Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jul 9, 2020

Advanced Molecular Detection Clips Content

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

NEWS

• A New Generation of Fast Coronavirus Tests Is Coming
  Wu KJ. New York Times, Jul6, 2020.
• CDC Combined COVID-19/Influenza Test Gets FDA Emergency Use Authorization
  GenomeWeb, Jul 3, 2020.
• A guide to R -- the pandemic's misunderstood metric
  Adam D. Nature, Jul 3, 2020.
• DNA Inherited From Neanderthals May Increase Risk of Covid-19
  Zimmer C. New York Times, Jul 4, 2020.
• The Pandemic's Big Mystery: How Deadly Is the Coronavirus?
  McNeil JG, Jr. New York Times, Jul 4, 2020.
• Did a Mutation Help the Coronavirus Spread? More Evidence, but Lingering Questions
  Carey B. New York Times, Jul 2, 2020.
• New journal will vet Covid-19 preprints, calling out misinformation and highlighting credible research
  Begley S. STAT, Jun 29, 2020.

POLICY

• Minutes of the International Committee on Systematics of Prokaryotes online discussion on the proposed use of gene sequences as type for naming of prokaryotes, and outcome of vote.
  Sutcliffe Iain C et al. International journal of systematic and evolutionary microbiology 2020 Jul

CONCEPTS / COMMENTS

• Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear
  Grubaugh N, et al. Cell, Jul 2, 2020.
• Advancing biological hazards risk assessment.
  Messens Winy et al. EFSA journal. European Food Safety Authority 2019 Jul (Suppl 1) e170714  

METHODS / TOOLS

• Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples.
  Xiao Minfeng et al. Genome medicine 2020 Jun (1) 57
• Rapid, Sensitive, Full-Genome Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2.
  Paden Clinton R et al. Emerging infectious diseases 2020 Jul (10) 
• Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV-2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding
  Freed NE, et al. bioRxiv, Jul 5, 2020.
• The Global Meningitis Genome Partnership.
  Rodgers Elizabeth et al. The Journal of infection 2020 Jun  
• STing: accurate and ultrafast genomic profiling with exact sequence matches.
  Espitia-Navarro Hector F et al. Nucleic acids research 2020 Jul
• Bioinformatics Pipeline for Human Papillomavirus Short Read Genomic Sequences Classification Using Support Vector Machine.
  Lomsadze Alexandre et al. Viruses 2020 Jun (7)
• Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions.
  Lees John A et al. mBio 2020 Jul (4)

EVOLUTION / ECOLOGY / POPULATIONS

• High genetic similarity between non-typhoidal Salmonella isolated from paired blood and stool samples of children in the Democratic Republic of the Congo.
  Phoba Marie-France et al. PLoS neglected tropical diseases 2020 Jul (7) e0008377
• Investigating the genomic landscape of novel coronavirus (2019-nCoV) to identify non-synonymous mutations for use in diagnosis and drug design.
  Tiwari Manish et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2020 07 104441
• Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission
  Sapoval N, et al. bioRxiv, Jul 2, 2020. 
• Genomic Characterization of Mycobacterium leprae to Explore Transmission Patterns Identifies New Subtype in Bangladesh.
  Tió-Coma Maria et al. Frontiers in microbiology 2020 1220
• Detection of Japanese Encephalitis Virus in Mosquitoes from Xinjiang during Next Generation Sequencing Arboviral Surveillance.
  Hameed Muddassar et al. Transboundary and emerging diseases 2020 Jul
• Application of Next-Generation Sequencing to Reveal How Evolutionary Dynamics of Viral Population Shape Dengue Epidemiology.
  Ko Hui-Ying et al. Frontiers in microbiology 2020 1371  
• Evidence for Reduced Malaria Parasite Population after Application of Population-Level Antimalarial Drug Strategies in Southern Province, Zambia.
  Daniels Rachel F et al. The American journal of tropical medicine and hygiene 2020 Jul 

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• The environmental contribution to the dissemination of carbapenem and (fluoro)quinolone resistance genes by discharged and reused wastewater effluents: The role of cellular and extracellular DNA.
  Oliveira Micaela et al. Water research 2020 Jun 116011
• SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain.
  Yurkovetskiy Leonid et al. bioRxiv : the preprint server for biology 2020 Jul
• No evidence of viral polymorphisms associated with Paediatric Inflammatory Multisystem Syndrome Temporally Associated With SARS-CoV-2 (PIMS-TS)
  Pang J, et al. medRxiv, Jul 8, 2020.
• Association of SARS-CoV-2 Genomic Load with COVID-19 Patient Outcomes
  Zacharioudakis IM, et al. medRxiv, Jul 4, 2020.
• Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus
  Korber B, et al. Cell, Jul 2, 2020.
• SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain
  Yurkovetskyi L, et al. bioRxiv, Jul 4, 2020.

