Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jun 11, 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
• Host-Microbe Interactions

NEWS

• Uncovering hidden antimicrobial resistance patterns within the hospital microbiome
  Haak BW, Wiersinga WJ. Nature, Jun 8, 2020.
• Metagenomic Survey of Hospital Sites Uncovers Two Ecological Niches Contributing to Infections
  GenomeWeb, Jun 8, 2020.
• The biggest mystery: what it will take to trace the coronavirus source
  Cyranoski D. Nature, Jun 5, 2020.
• A Living Library Filled With Killer Bacteria
  Pinkowski J. New York Times, Jun 8, 2020.
• COVID-19 vaccine development pipeline gears up
  Mullard A. Lancet, Jun 6, 2020.
• Genes May Leave Some People More Vulnerable to Severe Covid-19
  Zimmer C. New York Times, Jun 3, 2020.
• Two Genetic Regions Linked with Severe COVID-19
  Olena A. The Scientist, Jun 8, 2020.
• Italian Researchers Use Whole-Exome Sequencing to Unravel COVID-19 Disease Susceptibility
  Petrone J. GenomeWeb, Jun 10, 2020.
• NIH launches preprint pilot to expand discovery of NIH-funded research
  NLM, Jun 9, 2020.

EVENTS / TRAINING / WEB RESOURCES

• Updated BLAST RefSeq rRNA databases for identification and phylogenetic analysis
  (webinar) NCBI, June 17, 12:00 - 12:45 PM EDT
• New NCBI SARS-CoV-2 Resources Page
  (announcement) NCBI, Jun 9, 2020.

POLICY

• Guidance for research ethics committees for rapid review of research during public health emergencies
  WHO, 2020.

CONCEPTS / COMMENTS

• COVID-19 diagnostics in context.
  Weissleder Ralph et al. Science translational medicine 2020 06 (546)
• In silico veritas? Potential limitations for SARS-CoV-2 vaccine development based on T-cell epitope prediction.
  Silva-Arrieta Sandra et al. PLoS pathogens 2020 Jun (6) e1008607
• False Negative Tests for SARS-CoV-2 Infection - Challenges and Implications.
  Woloshin Steven et al. The New England journal of medicine 2020 Jun
• Building an international consortium for tracking coronavirus health status.
  Segal Eran et al. Nature medicine 2020 Jun
• Assessing Climate Change Impact on Ecosystems and Infectious Disease: Important Roles for Genomic Sequencing and a One Health Perspective.
  B Yeh Kenneth et al. Tropical medicine and infectious disease 2020 Jun (2)

METHODS / TOOLS

• Assessing the Performance of Dried-Blood-Spot DNA Extraction Methods in Next Generation Sequencing.
  Hendrix Miyono M et al. International journal of neonatal screening 2020 Apr (2) 1-15  
• Lessons learnt from the introduction of nanopore sequencing?
  Hays John et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2020 Jun 
• Ten recommendations for supporting open pathogen genomic analysis in public health
  Black A, et al. Nat Med, Jun 11, 2020.  
• Gen2EpiGUI: User-friendly Pipeline for Analyzing Whole Genome Sequencing Data for Epidemiological Studies of Neisseria gonorrhoeae.
  Singh Reema et al. Sexually transmitted diseases 2020 Jun
• Using viral genomics to estimate undetected infections and extent of superspreading events for COVID-19
  Li LM, Ayscue P. medRxiv, Jun 7, 2020.
• A Public Website for the Automated Assessment and Validation of SARS-CoV-2 Diagnostic PCR Assays
  Li PE, et al. arXiv, Jun 8, 2020. 
• Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic
  Pillay S, et al. bioRxiv, Jun 10, 2020. 
• Stability of SARS-CoV-2 Phylogenies
  Turakhia Y, et al. bioRxiv, Jun 9, 2020.
• PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing.
  Robitaille Alexis et al. BMC bioinformatics 2020 Jun (1) 233
• Development and Characterization of a Reverse-Genetics System for Influenza D Virus.
  Yu Jieshi et al. Journal of virology 2019 11 (21) 

EVOLUTION / ECOLOGY / POPULATIONS

• Coastal urbanization influences human pathogens and microdebris contamination in seafood.
  Littman Raechel A et al. The Science of the total environment 2020 May 139081
• Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada.
  Wang Lu Ya Ruth et al. Microbial genomics 2020 Jun
• Development and application of a core genome multilocus sequence typing scheme for the healthcare-associated pathogen Pseudomonas aeruginosa .
  Stanton Richard A et al. Journal of clinical microbiology 2020 Jun  
• Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment.
  Chng Kern Rei et al. Nature medicine 2020 Jun
• Within-Host Viral Diversity: A Window into Viral Evolution.
  Lauring Adam S et al. Annual review of virology 2020 Jun
• Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions.
  Butler Daniel J et al. bioRxiv : the preprint server for biology 2020 May
• The origin and underlying driving forces of the SARS-CoV-2 outbreak.
  Chaw Shu-Miaw et al. Journal of biomedical science 2020 Jun (1) 73
• Integrated genomic view of SARS-CoV-2 in India
  Kumar P, et al. bioRxiv, Jun 4, 2020.
• Movement of St. Louis encephalitis virus in the Western United States, 2014- 2018.
  Swetnam Daniele M et al. PLoS neglected tropical diseases 2020 Jun (6) e0008343 
• Biennial Upsurge and Molecular Epidemiology of Enterovirus D68 Infection in New York, United States, 2014-2018.
  Gilrane Victoria L et al. Journal of clinical microbiology 2020 Jun
• HIV-1 variants are archived throughout infection and persist in the reservoir.
  Brooks Kelsie et al. PLoS pathogens 2020 Jun (6) e1008378

