Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: May 14, 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
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• High-Throughput Diagnostic COVID-19 Sequencing Assays May Enable Large-Scale Testing
  Karow J. GenomeWeb, May 12, 2020.
• First CRISPR test for the coronavirus approved in the United States
  Guglielmi G. Nature, May 8, 2020.
• F.D.A. Paves Way for Home Testing of Coronavirus
  Jacobs A. New York Times, May 7, 2020.
• New Inflammatory Condition in Children Probably Linked to Coronavirus, Study Finds
  Belluck P. New York Times, May 13, 2020.
• AI Is Screening Billions of Molecules for Coronavirus Treatments
  Olena A. The Scientist, May 7, 2020.
• Coronavirus: Thousands of Covid patients to have genome studied
  Hamer M, et al. medRxiv, May 13, 2020.
• This course will train an army of contact tracers. You can take it, too.
  Guarino B. Washington Post, May 11, 2020.
• How swamped preprint servers are blocking bad coronavirus research
  Kwon D. Nature, May 7, 2020.
• Scientists are drowning in COVID-19 papers. Can new tools keep them afloat?
  Brainard J. Science, May 13, 2020.

EVENTS / TRAINING / WEB RESOURCES

• Thematic issue on Human Pathogens in the Environment: biology and risk factors.
  Holden Nicola et al. FEMS microbiology letters 2020 Apr (8)
• Ad hoc efforts for advancing data science education.
  DeMasi Orianna et al. PLoS computational biology 2020 May (5) e1007695

POLICY

• A strategic approach to COVID-19 vaccine R&D
  Corey L, et al. Science, May 11, 2020.

CONCEPTS / COMMENTS

• Ideas for how informaticians can get involved with COVID-19 research
  Moore JH, et al. BioData Mining, May 12, 2020.
• Better together: Elements of successful scientific software development in a distributed collaborative community.
  Koehler Leman Julia et al. PLoS computational biology 2020 May (5) e1007507
• Understanding, verifying and implementing Emergency Use Authorization molecular diagnostics for the detection of SARS-CoV-2 RNA.
  Mitchell Stephanie L et al. Journal of clinical microbiology 2020 May 
• Inner Workings: Molecular biologists offer "wartime service" in the effort to test for COVID-19.
  McDermott Amy et al. Proceedings of the National Academy of Sciences of the United States of America 2020 05 (18) 9656-9659 
• From the micro to the macro to improve health: microorganism ecology and society in teaching infectious disease epidemiology.
  Shahmanesh Maryam et al. The Lancet. Infectious diseases 2020 May
• Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
  Mavian Carla et al. Proceedings of the National Academy of Sciences of the United States of America 2020 May
• COVID-19 and Postinfection Immunity: Limited Evidence, Many Remaining Questions.
  Kirkcaldy Robert D et al. JAMA 2020 May 
• The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic
  The COVID-19 Host Genetics Initiative, Eur J Hum Genet, May 13, 2020.
• Moving from probiotics to precision probiotics
  Veiga P, et al. Nat Microbiol, May 11, 2020.

METHODS / TOOLS

• The coding capacity of SARS-CoV-2
  Finkel Y, et al. bioRxiv, May 7, 2020.
• VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data
  Yasumizu Y, et al. bioRxiv, May 9, 2020.
• Novel NGS Pipeline for Virus Discovery from a Wide Spectrum of Hosts and Sample Types
  Plyusnin I, et al. bioRxiv, May 8, 2020.
• A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2
  Gohl DM, et al. bioRxiv, May 11, 2020.
• Laboratory validation of an RNA/DNA hybrid tagmentation based mNGS workflow on SARS-CoV-2 and other respiratory RNA viruses detection
  Wei F, et al. medRxiv, May 14, 2020.
• Propagation, inactivation, and safety testing of SARS-CoV-2
  Jureka AS, et al. bioRxiv, May 14, 2020.
• A Computational Toolset for Rapid Identification of SARS-CoV-2, other Viruses, and Microorganisms from Sequencing Data
  Chen S, et al. bioRxiv, May 12, 2020.
• ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens
  Zamecnik CR, et al. medRxiv, May 13, 2020.
• Massive Multiplexing Can Deliver a $1 Test for COVID-19
  Hebert PD, et al. bioRxiv, May 8, 2020.
• 3D-Printing to Address COVID-19 Testing Supply Shortages.
  Cox Jesse L et al. Laboratory medicine 2020 May
• Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates.
  Gladstone Rebecca A et al. Microbial genomics 2020 Apr  
• COVID-19: Viral-host interactome analyzed by network based-approach model to study pathogenesis of SARS-CoV-2 infection.
  Messina F, et al. bioRxiv, May 7, 2020.
• An open source tool to infer epidemiological and immunological dynamics from serological data: Serosolver.
  Hay James A et al. PLoS computational biology 2020 May (5) e1007840
• COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.
  Ostaszewski Marek et al. Scientific data 2020 05 (1) 136