DETECTION / DIAGNOSIS

• Source Tracking Based on Core Genome SNV and CRISPR Typing of Salmonella enterica Serovar Heidelberg Isolates Involved in Foodborne Outbreaks in Québec, 2012.
  Yousfi Khadidja et al. Frontiers in microbiology 2020 1317
• Previously Derived Host Gene Expression Classifiers Identify Bacterial and Viral Etiologies of Acute Febrile Respiratory Illness in a South Asian Population.
  Tillekeratne L Gayani et al. Open forum infectious diseases 2020 Jun (6) ofaa194
• Hospital MRSA outbreaks: Multiplex PCR-reverse line blot binary typing as a screening method for WGS, and the role of the environment in transmission.
  McKew Genevieve et al. Infection, disease & health 2020 Jun 
• An epidemic CC1-MRSA-IV clone yields false-negative test results in molecular MRSA identification assays: a note of caution, Austria, Germany, Ireland, 2020.
  Monecke Stefan et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2020 Jun (25) 
• Clinical evaluation of self-collected saliva by RT-qPCR, direct RT-qPCR, RT-LAMP, and a rapid antigen test to diagnose COVID-19.
  Nagura-Ikeda Mayu et al. Journal of clinical microbiology 2020 Jul 
• Diagnostics and spread of SARS-CoV-2 in Western Africa: An observational laboratory-based study from Benin
  Yadouleton A, et al. medRxiv, Jul 8, 2020. 
• A CRISPR-based SARS-CoV-2 diagnostic assay that is robust against viral evolution and RNA editing
  Ooi KH, et al. bioRxiv, Jul 3, 2020.
• Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2
  Wyzelich C, et al. bioRxiv, Jul 1, 2020.
• Temporal detection and phylogenetic assessment of SARS-CoV-2 in municipal wastewater
  Nemudryi A, et al. medRxiv, Jul 5, 2020.
• Diagnosis of cytomegalovirus infection from clinical whole genome sequencing.
  Ramchandar Nanda et al. Scientific reports 2020 Jul (1) 11020
• Detection and differentiation of bacterial and fungal infection of neutrophils from peripheral blood using Raman spectroscopy.
  Arend Natalie et al. Analytical chemistry 2020 Jul

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Cohorting KPC+ Klebsiella pneumoniae (KPC-Kp)-positive patients: A genomic exposé of cross-colonization hazards in a long-term acute-care hospital (LTACH).
  Hawken Shawn E et al. Infection control and hospital epidemiology 2020 Jun 1-7 
• Epidemiological and Whole Genomic Sequencing Analysis of a Campylobacter jejuni Outbreak in Zhejiang Province, China, May 2019.
  Chen Honghu et al. Foodborne pathogens and disease 2020 Jul 
• COVID-19 in Latin America: Contrasting phylodynamic inference with epidemiological surveillance. (Molecular epidemiology of COVID-19 in Latin America)
  Rojas-Gallardo DM, et al. medRxiv, Jul 6, 2020.
• COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study.
  Sikkema Reina S et al. The Lancet. Infectious diseases 2020 Jul 
• Main Routes of Entry and Genomic Diversity of SARS-CoV-2, Uganda.
  Bugembe Daniel Lule et al. Emerging infectious diseases 2020 Jul (10)
• A genome epidemiological study of SARS-CoV-2 introduction into Japan
  Sekizuka T, et al. medRxiv, Jul 2, 2020.
• A Recent Human Immunodeficiency Virus Outbreak Among People Who Inject Drugs in Munich, Germany, Is Associated With Consumption of Synthetic Cathinones.
  Hanke Kirsten et al. Open forum infectious diseases 2020 Jun (6) ofaa192

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Phase 1/2 Study to Describe the Safety and Immunogenicity of a COVID-19 RNA Vaccine Candidate (BNT162b1) in Adults 18 to 55 Years of Age: Interim Report
  Mulligan MJ, et al. medRxiv, Jul 1, 2020.

HOST-MICROBE INTERACTIONS

• The major genetic risk factor for severe COVID-19 is inherited from Neandertals
  Zeberg H, P??bo S. bioRxiv, Jul 3, 2020.
• Genetic risk factors for death with SARS-CoV-2 from the UK Biobank
  Lu C, et al. medRxiv, Jul 5, 2020.
• A role for human leucocyte antigens in the susceptibility to SARS-Cov-2 infection observed in transplant patients.
  Poulton Kay et al. International journal of immunogenetics 2020 Jul
• PNPLA3 and TLL-1 polymorphisms affect disease severity in patients with COVID-19
  Grimaudo S, et al. ResearchSquare, Jul 7, 2020.
• Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes.
  Reitmeier Sandra et al. Cell host & microbe 2020 Jun

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.