Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: May 7, 2020

Advanced Molecular Detection Clips Content

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

NEWS

• Labs Across U.S. Join Federal Initiative to Study Coronavirus Genome
  Fink S. New York Times, Apr 30, 2020.
• Scientists Clone SARS-CoV-2 Genome with Quick Yeast-Based Method
  Williams R. The Scienstist, May 6, 2020.
• The Problem With Stories About Dangerous Coronavirus Mutations
  Yong E. Atlantic, May 6, 2020.
• Profile of a killer: the complex biology powering the coronavirus pandemic
  Cyranoski D. Nature, May 4, 2020.
• Lasers could speed up coronavirus diagnostics
  Terrone M. The Conversation, May 7, 2020.
• With Crispr, a Possible Quick Test for the Coronavirus
  Zimmer C. New York Times, May 5, 2020.
• Genetic sequencing supports Wisconsin stay-at-home order, shows clusters of coronavirus in Madison and Milwaukee
  Johnson.M, Milwaukee Journal Sentinel, May 4, 2020.
• Scores of coronavirus vaccines are in competition - how will scientists choose the best?
  Callaway Ewen et al. Nature 2020 Apr
• Children are falling ill with perplexing inflammatory syndrome thought to be linked to Covid-19
  Cha AE, Janes C. Washington Post, May 6, 2020.
• Your genes could determine whether the coronavirus puts you in the hospital -- and we're starting to unravel which ones matter
  Nguyen A, et al. The Conversation, May 5, 2020.
• Using human brain tissue in lab dishes, researchers show herpes link to Alzheimer's
  Begley S. STAT, May 6, 2020.
• Malaria 'completely stopped' by microbe
  Gallagher J. BBC, May 4, 2020.

EVENTS / TRAINING / WEB RESOURCES

• Coronavirus in context: Scite.ai tracks positive and negative citations for COVID-19 literature
  Khamsi R. Nature, May 1, 2020.
• Rapid Expert Consultations on the COVID-19 Pandemic
  (report) NASEM, March 14-April 8, 2020.

CONCEPTS / COMMENTS

• COVID-19: Epidemiology, Evolution, and Cross-Disciplinary Perspectives.
  Sun Jiumeng et al. Trends in molecular medicine 2020 05 (5) 483-495
• An ACE therapy for COVID-19
  Rodell CB. Sci Transl Med, Apr 29, 2020.

METHODS / TOOLS

• CoV-Seq: SARS-CoV-2 Genome Analysis and Visualization
  Liu B, et al. bioRxiv, May 2, 2020.
• Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform.
  Thao Tran Thi Nhu et al. Nature 2020 May
• Zika Virus Amplification Using Strand Displacement Isothermal Method and Sequencing Using Nanopore Technology.
  Hansen Sören et al. Methods in molecular biology (Clifton, N.J.) 2020 123-136
• Massively multiplexed nucleic acid detection using Cas13.
  Ackerman Cheri M et al. Nature 2020 Apr 
• Viral genomics in Ebola virus research.
  Di Paola Nicholas et al. Nature reviews. Microbiology 2020 May
• Clinical classifiers of COVID-19 infection from novel ultra-high-throughput proteomics
  Messner CB, et al. medRxiv, May 3, 2020.
• Ultra-Sensitive High-Resolution Profiling of Anti-SARS-CoV-2 Antibodies for Detecting Early Seroconversion in COVID-19 Patients
  Norman M, et al. medRxiv, May 2, 2020.
• Method for economic evaluation of bacterial whole genome sequencing surveillance compared to standard of care in detecting hospital outbreaks.
  Kumar Praveen et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 May 
• Animal Disease Surveillance in the 21st Century: Applications and Robustness of Phylodynamic Methods in Recent U.S. Human-Like H3 Swine Influenza Outbreaks.
  Alkhamis Moh A et al. Frontiers in veterinary science 2020 176

