Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Apr 16, 2020

Advanced Molecular Detection Clips Content

• News
• Events / Training / Web Resources
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• Coronavirus Tests Science's Need for Speed Limits
  Yan W. New York Times, Apr 14, 2020.
• UK Biobank makes infection and health data available to tackle COVID-19
  (news release) UK Biobank, Apr 14, 2020.
• SARS-CoV-2 Genomes Let Researchers Retrace Viral Spread, Mitigation Effects
  Anderson A. GenomeWeb, Apr 13, 2020.
• Bats are a key source of human viruses -- but they're not special
  Watson C. Nature, Apr 14, 2020.
• First Saliva Test for COVID-19 Approved for Emergency Use by FDA
  Winter L. The Scientist, Apr 14, 2020.
• FDA tightens enforcement on Covid-19 antibody tests
  Cohen E, Sayers D. CNN, Apr 14, 2020.
• Scientists tap CRISPR's search-and-detect skills to create a rapid Covid-19 test
  Brodwin E. STAT, Apr 16, 2020.
• Genetic Tracking Helped Us Fight Ebola. Why Can't It Halt COVID-19?
  Kiefer P. Five Thirty Eight, Apr 15, 2020.
• It was the saltshaker: How Germany meticulously traced its coronavirus outbreak
  WCarrel P, Poltz J. orld Economic Forum, Apr 12, 2020.
• Antibody tests may hold clues to COVID-19 exposure, immunity--but it's complicated
  Dall C. CIDRAP, Apr 15, 2020.
• What Do Antibody Tests For SARS-CoV-2 Tell Us About Immunity?
  Zimmer K. The Scientist, Apr 15, 2020.
• Who Is Immune to the Coronavirus?
  Lipsitch M. New York Times, Apr 15,32020.
• Antibody Points to Possible Weak Spot on Novel Coronavirus
  Collins F. NIH Director's Blog, Apr 14, 2020.
• Scientists Look for Genetic Clues Into Severe Coronavirus Cases
  Sternberg S. US News World Report, Apr 14, 2020.

EVENTS / TRAINING / WEB RESOURCES

• Open-Access Data and Computational Resources to Address COVID-19*
  Resource guide from datascience@nih.gov
• Rapid Expert Consultation on the Effectiveness of Fabric Masks for the COVID-19 Pandemic (April 8, 2020)
  (report) NASEM, Apr 8, 2020.
• Rapid Expert Consultation on SARS-CoV-2 Laboratory Testing for the COVID-19 Pandemic (April 8, 2020)
  (report) NASEM, Apr 8, 2020.
• Rapid Expert Consultation on SARS-CoV-2 Viral Shedding and Antibody Response for the COVID-19 Pandemic (April 8, 2020)
  (report) NASEM, Apr 8, 2020.
• NLM Webinar: Preprints in PubMed Central
  (webinar) Friday, May 8, 2020, 11:30AM-1:00PM EDT

METHODS / TOOLS

• BioLaboro: A bioinformatics system for detecting molecular assay signature erosion and designing new assays in response to emerging and reemerging pathogens
  Holland M, et al. bioRxiv, Apr 10, 2020.
• gplas: a comprehensive tool for plasmid analysis using short-read graphs.
  Arredondo-Alonso Sergio et al. Bioinformatics (Oxford, England) 2020 Apr
• PlasClass improves plasmid sequence classification.
  Pellow David et al. PLoS computational biology 2020 Apr (4) e1007781
• CoV Genome Tracker: tracing genomic footprints of Covid-19 pandemic
  Akther S, et al. bioRxiv, Apr 14, 2020.
• An Infectious cDNA Clone of SARS-CoV-2.
  Xie Xuping et al. Cell host & microbe 2020 Apr
• Non-specific Primers Reveal False-negative Risk in Detection of COVID-19 Infections
  Liu W. medRxiv, Apr 11, 2020.
• Rapid in silico design of antibodies targeting SARS-CoV-2 using machine learning and supercomputing
  Desautels T, et al. bioRxiv, Apr 10, 2020.
• Blueprint for a Pop-up SARS-CoV-2 Testing Lab
  Innovative Genomics Institute SARS-CoV-2 Testing Consortium, Doudna JA. medRxiv, Apr 12, 2020. 
• Applying next-generation sequencing to unravel the mutational landscape in viral quasispecies: A mini-review.
  Lu I-Na et al. Virus research 2020 Apr 197963
• Development of a workflow for identification of nuclear genotyping markers for Cyclospora cayetanensis.
  Houghton Katelyn A et al. Parasite (Paris, France) 2020 24 

EVOLUTION / ECOLOGY / POPULATIONS

• Insights on Population Structure and Within-Host Genetic Changes among Meningococcal Carriage Isolates from U.S. Universities.
  Joseph Sandeep J et al. mSphere 2020 Apr (2) 
• Genomic epidemiology and evolution of diverse lineages of clinical Campylobacter jejuni co-circulating in New Hampshire, USA, 2017.
  Park Cooper J et al. Journal of clinical microbiology 2020 Apr
• Persistence of Brucella abortus lineages revealed by genomic characterization and phylodynamic analysis.
  Suárez-Esquivel Marcela et al. PLoS neglected tropical diseases 2020 Apr (4) e0008235
• A comparative analysis of drinking water employing metagenomics.
  Brumfield Kyle D et al. PloS one 2020 (4) e0231210
• A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES.
  Tort Fernando L et al. Virus research 2020 Apr 197976
• Molecular Mechanism of Evolution and Human Infection with SARS-CoV-2.
  He Jiahua et al. Viruses 2020 Apr (4)
• The proximal origin of SARS-CoV-2.
  Andersen Kristian G et al. Nature medicine 2020 04 (4) 450-452
• The global population of SARS-CoV-2 is composed of six major subtypes
  Junior IJ, et al. bioRxiv, Apr 14, 2020.
• Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions
  Farkas C, et al. bioRxiv, Apr 12, 2020.
• Deep Sequencing Reveals Compartmentalized HIV-1 in the Semen of Men With and Without STI-Associated Urethritis.
  Council Olivia D et al. Journal of virology 2020 Apr
• Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape.
  Quadeer Ahmed A et al. Nature communications 2020 01 (1) 377

