Advanced Molecular Detection Clips Content (Published on 11/05/2020)
NEWS
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Tests Show Genetic Signature of Virus That May Have Infected President Trump
Glanz J. New York Times, Nov 1, 2020. -
A mutated coronavirus strain causes most new COVID-19 infections in Europe and was spread within the continent by tourists, scientists say
Dean G. Business Insider, Oct 29, 2020. -
A Rapid Virus Test Falters in People Without Symptoms, Study Finds
Wu KJ. New York Times, Nov 2, 2020. -
New polio vaccine poised to get emergency WHO approval
Irwin A. Nature, Oct 29, 2020. -
Identifying gut microbes that affect human health
Leviatan S, Segal E. Nature, Nov 4, 2020.
POLICY
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Request for Information (RFI): Inviting Comments and Suggestions on the NIH-Wide Strategic Plan for COVID-19 Research
(request for feedback by Dec 7, 2020) NIH NOT-OD-21-018, Oct 28, 2020.
CONCEPTS / COMMENTS
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The intersection of genomics and big data with public health: Opportunities for precision public health.
Khoury Muin J et al. PLoS medicine 2020 Oct (10) e1003373
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Food Safety Genomics and Connections to One Health and the Clinical Microbiology Laboratory.
Allard Marc W et al. Clinics in laboratory medicine 2020 Dec (4) 553-563
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Next slide please: data visualisation expert on what's wrong with the UK government's coronavirus charts
Cheshire J. The Conversation, Nov 3, 2020. -
Coronavirus biology and replication: implications for SARS-CoV-2.
V'kovski Philip et al. Nature reviews. Microbiology 2020 Oct -
Are infections seeding some cases of Alzheimer's disease?
Abbott A. Nature, Nov 4, 2020.
METHODS / TOOLS
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"METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI's sequence read archive".
Quiñones Mariam et al. BMC bioinformatics 2020 Sep (1) 378 -
A Digital CRISPR-based Method for the Rapid Detection and Absolute Quantification of Viral Nucleic Acids
Wu X, et al. medRxiv, Nov 5, 2020. -
Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies
Lau BT, et al. medRxiv, Nov 4, 2020. -
Novel SARS-CoV-2 Whole-genome sequencing technique using Reverse Complement PCR enables fast and accurate outbreak analysis
Wolters F, et al. bioRxiv, Oct 29, 2020. -
How to establish an academic SARS-CoV-2 testing laboratory.
Richter Alex et al. Nature microbiology 2020 Nov
EVOLUTION / ECOLOGY / POPULATIONS
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Complete and Circularized Genome Assemblies of the Kroppenstedtia eburnea Genus Type Strain and the Kroppenstedtia pulmonis Species Type Strain with MiSeq and MinION Sequence Data.
Gulvik Christopher A et al. Microbiology resource announcements 2020 Oct (44)
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The seventh pandemic of cholera in Europe revisited by microbial genomics.
Oprea Mihaela et al. Nature communications 2020 10 (1) 5347 -
Inferring evolutionary pathways and directed genotype networks of foodborne pathogens.
Cliff Oliver M et al. PLoS computational biology 2020 Oct (10) e1008401 -
High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States.
McNamara Ryan P et al. Cell reports 2020 Nov (5) 108352 -
Emergence of Novel SARS-CoV-2 Variants in the Netherlands
Urhan A, Abeel T. medRxiv, Nov 4, 2020. -
Genomic surveillance of COVID-19 cases in Beijing.
Du Pengcheng et al. Nature communications 2020 10 (1) 5503 -
Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area.
Long S Wesley et al. mBio 2020 Oct (6) -
Detection and Characterization of Swine-origin Influenza A(H1N1) Pandemic 2009 Viruses in Humans Following Zoonotic Transmission.
Cook Peter W et al. Journal of virology 2020 Oct
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Global and regional epidemiology of HIV-1 recombinants in 1990-2015: a systematic review and global survey.
Hemelaar Joris et al. The lancet. HIV 2020 Nov (11) e772-e781 -
An evolving genetic tapestry of HIV-1 recombinants.
Paraskevis Dimitrios et al. The lancet. HIV 2020 Nov (11) e733-e734 -
Nipah virus dynamics in bats and implications for spillover to humans.
Epstein Jonathan H et al. Proceedings of the National Academy of Sciences of the United States of America 2020 Nov -
Genetic Diversity of Nipah virus in Bangladesh.
Rahman M Z et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2020 Oct
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Atypical Mutation in Neisseria gonorrhoeae 23S rRNA Associated with High-Level Azithromycin Resistance.
Cau D Pham et al. Antimicrob Agents Chemother 2020 11 (2)
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Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes.
Berglund Fanny et al. Microbial genomics 2020 Oct -
Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone.
Tassinari Eleonora et al. Microbial genomics 2020 Oct -
Characteristics of HIV-1 molecular transmission networks and drug resistance among men who have sex with men in Tianjin, China (2014-2018).
Zheng Minna et al. Virology journal 2020 Nov (1) 169 -
A respiratory syncytial virus attachment (G) gene variant associated with more severe disease in infants decreases fusion (F) protein expression which may facilitate immune evasion.
