Advanced Molecular Detection Clips Content (Published on 01/16/2025)
NEWS
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Study warns of emergence, spread of resistance to new drug-resistant TB treatments
Dall C. CIDRAP, Jan 9, 2025. -
UK Launches National Pathogen-Agnostic Metagenomics Surveillance Effort
GenomeWeb, Jan 30, 2025. -
Uganda launches Ebola Sudan vaccine trial; sequencing shows no link to 2022 outbreak
Schnirring L. CIDRAP, Feb 3, 2025. -
GAO: Public-health workforce shortage undermines ability to respond to outbreaks, other emergencies
Van Beusekom M. CIDRAP, Jan 31, 2025. -
Mpox outbreak in DR Congo, neighboring countries underscores threat of clade 1b
Soucheray S. CIDRAP, Jan 30, 2025. -
Will bird flu spark a human pandemic? Scientists say the risk is rising
Kozlov M. Nature, Jan 30, 2025. -
Scientists May Have Found Traces of an Extinct Genetic Code That Came Before DNA
Stolte D. SciTech Daily, Feb 2, 2025. -
USDA milk testing shows different strain of H5N1 bird flu in Nevada dairy herds
Branswell H. STAT, Feb 5, 2025. -
China reports mpox clade 1b cluster
Schnirring L. CIDRAP, 2025. -
Mpox Clade I in the U.S. Should Be a Wake-Up Call
Madad S, et al. MedPage Today, Jan 12, 2024. -
Study reveals dangerous mutations in H5N1 bird flu
News-Medical, Jan 16, 2025. -
‘A Dangerous Virus’: Bird Flu Enters a New Phase
Mandavilli A. New York Times, Jan 27, 2024. -
Want to start a fight among virus experts? Ask about HIV’s new name
Mast J. STAT, Jan 9, 2025. -
In light of avian flu, seasonal flu, CDC urges clinicians to speed influenza A subtyping
Schnirring L. CIDRAP, Jan 16, 2025. -
Why the ‘Ferrari of viruses’ is surging through the Northern Hemisphere
Cohen J. Science, Jan 13, 2025. -
Tanzania health ministry reports negative test results in suspected Marburg virus outbreak
Schnirring L. CIDRAP, Jan 16, 2025. -
Scientists flock to DeepSeek: how they’re using the blockbuster AI model
Gibnety E. Nature, Jan 29, 2025. -
Asteroid fragments upend theory of how life on Earth bloomed
Witze A. Nature, Jan 29, 2025.
EVENTS / TRAINING / WEB RESOURCES
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Host genomics: lessons for infectious disease
(report) PHG Foundation (UK), Jan 2025.
CONCEPTS / COMMENTS
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Exploring the Frontiers of Nanopore Sequencing in Food Safety and Food Microbiology.
Arnav Sharma et al. Annu Rev Food Sci Technol 2025 1
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Oropouche virus and the urgent need for global surveillance.
Marta Giovanetti et al. Nat Microbiol 2025 1 (1) 2-3 -
Conference report of the 2024 Antimicrobial Resistance Meeting.
Charlotte E Chong et al. NPJ Antimicrob Resist 2025 1 (1) 43 -
A framework towards implementation of sequencing for antimicrobial-resistant and other health-care-associated pathogens.
Alison Laufer Halpin et al. Lancet Infect Dis 2025 1
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The issue of climate change and the spread of tropical diseases in Europe and Italy: vector biology, disease transmission, genome-based monitoring and public health implications.
Grazia Pavia et al. Infect Dis (Lond) 2024 12 (2) 121-136 -
Preparedness, prevention and control related to zoonotic avian influenza.
et al. EFSA J 2025 1 (1) e9191 -
Microbiome science needs more microbiologists.
Lauren C Radlinski et al. Nat Microbiol 2025 1 (2) 263-264 -
Explainable artificial intelligence evolves antimicrobial peptides.
Jeremie Alexander et al. Nat Microbiol 2025 1 (2) 267-269 -
Scarcity of research on breastfeeding and Ebola diseases is placing the lives of women and infants at risk: a call to specific action.
Catriona Waitt et al. Lancet Glob Health 2025 1 (2) e364-e371
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A Framework for Assessing Viral Pathogens: A Key Element of the BARDA Emerging Infectious Diseases Strategy.
Richard C White et al. Health Secur 2025 1 -
Molecular HIV Surveillance: Beyond Cluster Detection and Response.
Sanjay R Mehta et al. AIDS Res Hum Retroviruses 2025 1 -
Learning the language of life with AI
Topol E. Science, Jan 30, 2025. -
Campylobacter spreads colorectal cancer.
Andrea Du Toit et al. Nat Rev Microbiol 2024 12 (2) 68
METHODS / TOOLS
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Assessment of the Public Health Laboratory Capacity - Sierra Leone, 2021.
Esther Debora Ngegba et al. China CDC Wkly 2025 1 (1) 21-26
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BenchAMRking: a Galaxy-based platform for illustrating the major issues associated with current antimicrobial resistance (AMR) gene prediction workflows.
Nikolaos Strepis et al. BMC Genomics 2025 1 (1) 27 -
Solu: a cloud platform for real-time genomic pathogen surveillance.
Timo Saratto et al. BMC Bioinformatics 2025 1 (1) 12 -
Exploring SNP filtering strategies: the influence of strict vs soft core.
Mona L Taouk et al. Microb Genom 2025 1 (1) -
Influence of Sequencing Technology on Pangenome-level Analysis and Detection of Antimicrobial Resistance Genes in ESKAPE Pathogens.
Alba Frias-De-Diego et al. bioRxiv 2025 1
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High-throughput method characterizes hundreds of previously unknown antibiotic resistance mutations.
Matthew J Jago et al. Nat Commun 2025 1 (1) 780 -
VirDetector: A bioinformatic pipeline for virus surveillance using nanopore sequencing.
Nick Laurenz Kaiser et al. Bioinformatics 2025 1 -
ARGfore: A multivariate framework for forecasting antibiotic resistance gene abundances using time-series metagenomic datasets.
Joung Min Choi et al. bioRxiv 2025 1 -
Machine learning reveals the dynamic importance of accessory sequences for Salmonella outbreak clustering.
Chao Chun Liu et al. mBio 2025 1 e0265024 -
Wastewater-integrated pathogen surveillance dashboards enable real-time, transparent, and interpretable public health risk assessment and dissemination
Msomi NS, et al. medRxiv, Jan 25, 2025. -
Web Visualization for Spatiotemporal Genomic Epidemiology, Annotation, and Mutation Dynamics of Orthohantavirus hantanense Using Nextstrain.
Kyungmin Park et al. Am J Trop Med Hyg 2025 1 -
Genomics costing tool: considerations for improving cost-efficiencies through cross scenario comparison.
Marco Marklewitz et al. Front Public Health 2025 1 1498094
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Laboratory capacity-building during COVID-19 in Somalia: improving access to essential diagnostics for national health security in a fragile setting.
Salvador Figuereo et al. J Epidemiol Glob Health 2025 2 (1) 18
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Comparison of Illumina and Oxford Nanopore sequencing data quality for Clostridioides difficile genome analysis and their application for epidemiological surveillance.
Semeh Bejaoui et al. BMC Genomics 2025 1 (1) 92
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Improving Nanopore sequencing-based core genome MLST for global infection control: a strategy for GC-rich pathogens like Burkholderia pseudomallei.
Sarah Weigl et al. J Clin Microbiol 2025 2 e0156924 -
Harnessing Non-standard Nucleic Acids for Highly Sensitive Icosaplex (20-Plex) Detection of Microbial Threats for Environmental Surveillance.
Hinako Kawabe et al. ACS Synth Biol 2025 2 -
Whole-genome automated assembly pipeline for Chlamydia trachomatis strains from reference, in vitro and clinical samples using the integrated CtGAP pipeline.
Olusola Olagoke et al. NAR Genom Bioinform 2025 1 (1) lqae187 -
A simple phylogenetic approach to analyze hypermutated HIV proviruses reveals insights into their dynamics and persistence during antiretroviral therapy.
Aniqa Shahid et al. Virus Evol 2025 1 (1) veae094 -
Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment.
