Advanced Molecular Detection Clips Content (Published on 12/23/2021)
NEWS
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Understanding the omicron variant
Berkowitz B. Steckelberg A. Washington Post, Dec 16, 2021. -
Omicron blindspots: why it's hard to track coronavirus variants
Maxmen A. Nature, Dec 16, 2021. -
Omicron overpowers key COVID antibody treatments in early tests
Kozlov M. Nature, Dec 21, 2021. -
A computational biologist weighs in on Omicron, the future of vaccines, and the CDC's variant forecast
Branswell H. STAT, Dec 22, 2021. -
How COVID vaccines shaped 2021 in eight powerful charts
Mallapaty S, et al. Nature, Dec 16, 2021.
CONCEPTS / COMMENTS
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Winter of Omicron: The Evolving COVID-19 Pandemic
del Rio C, et al. JAMA, Dec 22, 2021. -
Diagnostics for COVID-19: moving from pandemic response to control
Peeling RW, et al. Lancet, Dec 20, 2021. -
One Year of COVID-19 Vaccines: A Shot of Hope, a Dose of Reality.
Cohn Amanda C et al. JAMA 2021 12
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Editorial: Codon Usage and Dinucleotide Composition of Virus Genomes: From the Virus-Host Interaction to the Development of Vaccines.
Pintó Rosa M et al. Frontiers in microbiology 2021 12 791750
METHODS / TOOLS
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An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes.
Perez-Sepulveda Blanca M et al. Genome biology 2021 12 (1) 349 -
Pandemic-scale phylogenetics.
Ye Cheng et al. bioRxiv : the preprint server for biology 2021 12 -
A proposed workflow for proactive virus surveillance and prediction of variants for vaccine design.
Baker Jordan J et al. PLoS computational biology 2021 12 (12) e1009624 -
CoxBase: an Online Platform for Epidemiological Surveillance, Visualization, Analysis, and Typing of Coxiella burnetii Genomic Sequences.
Fasemore Akinyemi M et al. mSystems 2021 12 (6) e0040321
EVOLUTION / ECOLOGY / POPULATIONS
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Whole-genome analysis-based phylogeographic investigation of Streptococcus pneumoniae serotype 19A sequence type 320 isolates in Japan.
Nakano Satoshi et al. Antimicrobial agents and chemotherapy 2021 12 AAC0139521 -
Treponema pallidum genome sequencing from six continents reveals variability in vaccine candidate genes and dominance of Nichols clade strains in Madagascar.
Lieberman Nicole A P et al. PLoS neglected tropical diseases 2021 12 (12) e0010063
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Genome sequencing of SARS-CoV-2 reveals the prevalence of variant B 1.1.7 in Egypt.
Seadawy Mohamed G et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 12 105191 -
Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York.
Duerr Ralf et al. medRxiv : the preprint server for health sciences 2021 12
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SARS-CoV-2 Circulation, Guinea, March 2020-July 2021.
Grayo Solène et al. Emerging infectious diseases 2021 12 (2) -
Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia.
Bermúdez Jubby Marcela Gálvez et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 12 105192 -
Striking lineage diversity of severe acute respiratory syndrome coronavirus 2 from non-human sources.
Muñoz Marina et al. One health (Amsterdam, Netherlands) 2021 12 100363 -
Delayed respiratory syncytial virus outbreak in 2020 in Taiwan was correlated with two novel RSV-A genotype ON1 variants.
Lee Chun Yi et al. Influenza and other respiratory viruses 2021 12 -
Genomic analyses of human adenoviruses unravel novel recombinant genotypes associated with severe infections in pediatric patients.
Akello Joyce Odeke et al. Scientific reports 2021 12 (1) 24038 -
Circulation of Type 2 Vaccine-Derived Poliovirus in China in 2018-2019.
Zhao Hehe et al. Open forum infectious diseases 2021 12 (12) ofab535
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Longitudinal monitoring in Cambodia suggests higher circulation of alpha and betacoronaviruses in juvenile and immature bats of three species.
Cappelle Julien et al. Scientific reports 2021 12 (1) 24145 -
Distinguishing gene flow between malaria parasite populations.
Brown Tyler S et al. PLoS genetics 2021 12 (12) e1009335 -
Insights from a comprehensive study of Trypanosoma cruzi: A new mitochondrial clade restricted to North and Central America and genetic structure of TcI in the region.
Lima-Cordón Raquel Asunción et al. PLoS neglected tropical diseases 2021 12 (12) e0010043 -
The bacterial biome of ticks and their wildlife hosts at the urban-wildland interface.
Egan Siobhon L et al. Microbial genomics 2021 12 (12)
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Worldwide distribution and environmental origin of the Adelaide imipenemase (AIM-1), a potent carbapenemase in Pseudomonas aeruginosa.
Amsalu Anteneh et al. Microbial genomics 2021 12 (12) -
Invasive Multidrug-Resistant emm93.0 Streptococcus pyogenes Strain Harboring a Novel Genomic Island, Israel, 2017-2019.