Human Stacey et al. Journal of virology 2020 Oct
DETECTION / DIAGNOSIS
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A Cluster of Non-tuberculous Mycobacterial Tenosynovitis following Hurricane Relief Efforts.
Turner Nicholas A et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Nov -
Identification of a Novel Pathogen Using Family-Wide PCR: Initial Confirmation of COVID-19 in Thailand.
Wacharapluesadee Supaporn et al. Frontiers in public health 2020 555013
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Reproducibility and sensitivity of 36 methods to quantify the SARS-CoV-2 genetic signal in raw wastewater: findings from an interlaboratory methods evaluation in the U.S.
Pecson BM, et al. medRxiv, Nov 4, 2020. -
SARS-CoV-2 viral load is associated with increased disease severity and mortality.
Fajnzylber Jesse et al. Nature communications 2020 10 (1) 5493 -
External Quality Assessment for Molecular Detection of Severe Acute Respiratory Syndrome Coronavirus 2 in Clinical laboratories.
Wang Zhe et al. The Journal of molecular diagnostics : JMD 2020 Oct
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Detection of SARS-COV N2 Gene: Very low amounts of viral RNA or false positive?
Falasca Francesca et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2020 Oct 104660 -
A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection
Fowler V, et al. medRxiv, Oct 25, 2020. -
HIV drug resistance profile in South Africa: Findings and implications from the 2017 national HIV household survey.
Moyo Sizulu et al. PloS one 2020 (11) e0241071
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Identifying septic pollution exposure routes during a waterborne norovirus outbreak - A new application for human-associated microbial source tracking qPCR.
Mia C Mattioli et al. J Microbiol Methods 2020 11 106091
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Identification of Candida auris and related species by multiplex PCR based on unique GPI protein-encoding genes.
Alvarado María et al. Mycoses 2020 Oct
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A real-time PCR assay for simultaneous detection and differentiation of four common Entamoeba species that infect humans.
Ali Ibne Karim M et al. Journal of clinical microbiology 2020 Oct
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Consensus Multilocus Sequence Typing Scheme for Pneumocystis jirovecii .
Pasic Lana et al. Journal of fungi (Basel, Switzerland) 2020 Oct (4)
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Genomic analysis revealed distinct transmission clusters of vancomycin-resistant Enterococcus faecium ST80 in Stockholm, Sweden.
Fang Hong et al. The Journal of hospital infection 2020 Oct -
Unravelling the modes of transmission of SARS-CoV-2 during a nursing home outbreak: looking beyond the church super-spread event.
Voeten Helene A C M et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Oct -
Multiple early introductions of SARS-CoV-2 into a global travel hub in the Middle East.
Tayoun Ahmad Abou et al. Scientific reports 2020 10 (1) 17720 -
SARS-CoV-2 transmission routes from genetic data: A Danish case study
Bluhm Andreas et al. PloS one 2020 (10) e0241405 -
Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020
Hodcroft EB, et al. medRxiv, Oct 28, 2020. -
Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread
Moreno GK, et al. Nat Commun, Nov 3, 2020.
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Viral genome sequencing places White House COVID-19 outbreak into phylogenetic context
Bedford T, et al. medRxiv, Nov 1, 2020. -
The genomic epidemiology of SARS-CoV-2 in Palestine
Qutob N, et al. bioRxiv, Oct 30, 2020.
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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A novel synthetic DNA vaccine elicits protective immune responses against Powassan virus.
Choi Hyeree et al. PLoS neglected tropical diseases 2020 Oct (10) e0008788 -
Fecal Microbiota Transplantations: Where Are We, Where Are We Going, and What Is the Role of the Clinical Laboratory?
Ransom Eric M et al. Clinical chemistry 2020 04 (4) 512-517
HOST-MICROBE INTERACTIONS
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Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis.
Liu Fang et al. Microbial genomics 2020 Oct -
The CCR5-delta32 variant might explain part of the association between COVID-19 and the chemokine-receptor gene cluster
Gomez J, et al. medRxiv, Nov 4, 2020. -
Within-Host Diversity of SARS-CoV-2 in COVID-19 Patients With Variable Disease Severities.
Al Khatib Hebah A et al. Frontiers in cellular and infection microbiology 2020 575613 -
The immune roadmap for understanding multi-system inflammatory syndrome in children: opportunities and challenges.
Martinez Olivia M et al. Nature medicine 2020 Nov -
Interferon deficiency can lead to severe COVID.
Meffre Eric et al. Nature 2020 Nov -
Exploring Host Genetic Polymorphisms Involved in SARS-CoV Infection Outcomes: Implications for Personalized Medicine in COVID-19.
Ramos-Lopez Omar et al. International journal of genomics 2020 6901217 -
Multi-ancestry fine mapping of interferon lambda and the outcome of acute hepatitis C virus infection.
Vergara Candelaria et al. Genes and immunity 2020 Oct
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Host variables confound gut microbiota studies of human disease
Vujkovic-Cvijin I, et al. Nature, Nov 4, 2020. -
The gut microbiota-brain axis in behaviour and brain disorders.
Morais Livia H et al. Nature reviews. Microbiology 2020 Oct
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 Public Health Genomics Branch 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.
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