EVOLUTION / ECOLOGY / POPULATIONS

• Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins.
  Xiao Kangpeng et al. Nature 2020 May
• Bioinformatic analysis indicates that SARS-CoV-2 is unrelated to known artificial coronaviruses.
  Dallavilla T et al. European review for medical and pharmacological sciences 2020 04 (8) 4558-4564 
• Characterization of SARS-CoV-2 viral diversity within and across hosts
  Sashittal P, et al. bioRxiv, May 13, 2020.
• "Frozen evolution" of an RNA virus suggests accidental release as a potential cause of arbovirus re-emergence.
  Pascall David J et al. PLoS biology 2020 Apr (4) e3000673 
• Molecular surveillance over 14 years confirms reduction of Plasmodium vivax and falciparum transmission after implementation of Artemisinin-based combination therapy in Papua, Indonesia.
  Pava Zuleima et al. PLoS neglected tropical diseases 2020 May (5) e0008295 
• Toxocara species environmental contamination of public spaces in New York City.
  Tyungu Donna L et al. PLoS neglected tropical diseases 2020 May (5) e0008249
• Fine-scale population genetic structure of dengue mosquito vector, Aedes aegypti, in metropolitan manila, Philippines.
  Carvajal Thaddeus M et al. PLoS neglected tropical diseases 2020 May (5) e0008279

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Complete Genome Sequences of Three Neisseria gonorrhoeae Isolates from Thailand with Multidrug Resistance and Multilocus Sequence Type 1903.
  Cherdtrakulkiat Thitima et al. Microbiology resource announcements 2020 May (19) 
• Ongoing dissemination of OXA-244 carbapenemase-producing Escherichia coli in Switzerland and their detection.
  Masseron Amandine et al. Diagnostic microbiology and infectious disease 2020 Apr (3) 115059 
• Antibiotic resistance by high-level intrinsic suppression of a frameshift mutation in an essential gene.
  Huseby Douglas L et al. Proceedings of the National Academy of Sciences of the United States of America 2020 02 (6) 3185-3191
• Molecular epidemiological analysis of Mycoplasma genitalium shows low prevalence of azithromycin resistance and a well-established epidemic in South Africa.
  Laumen Jolein G E et al. Sexually transmitted infections 2020 May
• HBV variants are common in the "immune-tolerant"phase of chronic hepatitis B.
  Yuen Lilly et al. Journal of viral hepatitis 2020 May
• Swine-Origin H1 Influenza Viruses Isolated from Humans Exhibit Sustained Infectivity in an Aerosol State.
  Pulit-Penaloza Joanna A et al. Applied and environmental microbiology 2019 05 (10) 
• Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensing.
  Bandara H M H N et al. Scientific reports 2020 May (1) 7769
• Local emergence in Amazonia of Plasmodium falciparum k13 C580Y mutants associated with in vitro artemisinin resistance.
  Mathieu Luana C et al. eLife 2020 May 
• The V410L knockdown resistance mutation occurs in island and continental populations of Aedes aegypti in West and Central Africa.
  Ayres Constância F J et al. PLoS neglected tropical diseases 2020 May (5) e0008216

