Advanced Molecular Detection Clips Content (Published on 09/09/2021)
NEWS
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UK scientists win L2.2m Breakthrough prize for DNA reading advances
Sample I. The Guardian, Sep 9, 2021. -
How the Delta variant's remarkable ability to replicate threw new twists into the Covid-19 pandemic
Joseph A. STAT, Sep 9, 2021. -
Call of the Wild: Why many scientists say it's unlikely that SARS-CoV-2 originated from a 'lab leak'
Cohen J. Science, Sep 2, 2021. -
Can Intranasal COVID Vaccines Help Stop the Spread?
Teres D, Stronsberg MA. MedPage Today, Sep 5, 2021. -
The Plan to Stop Every Respiratory Virus at Once
Zhang S. The Atlantic, Sep 7, 2021.
POLICY
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American Pandemic Preparedness: Transforming Our Capabilities
(plan) White House, Sep 2, 2021. -
Getting Ready for Future Pandemics an 'Economic and Moral Imperative': White House releases pandemic preparedness plan
Frieden J. MedPage Today, Sep 3, 2021.
CONCEPTS / COMMENTS
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Five keys to writing a reproducible lab protocol
Baker M. Nature, Sep 6, 2021. -
Building global health research capacity to address research imperatives following the COVID-19 pandemic.
Kilmarx Peter H et al. PLoS medicine 2021 9 (8) e1003753 -
What is the risk of a deadly adenovirus pandemic?
Kremer Eric J et al. PLoS pathogens 2021 9 (9) e1009814 -
Ethical Issues in Genetics and Infectious Diseases Research: An Interdisciplinary Expert Review.
Walker Alexis et al. Ethics, medicine, and public health 2021 7
METHODS / TOOLS
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MicrobeTrace: Retooling molecular epidemiology for rapid public health response.
Campbell Ellsworth M et al. PLoS computational biology 2021 9 (9) e1009300
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Whole-genome-based phylogenomic analysis of the Belgian 2016-2017 influenza A(H3N2) outbreak season allows improved surveillance.
Van Poelvoorde Laura A E et al. Microbial genomics 2021 9 (9)
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High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts.
Kapustina Žana et al. Microbial genomics 2021 9 (9) -
Probing T-cell response by sequence-based probabilistic modeling.
Bravi Barbara et al. PLoS computational biology 2021 9 (9) e1009297
EVOLUTION / ECOLOGY / POPULATIONS
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The rise and the fall of a Pseudomonas aeruginosa endemic lineage in a hospital.
Petitjean Marie et al. Microbial genomics 2021 9 (9) -
Complete Genome Sequence of Rhodococcus sp. Strain W8901, a Human Clinical Specimen, Assembled Using MiSeq and MinION Sequence Data.
Gulvik Christopher A et al. Microbiology resource announcements 2021 9 (35) e0061321
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Streptococcus pneumoniae genomic datasets from an Indian population describing pre-vaccine evolutionary epidemiology using a whole genome sequencing approach.
Nagaraj Geetha et al. Microbial genomics 2021 9 (9) -
Emergence of SARS-CoV-2 variant B.1.575.2 containing the E484K mutation in the spike protein in Pamplona (Spain) May-June 2021.
Trobajo-Sanmartín Camino et al. Journal of clinical microbiology 2021 9 JCM0173621 -
Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures.
Justo Arevalo Santiago et al. Scientific reports 2021 9 (1) 17755 -
A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
Wilkinson E, et al. Science, 2021.
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Coding-Complete Sequence of a SARS-CoV-2 B.1.1.25 Lineage Obtained from an 8-Day-Old Deceased Neonate.
Alam Muntasir et al. Microbiology resource announcements 2021 9 (35) e0075621
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The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages
Martin DP, et al. Cell, Sep 6, 2021. -
From one to many: The within-host rise of viral variants.
Bessière Pierre et al. PLoS pathogens 2021 9 (9) e1009811 -
Revisiting the heterogeneous global genomic population structure of Leishmania infantum.
