Advanced Molecular Detection Clips Content (Published on 12/16/2021)
NEWS
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SARS-CoV-2 genomics as a springboard for future disease mitigation in LMICs.
Belman Sophie et al. Nature reviews. Microbiology 2021 11 -
Omicron Is a Dress Rehearsal for the Next Pandemic
Anthes E. New York Times, Dec 14, 2021. -
Omicron spreading rapidly in U.S. and could bring punishing wave as soon as January, CDC warns
Sun LH, et al. Washington Post, Dec 14, 2021. -
Omicron found to grow 70 times faster than Delta in bronchial tissue
Devlin H. Guardian, Dec 15, 2021. -
C.D.C. Virus Tests Were Contaminated and Poorly Designed, Agency Says
Anthes E. New York Times, Dec 15, 2021. -
FDA Will Consider EUA Submissions for SARS-CoV-2 Variant Genotyping Assays
GenomeWeb, Dec 15, 2021. -
UCSD Developing SARS-CoV-2 At-Home, Molecular Test Leveraging CRISPR, Isothermal Amplification
O'Connor L. GenomeWeb, Dec 8, 2021. -
Omicron variant more resistant to vaccine but causes less severe covid, major South African study concludes
Wroughton L. Washington Post, Dec 14, 2021. -
Will we always need Covid-19 boosters? Experts have theories
Branswell H. STAT, Dec 15, 2021. -
The Pandemic of the Vaccinated Is Here
Gutman R. Atlantic, Dec 9, 2021. -
Waning COVID super-immunity raises questions about Omicron
Kozlov M. Nature, Nov 13, 2021. -
T-cell vaccines could top up immunity to COVID, as variants loom large
Dolgin E. Nat Biotechnol, Dec 13, 2021. -
Moderna data shows mRNA isn't a quick fix for the flu vaccine
Wetsman N. Verge, Dec 10, 2021.
EVENTS / TRAINING / WEB RESOURCES
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How to tell a compelling story in scientific presentations
Kirchoff B. Nature, Dec 1, 2021. -
Ten simple rules for creating a scientific web application.
Burnett Jessica L et al. PLoS computational biology 2021 12 (12) e1009574 -
Ten simple rules for developing bioinformatics capacity at an academic institution.
Aron Shaun et al. PLoS computational biology 2021 12 (12) e1009592 -
How Machines, a Pangolin, and Constellations are Guiding Us Through Waves of the COVID-19 Pandemic
Mackenzie K. Saskatchewan Provincial Laboratory. YouTube, Dec 14, 2021.
CONCEPTS / COMMENTS
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Vaccines 2020: The era of the digital vaccine is here
Pizza M, et al. Sci Transl Med, Dec 15, 2021. -
Current state of Ebola virus vaccines: A snapshot.
Woolsey Courtney et al. PLoS pathogens 2021 12 (12) e1010078 -
Infodemics: A new challenge for public health.
Briand Sylvie C et al. Cell 2021 12 (25) 6010-6014 -
A vision for spaceflight microbiology to enable human health and habitat sustainability.
Nickerson Cheryl A et al. Nature microbiology 2021 12
METHODS / TOOLS
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Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks.
Wagner Darlene D et al. PeerJ 2021 12 e12446
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Extracting novel antimicrobial emergence events from scientific literature and medical reports.
Mendelsohn Emma et al. F1000Research 2021 12 1320 -
Joint inference of migration and reassortment patterns for viruses with segmented genomes.
Stolz Ugne et al. Molecular biology and evolution 2021 12 -
Rapid screening and identification of viral pathogens in metagenomic data.
Song Shiyang et al. BMC medical genomics 2021 12 (Suppl 6) 289 -
Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows.
Lagerborg Kim A et al. Nature microbiology 2021 12 -
Genomics-informed outbreak investigations of SARS-CoV-2 using civet
O'Toole A, et al. medRxiv, Dec 14, 2021.