Ron Merav et al. Emerging infectious diseases 2021 12 (1) 118-126 -
The changing molecular epidemiology of Enterococcus faecium harbouring the van operon at a teaching hospital in Western Australia: A fifteen-year retrospective study.
Lee Terence et al. International journal of medical microbiology : IJMM 2021 12 (1) 151546 -
Epidemiology and genomic analysis of Shiga toxin-producing Escherichia coli clonal complex 165 in the UK.
Rodwell Ella V et al. Journal of medical microbiology 2021 12 (12) -
A 21-Year Survey of Escherichia coli from Bloodstream Infections (BSI) in a Tertiary Hospital Reveals How Community-Hospital Dynamics of B2 Phylogroup Clones Influence Local BSI Rates.
Rodríguez Irene et al. mSphere 2021 12 (6) e0086821 -
Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta.
Ulrich Lorenz et al. Nature 2021 12
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Long-term adaptation following influenza A virus host shifts results in increased within-host viral fitness due to higher replication rates, broader dissemination within the respiratory epithelium and reduced tissue damage.
Amat Julien A R et al. PLoS pathogens 2021 12 (12) e1010174 -
Library-based analysis reveals segment and length dependent characteristics of defective influenza genomes.
Mendes Marisa et al. PLoS pathogens 2021 12 (12) e1010125
DETECTION / DIAGNOSIS
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Metagenomics applied to the detection of diarrhea viruses in humans: Systematic Review.
David Everson Dos Santos et al. Acta tropica 2021 12 106287
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Clinical and public health utility of Mycobacterium tuberculosis whole genome sequencing.
Kizny Gordon Alice et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 3 S40-S42
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Metagenomics combined with comprehensive validation as a public health risk assessment tool for urban and agricultural run-off.
Fu Songzhe et al. Water research 2021 12 117941 -
Accuracy of an amplicon-sequencing nanopore approach to identify variants in tuberculosis drug-resistance-associated genes.
Mariner-Llicer Carla et al. Microbial genomics 2021 12 (12) -
Target-enriched sequencing enables accurate identification of bloodstream infections in whole blood.
Li Qian et al. Journal of microbiological methods 2021 12 106391 -
Monitoring microbial communities in intensive care units over one year in China.
Li Kexin et al. The Science of the total environment 2021 12 152353 -
Early detection and improved genomic surveillance of SARS-CoV-2 variants from deep sequencing data
Ramazzotti D, et al. medRxiv, Dec 16, 2021. -
Genomic and Virological Characterization of SARS-CoV-2 Variants in a Subset of Unvaccinated and Vaccinated U.S. Military Personnel
Smith DR, et al. medRxiv, Dec 16, 2021. -
Surveillance of SARS-CoV-2 in extensive monitoring of municipal wastewater: key issues to yield reliable results.
Cutrupi F et al. Water science and technology : a journal of the International Association on Water Pollution Research 2021 12 (12) 3508-3514
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Aptamer-Functionalized Nanochannels for One-Step Detection of SARS-CoV-2 in Samples from COVID-19 Patients.
Shi Liu et al. Analytical chemistry 2021 11 (49) 16646-16654 -
Monitoring International Travelers Arriving in Hong Kong for Genomic Surveillance of SARS-CoV-2.
Gu Haogao et al. Emerging infectious diseases 2021 12 (1) 247-250
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae.
Viehweger Adrian et al. Microbial genomics 2021 12 (12) -
Extensively Drug-Resistant Carbapenemase-Producing Pseudomonas aeruginosa and Medical Tourism from the United States to Mexico, 2018-2019.
Kracalik Ian et al. Emerging infectious diseases 2021 12 (1) 51-61
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Contact tracing outcomes among household contacts of fully vaccinated COVID-19 patients - San Francisco, California, January 29-July 2, 2021.
Sachdev Darpun D et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 12
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Population impact of SARS-CoV-2 variants with enhanced transmissibility and/or partial immune escape.
Bushman Mary et al. Cell 2021 12 -
Projected epidemiological consequences of the Omicron SARS-CoV-2 variant in England, December 2021 to April 2022
Barnard RC, et al. medRxiv, Dec 16, 2021.
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Comparative Effectiveness of Coronavirus Vaccine in Preventing Breakthrough Infections among Vaccinated Persons Infected with Delta and Alpha Variants.
Kislaya Irina et al. Emerging infectious diseases 2021 12 (2) -
Barcoded Asaia bacteria enable mosquito in vivo screens and identify novel systemic insecticides and inhibitors of malaria transmission.
Sturm Angelika et al. PLoS biology 2021 12 (12) e3001426 -
Vaccine effectiveness against SARS-CoV-2 infection with the Omicron or Delta variants following a two-dose or booster BNT162b2 or mRNA-1273 vaccination series: A Danish cohort study
Hansen CH, et al. medRxiv, Dec 21, 2021. -
Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York
Duerr R, et al. medRxiv, Dec 17, 2021.
HOST-MICROBE INTERACTIONS
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Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease.
Walker Rebecca L et al. