Advanced Molecular Detection Clips Content (Published on 03/26/2020)
NEWS
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UK COVID-19 Sequencing Consortium to Reveal Viral Spread, Evolution
Han AP, GenomeWeb, Mar 25, 2020. -
Genomic Study Points to Natural Origin of COVID-19
Collins F. NIH Director's Blog, Mar 26, 2020. -
Varied COVID-19 Strains Not a Problem for Vaccines -- For Now
Walker M. MedPage Today, Mar 25, 2020. -
Locally Made COVID-19 Tests Help Meet Demands
Jarvis C. The Scientist, Mar 25, 2020. -
Coronavirus tests: researchers chase new diagnostics to fight the pandemic
Subbaraman N. Nature, Mar 24, 2020. -
Fast, portable tests come online to curb coronavirus pandemic
Sheridan C. Nature, Mar 23, 2020. -
People Pretending to Be CDC Officials Are Knocking on Doors, Selling Fake Coronavirus Testing
Cohen M. Mother Jones, Mar 20, 2020. -
Coronavirus (COVID-19) Update: FDA Alerts Consumers About Unauthorized Fraudulent COVID-19 Test Kits
(news release) FDA, Mar 20, 2020. -
Wanted: A coronavirus test to identify people who were infected and then recovered
Healy M. Los Angeles Times, Mar 25, 2020. -
FDA Fleshes Out Emergency Guidance for Coronavirus Test Developers
Johnson M. GenomeWeb, Mar 26, 2020. -
Rockefeller-Led Team Launches Initiative to Study COVID-19 Genetic Vulnerability
GenomeWeb, Mar 26, 2020. -
COVID-19 Host Susceptibility Studies Ramp Up Internationally
Anderson A. GenomeWeb, Mar 26, 2020.
EVENTS / TRAINING / WEB RESOURCES
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The National Library of Medicine is Expanding Access to Coronavirus Literature through PubMed Central
(announcement) National Library of Medicine, Mar 25, 2020. -
COVID-19: Tackling the Novel Coronavirus
(free online course) London School of Hygiene and Tropical Medicine. -
Epidemiological data from the COVID-19 outbreak, real-time case information
(open access database) Xu B, et al. Sci Data, Mar 24, 2020. -
The COVID-19 Host Genetics Initiative
International esearch consortium.
CONCEPTS / COMMENTS
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Why the Coronavirus Has Been So Successful
Yong E. Atlantic, Mar 21, 2020. -
Scientometric Trends for Coronaviruses and Other Emerging Viral Infections
Kagan D, et al. bioRxiv, Mar 20, 2020. -
Mathematics of life and death: How disease models shape national shutdowns and other pandemic policies
Enserink M, Kupferschmidt K. Science, Mar 25, 2020.
METHODS / TOOLS
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F5N : Nanopore Sequence Analysis Toolkit for Android Smartphones
Samarakoon H, et al. bioRxiv, Mar 24, 2020. -
Automated quality control of next generation sequencing data using machine learning
Albrecht S, et al. bioRxiv, Mar 23, 2020. -
pyrpipe: a python package for RNA-Seq workflows
Singh U, et al. bioRxiv, Mar 23, 2020. -
Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform.
Szarvas Judit et al. Communications biology 2020 Mar (1) 137 -
Interpretable detection of novel human viruses from genome sequencing data
Bartoszewicz JM, et al. bioRxiv, Mar 23, 2020. -
VADR: validation and annotation of virus sequence submissions to GenBank
Schaffer AA, et al. bioRxiv, Mar 24, 2020. -
A proposal of alternative primers for the ARTIC Network's multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing
Itokawa K, et al. bioRxiv, Mar 25, 2020. -
Comparative Performance of SARS-CoV-2 Detection Assays using Seven Different Primer/Probe Sets and One Assay Kit
Casto AM, et al. medRxiv, Mar 17, 2020. -
Characterization of Molecular Cluster Detection and Evaluation of Cluster Investigation Criteria Using Machine Learning Methods and Statewide Surveillance Data in Washington State.
Erly Steven J et al. Viruses 2020 Jan (2)
EVOLUTION / ECOLOGY / POPULATIONS
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Discovery of a 382-nt deletion during the early evolution of SARS-CoV-2
Su YC, et al. bioRxiv, Mar 12, 2020. -
Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis
Sardar R, et al. bioRxiv, Mar 21, 2020. -
Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection
Li X, et al. bioRxiv, Mar 24, 2020. -
Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2
Patino-Galindo JA, et al. bioRxiv, Mar 23, 2020. -
Genetic characterization of mumps viruses associated with the resurgence of mumps in the United States: 2015-2017.