Jordan T Ort et al. bioRxiv 2025 1 -
Building a growing genomic repository for maternal and fetal health through the PING Consortium.
Clara M Abdelmalek et al. Pediatr Res 2025 1
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Recent advances in deep learning and language models for studying the microbiome.
Binghao Yan et al. Front Genet 2025 1 1494474
EVOLUTION / ECOLOGY / POPULATIONS
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Clinical epidemiology, genetic diversity, and drug susceptibility patterns by whole genome sequencing of Mycobacterium tuberculosis complex isolates in Gabon from 2012 to 2022.
Bayode R Adegbite et al. IJID Reg 2025 1 100501 -
Genomic epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli from humans and a river in Aotearoa New Zealand.
Holly A Gray et al. Microb Genom 2025 1 (1) -
Relating ecological diversity to genetic discontinuity across bacterial species.
Hemanoel Passarelli-Araujo et al. Genome Biol 2025 1 (1) 8 -
The mutational landscape of Staphylococcus aureus during colonisation.
Francesc Coll et al. Nat Commun 2025 1 (1) 302 -
Archival and Newly Isolated Historical Bacillus anthracis Strains Populate the Deeper Phylogeny of the A.Br.075(Sterne) Clade.
Markus Antwerpen et al. Pathogens 2025 1 (1) -
Identification of Bacillus anthracis Strains from Animal Cases in Ethiopia and Genetic Characterization by Whole-Genome Sequencing.
Abebe Olani et al. Pathogens 2025 1 (1) -
Novel introductions of human-origin H3N2 influenza viruses in swine, Chile.
Belen Monserrat Agüero et al. Front Vet Sci 2025 1 1505497 -
Urban waste piles are reservoirs for human pathogenic bacteria with high levels of multidrug resistance against last resort antibiotics: A comprehensive temporal and geographic field analysis.
Madalitso Mphasa et al. J Hazard Mater 2024 12 136639 -
Persistent cross-species transmission systems dominate Shiga toxin-producing Escherichia coli O157:H7 epidemiology in a high incidence region: A genomic epidemiology study.
Gillian A M Tarr et al. Elife 2025 1 -
A core genome MLST scheme for Borrelia burgdorferi sensu lato improves insights into the evolutionary history of the species complex.
Sabrina Hepner et al. Cell Rep Methods 2024 12 (1) 100935 -
Clostridioides difficile recovered from hospital patients, livestock and dogs in Nigeria share near-identical genome sequences.
Emmanuel O Ngbede et al. Microb Genom 2025 1 (1) -
Geographic origin and evolution of dengue virus serotypes 1 and 3 circulating in Africa.
Sindiso Nyathi et al. Virus Evol 2025 1 (1) veae116 -
Meta-analyses of Culex blood-meals indicates strong regional effect on feeding patterns.
Jet S Griep et al. PLoS Negl Trop Dis 2025 1 (1) e0012245 -
Molecular epidemiology, evolution, and transmission dynamics of raccoon rabies virus in Connecticut.
Gabriella Veytsel et al. Virus Evol 2025 1 (1) veae114 -
Comprehensive molecular epidemiology of influenza viruses in Brazil: insights from a nationwide analysis.
Isabela Carvalho Brcko et al. Virus Evol 2025 1 (1) veae102 -
Epidemiology and Genotype Dynamics of Dengue in Hospitalized Patients in Northern Vietnam Between 2020 and 2022.
Do Duc Anh et al. Open Forum Infect Dis 2025 1 (1) ofae753
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Ongoing measles outbreak in Romania: Clinical investigation and molecular epidemiology performed on whole genome sequences.
Robert Hohan et al. PLoS One 2025 1 (1) e0317045
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Coronavirus Cryptic Landscape and Draft Genome of a Novel CoV Clade Related to MERS From Bats Circulating in Northeastern Brazil.
Bruna Stefanie Silvério et al. J Med Virol 2025 1 (1) e70173 -
Bat coronavirus surveillance across different habitats in Yucatán, México.
Marco Antonio Jiménez-Rico et al. Virology 2025 1 110401 -
Genomic exploration of the journey of Plasmodium vivax in Latin America.