EVOLUTION / ECOLOGY / POPULATIONS

• Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni .
  Mourkas Evangelos et al. Proceedings of the National Academy of Sciences of the United States of America 2020 May
• Epidemiological and molecular characterization of Streptococcus pneumoniae carriage strains in pre-school children in Arkhangelsk, northern European Russia, prior to the introduction of conjugate pneumococcal vaccines.
  Vorobieva S Jensen V et al. BMC infectious diseases 2020 Apr (1) 279 
• Selectomic and Evolvability Analyses of the Highly Pathogenic Betacoronaviruses SARS-CoV-2, SARS-CoV, and MERS-CoV
  May M, et al. bioRxiv, May 5, 2020.
• Genetic diversity and evolution of SARS-CoV-2.
  Phan Tung et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 07 104260
• Genome-wide variations of SARS-CoV-2 infer evolution relationship and transmission route
  Zhang L, et al. medRxiv, May 3, 2020.
• SARS-CoV-2 is well adapted for humans. What does this mean for re-emergence?
  Zhan SH, et al. bioRxiv, May 2, 2020.
• Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas
  Long SW, et al. bioRxiv, May 3, 2020.
• Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses -- causes and consequences for their short and long evolutionary trajectories
  Simmonds P. bioRxiv, May 1, 2020.
• Phylogenetic network analysis of SARS-CoV-2 genomes.
  Forster Peter et al. Proceedings of the National Academy of Sciences of the United States of America 2020 04 (17) 9241-9243
• Could Environment Affect the Mutation of H1N1 Influenza Virus?
  Jiang Dong et al. International journal of environmental research and public health 2020 Apr (9)
• Under-the-Radar Dengue Virus Infections in Natural Populations of Aedes aegypti Mosquitoes.
  Boyles Sean M et al. mSphere 2020 Apr (2)

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Restricted Sequence Variation in Streptococcus pyogenes Penicillin Binding Proteins.
  Hayes Andrew et al. mSphere 2020 Apr (2)
• Emergence and genomic characterization of the ceftriaxone-resistant Neisseria gonorrhoeae FC428 clone in Chengdu, China.
  Wang Hongren et al. The Journal of antimicrobial chemotherapy 2020 May 
• Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital.
  Hastak Priyanka et al. Microbial genomics 2020 May
• Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2
  Korber B, et al. bioRxiv, Apr 30, 2020.
• The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC.
  Verity Robert et al. Nature communications 2020 Apr (1) 2107  

DETECTION / DIAGNOSIS

• Species identification of Enterococcus spp: Whole genome sequencing compared to three biochemical test-based systems and two Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) systems.
  Garza-González Elvira et al. Journal of clinical laboratory analysis 2020 May e23348 
• A New Whole Genome Culture-Independent Diagnostic Test (WG-CIDT) for Rapid Detection of Salmonella in Lettuce.
  Ogunremi Dele et al. Frontiers in microbiology 2020 602
• Molecular Evidence of Bacteria in Clothes Lice Collected from Homeless People Living in Shelters in Marseille.
  Ly Tran Duc Anh et al. Vector borne and zoonotic diseases (Larchmont, N.Y.) 2020 May
• Molecular testing for acute respiratory tract infections: clinical and diagnostic recommendations from the IDSA's Diagnostics Committee.
  Hanson Kimberly E et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 May 
• Adapting microarray gene expression signatures for early melioidosis diagnosis.
  Sangwichian Ornuma et al. Journal of clinical microbiology 2020 Apr
• Resistance-conferring mutations on whole-genome sequencing of fluoroquinolone-resistant and -susceptible M. tuberculosis isolates: a proposed threshold for identifying resistance.
  Maruri Fernanda et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Apr
• Rapid detection of Mycobacterium tuberculosis DNA and genetic markers for Isoniazid resistance in Ziehl-Neelsen stained slides.
  Bello Graziele Lima et al. Memorias do Instituto Oswaldo Cruz 2020 e190407
• Evaluation of lockdown impact on SARS-CoV-2 dynamics through viral genome quantification in Paris wastewaters
  Wurtzer S, et al. medRxiv, May 6, 2020.
• Multi-Tiered Screening and Diagnosis Strategy for COVID-19: A Model for Sustainable Testing Capacity in Response to Pandemic.
  Pulia Michael S et al. Annals of medicine 2020 May 1-20
• Navigating the Pandemic Response Life Cycle: Molecular Diagnostics and Immunoassays in the Context of COVID-19 Management.
  Zhang Jingwei et al. IEEE reviews in biomedical engineering 2020 Apr
• Evaluation of COVID-19 RT-qPCR test in multi-sample pools.
  Yelin Idan et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 May
• False positives in reverse transcription PCR testing for SARS-CoV-2
  Cohen AN, Kessel B. medRxiv, May 1, 2020. 
• Performance & Quality Evaluation of Marketed COVID-19 RNA Detection Kits
  Kapitula DS, et al. medRxiv, May 1, 2020. 
• Highly sensitive and specific detection of HBV DNA and drug resistance mutations utilizing the PCR-based CRISPR-Cas13a system.
  Wang Shan et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2020 Apr
• Validation of a Laboratory-Developed Triplex Molecular Assay for Simultaneous Detection of Gastrointestinal Adenovirus and Rotavirus in Stool Specimens.
  Higgins Rachel R et al. Pathogens (Basel, Switzerland) 2020 Apr (5)

