Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jul 30, 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

• Smallpox and other viruses plagued humans much earlier than suspected
  Spinney L. Nature, Jul 23, 2020.
• Influenza virus with "pre-pandemic potential" pinpointed in European pig surveillance study
  GenomeWeb, Jul 27, 2020.
• Saliva samples slow to catch on for large-scale coronavirus testing
  Karow J. GenomeWeb, Jul 29, 2020.
• SARS-CoV-2 lineage may go back decades in bats, phylogenetic analysis suggests
  GenomeWeb, Jul 28, 2020.
• 'Immune Profiles' Shed Light on COVID-19 Disease Course
  Walker M. MedPage Today, Jul 28, 2020.
• Rare TLR7 Variants Implicated in COVID-19 Severity in Case Study of Affected Brothers
  GenomeWeb, Jul 24, 2020.
• Phase 3 clinical trial of investigational vaccine for COVID-19 begins
  (news release) NIH, Jul 27, 2020.
• Coronavirus research updates: Mutations allow virus to elude antibodies
  Nature, Jul 28, 2020.
• NIH Launches Platform to Serve as Depository for COVID-19 Medical Data
  Rubin R. JAMA, Jul 28, 2020.
• Data secrecy may cripple U.S. attempts to slow pandemic
  Piller C. Science, Jul 24, 2020.

EVENTS / TRAINING / WEB RESOURCES

• COVID-19 Genomics UK Consortium
  (website) COG-UK, updated Jul 22, 2020.
• Nine quick tips for efficient bioinformatics curriculum development and training.
  McClatchy Susan et al. PLoS computational biology 2020 Jul (7) e1008007

POLICY

• Need for sustainable biobanking networks for COVID-19 and other diseases of epidemic potential
  Peeling RW, et al. Lancet Infect Dis, Jul 24, 2020.
• Coronavirus (COVID-19) Update: FDA Posts New Template for At-Home and Over-the-Counter Diagnostic Tests for Use in Non-Lab Settings, Such as Homes, Offices or Schools
  FDA, Jul 29, 2020.

CONCEPTS / COMMENTS

• A Public Health Laboratory Response to the Pandemic
  Pabbaraju K, et al. J Clin Microbiol doi: 10.1128/JCM.01110-20
• Mathematical models to guide pandemic response.
  Metcalf C Jessica E et al. Science (New York, N.Y.) 2020 Jul (6502) 368-369
• Genomics and epidemiological surveillance.
  Lo Stephanie W et al. Nature reviews. Microbiology 2020 Jul
• Understanding, Verifying, and Implementing Emergency Use Authorization Molecular Diagnostics for the Detection of SARS-CoV-2 RNA
  Mitchell SL, et al. J Clin Microbiol, doi:10.1128/JCM.00796-20
• The First Quarter of SARS-CoV-2 Testing: the University of Washington Medicine Experience.
  Greninger Alexander L et al. Journal of clinical microbiology 2020 Jul (8)
• The cause of Severe Acute Respiratory Syndrome: What did we learn from it?
  Peiris Malik et al. Clinical chemistry 2020 Jul
• The challenges of informative wastewater sampling for SARS-CoV-2 must be met: lessons from polio eradication
  O'Reilly KM, et al. Lancet Microbe, Jul 28, 2020.
• Pan-resistant HIV-1: what's next?
  Hamers RL, Inzaule SC. Lancet Microbe. 2020;1:E97-98.
• Towards a Sustainable One Health Approach to Crimean-Congo Hemorrhagic Fever Prevention: Focus Areas and Gaps in Knowledge.
  Sorvillo Teresa E et al. Tropical medicine and infectious disease 2020 Jul (3)  
• Environmental Surveillance as a Tool for Identifying High-risk Settings for Typhoid Transmission.
  Andrews Jason R et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jul (Supplement_2) S71-S78