DETECTION / DIAGNOSIS

• Increased Discrimination of Treponema pallidum Strains by Subtyping With a 4-Component System Incorporating a Mononucleotide Tandem Repeat in rpsA.
  Pillay Allan et al. Sexually transmitted diseases 2019 04 (4) e42-e45 
• Mycobacterium bovis : From Genotyping to Genome Sequencing.
  Guimaraes Ana M S et al. Microorganisms 2020 May (5) 
• Detection of drug resistant Mycobacterium tuberculosis by high-throughput sequencing of DNA isolated from acid fast bacilli smears.
  Rowneki Mazhgan et al. PloS one 2020 (5) e0232343
• Performance of the rapid Nucleic Acid Amplification by Abbott ID NOW COVID-19 in nasopharyngeal swabs transported in viral media and dry nasal swabs, in a New York City academic institution
  Basu A, et al. biorxiv, May 12, 2020.
• Comparison of SARS-CoV-2 Indirect and Direct Detection Methods
  Bremner R, et al. bioRxiv, May 13, 2020.
• Escalating infection control response to the rapidly evolving epidemiology of the coronavirus disease 2019 (COVID-19) due to SARS-CoV-2 in Hong Kong.
  Cheng Vincent C C et al. Infection control and hospital epidemiology 2020 05 (5) 493-498 
• A Droplet Digital PCR Assay to Detect SARS-CoV-2 RNA
  Romeo MJ, et al. medRxiv, May 11, 2020.
• Screening for SARS-CoV-2 infections with colorimetric RT-LAMP and LAMP sequencing
  Thi VL, et al. medRxiv, May 9, 2020.
• US CDC Real-Time Reverse Transcription PCR Panel for Detection of Severe Acute Respiratory Syndrome Coronavirus 2.
  Lu Xiaoyan et al. Emerging infectious diseases 2020 May (8) 
• Point-of-care testing for COVID-19 using SHERLOCK diagnostics
  Joung J, et al. medRxiv, May 8, 2020.
• Clinical Performance of SARS-CoV-2 Molecular Testing
  Green DA, et al. medRxiv, May 8, 2020. 
• Occurrence and Timing of Subsequent SARS-CoV-2 RT-PCR Positivity Among Initially Negative Patients
  Long DR, et al. medRxiv, May 8, 2020. 
• A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs.
  Rocca MF, et al. bioRxiv, May 7, 2020.
• Making the best use of test kits for COVID-19.
  Weinberg Clarice R et al. American journal of epidemiology 2020 May
• Candida auris : An Emerging Yeast Pathogen Posing Distinct Challenges for Laboratory Diagnostics, Treatment, and Infection Prevention.
  Hata D Jane et al. Archives of pathology & laboratory medicine 2020 01 (1) 107-114  
• Analysis of the serum peptidome associated with Toxoplasma gondii infection.
  Zhou Chun-Xue et al. Journal of proteomics 2020 May 103805

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• A protracted iGAS outbreak in a long-term care facility 2014-2015: control measures and the use of whole-genome sequencing.
  Degala S et al. The Journal of hospital infection 2020 May (1) 70-77
• Genomic Comparison of Salmonella Enteritidis Strains Isolated from Laying Hens and Humans in the Abruzzi Region during 2018.
  Di Marcantonio Lisa et al. Pathogens (Basel, Switzerland) 2020 May (5) 
• Consecutive outbreaks of Burkholderia cepacia complex caused by intrinsically contaminated chlorhexidine mouthwashes.
  Dos Santos Saalfeld Silvia Maria et al. American journal of infection control 2020 May 
• Defining the Pandemic at the State Level: Sequence-Based Epidemiology of the SARS-CoV-2 virus by the Arizona COVID-19 Genomics Union (ACGU)
  Ladner JT, et al. medRxiv, May 13, 2020.
• Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States.
  Fauver Joseph R et al. Cell 2020 May
• The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing.
  Xavier J, et al. medRxiv, May 11, 2020.
• Using viral genomics to estimate undetected infections and extent of superspreading events for COVID-19
  Li LM, Ayscue P. medRxiv, May 9, 2020.
• Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission.
  Rivett Lucy et al. eLife 2020 May

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• In Silico Design of Antiviral Peptides Targeting the Spike Protein of SARS-CoV-2.
  Ling Rongsong et al. Peptides 2020 May 170328
• SARS-CoV-2 RNA polymerase as target for antiviral therapy.
  Buonaguro Luigi et al. Journal of translational medicine 2020 05 (1) 185
• The Current and Future State of Vaccines, Antivirals and Gene Therapies Against Emerging Coronaviruses.
  Tse Longping V et al. Frontiers in microbiology 2020 658
• Rapid isolation and profiling of a diverse panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein
  Zost SJ, et al. bioRxiv, May 13, 2020.

HOST-MICROBE INTERACTIONS

• The Bacterial Gut Microbiota of Adult Patients Infected, Colonized or Noncolonized by Clostridioides difficile .
  Crobach Monique J T et al. Microorganisms 2020 May (5)
• The landscape of host genetic factors involved in infection to common viruses and SARS-CoV-2
  Kachuri L, et al. bioRxiv, May 7, 2020.

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.