Advanced Molecular Detection Clips Content (Published on 11/12/2020)
NEWS
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Metagenomic Sequencing Can Quickly Identify Pathogens in Body Fluids, New Study Finds
GenomeWeb, Nov 9, 2020. -
Where did COVID come from? WHO investigation begins but faces challenges
Mallapaty S. Nature, Nov 11, 2020. -
Coronavirus testing finally gathers speed
Sheridan C. Nature, Nov 5, 2020. -
MIT Team Uses Traditional Physics Technology to Develop Rapid COVID-19 Testing
Ketchum K. 360dx, Nov 6, 2020. -
Navy Research Confirms Need for Strict Coronavirus Testing Protocols
Carey B. New York Times, Nov 11, 2020. -
A woman shed infectious coronavirus particles for at least 70 days without showing symptoms, a study found
Neilson S. Business Insider, Nov 8, 2020. -
Spread of mutated coronavirus in Danish mink "hits all the scary buttons," but fears may be overblown
Branswell H. STAT, Nov 5, 2020. -
The story of mRNA: How a once-dismissed idea became a leading technology in the Covid vaccine race
Garde D, Saltzman J. STAT, Nov 10, 2020. -
Covid-19 vaccine from Pfizer and BioNTech is strongly effective, early data from large trial indicate
Herper M. STAT, Nov 9, 2020.
POLICY
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Pandemic diseases preparedness and response in the age of COVID-19-a symposium report.
Jennifer Cable et al. Ann N Y Acad Sci 2020 11 (1) 17-29 -
SARS-CoV-2 sequencing: The technological initiative to strengthen early warning systems for public health emergencies in Latin America and the Caribbean
Álvarez-Díaz Diego A et al. Biomedica : revista del Instituto Nacional de Salud 2020 10 (Supl. 2) 188-197
CONCEPTS / COMMENTS
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Inferring public health and vaccine policies from epidemiology and whole genome sequencing of invasive pneumococcal isolates from a surveillance network.
Pelton Stephen I et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Nov -
Using genomics to improve preparedness and response of future epidemics or pandemics in Africa
Chaguza C. Lancet Microbe, Nov 1, 2020. -
Coronavirus Detection in the Clinical Microbiology Laboratory: Are We Ready for Identifying and Diagnosing a Novel Virus?
Uhteg Katharine et al. Clinics in laboratory medicine 2020 12 (4) 459-472 -
The engines of SARS-CoV-2 spread.
Lee Elizabeth C et al. Science (New York, N.Y.) 2020 10 (6515) 406-407 -
Investigating the Concept and Origin of Viruses.
Nasir Arshan et al. Trends in microbiology 2020 Sep
METHODS / TOOLS
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Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework.
Dellicour Simon et al. Nature communications 2020 Nov (1) 5620 -
IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring.
Kalantar Katrina L et al. GigaScience 2020 10 (10) -
Optimized use of Oxford Nanopore flowcells for hybrid assemblies.
Lipworth Samuel et al. Microbial genomics 2020 Nov -
Rapid and robust assembly and decoding of molecular tags with DNA-based nanopore signatures.
Doroschak Kathryn et al. Nature communications 2020 11 (1) 5454 -
Ten simple rules for writing Dockerfiles for reproducible data science.
Nüst Daniel et al. PLoS computational biology 2020 Nov (11) e1008316 -
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.
Hufsky Franziska et al. Briefings in bioinformatics 2020 Nov -
COVID-19 Wastewater Epidemiology: A Model to Estimate Infected Populations
McMahan CS, et al. medRxiv, Nov 7, 2020. -
Amplicon-Based, Next-Generation Sequencing Approaches to Characterize Single Nucleotide Polymorphisms of Orthohantavirus Species.
Taylor Mariah K et al. Frontiers in cellular and infection microbiology 2020 565591 -
Genomic Epidemiology of Historical Clostridium perfringens Outbreaks in New York State Using Two Web-based Platforms: National Center for Biotechnology Information-Pathogen Detection and FDA-GalaxyTrakr
Carey J, et al. J Clin Microbiol, 2020 Nov 11;JCM.02200-20.
EVOLUTION / ECOLOGY / POPULATIONS
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Invasive Pneumococcal Strain Distributions and Isolate Clusters Associated With Persons Experiencing Homelessness During 2018.
Benjamin J Metcalf et al. Clin Infect Dis 2020 11 (12) e948-e956 -
Global genomic epidemiology of Streptococcus pyogenes.
Jespersen Magnus G et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 Nov 104609 -
Whole-Genome Analysis of Clinical Vibrio cholerae O1 in Kolkata, India, and Dhaka, Bangladesh, Reveals Two Lineages of Circulating Strains, Indicating Variation in Genomic Attributes.
Morita Daichi et al. mBio 2020 Nov (6) -
Trends of mutation accumulation across global SARS-CoV-2 genomes: Implications for the evolution of the novel coronavirus.
Roy Chayan et al. Genomics 2020 Nov -
The evolution of dengue-2 viruses in Malindi, Kenya and greater East Africa: Epidemiological and immunological implications.
Pollett Simon et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 Nov 104617 -
Drivers of within-host genetic diversity in acute infections of viruses.
Gelbart Maoz et al. PLoS pathogens 2020 Nov (11) e1009029 -
Emergence of a novel chikungunya virus strain bearing the E1:V80A substitution, out of the Mombasa, Kenya 2017-2018 outbreak.
Eyase Fredrick et al. PloS one 2020 (11) e0241754 -
A novel Sporothrix brasiliensis genomic variant in Midwestern Brazil: evidence for an older and wider sporotrichosis epidemic.
