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| Open AccessSeasonal antigenic prediction of influenza A H3N2 using machine learning
This study presents a machine learning model that accurately predicts seasonal antigenic changes of influenza A H3N2 using genetic data. The model’s predictions can aid influenza surveillance, vaccine strain selection, and public health management.
- Syed Awais W. Shah
- , Daniel P. Palomar
- & Matthew R. McKay
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Perspective
| Open AccessEcological countermeasures to prevent pathogen spillover and subsequent pandemics
In this Perspective, the authors discuss the importance of preventing zoonotic spillover to prevent pandemics. They highlight mechanisms by which environmental changes can enable spillover, identify ecological interventions for spillover prevention and suggest policy frameworks through which interventions can be implemented.
- Raina K. Plowright
- , Aliyu N. Ahmed
- & Annika T. H. Keeley
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Article
| Open AccessEstimating 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
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Article
| Open AccessAsymptomatic immunodeficiency-associated vaccine-derived poliovirus infections in two UK children
There is increasing incidence of vaccine-derived poliovirus (VDPV) in countries thought to be polio free. Here, the authors report detection of VDPV in 2 UK children with primary immunodeficiency. The children did not develop paralysis, but isolated viruses showed intra-host evolution and neurovirulent potential.
- Anika Singanayagam
- , Dimitra Klapsa
- & Maria Zambon
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Article
| Open AccessWithin-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals
There is limited data on within-host SARS-CoV-2 genetic diversity and how it is affected by vaccination. The authors analysed intra-host sequence diversity and found that VOCs may have more sequence variations than non-VOCs and that breakthrough infections in vaccinated individuals do not seem to increase non-silent mutations.
- Haogao Gu
- , Ahmed Abdul Quadeer
- & Leo L. M. Poon
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Article
| Open AccessNon-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
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Article
| Open AccessComparison of fecal and blood metabolome reveals inconsistent associations of the gut microbiota with cardiometabolic diseases
Here, analyzing paired fecal and blood metabolomics and metagenomics data in a large cohort, Deng et al. uncover disparate associations of the gut microbiota with cardiometabolic diseases when utilizing either fecal or blood metabolome data, suggesting that sampling criteria may be a relevant factor in metabolomics-based association studies.
- Kui Deng
- , Jin-jian Xu
- & Yu-ming Chen
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Article
| Open AccessRapid emergence of extensively drug-resistant Shigella sonnei in France
There have been increasing reports of extensively drug-resistant (XDR) Shigella sonnei infections in recent years. In this laboratory surveillance study from France, the authors document the rise of XDR isolates from 2005 to 2021 and perform whole genome sequencing to investigate their genomic diversity and evolutionary history.
- Sophie Lefèvre
- , Elisabeth Njamkepo
- & François-Xavier Weill
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Article
| Open AccessGenomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
Understanding the emergence, evolution, and transmission of antibiotic resistance genes (ARGs) is essential to combat antimicrobial resistance. Here, Munk et al. analyse ARGs in hundreds of sewage samples from 101 countries and describe regional patterns, diverse genetic environments of common ARGs, and ARG-specific transmission patterns.
- Patrick Munk
- , Christian Brinch
- & Frank M. Aarestrup
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Article
| Open AccessA Shigella sonnei clone with extensive drug resistance associated with waterborne outbreaks in China
Shigella sonnei is a major contributor to the global burden of dysenteric diarrhoea in developed countries. In this work, authors report a S. sonnei clone which has caused numerous waterborne shigellosis outbreaks in China from 2015 to 2020.
- Shaofu Qiu
- , Kangkang Liu
- & Hongbin Song
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Article
| Open AccessSpike-antibody responses to COVID-19 vaccination by demographic and clinical factors in a prospective community cohort study
Vaccination can provide reliable and long-lasting protection against COVID-19, however the immune response to vaccination can vary between individuals and can decline over time, leading to differences in protective effects. Here the authors assess the immune response to COVID-19 vaccination across a large cohort of previously uninfected adults and demonstrate lower post-vaccination antibody levels amongst those with immune-suppressing conditions and medications, as well as those with several other more common chronic conditions.
- Madhumita Shrotri
- , Ellen Fragaszy
- & Robert W. Aldridge
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Article
| Open AccessSARS-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
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Article
| Open AccessSARS-CoV-2 antibody trajectories after a single COVID-19 vaccination with and without prior infection
The impact of prior infection on the immune response to COVID-19 vaccination has not been fully characterised. Here, the authors use data from ~100,000 adults in the UK and find that a single vaccine dose in those with prior infection produces a comparable or stronger response to two doses in those without infection.