METHODS / TOOLS

• Freshwater monitoring by nanopore sequencing
  Urban L, et al. bioRxiv, Jul 25, 2020.
• NAuRA: Genomic Tool to Identify Staphylococcal Enterotoxins in Staphylococcus aureus Strains Responsible for FoodBorne Outbreaks.
  Merda Déborah et al. Frontiers in microbiology 2020 1483
• Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses.
  Pérez-Cobas Ana Elena et al. Microbial genomics 2020 Jul
• Analysis of Treponema pallidum strains from China using improved methods for whole-genome sequencing from primary syphilis chancres.
  Chen Wentao et al. The Journal of infectious diseases 2020 Jul
• Predicting the Emergence of SARS-CoV-2 Clades
  Jain S, et al. bioRxiv, Jul 27, 2020.
• SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission.
  Harilal Divinlal et al. Clinical chemistry 2020 Jul
• High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs
  Gorzynski JE, et al. medRxiv, Jul 29, 2020.
• An integrated national scale SARS-CoV-2 genomic surveillance network
  The COVID-19 Genomics UK (COG-UK) consortium, Lancet Microbe, Jun 20, 2020. 
• PACIFIC: A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
  Mateos PA, et al. bioRxiv, Jul 24, 2020.
• A Scalable, Easy-to-Deploy, Protocol for Cas13-Based Detection of SARS-CoV-2 Genetic Material
  Rauch JN, et al. bioRxiv, Jul 24, 2020.
• High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics.
  I Sardi Silvia et al. Viruses 2020 Jul (7)
• Simultaneous Viral Whole-Genome Sequencing and Differential Expression Profiling in Respiratory Syncytial Virus Infection of Infants.
  Lin Gu-Lung et al. The Journal of infectious diseases 2020 Jul

EVOLUTION / ECOLOGY / POPULATIONS

• Understanding leptospirosis eco-epidemiology by environmental DNA metabarcoding of irrigation water from two agro-ecological regions of Sri Lanka.
  Gamage Chandika D et al. PLoS neglected tropical diseases 2020 Jul (7) e0008437
• Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2.
  Su Yvonne C F et al. mBio 2020 07 (4)
• Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes.
  Guo Hua et al. Journal of virology 2020 Jul
• Evolution And Genetic Diversity Of SARSCoV-2 In Africa Using Whole Genome Sequences
  Motayo BO, et al, bioRxiv, Jul 27, 2020.
• Evolution of viral quasispecies during SARS-CoV-2 infection.
  Jary A et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2020 Jul
• Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
  Boni MF, et al. Nat Microbiol, Jul 28, 2020.
• Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age.
  Mühlemann Barbara et al. Science (New York, N.Y.) 2020 Jul (6502)
• Genetic diversity and evolutionary history of Korean isolates of severe fever with thrombocytopenia syndrome virus from 2013-2016.
  Yun Mi-Ran et al. Archives of virology 2020 Jul
• Evolution and Antigenic Drift of Influenza A (H7N9) Viruses, China, 2017-2019.
  Zhang Jiahao et al. Emerging infectious diseases 2020 Aug (8) 1906-1911
• Heartland Virus in Lone Star Ticks, Alabama, USA.
  Newman Brent C et al. Emerging infectious diseases 2020 Aug (8) 1954-1956 
• Integrating population genetic structure, microbiome, and pathogens presence data in Dermacentor variabilis .
  Lado Paula et al. PeerJ 2020 e9367 
• Population Genomic Structure and Recent Evolution of Plasmodium knowlesi, Peninsular Malaysia.
  Hocking Suzanne E et al. Emerging infectious diseases 2020 Aug (8) 1749-1758
• Genetic tools discriminate strains of Leishmania infantum isolated from  humans and dogs in Sicily, Italy.
  Castelli Germano et al. PLoS neglected tropical diseases 2020 Jul (7) e0008465

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Validation of the T86I mutation in the gyrA gene as a highly reliable real time PCR target to detect Fluoroquinolone-resistant Campylobacter jejuni.
  Espinoza Nereyda et al. BMC infectious diseases 2020 Jul (1) 518
• Identification of Antimicrobial Resistance-Associated Genes through Whole Genome Sequencing of Mycoplasma bovis Isolates with Different Antimicrobial Resistances.
  Ledger Lisa et al. Pathogens (Basel, Switzerland) 2020 Jul (7)
• Genotypic Heterogeneity of Orientia tsutsugamushi in Scrub Typhus Patients and Thrombocytopenia Syndrome Co-infection, Myanmar.
  Win Aye Marlar et al. Emerging infectious diseases 2020 Aug (8) 1878-1881
• Surveillance of European Domestic Pig Populations Identifies an Emerging Reservoir of Potentially Zoonotic Swine Influenza A Viruses.
  Henritzi Dinah et al. Cell host & microbe 2020 Jul
• Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants
  Weisblum Y, et al. bioRxiv, Jul 22, 2020.
• Mutations Strengthened SARS-CoV-2 Infectivity.
  Chen Jiahui et al. Journal of molecular biology 2020 Jul
• Use of Drug-Level Testing and Single-Genome Sequencing to Unravel a Case of HIV Seroconversion on PrEP.
  Spinelli Matthew A et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jul  
• The Frequency of Sex: Population Genomics Reveals Differences in Recombination and Population Structure of the Aflatoxin-Producing Fungus Aspergillus flavus.
  Drott Milton T et al. mBio 2020 Jul (4)

