline health status and demographics.
- Yan Xie
- , Benjamin Bowe
- & Ziyad Al-Aly
-
Article
| Open AccessA novel SARS-CoV-2 related coronavirus in bats from Cambodia
In this study, Delaune et al., isolate and characterise a SARS-CoV-2-related coronavirus from two bats sampled in Cambodia. Their findings suggest that the geographic distribution of SARS-CoV-2-related viruses is wider than previously reported.
- Deborah Delaune
- , Vibol Hul
- & Veasna Duong
-
Article
| Open AccessPotential global impacts of alternative dosing regimen and rollout options for the ChAdOx1 nCoV-19 vaccine
The ChAdOx1 nCoV-19 vaccine requires two doses, but under limited supply single dose regimens have also been considered. Here, the authors show using static transmission modelling that under certain conditions it is optimal to more expediently administer a single dose to a larger proportion of the population.
- Ricardo Aguas
- , Anouska Bharath
- & Rima Shretta
-
Article
| Open AccessUsing secondary cases to characterize the severity of an emerging or re-emerging infection
Estimates of the severity of emerging infections did not consider the case ascertainment method, but secondary cases identified by contact tracing of index cases may be more reliable as they are less susceptible to ascertainment bias. Here, the authors perform a systematic review to quantify these differences and model their impacts for COVID-19.
- Tim K. Tsang
- , Can Wang
- & Benjamin J. Cowling
-
Article
| Open AccessUnderstanding how Victoria, Australia gained control of its second COVID-19 wave
The state of Victoria, Australia experienced a substantial second wave of COVID-19 but brought it under control with strict non-pharmaceutical interventions. Here, the authors model the second wave in Victoria to estimate the impacts of the different interventions.
- James M. Trauer
- , Michael J. Lydeamore
- & Romain Ragonnet
-
Article
| Open AccessClinical outcomes and cost-effectiveness of COVID-19 vaccination in South Africa
Cost, supply and logistics present challenges to COVID-19 vaccine rollout in low and middle income countries. Here, the authors model vaccination programmes in South Africa and demonstrate the importance of the pace of vaccine rollout, with even moderately efficacious vaccines likely to be cost-effective.
- Krishna P. Reddy
- , Kieran P. Fitzmaurice
- & Mark J. Siedner
-
Article
| Open AccessThe impact of the timely birth dose vaccine on the global elimination of hepatitis B
The timely hepatitis B birth dose vaccination is recommended for all new-borns by the WHO, but coverage is inconsistent. Here, the authors model the impact of scaling-up coverage in 110 low and middle income countries and assess how it may be affected by delays for example caused by the COVID-19 pandemic.
- Margaret J. de Villiers
- , Shevanthi Nayagam
- & Timothy B. Hallett
-
Article
| Open AccessUnderstanding the effectiveness of government interventions against the resurgence of COVID-19 in Europe
European governments control resurging waves of COVID-19 using nonpharmaceutical interventions. Here, the authors estimate the effectiveness of 17 interventions in Europe’s second wave, and analyse differences to the first wave as well as implications for the future of the pandemic.
- Mrinank Sharma
- , Sören Mindermann
- & Jan Markus Brauner
-
Article
| Open AccessGenomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity
Genomic surveillance of SARS-CoV-2 can inform regional transmission dynamics and inform public health interventions. Here, the authors sequence ~200 samples from Rwanda, identify shifts in predominating strains from May 2020 to February 2021, and infer geographic origins.
- Yvan Butera
- , Enatha Mukantwari
- & Nadine Rujeni
-
Article
| Open AccessDevelopment of a model-inference system for estimating epidemiological characteristics of SARS-CoV-2 variants of concern
Quantification of the transmissibility and immune escape properties of SARS-CoV-2 variants is necessary to support pandemic planning. Here, the authors develop a model inference system to estimate these properties using incidence and mortality data for three variants of concern.
