Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Oct 8, 2020

Advanced Molecular Detection Clips Content

• News
• Events / Training / Web Resources
• Policy
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission

NEWS

• Trio wins Nobel Prize in medicine for discovery of hepatitis C virus
  Cooney E. STAT, Oct 5, 2020.
• Pioneers of revolutionary CRISPR gene editing win chemistry Nobel
  Ledford H, Callaway E. Nature, Oct 7, 2020.
• Genomic Data Helps Explain Yaws Re-emergence, Antibiotic Resistance in Papua New Guinea
  GenomeWeb, Oct 8, 2020.
• Harvard Team Builds Comprehensive Profile of Antibody Response to SARS-CoV-2
  Bonislawski A. 360dx, Oct 1, 2020.
• Rogue Antibodies and Gene Mutations Explain Some Cases of Severe COVID-19
  Collins F. NIH Director's Blog, Oct 6, 2020.
• Newly found viruses suggest rubella originated in animals
  Gibbons A. Science, Oct 8, 2020.

EVENTS / TRAINING / WEB RESOURCES

• Real-time audio and visual display of the Coronavirus genome.
  Temple Mark D et al. BMC bioinformatics 2020 Oct (1) 431

POLICY

• FDA Will No Longer Review EUA Submissions for SARS-CoV-2 Lab-Developed Tests
  Johnson M. GenomeWeb, Oct 7, 2020.

CONCEPTS / COMMENTS

• Microbe hunting in the modern era: reflecting on a decade of microbial genomic epidemiology.
  Baker Kate S et al. Current biology : CB 2020 Oct (19) R1124-R1130
• A call for diagnostic tests to report viral load.
  Service Robert F et al. Science (New York, N.Y.) 2020 10 (6512) 22
• Harnessing genomics to trace the path of a viral outbreak in African lions.
  Kamath Pauline L et al. Molecular ecology 2020 Oct
• Contextualizing bats as viral reservoirs
  Streicker DG, Gilbert AT. Science, Oct 9, 2020.
• Inhibiting Ebola virus and SARS-CoV-2 entry
  Wells AI, Coyne CB. Science, Oct 9, 2020.
• Implementation of environmental surveillance for SARS-CoV-2 virus to support public health decisions: opportunities and challenges.
  Medema Gertjan et al. Current opinion in environmental science & health 2020 Oct 
• Insight on Sex-Based Immunity Differences, With COVID-19 Implications.
  Hampton Tracy et al. JAMA 2020 Oct (13) 1274

METHODS / TOOLS

• metaFlye: scalable long-read metagenome assembly using repeat graphs.
  Kolmogorov Mikhail et al. Nature methods 2020 Oct
• Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries.
  Rivière Emmanuel et al. Briefings in bioinformatics 2020 Oct 
• COVID-19 CG: Tracking SARS-CoV-2 mutations by locations and dates of interest.
  Chen Albert Tian et al. bioRxiv : the preprint server for biology 2020 Sep
• A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data.
  Chen Shifu et al. Briefings in bioinformatics 2020 Oct
• A database resource and online analysis tools for coronaviruses on a historical and global scale.
  Zhu Zhenglin et al. Database : the journal of biological databases and curation 2020 Oct

EVOLUTION / ECOLOGY / POPULATIONS

• Broad host range of SARS-CoV-2 and the molecular basis for SARS-CoV-2 binding to cat ACE2.
  Wu Lili et al. Cell discovery 2020 68

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Identification of the first erm(B) + Campylobacter jejuni and Campylobacter coli associated with novel multidrug resistance genomic islands in Australia.
  Wallace Rhiannon L et al. Journal of global antimicrobial resistance 2020 Sep
• Predicting antimicrobial susceptibility from the bacterial genome: A new paradigm for one health resistance monitoring.
  McDermott Patrick F et al. Journal of veterinary pharmacology and therapeutics 2020 Oct
• Exploration of the Neisseria Resistome Reveals Resistance Mechanisms in Commensals That May Be Acquired by N. gonorrhoeae through Horizontal Gene Transfer.
  Fiore Michael A et al. Antibiotics (Basel, Switzerland) 2020 Sep (10)
• Azithromycin susceptibility of Neisseria gonorrhoeae in the USA in 2017: a genomic analysis of surveillance data.
  Gernert Kim M et al. The Lancet. Microbe 2020 Aug (4) e154-e164  
• Bacterial Genome Wide Association Studies (bGWAS) and Transcriptomics Identifies Cryptic Antimicrobial Resistance Mechanisms in Acinetobacter baumannii .
  Roe Chandler et al. Frontiers in public health 2020 451
• Yaws re-emergence and bacterial drug resistance selection after mass administration of azithromycin: a genomic epidemiology investigation
  Beale MA, et al. Lancet Microbe, Oct 1, 2020.
• Machine learning methods accurately predict host specificity of coronaviruses based on spike sequences alone.
  Kuzmin Kiril et al. Biochemical and biophysical research communications 2020 Sep
• Remdesivir targets a structurally analogous region of the Ebola virus and SARS-CoV-2 polymerases
  Lo MK, et al. Proc Natl Acad Sci USA. 2020 Oct 7;202012294.
• Fun(gi)omics: Advanced and Diverse Technologies to Explore Emerging Fungal Pathogens and Define Mechanisms of Antifungal Resistance.
  Ball B et al. mBio 2020 Oct (5)
• Mechanisms associated with pyrethroid resistance in populations of Aedes aegypti (Diptera: Culicidae) from the Caribbean coast of Colombia.
  Pareja-Loaiza Paula X et al. PloS one 2020 (10) e0228695 

