Advanced Molecular Detection Clips Content (Published on 12/17/2020)
NEWS
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Update on new SARS-CoV-2 variant and how COG-UK tracks emerging mutations
COG-UK, Dec 14, 2020. -
New At-Home Covid Test Gets Green Light From F.D.A.
Wu KJ. New York Times, Dec 15, 2020. -
Cold Spring Harbor Lab Develops iPhone App for Mobile Sequencing Analysis
Versel N. GenomeWeb, Dec 11, 2020. -
Imperial College London, Moredun Research Developing Silicon-Based Test for Infectious Disease Screening
O'Connor L. GenomeWeb, Dec 15, 2020. -
What Happens When a Superspreader Event Keeps Spreading
Wines M, Harmon A. New York Times, Dec 11, 2020. -
FDA review clears path for second coronavirus vaccine, this one developed by Moderna
Johnson CY. Washington Post, Dec 15, 2020. -
F.D.A. Advisory Panel Gives Green Light to Pfizer Vaccine
Thomas K, et al. New York Times, Dec 10, 2020. -
Study finds no link between COVID-19, Guillain-Barre' syndrome
Paulsen SK. CIDRAP, Dec 14, 2020. -
Covid: Genes hold clues to why some people get severely ill
Morelle R. BBC, Dec 11, 2020. -
How a torrent of COVID science changed research publishing in seven charts
Else H. Nature, Dec 16, 2020.
EVENTS / TRAINING / WEB RESOURCES
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How do we collect and sequence SARS-CoV-2 samples?
(blog post) COG-UK, Dec 4, 2020. -
In Vitro Diagnostics EUAs (SARS-CoV-2)
(website) FDA, updated Dec 15, 2020.
CONCEPTS / COMMENTS
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Mathematical Model of the Role of Asymptomatic Infection in Outbreaks of Some Emerging Pathogens.
Siewe Nourridine et al. Tropical medicine and infectious disease 2020 Dec (4)
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Design and evaluation of a data anonymization pipeline to promote Open Science on COVID-19.
Jakob Carolin E M et al. Scientific data 2020 12 (1) 435 -
Targeting viral genome synthesis as broad-spectrum approach against RNA virus infections.
Huchting Johanna et al. Antiviral chemistry & chemotherapy 2040206620976786 -
Emergence of a Highly Fit SARS-CoV-2 Variant.
Baric Ralph S et al. The New England journal of medicine 2020 Dec
METHODS / TOOLS
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iGenomics: Comprehensive DNA sequence analysis on your Smartphone.
Palatnick Aspyn et al. GigaScience 2020 Dec (12) -
DarkQ: Continuous genomic monitoring using message queues
Viehweger A, et al. bioRxiv, Nov 14, 2020. -
Web-Based Genome Analysis of Bacterial Meningitis Pathogens for Public Health Applications Using the Bacterial Meningitis Genomic Analysis Platform (BMGAP).
Buono Sean A et al. Frontiers in genetics 2020 12 601870
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Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus : a genomic epidemiology analysis.
Coll Francesc et al. The Lancet. Microbe 2020 Dec (8) e328-e335 -
Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals
Doddapaneni H, et al. bioRxiv, Dec 11, 2020. -
Phylogenetic analysis of SARS-CoV-2 data is difficult.
Morel Benoit et al. Molecular biology and evolution 2020 Dec -
A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages.
Dellicour Simon et al. Molecular biology and evolution 2020 Nov -
Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny.
Pipes Lenore et al. Molecular biology and evolution 2020 Dec -
NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index.
Martí-Carreras Joan et al. Viruses 2020 Dec (12)
EVOLUTION / ECOLOGY / POPULATIONS
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Features of Streptococcus agalactiae strains recovered from pregnant women and newborns attending different hospitals in Ethiopia.
Ali Musa Mohammed et al. BMC infectious diseases 2020 Nov (1) 848
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An assessment of the persistence of putative pathogenic bacteria in chloraminated water distribution systems.
Bal Krishna K C et al. Water research 2020 Nov 116677
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Isolation and characterization of human pathogenic multidrug resistant bacteria associated with plastic litter collected in Zanzibar.
Rasool Farah N et al. Journal of hazardous materials 2020 Nov 124591 -
No detectable signal for ongoing genetic recombination in SARS-CoV-2
Richard D, et al. bioRxiv, Dec 15, 2020. -
Recurrent emergence and transmission of a SARS-CoV-2 Spike deletion delta-H69/delta-V70
Kemp SA, et al. bioRxiv, Dec 15, 2020. -
One Year of SARS-CoV-2: How Much Has the Virus Changed?
Vilar S, Isom DG. bioRxiv, Dec 16, 2020. -
Evolution and epidemiologic dynamics of dengue virus in Nicaragua during the emergence of chikungunya and Zika viruses.