- Wan Yang
- & Jeffrey Shaman
-
Article
| Open AccessContact tracing is an imperfect tool for controlling COVID-19 transmission and relies on population adherence
Evaluations of the UK’s contact tracing programme have shown that it has had limited impact on COVID-19 control. Here, the authors show that with high levels of reporting and adherence, contact tracing could reduce transmission, but it should not be used as the sole control measure.
- Emma L. Davis
- , Tim C. D. Lucas
- & Petra Klepac
-
Article
| Open AccessA pre-registered short-term forecasting study of COVID-19 in Germany and Poland during the second wave
Forecasting models have been used extensively to inform decision making during the COVID-19 pandemic. In this preregistered and prospective study, the authors evaluated 14 short-term models for Germany and Poland, finding considerable heterogeneity in predictions and highlighting the benefits of combined forecasts.
- J. Bracher
- , D. Wolffram
- & Frost Tianjian Xu
-
Article
| Open AccessGlobal spread of Salmonella Enteritidis via centralized sourcing and international trade of poultry breeding stocks
Salmonella enterica serotype Enteritidis is a pathogen of poultry that can cause outbreaks in humans. Here the authors use genomic and trade data to investigate a pandemic in the 1980s, finding evidence that international trade of breeding stocks led to global spread of the pathogen.
- Shaoting Li
- , Yingshu He
- & Xiangyu Deng
-
Article
| Open AccessThe risk of indoor sports and culture events for the transmission of COVID-19
Mass gathering events represent a risk for transmission of SARS-CoV-2. Here, the authors describe an experimental indoor test event in which individual contacts were measured and use aerosol and epidemiological modelling to evaluate transmission risks of different types of restrictions in the arena.
- Stefan Moritz
- , Cornelia Gottschick
- & Rafael Mikolajczyk
-
Article
| Open AccessEtiological and epidemiological features of acute respiratory infections in China
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 AccessHigh COVID-19 transmission potential associated with re-opening universities can be mitigated with layered interventions
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 AccessTracking the introduction and spread of SARS-CoV-2 in coastal Kenya
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 AccessDetection and characterization of the SARS-CoV-2 lineage B.1.526 in New York
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 AccessCOVID-19 spread, detection, and dynamics in Bogota, Colombia
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 AccessHeatstroke predictions by machine learning, weather information, and an all-population registry for 12-hour heatstroke alerts
In the context of climate change, heatstroke is expected to become an increasingly relevant public health concern. Here, the authors develop and validate prediction models for the number of all heatstroke cases in different cities in Japan.
- Soshiro Ogata
- , Misa Takegami
- & Kunihiro Nishimura
-
Article
| Open AccessLineage-specific protection and immune imprinting shape the age distributions of influenza B cases
The earliest infections with influenza A shape the immune responses to future infections, but it is not known if this phenomenon applies to influenza B. Here, the authors use influenza B case data from New Zealand and find evidence for both lineage-specific and imprinting protection.
- Marcos C. Vieira
- , Celeste M. Donato
- & Sarah Cobey
-
Article
| Open AccessThe epidemiology of Plasmodium vivax among adults in the Democratic Republic of the Congo
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 AccessA genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex
Klebsiella pneumoniae is a pathogen of increasing public health concern and antimicrobial resistance is becoming more prevalent. Here, the authors describe a K. pneumoniae genotyping tool, Kleborate, that can be used to identify lineages and detect antimicrobial resistance and virulence loci.
- Margaret M. C. Lam
- , Ryan R. Wick
- & Kathryn E. Holt
-
Article
| Open AccessLack of consideration of sex and gender in COVID-19 clinical studies
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 AccessTemporal trends of SARS-CoV-2 seroprevalence during the first wave of the COVID-19 epidemic in Kenya
The reported burden of SARS-CoV-2 has been relatively low in tropical Africa compared to Europe and the Americas, but estimating true infection rates is challenging. Here, the authors screen blood donors in Kenya for SARS-CoV-2 antibodies and describe spatiotemporal seroprevalence dynamics.
