Advanced Molecular Detection Clips Content (Published on 07/08/2021)
NEWS
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Delta, as expected, is now the dominant virus variant in the U.S., the C.D.C. estimates.
Anthes E. New York Times, Jul 7, 2021. -
The Gamma Variant's Rise in Washington State
Grant K. Medpage Today, Jul 2, 2021. -
Delta variant confirmed in samples from church camp outbreak
(video) Fox 26, Houston, Jul 7, 2021. -
From Wuhan to Paris to Milan, the search for 'patient zero'
Dou E, et al. Washington Post, Jul 7, 2021. -
Scientists quit journal board, protesting 'grossly irresponsible' study claiming COVID-19 vaccines kill
Waldman M. Science, Jul 1, 2021. -
New study on delta variant reveals importance of receiving both vaccine shots, highlights challenges posed by mutations
Achenbach J. Washington Post, Jul 8, 2021.
EVENTS / TRAINING / WEB RESOURCES
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Cov2Tree: interactive SARS-CoV-2 phylogeny
(website) Sanderson T. cov2tree.org
POLICY
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Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021).
Walker Peter J et al. Archives of virology 2021 7
CONCEPTS / COMMENTS
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The importance of molecular diagnostics for infectious diseases in low-resource settings.
Okeke Iruka N et al. Nature reviews. Microbiology 2021 6 -
Thinking clearly about social aspects of infectious disease transmission.
Buckee Caroline et al. Nature 2021 7 (7866) 205-213 -
Science, not speculation, is essential to determine how SARS-CoV-2 reached humans
Calisher CH, et al. Lancet, Jul 5, 2021. -
Increasing threats from SARS-CoV-2 variants: Time to establish global surveillance
Layne SP, Taubenberger JK. Sci Transl Med, Jul 7, 2021. -
Human genetic variants identified that affect COVID susceptibility and severity
Asgari S, Pouzas LA. Nature, Jul 8, 2021. -
The Enterovirus Theory of Disease Etiology in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Critical Review.
O'Neal Adam J et al. Frontiers in medicine 2021 7 688486
METHODS / TOOLS
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Monitoring SARS-CoV-2 in sewage: toward sentinels with analytical accuracy
Calderon-Franco D, et al. medRxiv, Jul 5, 2021. -
Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST.
Deneke Carlus et al. Frontiers in microbiology 2021 7 649517 -
High-precision and cost-efficient sequencing for real-time COVID-19 surveillance.
Park Sung Yong et al. Scientific reports 2021 7 (1) 13669 -
Sequencing SARS-CoV-2 Genomes from Saliva
Alpert T, et al. medRxiv, Jun 21, 2021. -
Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction.
Knyazev Sergey et al. Nucleic acids research 2021 7 -
A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex
Lam MM, et al. Nat Commun, Jul 7, 2021. -
VirusViz: comparative analysis and effective visualization of viral nucleotide and amino acid variants.
Bernasconi Anna et al. Nucleic acids research 2021 6
EVOLUTION / ECOLOGY / POPULATIONS
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Whole-Genome Sequencing for Tracing the Genetic Diversity of Brucella abortus and Brucella melitensis Isolated from Livestock in Egypt.
Khan Aman Ullah et al. Pathogens (Basel, Switzerland) 2021 7 (6) -
Characterization of a novel transitional group Rickettsia species (Rickettsia tillamookensis sp. nov.) from the western black-legged tick, Ixodes pacificus.
Gauthier David T et al. International journal of systematic and evolutionary microbiology 2021 7 (7) -
Characterization of genetic diversity and clonal complexes by whole genome sequencing of Mycobacterium tuberculosis isolates from Jalisco, Mexico.
Rendón-Bautista Luis Alfredo et al. Tuberculosis (Edinburgh, Scotland) 2021 7 102106 -
The Origins of SARS-CoV-2: A Critical Review
Holmes EC, et al. zenodo, Jul 7, 2021. -
Predicted dominance of variant Delta of SARS-CoV-2 before Tokyo Olympic Games, Japan, July 2021
Ito K, et al. Eurosurveill, Jul 8, 2021. -
A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic.
Chrysostomou Andreas C et al. Viruses 2021 7 (6) -
The Emergence of SARS-CoV-2 Variant Lambda (C.37) in South America
Romero PE, et al. medRxiv, Jul 3, 2021. -
COVID-19 vaccines dampen genomic diversity of SARS-CoV-2: Unvaccinated patients exhibit more antigenic mutational variance
Niesen M, et al. medRxiv, Jul 5, 2021. -
Review of the early reports of the epidemiological characteristics of the B.1.1.7 variant of SARS-CoV-2 and its spread worldwide.
Kim Yeonju et al. Osong public health and research perspectives 2021 7 (3) 139-148 -
Two decades of one health surveillance of Nipah virus in Thailand.
Wacharapluesadee Supaporn et al. One health outlook 2021 7 (1) 12
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Exploring the evolution and epidemiology of European CC1-MRSA-IV: tracking a multidrug-resistant community-associated meticillin-resistant Staphylococcus aureus clone.
Earls Megan R et al. Microbial genomics 2021 7 (7) -
A genetic cluster of MDR Enterobacter cloacae complex ST78 harbouring a plasmid containing bla and mcr-9 in the Netherlands.