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Concordance between epidemiological evaluation of probability of transmission and whole genome sequence relatedness among hospitalized patients acquiring KPC-producing Klebsiella pneumoniae.
  Hassoun-Kheir Nasreen et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2020 Apr 
• Nosocomial outbreak linked to a flexible gastrointestinal endoscope contaminated with an amikacin-resistant ST17 clone of Pseudomonas aeruginosa.
  Fernández-Cuenca Felipe et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2020 May 
• Whole-genome sequencing and epidemiological analysis of a tuberculosis outbreak in a high school of southern China.
  Yu Hongying et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 Apr 104343 
• Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China
  Lu J, et al. Cell, Apr 30, 2020.
• The natural history and transmission potential of asymptomatic SARS-CoV-2 infection
  Chau NV, et al. medRxiv, Apr 29, 2020.
• Determining the source of transmission of SARS-CoV-2 infection in a healthcare worker
  Safdar N. medRxiv, May 1, 2020.
• Use of whole-genome sequencing to detect an outbreak of Malassezia pachydermatis infection and colonization in a neonatal intensive care unit-California, 2015-2016.
  Chow Nancy A et al. Infection control and hospital epidemiology 2020 May 1-3  

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Structural and Evolutionary Analysis Indicate That the SARS-CoV-2 Mpro Is a Challenging Target for Small-Molecule Inhibitor Design.
  Bzówka Maria et al. International journal of molecular sciences 2020 Apr (9)
• An Evidence Based Perspective on mRNA-SARS-CoV-2 Vaccine Development.
  Wang Fuzhou et al. Medical science monitor : international medical journal of experimental and clinical research 2020 May e924700

HOST-MICROBE INTERACTIONS

• Considering the Immune System during Fecal Microbiota Transplantation for Clostridioides difficile Infection.
  Frisbee Alyse L et al. Trends in molecular medicine 2020 May (5) 496-507
• Pathobionts in the Vaginal Microbiota: Individual Participant Data Meta-Analysis of Three Sequencing Studies.
  van de Wijgert Janneke H H M et al. Frontiers in cellular and infection microbiology 2020 129 
• Plasma IP-10 and MCP-3 levels are highly associated with disease severity and predict the progression of COVID-19.
  Yang Yang et al. The Journal of allergy and clinical immunology 2020 Apr
• Imbalanced host response to SARS-CoV-2 drives development of COVID-19
  Blanco-Melo D, et al. Cell, Apr 26, 2020. doi: 10.1016/j.cell.2020.04.026
• Global Spread of SARS-CoV-2 Subtype with Spike Protein Mutation D614G is Shaped by Human Genomic Variations that Regulate Expression of TMPRSS2 and MX1 Genes
  Bhattacharyya C, et al. bioRxiv, May 5, 2020.
• COVID-2019 associated overexpressed Prevotella proteins mediated host-pathogen interactions and their role in coronavirus outbreak.
  Khan Abdul Arif et al. Bioinformatics (Oxford, England) 2020 May
• Fetal inheritance of chromosomally integrated human herpesvirus 6 predisposes the mother to pre-eclampsia.
  Gaccioli Francesca et al. Nature microbiology 2020 May

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.