- Ifedayo M. O. Adetifa
- , Sophie Uyoga
- & George M. Warimwe
-
Article
| Open AccessDesign of COVID-19 staged alert systems to ensure healthcare capacity with minimal closures
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 AccessControlling the pandemic during the SARS-CoV-2 vaccination rollout
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 AccessMolecular benchmarks of a SARS-CoV-2 epidemic
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 AccessInsights into household transmission of SARS-CoV-2 from a population-based serological survey
Household-based studies can provide insights into SARS-CoV-2 transmission. Here, the authors fit transmission models to serological data from Geneva, Switzerland, and estimate that the risk of infection from single household exposure (17.3%) was higher than for extra-household exposure (5.1%).
- Qifang Bi
- , Justin Lessler
- & Didier Trono
-
Article
| Open AccessRole of meteorological factors in the transmission of SARS-CoV-2 in the United States
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 AccessMaps and metrics of insecticide-treated net access, use, and nets-per-capita in Africa from 2000-2020
Insecticide treated nets (ITNs) are an important part of malaria control in Africa and WHO targets aim for 80% coverage. This study estimates the spatio-temporal access and use of ITNs in Africa from 2000-2020, and shows that both metrics have improved over time but access remains below WHO targets.
- Amelia Bertozzi-Villa
- , Caitlin A. Bever
- & Samir Bhatt
-
Article
| Open AccessEffect of specific non-pharmaceutical intervention policies on SARS-CoV-2 transmission in the counties of the United States
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 AccessThe geometry of clinical labs and wellness states from deeply phenotyped humans
Longitudinal multi-omics measurements are highly valuable in studying heterogeneity in health and disease phenotypes. Here, the authors apply Pareto Task Inference to analyze the clinical lab tests of 3094 individuals and find three wellness states, and one aberrant health state defining this cohort.
- Anat Zimmer
- , Yael Korem
- & Nathan D. Price
-
Article
| Open AccessImpact of COVID-19 outbreaks and interventions on influenza in China and the United States
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 AccessImpacts of social distancing policies on mobility and COVID-19 case growth in the US
In response to COVID-19, many states have implemented social distancing orders, but the effect of these orders on population mobility has not been fully quantified. Here, the authors use data from the US to show that state-level social distancing orders substantially reduced mobility and limited the spread of disease.
- Gregory A. Wellenius
- , Swapnil Vispute
- & Evgeniy Gabrilovich
-
Article
| Open AccessThe effect of generic market entry on antibiotic prescriptions in the United States
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 AccessA global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch
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 AccessCirculation of pertussis and poor protection against diphtheria among middle-aged adults in 18 European countries
Recent outbreaks of pertussis have highlighted the importance of surveillance of vaccine-preventable diseases. Here, the authors performed a cross-sectional seroprevalence study of pertussis, diphtheria, and tetanus in Europe and found evidence of circulation of pertussis in middle-aged adults.
- Guy Berbers
- , Pieter van Gageldonk
- & Jussi Mertsola
-
Article
| Open AccessUsing mobile phone data to reveal risk flow networks underlying the HIV epidemic in Namibia
Human mobility influences the spatial distribution of infectious diseases such as HIV. Here, the authors use call data records from mobile phones to model HIV networks in Namibia and estimate that ~40% of the risk of HIV acquisition is driven by mobility.
- Eugenio Valdano
- , Justin T. Okano
- & Sally Blower
-
Article
| Open AccessEstimating COVID-19 mortality in Italy early in the COVID-19 pandemic
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 AccessThe impact of stopping and starting indoor residual spraying on malaria burden in Uganda
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 AccessEtiological, epidemiological, and clinical features of acute diarrhea in China
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 AccessLeveraging community mortality indicators to infer COVID-19 mortality and transmission dynamics in Damascus, Syria
Reported COVID-19 mortality rates have been relatively low in Syria, but there has been concern about overwhelmed health systems. Here, the authors use community mortality indicators and estimate that <3% of COVID-19 deaths in Damascus were reported as of 2 September 2020.
- Oliver J. Watson
- , Mervat Alhaffar
- & Patrick Walker
-
Article
| Open AccessAssociation of sleep duration in middle and old age with incidence of dementia
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 AccessGenetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions
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