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| 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
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| Open AccessAnalyses of child cardiometabolic phenotype following assisted reproductive technologies using a pragmatic trial emulation approach
Huang and colleagues used machine-learning estimators to analyse a broad range of parameters in a prospective cohort consisting ART and spontaneously conceived children. Small differences in stature and growth could not be explained by parental or perinatal environment factors, nor differences in fetal DNA methylation. No strong differences in metabolic parameters were seen.
- Jonathan Yinhao Huang
- , Shirong Cai
- & Shiao-Yng Chan
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| Open AccessSARS-CoV-2 mucosal antibody development and persistence and their relation to viral load and COVID-19 symptoms
There has been limited research on the role of the mucosal immune response to SARS-CoV-2 infection. Here, the authors perform a prospective observational household study and find that mucosal antibody responses are associated with decreased viral load and faster resolution of systemic symptoms.
- Janeri Fröberg
- , Joshua Gillard
- & Dimitri A. Diavatopoulos
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| 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
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| Open AccessModelling the persistence and control of Rift Valley fever virus in a spatially heterogeneous landscape
Rift Valley fever is a zoonotic haemorrhagic fever with complex transmission dynamics influenced by environmental variables and animal movements. Here, the authors develop a metapopulation model incorporating these factors and use it to identify the main drivers of transmission in the Comoros archipelago.
- Warren S. D. Tennant
- , Eric Cardinale
- & Raphaëlle Métras
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| 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
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| 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
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| 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
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| 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
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| 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
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| 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
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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
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| 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
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| 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
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| Open AccessTime-varying optimization of COVID-19 vaccine prioritization in the context of limited vaccination capacity
In the context of limited supply, strategies for optimising allocation of COVID-19 vaccines are needed. Here, the authors explore time-varying strategies that adapt to the epidemiological situation and simultaneously optimise for multiple objectives including reducing numbers of infections, hospitalisations, and deaths.
- Shasha Han
- , Jun Cai
- & Hongjie Yu
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| Open AccessAn umbrella review of the evidence associating diet and cancer risk at 11 anatomical sites
Diet and food intake have been associated with a risk of developing different types of cancer but individual nutritional epidemiology studies are prone to inherent bias. Here, the authors perform an umbrella review of meta-analyses of observational studies and show the level of evidence for associating food and nutrients to cancer risk.
- Nikos Papadimitriou
- , Georgios Markozannes
- & Konstantinos K. Tsilidis
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| Open AccessImpact of tiered restrictions on human activities and the epidemiology of the second wave of COVID-19 in Italy
Italy introduced a system of tiered SARS-CoV-2 control measures in November 2020. Here, the authors quantify the effect of these measures on SARS-CoV-2 transmissibility and hospitalisation, and find reductions across all tiers with the greatest impacts associated with the most restrictive level.
- Mattia Manica
- , Giorgio Guzzetta
- & Stefano Merler
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| Open AccessSARS-CoV-2 antibody dynamics and transmission from community-wide serological testing in the Italian municipality of Vo’
Vo’, Italy, is a unique setting for studying SARS-CoV-2 antibody dynamics because mass testing was conducted there early in the pandemic. Here, the authors perform two follow-up serological surveys and estimate seroprevalence, the extent of within-household transmission, and the impact of contact tracing.
- Ilaria Dorigatti
- , Enrico Lavezzo
- & Andrea Crisanti
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| 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
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| 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
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| 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
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| 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
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| 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
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| Open AccessImpact of an accelerated melting of Greenland on malaria distribution over Africa
Release of freshwater into the oceans as a result of ice sheet melting could impact the distribution of climate-sensitive diseases. Here, the authors show that a rapid ice sheet melting in Greenland could cause an emergence of malaria in Southern Africa whilst transmission risks in West Africa may decline.
- Alizée Chemison
- , Gilles Ramstein
- & Cyril Caminade
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| Open AccessPhylogenomic analysis reveals persistence of gonococcal strains with reduced-susceptibility to extended-spectrum cephalosporins and mosaic penA-34
Resistance of Neisseria gonorrhoeae to extended spectrum cephalosporins is an increasing concern. Here, the authors conduct whole genome sequencing of isolates from the United States and find that most resistant isolates were associated with a persistent circulating lineage.
- Jesse C. Thomas IV
- , Sandeep J. Joseph
- & Zach Perry
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| 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
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| Open AccessCommunity factors and excess mortality in first wave of the COVID-19 pandemic in England
COVID-19-related mortality in England shows geographical variation but the reasons for this are not well understood. This study estimated excess mortality in the first wave of the pandemic and found associations with higher density of care homes, overcrowding, and economic deprivation, but not with population density or air pollution.