Eudes Filho João et al. Emerging microbes & infections 2020 Nov 1-26 -
Genetic epidemiology of lymphatic filariasis in American Samoa after mass drug administration.
Hedtke Shannon M et al. International journal for parasitology 2020 Nov
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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A highly rifampicin resistant Mycobacterium tuberculosis strain emerging in Southern Brazil.
Rossetti Maria Lucia et al. Tuberculosis (Edinburgh, Scotland) 2020 Oct 102015 -
Characterization of the Plasmidome Encoding Carbapenemase and Mechanisms for Dissemination of Carbapenem-Resistant Enterobacteriaceae .
Abe Ryuichiro et al. mSystems 2020 Nov (6) -
Snapshot Study of Whole Genome Sequences of Escherichia coli from Healthy Companion Animals, Livestock, Wildlife, Humans and Food in Italy.
Massella Elisa et al. Antibiotics (Basel, Switzerland) 2020 Nov (11) -
Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains.
Kopotsa Katlego et al. Microbial genomics 2020 Nov -
Genomic epidemiology of Corynebacterium striatum from three regions of China: an emerging national nosocomial epidemic.
Wang Xuebing et al. The Journal of hospital infection 2020 Nov -
HIV-1 gp41 genetic diversity and enfuvirtide resistance-associated mutations among enfuvirtide-naïve patients in southern China.
Chang Le et al. Virus research 2020 Nov 198215 -
Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART.
Wan Chenjie et al. Nature communications 2020 11 (1) 5542 -
Reduced long-lasting insecticidal net efficacy and pyrethroid insecticide resistance are associated with over-expression of CYP6P4, CYP6P3 and CYP6Z1 in populations of Anopheles coluzzii from South-East Côte d'Ivoire.
Meiwald Anne et al. The Journal of infectious diseases 2020 Nov
DETECTION / DIAGNOSIS
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MALDI-TOF MS and genomic analysis can make the difference in the clarification of canine brucellosis outbreaks.
da Silva David Attuy Vey et al. Scientific reports 2020 Nov (1) 19246 -
Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids.
Gu Wei et al. Nature medicine 2020 Nov -
Wastewater Analysis of SARS-CoV-2 as a Predictive Metric of Positivity Rate for a Major Metropolis
Stadler LB, et al. medRxiv, Nov 6, 2020. -
Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION.
Gigante Crystal M et al. Viruses 2020 Nov (11) -
A machine learning-based treatment prediction model using whole genome variants of hepatitis C virus.
Haga Hiroaki et al. PloS one 2020 (11) e0242028 -
Impact of Plasmodium falciparum gene deletions on malaria rapid diagnostic test performance.
Gatton Michelle L et al. Malaria journal 2020 Nov (1) 392
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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A Dominant Strain of Elizabethkingia anophelisEmerged from Hospital Water System to Cause a Three-year Outbreak in A Respiratory Care Center.
Lee Yu-Lin et al. The Journal of hospital infection 2020 Nov -
Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data.
Xu Yuanwei et al. Microbial genomics 2020 Nov -
Genotypic correlation between post discharge Clostridiodes difficle infection (CDI) and previous unit-based contacts.
Babady N Esther et al. The Journal of hospital infection 2020 Nov -
Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans.
Oude Munnink Bas B et al. Science (New York, N.Y.) 2020 Nov -
Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel.
Miller Danielle et al. Nature communications 2020 11 (1) 5518 -
Symptomatic SARS-CoV-2 re-infection of a health care worker in a Belgian nosocomial outbreak despite primary neutralizing antibody response.
Selhorst P, et al. medRxiv, Nov 9, 2020. -
A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan
Sekizuka T, et al. mSphere, Nov 11, 2020. -
SARS-CoV-2 Transmission among Marine Recruits during Quarantine.
Letizia Andrew G et al. The New England journal of medicine 2020 Nov -
SARS-CoV-2 spread across the Colombian-Venezuelan border.
Paniz-Mondolfi Alberto et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 Nov 104616 -
HCV Genetic Diversity Can Be Used to Infer Infection Recency and Time since Infection.
Carlisle Louisa A et al. Viruses 2020 Oct (11) -
Factors associated with phylogenetic clustering of hepatitis C among people who inject drugs in Baltimore.
Falade-Nwulia Oluwaseun et al. BMC infectious diseases 2020 Nov (1) 815
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Elicitation of potent neutralizing antibody responses by designed protein nanoparticle vaccines for SARS-CoV-2
Walls AC, et al. Cell, Oct 31, 2020.
HOST-MICROBE INTERACTIONS
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Genetic variants are identified to increase risk of COVID-19 related mortality from UK Biobank data
Hu J, et al. medRxiv, Nov 9, 2020. -
Longitudinal Analysis of T and B Cell Receptor Repertoire Transcripts Reveal Dynamic Immune Response in COVID-19 Patients.
Niu Xuefeng et al. Frontiers in immunology 2020 582010 -
Host Genomics of the HIV-1 Reservoir Size and Its Decay Rate During Suppressive Antiretroviral Treatment.
Thorball Christian W et al. Journal of acquired immune deficiency syndromes (1999) 2020 Dec (4) 517-524 -
Asymptomatic Infection of Marburg Virus Reservoir Bats Is Explained by a Strategy of Immunoprotective Disease Tolerance.
Guito Jonathan C et al. Current biology : CB 2020 Oct -
Opioid agonist and antagonist use and the gut microbiota: associations among people in addiction treatment.
Gicquelais Rachel E et al. Scientific reports 2020 Nov (1) 19471
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.
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