- Jia Wei
- , Philippa C. Matthews
- & Chris Cunningham
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Comment
| Open AccessLearnings from Thailand in building strong surveillance for malaria elimination
On the cusp of Plasmodium falciparum (Pf) elimination, Thailand is accelerating towards zero malaria by 2024. This commentary reviews the heart of its success—effective surveillance—and what else may be needed to reach zero on time.
- Jui A. Shah
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Article
| Open AccessHuman seasonal influenza under COVID-19 and the potential consequences of influenza lineage elimination
COVID-19 control measures have suppressed circulation of other infections including influenza. Here, the authors analyse WHO global influenza sequence and case report data and describe changes in the phylogenetic and geographic distribution of influenza lineages during the COVID-19 pandemic.
- Vijaykrishna Dhanasekaran
- , Sheena Sullivan
- & Ian G. Barr
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Article
| Open AccessGenomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission
Post-international travel quarantine has been widely implemented to mitigate SARS-CoV-2 transmission, but the impacts of such policies are unclear. Here, the authors used linked genomic and contact tracing data to assess the impacts of a 14-day quarantine on return to England in summer 2020.
- Dinesh Aggarwal
- , Andrew J. Page
- & Ewan M. Harrison
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Comment
| Open AccessAusTrakka: Fast-tracking nationalized genomics surveillance in response to the COVID-19 pandemic
The COVID-19 pandemic has accelerated the demand for near real-time analysis and dissemination of pathogen genomic data. In this comment, the authors describe how Australia has developed and rolled out its SARS-CoV-2 genomics platform, AusTrakka, and used it to support public health action.
- Tuyet Hoang
- , Anders Gonçalves da Silva
- & Torsten Seemann
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Article
| Open AccessPopulation structure analysis and laboratory monitoring of Shigella by core-genome multilocus sequence typing
Lab-based surveillance of Shigella has traditionally been based on serotyping but increasing availability of whole genome sequencing could enable higher resolution typing. Here, the authors apply a core genome multilocus sequence typing scheme to Shigella sequence data and describe its population structure.
- Iman Yassine
- , Sophie Lefèvre
- & François-Xavier Weill
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Comment
| Open AccessPandemic preparedness: synthetic biology and publicly funded biofoundries can rapidly accelerate response time
Synthetic biology has played a key role in responding to the current pandemic. Biofoundries are critical synthetic biology infrastructure which should be available to all nations as a part of their independent bioengineering, biosecurity, and countermeasure response systems.
- Claudia E. Vickers
- & Paul S. Freemont
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Article
| Open AccessTwenty-year trends in antimicrobial resistance from aquaculture and fisheries in Asia
Trends in antimicrobial resistance (AMR) in aquatic food animals are seldom documented, particularly in Asia. Here, Schar et al. review 749 point prevalence surveys, describing AMR trends in Asian aquaculture and fisheries over two decades, and identifying resistance hotspots as well as regions that would benefit most from future surveillance efforts.
- Daniel Schar
- , Cheng Zhao
- & Thomas P. Van Boeckel
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Article
| Open AccessAn omics-based framework for assessing the health risk of antimicrobial resistance genes
Antibiotic resistance genes are common but not all are of high risk to human health. Here, the authors develop an omics-based framework for ranking genes by risk that incorporates level of enrichment in human associated environments, gene mobility, and host pathogenicity.
- An-Ni Zhang
- , Jeffry M. Gaston
- & Tong Zhang
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Article
| Open AccessBNT162b2 vaccine uptake and effectiveness in UK healthcare workers – a single centre cohort study
Several vaccines for COVID-19 have received emergency approval. Here, the authors describe BNT162B2 vaccine uptake and effectiveness among UK healthcare workers in a single centre cohort study during a time of high community COVID-19 prevalence.
- Tariq Azamgarhi
- , Michelle Hodgkinson
- & Simon Warren
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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
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Article
| Open AccessThe effect of eviction moratoria on the transmission of SARS-CoV-2
Massive unemployment during the COVID-19 pandemic could result in an eviction crisis in US cities. Here, the authors model the effect of evictions on SARS-CoV-2 epidemics, simulating viral transmission within and among households in a theoretical and applied urban settings.
- Anjalika Nande
- , Justin Sheen
- & Alison L. Hill
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Article
| Open AccessSmell and taste changes are early indicators of the COVID-19 pandemic and political decision effectiveness
Syndromic surveillance for COVID-19 could help to identify areas with increasing transmission. Here, the authors show that increased reports of changes in smell and taste measured at the population level are correlated with the increased COVID-19-related hospital admissions.