Hendrickx Antoni P A et al. JAC-antimicrobial resistance 2021 7 (2) dlab046 -
Prevalence of Mycobacterium tuberculosis resistant to Bedaquiline and Delamanid in China.
He Wencong et al. Journal of global antimicrobial resistance 2021 7 -
Progressive Increase in Virulence of Novel SARS-CoV-2 Variants in Ontario, Canada, February to June, 2021
Fisman D, Tuite A. medRxiv, Jul 7, 2021. -
What do we know about the biology of the emerging fungal pathogen of humans Candida auris?
Bravo Ruiz Gustavo et al. Microbiological research 2020 10 126621
DETECTION / DIAGNOSIS
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Molecular Detection of Carbapenemases in Enterobacterales: A Comparison of Real-Time Multiplex PCR and Whole-Genome Sequencing.
Probst Katja et al. Antibiotics (Basel, Switzerland) 2021 7 (6) -
Reporter-Phage-Based Detection and Antibiotic Susceptibility Testing of Yersinia pestis for a Rapid Plague Outbreak Response.
Moses Sarit et al. Microorganisms 2021 7 (6) -
Application of MALDI-TOF mass spectrometry, and DNA sequencing-based SLST and MLST analysis for the identification of Cronobacter spp. isolated from environmental surveillance samples.
Sulaiman Irshad M et al. Archives of microbiology 2021 7 -
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Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season
Xu Y, et al. Eurosurveill, Jul 8, 2021.
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Phylogeography and transmission of M. tuberculosis in Moldova
Yang C, et al. medRxiv, Jul 5, 2021. -
Genomic evidence for prisons as amplifiers of community tuberculosis epidemics
Walter KS, et al. medRxiv, Jun 24, 2021. -
Molecular Epidemiology of Drug-Resistant Mycobacterium Tuberculosis in Japan.
Mizukoshi Fuminori et al. mSphere 2021 7 e0097820 -
Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response
Liu R, et al. Sci Rep. 2021 Jul 7;11(1):13971. -
Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages
Petrone ME, et al. medRxiv, Jul 2, 2021. -
Mathematical modelling of SARS-CoV-2 variant outbreaks reveals their probability of extinction
Schioler H, et al. medRxiv, Jul 7, 2021. -
An outbreak caused by the SARS-CoV-2 Delta (B.1.617.2) variant in a care home after partial vaccination with a single dose of the COVID-19 vaccine Vaxzevria, London, England, April 2021
Williams SV, et al. Eurosurveill, Jul 8, 2021. -
Transmission event of SARS-CoV-2 Delta variant reveals multiple vaccine breakthrough infections
Farinholt T, et al. medRxiv, Jul 4, 2021. -
Human Immunodeficiency Virus (HIV) Drug Resistance, Phylogenetic Analysis, and Superinfection Among Men Who Have Sex with Men and Transgender Women in Sub-Saharan Africa: HIV Prevention Trials Network (HPTN) 075 Study.
Sivay Mariya V et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 8 (1) 60-67
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Global genomic pathogen surveillance to inform vaccine strategies: a decade-long expedition in pneumococcal genomics.
Bentley Stephen D et al. Genome medicine 2021 5 (1) 84 -
Will Vaccine-derived Protective Immunity Curtail COVID-19 Variants in the US?
Mancuso M, et al. medRxiv, Jul 5, 2021. -
Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization
Planas D, et al. Nature, Jul 8, 2021. -
An observational cohort study on the incidence of SARS-CoV-2 infection and B.1.1.7 variant infection in healthcare workers by antibody and vaccination status.
Lumley Sheila F et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 7 -
Ultrapotent antibodies against diverse and highly transmissible SARS-CoV-2 variants.
Wang Lingshu et al. Science (New York, N.Y.) 2021 7 -
Age-related immune response heterogeneity to SARS-CoV-2 vaccine BNT162b2.
Collier Dami A et al. Nature 2021 7 -
Post-vaccination SARS-COV-2 among healthcare workers in New Jersey: a genomic epidemiological study
Mathema B, et al. medRxiv, Jul 5, 2021. -
Screening and Identification of Lujo Virus Inhibitors Using a Recombinant Reporter Virus Platform.
Welch Stephen R et al. Viruses 2021 7 (7)
HOST-MICROBE INTERACTIONS
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The infant gut resistome is associated with E. coli and early-life exposures.
Lebeaux Rebecca M et al. BMC microbiology 2021 7 (1) 201 -
A Listeria monocytogenes clone in human breast milk associated with severe acute malnutrition in West Africa: A multicentric case-controlled study
Sar M, et al. PLoS Negl Trop Dis, Jun 29, 2021. -
Mapping the human genetic architecture of COVID-19
COVID-19 Host Genetics Initiative. Nature, Jul 8, 2021. -
An integrative multiomics analysis identifies putative causal genes for COVID-19 severity.
Wu Lang et al. Genetics in medicine : official journal of the American College of Medical Genetics 2021 6 -
Global patterns of genetic variation and association with clinical phenotypes at genes involved in SARS-CoV-2 infection
Zhang C, et al. medRxiv, Jul 1, 2021. -
Predicted Impact of the Viral Mutational Landscape on the Cytotoxic Response against SARS-CoV-2
Foix A, et al. bioRxiv, Jul 5, 2021.
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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- Page last updated:Apr 11, 2024
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