Margaux J M Lefebvre et al. PLoS Pathog 2025 1 (1) e1012811 -
Systematic bias in malaria parasite relatedness estimation.
Somya Mehra et al. G3 (Bethesda) 2025 1 -
Filarial parasite infection prevalence in field-caught mosquitoes from Connecticut, United States.
Meredith S Bagger et al. J Med Entomol 2025 1
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Diversification of bla -harbouring plasmids among carbapenemase-producing Enterobacterales, 11 years after a large outbreak in a general hospital in the Netherlands.
Pieter W Smit et al. Microb Genom 2025 1 (1) -
Tracking clonal and plasmid transmission in colistin- and carbapenem-resistant Klebsiella pneumoniae.
Ifeoluwa Akintayo et al. mSystems 2025 1 e0112824 -
Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic.
Wilhelm Furnon et al. Nat Microbiol 2025 1 (1) 77-93 -
Global dissemination of the beta-lactam resistance gene blaTEM-1 among pathogenic bacteria.
Adeel Farooq et al. Sci Total Environ 2025 1 178521 -
Hybrid strains of enterotoxigenic/Shiga toxin-producing Escherichia coli, United Kingdom, 2014-2023.
Ella V Rodwell et al. J Med Microbiol 2025 1 (1) -
Salmonella enterica serovar Schwarzengrund: Distribution, Virulence, and Antimicrobial Resistance.
Monique A Felix et al. Microorganisms 2025 1 (1) -
One day in Denmark: whole-genome sequence-based analysis of Escherichia coli isolates from clinical settings.
Ana Rita Rebelo et al. J Antimicrob Chemother 2025 1
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Progression of antibiotic resistance in Neisseria meningitidis.
Emilio Rodriguez et al. Clin Microbiol Rev 2025 1 e0021524
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Short-term evolution and dispersal patterns of fluconazole-resistance in Candida auris clade III.
Irving Cancino-Muñoz et al. mBio 2024 12 (2) e0316424 -
HIV Replication Under High-Level Cabotegravir Is Associated with the Appearance of 3'-PPT Mutations, Circular DNA Transcription and Recombination.
Xierong Wei et al. Viruses 2025 1 (12)
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Haplotypes of Chloroquine Resistance Marker Genes Among Uncomplicated Malaria Cases in Lagos, Nigeria.
Uche Thecla Igbasi et al. Biochem Genet 2025 1 -
Detection of low frequency artemisinin resistance mutations, C469Y, P553L and A675V, and fixed antifolate resistance mutations in asymptomatic primary school children in Kenya.
Victor Osoti et al. BMC Infect Dis 2025 1 (1) 73
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Changes in susceptibility of Plasmodium falciparum to antimalarial drugs in Uganda over time: 2019-2024.
Martin Okitwi et al. medRxiv 2025 1
DETECTION / DIAGNOSIS
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Aptamer-molecularly imprinted polymer sensors for the detection of bacteria in water.
Meltem Agar et al. Biosens Bioelectron 2025 1 117136 -
Cost-effectiveness of targeted next-generation sequencing (tNGS) for detection of tuberculosis drug resistance in India, South Africa and Georgia: a modeling analysis.
Suvesh Shrestha et al. EClinicalMedicine 2025 1 103003
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Rapid, Inexpensive Multiplex Pathogen Detection Using Resequencing Microarrays.
Kendall Hoff et al. J Virol Methods 2025 1 115109 -
On the ability to extract MLVA profiles of Vibrio cholerae isolates from WGS data generated with Oxford Nanopore Technologies.
Jérôme Ambroise et al. BMC Res Notes 2025 1 (1) 18
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Molecular identification and antibiotic clearance of Mycoplasma arginini and Mycoplasma orale from cell cultures infected with Rickettsia or Ehrlichia species.
Michelle E J Allerdice et al. Microbiol Spectr 2025 1 e0174324
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From Traditional Typing to Genomic Precision: Whole-Genome Sequencing of Listeria monocytogenes Isolated from Refrigerated Foods in Chile.
Julio Parra-Flores et al. Foods 2025 1 (2)
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Silent outbreaks of psittacosis revealed using targeted next-generation sequencing.