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Comparative genomic analysis provides insight into the phylogeny and virulence of atypical enteropathogenic Escherichia coli strains from Brazil.
  Hernandes Rodrigo T et al. PLoS neglected tropical diseases 2020 Jun (6) e0008373
• Inherent colistin resistance in genogroups of the Enterobacter cloacae complex: epidemiological, genetic and biochemical analysis from the BSAC Resistance Surveillance Programme.
  Mushtaq Shazad et al. The Journal of antimicrobial chemotherapy 2020 Jun
• A whole-genome screen identifies Salmonella enterica serovar Typhi genes involved in fluoroquinolone susceptibility.
  Turner A Keith et al. The Journal of antimicrobial chemotherapy 2020 Jun
• Spill-Over from Public Health? First Detection of an OXA-48-Producing Escherichia coli in a German Pig Farm.
  Irrgang Alexandra et al. Microorganisms 2020 Jun (6)
• An Africa-wide genomic evolution of insecticide resistance in the malaria vector Anopheles funestus involves selective sweeps, copy number variations, gene conversion and transposons.
  Weedall Gareth D et al. PLoS genetics 2020 Jun (6) e1008822

DETECTION / DIAGNOSIS

• Carriage of Neisseria meningitidis in men who have sex with men presenting to public sexual health clinics, New York City.
  Ngai Stephanie et al. Sexually transmitted diseases 2020 Jun 
• HiDRA-seq: High-Throughput SARS-CoV-2 Detection by RNA Barcoding and Amplicon Sequencing
  Yanguez E, et al. bioRxiv, Jun 2, 2020.
• Identification of nsp1 gene as the target of SARS-CoV-2 real-time RT-PCR using nanopore whole genome sequencing.
  Chan Wan-Mui et al. Journal of medical virology 2020 Jun
• CRISPR-Cas12-based detection of SARS-CoV-2.
  Broughton James P et al. Nature biotechnology 2020 Apr
• Detection of SARS-Coronavirus-2 in wastewater, using the existing environmental surveillance network: An epidemiological gateway to an early warning for COVID-19 in communities.
  Sharif S Sr, et al. medRxiv, Jun 7, 2020.
• Longitudinal Surveillance for SARS-CoV-2 RNA Among Asymptomatic Staff in Five Colorado Skilled Nursing Facilities: Epidemiologic, Virologic and Sequence Analysis
  Quicke K, et al. medRxiv, Jun 9, 2020.
• Point-of-Care Devices to Detect Zika and Other Emerging Viruses.
  de Puig Helena et al. Annual review of biomedical engineering 2020 Jun 371-386 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Management of an outbreak of postpartum Streptococcus pyogenes emm75 infections.
  Trell Kristina et al. The Journal of hospital infection 2020 Jun 
• Tuberculosis transmission across three states: the story of a solid organ donor born in an endemic country, 2018.
  Jones Jefferson M et al. Transplant infectious disease : an official journal of the Transplantation Society 2020 Jun e13357 
• Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China.
  Lu Jing et al. Cell 2020 05 (5) 997-1003.e9
• Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.
  Deng Xianding et al. Science (New York, N.Y.) 2020 Jun

HOST-MICROBE INTERACTIONS

• Inflammasome genetics and complex diseases: a comprehensive review.
  Fernandes Fernanda Pereira et al. European journal of human genetics : EJHG 2020 Jun
• Class I HLA allele restricted antigenic coverage for Spike and N proteins is associated with divergent outcomes for COVID-19
  Pretti MA, et al. medRxiv, Jun 5, 2020.
• Proteomic Profiling in Biracial Cohorts Implicates DC-SIGN as a Mediator of Genetic Risk in COVID-19
  Katz DH, et al. medRxiv, Jun 11, 2020.
• Initial Study of Human Genetic Contribution to COVID-19 Severity and Susceptibility
  Wang F, et a. medRxiv, Jun 11, 2020.
• TMPRSS2 variants and their susceptibility to COVID-19: focus in East Asian and European populations.
  Santos NP, et al. medRxiv, Jun 11, 2020.
• Association of gene polymorphisms of CD55 with susceptibility to and severity of hand, foot, and mouth disease caused by enterovirus 71 in the Han Chinese population.
  Li Mei et al. Journal of medical virology 2020 May
• Genetic variation in toll like receptors 2, 7, 9 and interleukin-6 is associated with cytomegalovirus infection in late pregnancy.
  Mhandire Doreen Z et al. BMC medical genetics 2020 May (1) 113

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.