Rebecca J McNall et al. Virus Res 2020 3 197935 -
Dynamic Shifts in the HIV Proviral Landscape During Long Term Combination Antiretroviral Therapy: Implications for Persistence and Control of HIV Infections.
Anderson Elizabeth M et al. Viruses 2020 Jan (2)
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Identification of novel mobile colistin resistance gene mcr-10 .
Wang Chengcheng et al. Emerging microbes & infections 2020 (1) 508-516 -
Comparative genomics and antimicrobial resistance profiling of Elizabethkingia isolates reveals nosocomial transmission and in vitro susceptibility to fluoroquinolones, tetracyclines and trimethoprim-sulfamethoxazole
Burnard D, et al. medRxiv, Mar 17, 2020. -
Genome-Wide Screens Identify Group A Streptococcus Surface Proteins Promoting Female Genital Tract Colonization and Virulence.
Zhu Luchang et al. The American journal of pathology 2020 Mar -
Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli .
Davies Timothy J et al. Antimicrobial agents and chemotherapy 2020 Mar -
SARS-CoV-2 launches a unique transcriptional signature from in vitro, ex vivo, and in vivo systems
Blanco-Melo D, et al. bioRxiv, Mar 24, 2020. -
Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses.
Qi Furong et al. Biochemical and biophysical research communications 2020 Mar
DETECTION / DIAGNOSIS
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Paper-based nuclease protection assay with on-chip sample pretreatment for point-of-need nucleic acid detection.
Noviana Eka et al. Analytical and bioanalytical chemistry 2020 Mar -
Laboratory Diagnosis of Emerging Human Coronavirus Infections - The State of the Art.
Loeffelholz Michael J et al. Emerging microbes & infections 2020 Mar 1-26 -
RT-qPCR Detection Of Sars-Cov-2 RNA from Patient Nasopharyngeal Swab Using Qiagen RNeasy Kits or Directly via Omission of an RNA Extraction Step
Bruce EA, et al. bioRxiv, Mar 21, 2020. -
Accurate Identification of SARS-CoV-2 from Viral Genome Sequences using Deep Learning
Lopez-Rincon A, et al. bioRxiv, Mar 20, 2020. -
Development of Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) Assays Targeting SARS-CoV-2
Park GS, et al. bioRxiv, Mar 24, 2020. -
CRISPR-based surveillance for COVID-19 using genomically-comprehensive machine learning design
Metsky HC, et al. bioRxiv, Mar 2, 2020. -
Laboratory readiness and response for novel coronavirus (2019-nCoV) in expert laboratories in 30 EU/EEA countries, January 2020.
Reusken Chantal B E M et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2020 02 (6)
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Genotyping and Subtyping Cryptosporidium To Identify Risk Factors and Transmission Patterns - Nebraska, 2015-2017.
Loeck Brianna K et al. MMWR. Morbidity and mortality weekly report 2020 3 (12) 335-338 -
Notes from the Field: Ongoing Cluster of Highly Related Disseminated Gonococcal Infections - Southwest Michigan, 2019.
Nettleton William D et al. MMWR. Morbidity and mortality weekly report 2020 3 (12) 353-354 -
Improving tuberculosis surveillance by detecting international transmission using publicly available whole-genome sequencing data
Sanchini A, et al. bioRxiv, Mar 23, 2020. -
Public Health Responses to COVID-19 Outbreaks on Cruise Ships - Worldwide, February-March 2020.
Leah F Moriarty et al. MMWR Morb Mortal Wkly Rep 2020 3 (12) 347-352 -
A doubt of multiple introduction of SARS-CoV-2 in Italy: a preliminary overview.
Giovanetti Marta et al. Journal of medical virology 2020 Mar -
Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda.
Bbosa Nicholas et al. Viruses 2020 Mar (3)
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Nucleotide Analogues as Inhibitors of SARS-CoV-2 Polymerase
Chien M, et al. bioRxiv, Mar 20, 2020. -
COVID-19 Vaccine Candidates: Prediction and Validation of 174 SARS-CoV-2 Epitopes
Prachar M, et al. bioRxiv, Mar 23, 2020. -
COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning
Ong E, et al. bioRxiv, Mar 23, 2020.
HOST-MICROBE INTERACTIONS
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Colonization with the commensal fungus Candida albicans perturbs the gut-brain axis through dysregulation of endocannabinoid signaling
Markey L, et al. bioRxiv, Mar 24, 2020.


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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