Tian Qin et al. Lancet Microbe 2025 1 101061
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Evaluation of nationwide analysis surveillance for methicillin-resistant Staphylococcus aureus within Genomic Medicine Sweden.
Erika Tång Hallbäck et al. Microb Genom 2025 1 (1)
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Two Years of SARS-CoV-2 Omicron Genomic Evolution in Brazil (2022-2024): Subvariant Tracking and Assessment of Regional Sequencing Efforts.
Ueric José Borges de Souza et al. Viruses 2025 1 (1)
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A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission.
Benjamin Sobkowiak et al. Genome Med 2025 1 (1) 8 -
Unsupervised detection of novel SARS-CoV-2 mutations and lineages in wastewater samples using long-read sequencing.
Ignacio Garcia et al. BMC Genomics 2025 1 (1) 87
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Assessment of different genotyping markers and algorithms for distinguishing Plasmodium falciparum recrudescence from reinfection in Uganda.
Alex Mwesigwa et al. Sci Rep 2025 2 (1) 4375
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One-Step Multiplex Polymerase Chain Reaction Assay for the Detection of Major Disease-Transmitting Mosquito Vectors in India.
Mintu Karan et al. Am J Trop Med Hyg 2024 11 (2) 296-303 -
Development and evaluation of a next-generation sequencing methodology for measles virus using Oxford Nanopore Technology.
Vanessa Zubach et al. J Clin Microbiol 2025 2 e0145624 -
Comprehensive genomic surveillance reveals transmission profiles of extensively drug-resistant tuberculosis cases in Pará, Brazil.
Davi Josué Marcon et al. Front Microbiol 2025 2 1514862
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Consistency between metagenomic next-generation sequencing versus traditional microbiological tests for infective disease: systemic review and meta-analysis.
Chengxi Liu et al. Crit Care 2025 2 (1) 55 -
The SARS-CoV-2 test scale-up in the USA: an analysis of the number of tests produced and used over time and their modelled impact on the COVID-19 pandemic.
Steven Santos et al. Lancet Public Health 2025 1 (1) e47-e57
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Hyperplex PCR enables highly multiplexed analysis of point mutations in wastewater: Long-term SARS-CoV-2 variant surveillance in Sweden as a case study.
Ruben R G Soares et al. Water Res 2025 1 123154
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Detection of circulating vaccine-derived poliovirus type 2 (cVDPV2) in wastewater samples: a wake-up call, Finland, Germany, Poland, Spain, the United Kingdom, 2024.
Sindy Böttcher et al. Euro Surveill 2025 1 (3)
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Eight Years of Norovirus Surveillance in Urban Wastewater: Insights from Next-Generation.
Giusy Bonanno Ferraro et al. Viruses 2025 1 (1)
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Insect-specific RNA viruses detection in Field-Caught Aedes aegypti mosquitoes from Argentina using NGS technology.
Lucas Ripoll et al. PLoS Negl Trop Dis 2025 1 (1) e0012792 -
Testing of Retail Cheese, Butter, Ice Cream, and Other Dairy Products for Highly Pathogenic Avian Influenza in the US.
David L Suarez et al. J Food Prot 2024 12 (1) 100431 -
Development and validation of a high-throughput qPCR platform for the detection of soil-transmitted helminth infections.
Nils Pilotte et al. PLoS Negl Trop Dis 2025 1 (1) e0012760
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Incidence and estimated risk of residual transmission of hepatitis a virus and parvovirus B19 by blood transfusion in the state of Rio De Janeiro - Brazil: a retrospective study.
Arthur Daniel Rocha Alves et al. Virol J 2025 1 (1) 15 -
The origin and transmission of HIV-1 CRF80_0107 among two major first-tier cities in China.
Xiaorui Wang et al. BMC Infect Dis 2025 1 (1) 104 -
Hospital toilets and drainage systems as a reservoir for a long-term polyclonal outbreak of clinical infections with multidrug-resistant Klebsiella oxytoca species complex.
Astri Lervik Larsen et al. Infect Prev Pract 2025 1 (1) 100430
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Sources and Transmission Routes of Carbapenem-Resistant Pseudomonas aeruginosa: Study Design and Methodology of the SAMPAN Study.