DETECTION / DIAGNOSIS

• Centrifugal microfluidic lab-on-a-chip system with automated sample lysis, DNA amplification and microarray hybridization for identification of enterohemorrhagic Escherichia coli culture isolates.
  Geissler Matthias et al. The Analyst 2020 Oct
• Detection of SARS-CoV-2 RNA by multiplex RT-qPCR.
  Kudo Eriko et al. PLoS biology 2020 Oct (10) e3000867
• Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step.
  Bruce Emily A et al. PLoS biology 2020 Oct (10) e3000896
• Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone
  Fozouni P, et al. medRxiv, Sep 30, 2020.
• Ultra-rapid detection of SARS-CoV-2 in public workspace environments
  Yaren O, et al. medRxiv, Sep 30, 2020.
• SARS-CoV-2 RapidPlex: A Graphene-based Multiplexed Telemedicine Platform for Rapid and Low-Cost COVID-19 Diagnosis and Monitoring
  Torrente-Rodgriguez RM, et al. Matter, Oct 1, 2020.
• Temporal, Spatial, and Epidemiologic Relationships of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Gene Cycle Thresholds: A Pragmatic Ambi-directional Observation.
  Lesho Emil et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Aug
• A One-Minute Blood Test to Monitor Immune Responses in COVID-19 Patients and Predict Clinical Risks of Developing Moderate to Severe Symptoms
  Deb C, et al. medRxiv, Oct 5, 2020.
• Comparison of participant-collected nasal and staff-collected oropharyngeal specimens for human ribonuclease P detection with RT-PCR during a community-based study.
  Arnold Mitchell T et al. PloS one 2020 (10) e0239000 
• Progress Toward Poliomyelitis Eradication -- Afghanistan, January 2019-July 2020
  Martinez M, et al. MMWR, Oct 9, 2020.  

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• A persistent recurring cluster of meticillin-resistant Staphylococcus aureus (MRSA) colonisations in a special care baby unit: a matched case-control study.
  Love Nicola K et al. The Journal of hospital infection 2020 Oct
• SARS-CoV-2 outbreak investigation in a German meat processing plant.
  Günther Thomas et al. EMBO molecular medicine 2020 Oct e202013296
• Large scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management
  Page AJ, et al. medRxiv, Sep 30, 2020.
• Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State
  Mueller NF, et al. medRxiv, Sep 30, 2020.
• SARS-CoV-2 variant tracing within the first COVID-19 clusters in Northern Germany.
  Pfefferle Susanne et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2020 Sep
• Comprehensive Genome Analysis of 6,000 USA SARS-CoV-2 Isolates Reveals Haplotype Signatures and Localized Transmission Patterns by State and by Country.
  Shen Lishuang et al. Frontiers in microbiology 2020 573430
• Molecular epidemiology of the first wave of severe acute respiratory syndrome coronavirus 2 infection in Thailand in 2020.
  Puenpa Jiratchaya et al. Scientific reports 2020 Oct (1) 16602
• Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic.
  Zhang Wenjuan et al. JAMA network open 2020 Oct (10) e2024191
• Inference of person-to-person transmission of COVID-19 reveals hidden super-spreading events during the early outbreak phase.
  Wang Liang et al. Nature communications 2020 10 (1) 5006
• Application of Human Adenovirus Genotyping by Phylogenetic Analysis in an Outbreak to Identify Nosocomial Infection.
  Yang Chuanyu et al. Virologica Sinica 2020 Oct

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