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid.
  Alba Patricia et al. Microbial genomics 2020 Apr
• The spread of chloramphenicol-resistant Neisseria meningitidis in Southeast Asia.
  Batty Elizabeth M et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2020 Apr
• Food workers as a reservoir of extended-spectrum cephalosporin-resistant Salmonella in Japan.
  Shigemura Hiroaki et al. Applied and environmental microbiology 2020 Apr
• Adaptive evolution of virulence and persistence in carbapenem-resistant Klebsiella pneumoniae.
  Ernst Christoph M et al. Nature medicine 2020 Apr
• Genetic evolution of invasive emm28 Streptococcus pyogenes strains and significant association with puerperal infections in young women, Finland.
  Gröndahl-Yli-Hannuksela Kirsi et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2020 Apr
• Amino Acid Substitutions in Positions 385 and 393 of the Hydrophobic Region of VP4 May Be Associated with Rotavirus Attenuation and Cell Culture Adaptation.
  Guo Yusheng et al. Viruses 2020 Apr (4) 

DETECTION / DIAGNOSIS

• Evaluation of Commercial Molecular Diagnostic Methods for the Detection and Determination of Macrolide Resistance in Mycoplasma pneumoniae .
  Leal Sixto M et al. Journal of clinical microbiology 2020 Apr  
• SARS-CoV-2 detection with CRISPR diagnostics
  Lu G, et al. bioRxiv, Apr 11, 2020.
• A streamlined approach to rapidly detect SARS-CoV-2 infection, avoiding RNA extraction
  Marzinotto S, et al. medRxiv, Apr 11, 2020.
• Triplex Real-Time RT-PCR for Severe Acute Respiratory Syndrome Coronavirus 2
  Waggoner JJ, et al. Emerg Infect Dis, Apr 15, 2020.
• Significance of Serology Testing to Assist Timely Diagnosis of SARS-CoV-2 infections: Implication from a Family Cluster.
  Xu Yan et al. Emerging microbes & infections 2020 Apr 1-12
• Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR
  Wikmaramatra P, et al. medRxiv, Apr 14, 2020.
• CRISPR-Cas12-based detection of SARS-CoV-2
  Broughton JP, et al. Nat Biotechnol, Apr 16, 2020.
• Field evaluation of DNA detection of human filarial and malaria parasites using mosquito excreta/feces.
  Minetti Corrado et al. PLoS neglected tropical diseases 2020 Apr (4) e0008175
• Species identification of Trichinella originated from various host and different geographical location by MALDI-TOF.
  Karadjian Gregory et al. Experimental parasitology 2020 Apr 107890

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Molecular and epidemiological analysis of a Burkholderia cepacia sepsis outbreak from a tertiary care hospital in Bangladesh.
  Farzana Refath et al. PLoS neglected tropical diseases 2020 Apr (4) e0008200
• Molecular epidemiology of Mycobacterium tuberculosis to describe the transmission dynamics among Inuit residing in Iqaluit Nunavut using whole genome sequencing.
  Alvarez Gonzalo G et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Apr
• Detection of SARS-CoV-2 Among Residents and Staff Members of an Independent and Assisted Living Community for Older Adults - Seattle, Washington, 2020.
  Roxby Alison C et al. MMWR. Morbidity and mortality weekly report 2020 Apr (14) 416-418  
• Introductions and early spread of SARS-CoV-2 in the New York City area
  Gonzalez-Reiche AS, et al. medRxiv, Apr 11, 2020.
• Spread of SARS-CoV-2 in the Icelandic Population.
  Gudbjartsson Daniel F et al. The New England journal of medicine 2020 Apr
• Temporal dynamics in viral shedding and transmissibility of COVID-19
  He X, et al. Nat Med, Apr 15, 2020.
• Incident infection in high-priority HIV molecular transmission clusters in the united states.
  Wertheim Joel O et al. AIDS (London, England) 2020 Apr 

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• In silico identification of vaccine targets for 2019-nCoV.
  Hyun-Jung Lee Chloe et al. F1000Research 2020 145
• A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2.
  Grifoni Alba et al. Cell host & microbe 2020 04 (4) 671-680.e2

HOST-MICROBE INTERACTIONS

• Biomarkers of biological age as predictors of COVID-19 disease severity.
  Lauc Gordan et al. Aging 2020 Apr
• Human ACE2 receptor polymorphisms predict SARS-CoV-2 susceptibility
  Stawiski EW, et al. bioRxiv, Apr 10, 2020.
• Human leukocyte antigen susceptibility map for SARS-CoV-2
  Nguyen A, et al. medRxiv, Apr 15, 2020.
• The landscape of viral associations in human cancers.
  Zapatka Marc et al. Nature genetics 2020 03 (3) 320-330

Note:  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 the CDC Office of Public Health Genomics 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.