Patino Luz H et al. Microbial genomics 2021 9 (9)
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Whole Genome Sequencing of Pediatric Klebsiella pneumoniae Strains Reveals Important Insights Into Their Virulence-Associated Traits.
Flores-Valdez Mauricio et al. Frontiers in microbiology 2021 9 711577 -
Genomic Epidemiology and Global Population Structure of Exfoliative Toxin A-Producing Staphylococcus aureus Strains Associated With Staphylococcal Scalded Skin Syndrome.
Azarian Taj et al. Frontiers in microbiology 2021 9 663831 -
Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK.
Lipworth Samuel et al. Genome medicine 2021 9 (1) 144 -
Genetic variants and their association with phenotypic resistance to bedaquiline in Mycobacterium tuberculosis: a systematic review and individual isolate data analysis
Ismail N, et al. Lancet Microbe, Aug 31, 2021. -
Evolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase (pks) Island.
Suresh Arya et al. mBio 2021 3 (1) -
SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion.
Mlcochova Petra et al. Nature 2021 9 -
Functional comparison of MERS-coronavirus lineages reveals increased replicative fitness of the recombinant lineage 5.
Schroeder Simon et al. Nature communications 2021 9 (1) 5324
DETECTION / DIAGNOSIS
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Molecular diagnostics in the era of COVID-19.
Jayakody Harindi et al. Analytical methods : advancing methods and applications 2021 9 (34) 3744-3763
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Next-Generation Sequencing (NGS) in COVID-19: A Tool for SARS-CoV-2 Diagnosis, Monitoring New Strains and Phylodynamic Modeling in Molecular Epidemiology.
John Goldin et al. Current issues in molecular biology 2021 8 (2) 845-867
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Using Wastewater Surveillance Data to Support the COVID-19 Response - United States, 2020-2021.
Kirby Amy E et al. MMWR. Morbidity and mortality weekly report 2021 9 (36) 1242-1244
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The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology
Munnink BB, et al. Nat Med, Sep 9, 2021. -
Simultaneous detection of SARS-CoV-2 RNA and host antibodies enabled by a multiplexed electrochemical sensor platform
de Puig H, et al. medRxiv, Sep 5, 2021. -
Mathematical modeling and adequate environmental sampling plans are essential for the public health assessment of COVID-19 pandemics : development of a monitoring indicator for SARS-CoV-2 in wastewater
Cluzel N, et al. medRxiv, Sep 3, 2021.
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Wastewater-Based Epidemiology and Whole-Genome Sequencing for Community-Level Surveillance of SARS-CoV-2 in Selected Urban Communities of Davao City, Philippines: A Pilot Study
Otero MC, et al. medRxiv, Sep 3, 2021. -
High-Throughput Adaptable SARS-CoV-2 Screening for Rapid Identification of Dominant and Emerging Regional Variants
Hubler Z, et al. medRxiv, Sep 2, 2021.
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Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification
Baaijens J, et al. medRxiv, Sep 2, 2021. -
SARS-CoV-2 Wastewater Surveillance for Public Health Action.
McClary-Gutierrez Jill S et al. Emerging infectious diseases 2021 8 (9) 1-8
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Effective Human Immunodeficiency Virus Molecular Surveillance Requires Identification of Incident Cases of Infection.
Little Susan J et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 9 (5) 842-849 -
Metagenomic evidence for a polymicrobial signature of sepsis.
Tan Cedric Chih Shen et al. Microbial genomics 2021 9 (9)
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Sustained Transmission of Neisseria gonorrhoeae with High-Level Resistance to Azithromycin, in Indianapolis, Indiana, 2017-2018.
Justin L Holderman et al. Clin Infect Dis 2021 9 (5) 808-815
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Increased Rates of Secondary Bacterial Infections, Including Enterococcus Bacteremia, in Patients Hospitalized with COVID-19.
DeVoe Catherine et al. Infection control and hospital epidemiology 2021 9 1-33 -
Defining nosocomial transmission of Escherichia coli and antimicrobial resistance genes: a genomic surveillance study.