EVOLUTION / ECOLOGY / POPULATIONS
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Global Genome Diversity and Recombination in Mycoplasma pneumoniae
Hsieh YC, et al. Emerg Infect Dis, Dec 3 2021. -
The evolutionary history of Shigella flexneri serotype 6 in Asia
Mai ST, et al. Microb Genom. 2021 Dec;7(12). -
Whole-genome sequencing links Clostridium (Clostridioides) difficile in a single hospital to diverse environmental sources in the community.
Lim Su-Chen et al. Journal of applied microbiology 2021 12 -
Genomic comparisons of Escherichia coli ST131 from Australia.
Li Dmitriy et al. Microbial genomics 2021 12 (12) -
(SARS-CoV-2) COVID 19: Genomic surveillance and evaluation of the impact on the population speaker of indigenous language in Mexico
Ramirez CM, et al. medRxiv, Dec 11, 2021. -
Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal.
Ahouidi Ambroise D et al. Scientific reports 2021 12 (1) 23644 -
Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals.
Islam Ariful et al. PloS one 2021 12 (12) e0260635 -
Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia.
Mio Catia et al. PloS one 2021 12 (12) e0261229 -
Origin and evolution of HIV-1 subtype A6.
Abidi Syed Hani et al. PloS one 2021 12 (12) e0260604 -
Analysis of entire hepatitis B virus genomes reveals reversion of mutations to wild type in natural infection, a 15 year follow-up study.
Chen Qin-Yan et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 12 105184 -
Four genomic clades of Candida auris identified in Canada, 2012-2019.
De Luca Domenica G et al. Medical mycology 2021 12 -
Genetic diversity of Anopheles stephensi in Ethiopia provides insight into patterns of spread.
Carter Tamar E et al. Parasites & vectors 2021 12 (1) 602
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Genomic diversity of antimicrobial resistance in non-typhoidal Salmonella in Victoria, Australia
Sia CM, et al. Microb Genom. 2021 Dec;7(12). -
Prophages encoding human immune evasion cluster genes are enriched in Staphylococcus aureus isolated from chronic rhinosinusitis patients with nasal polyps
Nepal R, et al. Microb Genom. 2021 Dec;7(12). -
Genomic insights into the circulation of pandemic fluoroquinolone-resistant extra-intestinal pathogenic Escherichia coli ST1193 in Vietnam
Nguyen Q, et al. Microb Genom. 2021 Dec;7(12). -
Epidemiology and population structure of Haemophilus influenzae causing invasive disease
Carrera-Salinas A, et al. Microb Genom. 2021 Dec;7(12). -
Whole genome sequencing reveals large deletions and other loss of function mutations in Mycobacterium tuberculosis drug resistance genes.
Gomes Laura C et al. Microbial genomics 2021 12 (12) -
Whole-Genome Sequencing to Identify Missed Rifampicin and Isoniazid Resistance Among Tuberculosis Isolates-Chennai, India, 2013-2016.
Tamilzhalagan Sembulingam et al. Frontiers in microbiology 2021 12 720436
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Increase in antimicrobial resistance in Escherichia coli in food animals between 1980 and 2018 assessed using genomes from public databases.
Pires João et al. The Journal of antimicrobial chemotherapy 2021 12 -
Characterization of a Novel Plasmid in Serratia marcescens Harbouring bla Isolated from a Nosocomial Outbreak in Japan.
Nakanishi Noriko et al. The Journal of hospital infection 2021 12 -
De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: A case report.
Gandhi Shiv et al. medRxiv : the preprint server for health sciences 2021 12 -
Estimated Effectiveness of COVID-19 Messenger RNA Vaccination Against SARS-CoV-2 Infection Among Older Male Veterans Health Administration Enrollees, January to September 2021
Young-Xu Y, et al. JAMA Network Open, Dec 15, 2021.
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Temporal evolution of the resistance genotypes of Plasmodium falciparum in isolates from Equatorial Guinea during 20 years (1999 to 2019).
Berzosa Pedro et al. Malaria journal 2021 12 (1) 463 -
Dynamic changes in genetic diversity, drug resistance mutations, and treatment outcomes of falciparum malaria from the low-transmission to the pre-elimination phase on the islands of São Tomé and Príncipe.
Chen Ying-An et al. Malaria journal 2021 12 (1) 467
DETECTION / DIAGNOSIS
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GBS-SBG - GBS Serotyping by Genome Sequencing.