- Bethan Davies
- , Brandon L. Parkes
- & Paul Elliott
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| Open AccessAssociation of social distancing and face mask use with risk of COVID-19
Estimating the effectiveness of COVID-19 control measures requires large prospective data including symptoms and personal risk factors. Here, the authors used data from smartphone-based application and found that individual face mask use was associated with a 64% reduced risk of COVID-19 symptoms.
- Sohee Kwon
- , Amit D. Joshi
- & Andrew T. Chan
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| Open AccessMultianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2
Here, Roxhed et al. develop a multiplexed approach to screen IgG and IgM levels against several SARS-CoV-2 proteins in home-sampled dried blood spots and estimate seroprevalence of 12.5% in Stockholm in spring of 2020.
- Niclas Roxhed
- , Annika Bendes
- & Jochen M. Schwenk
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| Open AccessModeling the effectiveness of olfactory testing to limit SARS-CoV-2 transmission
A central problem in the COVID-19 pandemic is that there is not enough testing to prevent infectious spread of SARS-CoV-2, causing surges and lockdowns with human and economic toll. Here, the authors evaluate an alternative strategy based on the monitoring of olfactory dysfunction with a mathematical model.
- Daniel B. Larremore
- , Derek Toomre
- & Roy Parker
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| 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
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| 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
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| 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
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| 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
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| 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
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| 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
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| Open AccessCitywide serosurveillance of the initial SARS-CoV-2 outbreak in San Francisco using electronic health records
Population-based surveys are the gold standard for estimating seroprevalence but are expensive and often only capture a small geographic area or window of time. This study describes a new platform, SCALE-IT, for serosurveillance based on algorithmic sampling of electronic health records, and uses it to estimate the seroprevalence of SARS-CoV-2 in San Francisco.
- Isobel Routledge
- , Adrienne Epstein
- & Isabel Rodriguez-Barraquer
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| Open AccessLarge variation in anti-SARS-CoV-2 antibody prevalence among essential workers in Geneva, Switzerland
Many job sectors classified as ‘essential’ have continued operating with limited restrictions during the COVID-19 pandemic, potentially placing workers at higher risk of infection. Here, the authors show that seropositivity rates in workers vary widely across and between job sectors in Geneva, Switzerland.
- Silvia Stringhini
- , María-Eugenia Zaballa
- & Idris Guessous
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| Open AccessMolecular evidence of SARS-CoV-2 in New York before the first pandemic wave
Matthew M. Hernandez and Ana S. Gonzalez-Reiche and colleagues report evidence of SARSCoV-2 infections in respiratory pathogen-negative nasopharyngeal specimens collected in New York, which date back to over one month before the first officially documented case in the state. The findings provide insights in to the origins of the virus in New York.
- Matthew M. Hernandez
- , Ana S. Gonzalez-Reiche
- & Emilia Mia Sordillo
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| 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
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Article
| Open AccessOpen fire exposure increases the risk of pregnancy loss in South Asia
Open fires can increase heavy exposure to hazardous particulate matters, and thus harm human health, particularly among the vulnerable individuals, such as pregnant women. Here, the authors show an association between maternal exposure to fire smoke and increased risk of pregnancy loss in South Asia.
- Tao Xue
- , Guannan Geng
- & Tong Zhu
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Article
| Open AccessPrevalence of SARS-CoV-2 antibodies in France: results from nationwide serological surveillance
The percentage of national populations infected during the first stages of the COVID-19 pandemic are unclear owing to limited early testing. Here the authors provide a nation-wide prevalence study of SARS-CoV-2 antibodies in France from the first wave of COVID-19 in 2020, including stratification based on age, sex and region.
- Stéphane Le Vu
- , Gabrielle Jones
- & Harold Noel
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Article
| Open AccessControlling COVID-19 via test-trace-quarantine
Initial COVID-19 containment in the United States focused on limiting mobility, including school and workplace closures, with enormous societal and economic costs. Here, the authors demonstrate the feasibility of a test-trace-quarantine strategy using an agent-based model and detailed data on the Seattle region.
- Cliff C. Kerr
- , Dina Mistry
- & Daniel J. Klein
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Article
| Open AccessMultiscale influenza forecasting
Influenza forecasting in the United States is challenging and consequential, with the ability to improve the public health response. Here the authors show the performance of the multiscale flu forecasting model, Dante, that won the CDC’s 2018/19 national, regional and state flu forecasting challenges.
- Dave Osthus
- & Kelly R. Moran
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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
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| 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
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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
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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
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Article
| Open AccessThe role of maternal preconception vitamin D status in human offspring sex ratio
Higher vitamin D is associated with improved pregnancy and live birth rates, but its potential role in the human offspring sex ratio in unknown. Here, the authors show that the levels of vitamin D at preconception are positively associated with male live birth, particularly among women presenting inflammatory markers.
- Alexandra C. Purdue-Smithe
- , Keewan Kim
- & Sunni L. Mumford