- Denis Pierron
- , Veronica Pereda-Loth
- & Moustafa Bensafi
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Article
| Open AccessChanging travel patterns in China during the early stages of the COVID-19 pandemic
COVID-19-related travel restrictions were imposed in China around the same time as major annual holiday migrations, with unknown combined impacts on mobility patterns. Here, the authors show that restructuring of the travel network in response to restrictions was temporary, whilst holiday-related travel increased pressure on healthcare services with lower capacity.
- Hamish Gibbs
- , Yang Liu
- & Rosalind M. Eggo
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Article
| Open AccessBridging of Neisseria gonorrhoeae lineages across sexual networks in the HIV pre-exposure prophylaxis era
Here, Williamson et al. combine epidemiological and genomic analysis of 2,186 Neisseria gonorrhoeae isolates from Australia and show that men who have sex with men and women are a possible ‘bridging’ population between men who have sex with men and heterosexuals.
- Deborah A. Williamson
- , Eric P. F. Chow
- & Benjamin P. Howden
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Article
| Open AccessOmpK36-mediated Carbapenem resistance attenuates ST258 Klebsiella pneumoniae in vivo
Carbapenem-resistance in Klebsiella pneumoniae sequence type ST258 can be enhanced by modification of the porins OmpK35 and OmpK36. Here, Wong et al. solve the crystal structure of a clinical ST258 OmpK36 variant, elucidating the mechanism of resistance and consequences on pathogenicity in vivo.
- Joshua L. C. Wong
- , Maria Romano
- & Gad Frankel
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Article
| Open AccessFDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science
To be able to use infectious disease next generation sequencing as a diagnostic tool, appropriate reference datasets are required. Here, Sichtig et al. describe FDA-ARGOS, a reference database for high-quality microbial reference genomes, and demonstrate its utility on the example of two use cases.
- Heike Sichtig
- , Timothy Minogue
- & Uwe Scherf
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Article
| Open AccessCopper-containing glass ceramic with high antimicrobial efficacy
Copper is well known for its high antimicrobial efficacy; however, cost, appearance and metallic properties limit application. Here the authors describe a stable, water dispersible copper-glass ceramic powder with long-term antimicrobial activity as an additive for antimicrobial surfaces.
- Timothy M. Gross
- , Joydeep Lahiri
- & Michael J. Snyder
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Article
| Open AccessMapping vaccination coverage to explore the effects of delivery mechanisms and inform vaccination strategies
The success of vaccination programs depends largely on the mechanisms used in vaccine delivery. Here, the authors evaluate the relative effectiveness of two major vaccine delivery strategies, namely routine immunization and supplementary immunization activities in five study countries.
- C. Edson Utazi
- , Julia Thorley
- & Andrew J. Tatem
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Article
| Open AccessRETRACTED ARTICLE: A switch in the poly(dC)/RmlB complex regulates bacterial persister formation
The mechanisms underlying bacterial persisters formation remain poorly understood. Here, Chen et al. identify a complex formed by extracellular poly(dC) and the binding protein RmlB that controls Pseudomonas aeruginosa persister formation in response to environmental stimuli.
- Xu Chen
- , Gen Li
- & Kouhong Sun
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Article
| Open AccessMathematical modelling of the impact of expanding levels of malaria control interventions on Plasmodium vivax
Plasmodium vivax poses a unique challenge for malaria elimination worldwide. Here, White et al. develop an individual-based mathematical model of P. vivax transmission and evaluate intervention strategies in Papua New Guinea.
- Michael T. White
- , Patrick Walker
- & Ivo Mueller
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Article
| Open AccessThe geography of measles vaccination in the African Great Lakes region
The WHO targets measles elimination by 2020, a goal that relies on high vaccination coverage. Here, Takahashiet al. identify ‘coldspots’ in the African Great Lakes region where measles vaccine coverage is below 80%, suggesting that these regions should be targeted in future vaccination campaigns.
- Saki Takahashi
- , C. Jessica E. Metcalf
- & Justin Lessler
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Article
| Open AccessContrasting benefits of different artemisinin combination therapies as first-line malaria treatments using model-based cost-effectiveness analysis
Several drug combinations with different properties are used for malaria treatment. Here, Okell et al. use a mathematical model to simulate malaria transmission and treatment with two drug combinations in Africa, and find that locally optimized policies can be highly cost effective for reducing malaria burden.
- Lucy C. Okell
- , Matthew Cairns
- & Azra C. Ghani