Tiruvayipati Suma et al. Microbial genomics 2021 12 (12) -
Rapid absolute quantification of pathogens and ARGs by nanopore sequencing.
Yang Yu et al. The Science of the total environment 2021 12 152190
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Effect of Time Since Death on Multipathogen Molecular Test Results of Postmortem Specimens Collected Using Minimally Invasive Tissue Sampling Techniques.
Dawa Jeanette et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 12 (Supplement_5) S360-S367
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Monitoring COVID-19 through SARS-CoV-2 quantification in wastewater: progress, challenges and prospects.
Alhama José et al. Microbial biotechnology 2021 12
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Track Omicron's spread with molecular data.
Scott L, et al. Science, Dec 9, 2021. -
Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform.
He Changsheng et al. Biosensors & bioelectronics 2021 12 113857 -
Analysis of the initial lot of the CDC 2019-Novel Coronavirus (2019-nCoV) real-time RT-PCR diagnostic panel.
Lee Justin S et al. PloS one 2021 12 (12) e0260487
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SARS-CoV-2 B.1.1.529 (Omicron) Variant--United States, December 1-8, 2021
CDC COVID-19 Response Team, MMWR, Dec 17, 2021.
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Novel and extendable genotyping system for human respiratory syncytial virus based on whole-genome sequence analysis.
Chen Jiani et al. Influenza and other respiratory viruses 2021 12
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Comparative genomic analysis of clinical Candida glabrata isolates identifies multiple polymorphic loci that can improve existing multilocus sequence typing strategy.
Arastehfar A et al. Studies in mycology 2021 12 100133
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Diagnosis of Taenia solium infections based on "mail order" RNA-sequencing of single tapeworm egg isolates from stool samples.
Sadlowski Henrik et al. PLoS neglected tropical diseases 2021 12 (12) e0009787
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Linkage of Whole Genome Sequencing, Epidemiological, and Clinical Data to Understand the Genetic Diversity and Clinical Outcomes of Shigella flexneri among Men Who Have Sex with Men in England.
Mitchell Holly D et al. Microbiology spectrum 2021 12 e0121321
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Extensively Drug-Resistant Carbapenemase-Producing Pseudomonas aeruginosa and Medical Tourism from the United States to Mexico, 2018-2019
Kracalik I, et al. Emerg Infect Dis, Dec 15, 2021.
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Reconstructing SARS-CoV-2 infection dynamics through the phylogenetic inference of unsampled sources of infection.
Perera Deshan et al. PloS one 2021 12 (12) e0261422 -
Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020.
Leung Kathy et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 12 (49) -
Propagation of a hospital-associated cluster of COVID-19 in Malaysia.
Chong Diane Woei-Quan et al. BMC infectious diseases 2021 12 (1) 1238 -
Transmission of SARS-CoV-2 from humans to a 16-year-old domestic cat with comorbidities in Pennsylvania, USA.
Tewari Deepanker et al. Veterinary medicine and science 2021 12
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Transfusion-Transmitted Hepatitis A Virus, France, 2018
LeFeuvre C, et al. Emerg Infect Dis, Dec 8, 2021.
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Universal Coronavirus Vaccines - An Urgent Need.
Morens David M et al. The New England journal of medicine 2021 12 -
Effectiveness of COVID-19 vaccines against the Omicron (B.1.1.529) variant of concern
Andrews N, et al. medRxiv, Dec 14, 2021.
HOST-MICROBE INTERACTIONS
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A Phenome Wide Association Study of Severe COVID-19 Genetic Risk Variants
Regan JA, et al. medRxiv, Dec 11, 2021. -
Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity.
Fallerini Chiara et al. Human genetics 2021 12 -
Signatures of immune selection in intact and defective proviruses distinguish HIV-1 elite controllers
Liang X, et al. Sci Transl Med, Dec 15, 2021. -
Malaria protection due to sickle haemoglobin depends on parasite genotype.
Band Gavin et al. Nature 2021 12
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 Genomics and Precision Public Health 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.
- Page last reviewed:Oct 1, 2023
- Page last updated:Nov 16, 2023
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