Edgerton Sean V et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 Dec 104680 -
Genetic diversity, phylogeography, and evolutionary dynamics of highly pathogenic avian influenza A (H5N6) viruses.
Zhang Jiahao et al. Virus evolution 2020 Jul (2) veaa079 -
Non-B variants of HIV-1 in San Francisco, California.
Kara J O'Keefe et al. Infect Genet Evol 2020 12 104677
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence.
Murray Gemma G R et al. Molecular biology and evolution 2020 Dec -
Emergence of artemisinin-resistant Plasmodium falciparum with kelch13 C580Y mutations on the island of New Guinea.
Miotto Olivo et al. PLoS pathogens 2020 Dec (12) e1009133
DETECTION / DIAGNOSIS
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The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock.
Lamb Harrison J et al. Genes 2020 Dec (12) -
Disposable silicon-based all-in-one micro-qPCR for rapid on-site detection of pathogens.
Nunez-Bajo Estefania et al. Nature communications 2020 12 (1) 6176 -
Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies.
Napier Gary et al. Genome medicine 2020 Dec (1) 114 -
Rapid detection of SARS-CoV-2 with Cas13
Agrawal S, et al. medRxiv, Dec 16, 2020. -
Diagnostic accuracy of Loop mediated isothermal amplification coupled to Nanopore sequencing for the detection of SARS-CoV-2 infection at scale in symptomatic and asymptomatic populations
Ptasinska A, et al. medRxiv, Dec 16, 2020. -
Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy.
Fozouni Parinaz et al. Cell 2020 Dec -
Symptomatic SARS-CoV-2 reinfection of a health care worker in a Belgian nosocomial outbreak despite primary neutralizing antibody response.
Selhorst Philippe et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Dec -
Development of a Subtyping Tool for Zoonotic Pathogen Cryptosporidium Canis .
Jiang Wen et al. Journal of clinical microbiology 2020 Dec
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Outbreak of community-acquired Staphylococcus aureus skin infections in an Australian professional football team.
Shaban Ramon Z et al. Journal of science and medicine in sport 2020 Nov -
Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil.
Paiva Marcelo Henrique Santos et al. Viruses 2020 12 (12)
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Assessment of the risk of SARS-CoV-2 reinfection in an intense re-exposure setting.
Abu-Raddad Laith J et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Dec -
Timely intervention and control of a novel coronavirus (COVID-19) outbreak at a large skilled nursing facility-San Francisco, California, 2020.
Ellora N Karmarkar et al. Infect Control Hosp Epidemiol 2020 12 (10) 1173-1180
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SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay.
Elizondo Victoria et al. Emerging microbes & infections 2020 Dec 1-52 -
Combining traditional and molecular epidemiology methods to quantify local HIV transmission among foreign-born residents of King County, Washington.
Tordoff Diana M et al. AIDS (London, England) 2020 Dec -
Genomic analysis reveals G3P[13] porcine rotavirus A interspecific transmission to human from pigs in a swine farm with diarrhoea outbreak.
Yan Nan et al. The Journal of general virology 2020 Dec -
General hospital outbreak of invasive candidiasis due to azole-resistant Candida parapsilosis associated with an Erg11 Y132F mutation.
Corzo-Leon Dora E et al. Medical mycology 2020 Dec
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Safety and immunogenicity of two novel type 2 oral poliovirus vaccine candidates compared with a monovalent type 2 oral poliovirus vaccine in healthy adults: two clinical trials.
De Coster Ilse et al. Lancet (London, England) 2020 Dec
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Safety and immunogenicity of two novel type 2 oral poliovirus vaccine candidates compared with a monovalent type 2 oral poliovirus vaccine in children and infants: two clinical trials.
Sáez-Llorens Xavier et al. Lancet (London, England) 2020 Dec
HOST-MICROBE INTERACTIONS
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Genetic mechanisms of critical illness in Covid-19.
Pairo-Castineira Erola et al. Nature 2020 Dec -
Shared genetic etiology between idiopathic pulmonary fibrosis and COVID-19 severity
Fadista J, et al. medRxiv, Dec 16, 2020. -
Common genetic variants identify therapeutic targets for COVID-19 and individuals at high risk of severe disease
Horowitz JE, et al. medRxiv, Dec 16, 2020. -
The MERS-CoV receptor gene is among COVID-19 risk factors inherited from Neandertals
Zeberg H, Paabo S. bioRxiv, Dec 12, 2020. -
Comparative Transcriptome Analysis Reveals the Intensive Early Stage Responses of Host Cells to SARS-CoV-2 Infection.
Sun Jiya et al. Frontiers in microbiology 2020 593857
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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