DETECTION / DIAGNOSIS

• Incremental value of metagenomic next generation sequencing for the diagnosis of suspected focal infection in adults.
  Zhang Hao-Cheng et al. The Journal of infection 2019 11 (5) 419-425 
• Diagnostic accuracy of IP-10 mRNA release assay for tuberculosis
  Blauenfeldt T, et al. J Clin Microbiol, Jul 22, 2020.
• A multiplex assay for characterization of antimicrobial resistance in Neisseria gonorrhoeae using multi-PCR coupled with mass spectrometry.
  Li Yamei et al. The Journal of antimicrobial chemotherapy 2020 Jul
• A loop-mediated isothermal amplification (LAMP) assay for the consensus detection of human pathogenic Campylobacter species.
  Babu Uma S et al. Journal of microbiological methods 2020 Jul 106009
• Evidence of exposure to SARS-CoV-2 in cats and dogs from households in Italy
  Patterson EI, et al. bioRxiv, Jul 23, 2020.
• Relationship Between serum SARS-CoV-2 nucleic acid(RNAemia) and Organ Damage in COVID-19 Patients: A Cohort Study.
  Xu Dan et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jul
• Saliva sampling and its direct lysis, an excellent option to increase the number of SARS CoV2 diagnostic tests in settings with supply shortages.
  Moreno-Contreras Joaquín et al. Journal of clinical microbiology 2020 Jul
• Clinical Performance of SARS-CoV-2 Molecular Tests.
  Green Daniel A et al. Journal of clinical microbiology 2020 Jul (8) 
• Viral RNA level, serum antibody responses, and transmission risk in discharged COVID-19 patients with recurrent positive SARS-CoV-2 RNA test results: a population-based observational cohort study
  Yang C, et al. medRxiv, Jul 26, 2020. 
• Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal specimens without extraction of viral RNA.
  Hasan Mohammad Rubayet et al. PloS one 2020 (7) e0236564
• Spatial and temporal dynamics of SARS-CoV-2 in COVID-19 patients: A systematic review and meta-analysis.
  Weiss Anne et al. EBioMedicine 2020 Jul 102916
• A new pleosporalean fungus isolated from superficial to deep human clinical specimens.
  Valenzuela-Lopez Nicomedes et al. Medical mycology 2020 Jul
• One-step PCR: A novel protocol for determination of pfhrp2 deletion status in Plasmodium falciparum.
  Jones Sophie et al. PloS one 2020 (7) e0236369 
• Rapid, Noninvasive Diagnosis of Balamuthia mandrillaris Encephalitis by a Plasma-Based Next-Generation Sequencing Test.
  Kalyatanda Gautam et al. Open forum infectious diseases 2020 Jul (7) ofaa189  

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Investigation of sequential outbreaks of Burkholderia cepacia and multidrug-resistant extended spectrum beta-lactamase producing Klebsiella species in a West African tertiary hospital neonatal unit: a retrospective genomic analysis
  Okomo U, et al. Lancet Microbe, Jul 1, 2020. 
• Toilet drain water as a potential source of hospital room-to-room transmission of carbapenemase-producing Klebsiella pneumoniae.
  Heireman L et al. The Journal of hospital infection 2020 Jul 
• Evolution and epidemic spread of SARS-CoV-2 in Brazil.
  Candido Darlan S et al. Science (New York, N.Y.) 2020 Jul
• Fingerprinting of human noroviruses co-infections in a possible foodborne outbreak by metagenomics.
  Liu Danlei et al. International journal of food microbiology 2020 Jul 108787 
• Outbreak of Human Metapneumovirus Infection in Zoo, Slovenia.
  Uršic Tina et al. Emerging infectious diseases 2020 Aug (8) 1949-1951 

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Evaluation of the mRNA-1273 Vaccine against SARS-CoV-2 in Nonhuman Primates.
  Corbett Kizzmekia S et al. The New England journal of medicine 2020 07

HOST-MICROBE INTERACTIONS

• Presence of Genetic Variants Among Young Men With Severe COVID-19.
  van der Made Caspar I et al. JAMA 2020 Jul
• Molecular Underpinnings of Severe Coronavirus Disease 2019.
  Plenge Robert M et al. JAMA 2020 Jul 
• HLA-B*44 and C*01 Prevalence Correlates with Covid19 Spreading across Italy.
  Correale Pierpaolo et al. International journal of molecular sciences 2020 Jul (15)
• The genome-wide methylation profile of CD4+ T cells from HIV-infected individuals identifies distinct patterns associated with disease progression.
  Moron-Lopez Sara et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jul
• Otitis media susceptibility and shifts in the head and neck microbiome due to SPINK5 variants.
  Frank Daniel N et al. Journal of medical genetics 2020 Jul

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.