Ludden Catherine et al. The Lancet. Microbe 2021 9 (9) e472-e480 -
Epidemiological investigation of a typhoid fever outbreak in Sekhukhune District, Limpopo province, South Africa - 2017.
Makungo Unarine B et al. Southern African journal of infectious diseases 2021 9 (1) 107
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Substantial Decrease in Vancomycin-Resistant Enterococcus faecium Outbreak Duration and Number of Patients During the Danish COVID-19 Lockdown: A Prospective Observational Study.
Gisselø Katrine Lauridsen et al. Microbial drug resistance (Larchmont, N.Y.) 2021 9
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Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination.
Chaintoutis Serafeim C et al. PLoS pathogens 2021 9 (9) e1009883
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Nosocomial or not? A combined epidemiological and genomic investigation to understand hospital-acquired COVID-19 infection on an elderly care ward.
Wenlock R D et al. Infection prevention in practice 2021 9 100165
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Multiple Variants of SARS-CoV-2 in a University Outbreak After Spring Break - Chicago, Illinois, March-May 2021.
Doyle Kate et al. MMWR. Morbidity and mortality weekly report 2021 9 (35) 1195-1200
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Transmitted drug resistance and transmission clusters among HIV-1 treatment-naïve patients in Guangdong, China: a cross-sectional study.
Lan Yun et al. Virology journal 2021 9 (1) 181 -
Phylogenetic and Drug-Resistance Analysis of HIV-1 Sequences From an Extensive Paediatric HIV-1 Outbreak in Larkana, Pakistan.
Abidi Syed Hani et al. Frontiers in microbiology 2021 9 658186
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Using molecular transmission networks to understand the epidemic characteristics of HIV-1 CRF08_BC across China.
Li Kang et al. Emerging microbes & infections 2021 3 (1) 497-506 -
Rapid Assessment and Containment of Candida auris Transmission in Postacute Care Settings-Orange County, California, 2019.
Ellora N Karmarkar et al. Ann Intern Med 2021 9 (11) 1554-1562
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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The Effect of Disinfectants on the Microbial Community on Environmental Healthcare Surfaces using Next Generation Sequencing.
Perry-Dow K A et al. American journal of infection control 2021 9
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Surveillance for Adverse Events After COVID-19 mRNA Vaccination.
Klein Nicola P et al. JAMA 2021 9
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Effectiveness of COVID-19 Vaccines Against SARS-CoV-2 Infection During a Delta Variant Epidemic Surge in Multnomah County, Oregon, July 2021
Barlow RS, et al. medRxiv, Sep 3, 2021.
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Effectiveness of Covid-19 Vaccines in Ambulatory and Inpatient Care Settings.
Thompson Mark G et al. The New England journal of medicine 2021 9
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Covid-19 Vaccine Effectiveness and the Test-Negative Design.
Dean Natalie E et al. The New England journal of medicine 2021 9
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Novel virus-like nanoparticle vaccine effectively protects animal model from SARS-CoV-2 infection.
Geng Qibin et al. PLoS pathogens 2021 9 (9) e1009897 -
Japanese encephalitis virus live attenuated vaccine strains display altered immunogenicity, virulence and genetic diversity.
Davis Emily H et al. NPJ vaccines 2021 9 (1) 112
HOST-MICROBE INTERACTIONS
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A year of Covid-19 GWAS results from the GRASP portal reveals potential SARS-CoV-2 modifiers
Thibord F, et al. medRxiv, Sep 5, 2021. -
COVID-19 susceptibility variants associate with blood clots, thrombophlebitis and circulatory diseases.
Papadopoulou Areti et al. PloS one 2021 9 (9) e0256988 -
Human host genetics and susceptibility to ZIKV infection.
Ferraris Pauline et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 9 105066 -
Association of HLA-DPA1, HLA-DPB1, and HLA-DQB1 Alleles With the Long-Term and Booster Immune Responses of Young Adults Vaccinated Against the Hepatitis B Virus as Neonates.
Wang Wen-Chang et al. Frontiers in immunology 2021 9 710414
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.
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