Anneloes van Veen et al. Antibiotics (Basel) 2025 1 (1) -
Genomic evaluation of phenotypic antibiotic susceptibility patterns as a surrogate for MRSA relatedness and putative transmission during outbreak investigations.
Francesc Coll et al. Infect Prev Pract 2025 1 (1) 100435 -
Whole genome sequencing and phylogenetic analysis to examine acquisition of Escherichia coli clones during international travel.
Samantha Dos S Tufic-Garutti et al. Diagn Microbiol Infect Dis 2025 1 (3) 116701 -
Severe Non-Donor-Derived Lymphocytic Choriomeningitis Virus Infection in 2 Solid Organ Transplant Recipients.
Leanna E Sayyad et al. Open Forum Infect Dis 2025 2 (2) ofaf002
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Transmission patterns of hepatitis E virus.
Jil A Haase et al. Curr Opin Virol 2025 2 101451 -
Metabarcoding captures genetic diversity and links cases in outbreaks of cryptosporidiosis in New Zealand.
Paul Ogbuigwe et al. J Infect 2025 1 106427 -
Segmentation of the response of a neuronal network into clusters with similar activity.
P Parodi et al. Biosystems 1999 1 (1-3) 171-8
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Dynamics of clustering rates in the Rhode Island HIV-1 epidemic.
Vlad Novitsky et al. AIDS 2024 11 (2) 105-114 -
Leveraging mobility data to analyze persistent SARS-CoV-2 mutations and inform targeted genomic surveillance.
Riccardo Spott et al. Elife 2025 1 -
Identification of patient demographic, clinical, and SARS-CoV-2 genomic factors associated with severe COVID-19 using supervised machine learning: a retrospective multicenter study.
Kuganya Nirmalarajah et al. BMC Infect Dis 2025 1 (1) 132 -
Benefits of HIV-1 transmission cluster surveillance: a French retrospective observational study of the molecular and epidemiological co-evolution of recent circulating recombinant forms 94 and 132.
Marc Wirden et al. J Int AIDS Soc 2025 1 (2) e26416 -
Outbreak of Rotavirus Diarrheal Infection among Adults in King County, Washington, January-June 2023.
Jimmy Ma et al. J Infect Dis 2025 1
HOST-MICROBE INTERACTIONS
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Shaping current European mitochondrial haplogroup frequency in response to infection: the case of SARS-CoV-2 severity.
José Luis Cabrera-Alarcon et al. Commun Biol 2025 1 (1) 33 -
Blood DNA virome associates with autoimmune diseases and COVID-19.
Noah Sasa et al. Nat Genet 2025 1 (1) 65-79 -
Lessons from the Use of Monoclonal Antibodies to SARS-CoV-2 Spike Protein During the COVID-19 Pandemic.
Arturo Casadevall et al. Annu Rev Med 2024 12 (1) 1-12 -
Differential protection against SARS-CoV-2 reinfection pre- and post-Omicron
Chemaitelly H, et al. Nature, Feb 5, 2025. -
Targets of influenza human T-cell response are mostly conserved in H5N1.
John Sidney et al. mBio 2024 12 (2) e0347924
indicates that at least one CDC-affiliated author;
indicates that the article addresses aspects of implementation or evaluation in clinical or public health practice. Disclaimer: Articles listed in the Advanced Molecular Detection Clips are selected by Public Health Genomics Branch to provide current awareness of the scientific literature and news. Inclusion in the clips does not necessarily represent the views of the Centers for Disease Control and Prevention nor does it imply endorsement of the article's methods or findings. CDC and DHHS assume no responsibility for the factual accuracy of the items presented. The selection, omission, or content of items does not imply any endorsement or other position taken by CDC or DHHS. Opinion, findings and conclusions expressed by the original authors of items included in the Clips, or persons quoted therein, are strictly their own and are in no way meant to represent the opinion or views of CDC or DHHS. References to publications, news sources, and non-CDC Websites are provided solely for informational purposes and do not imply endorsement by CDC or DHHS.
- Page last reviewed:Feb 1, 2024
- Page last updated:Jan 16, 2025

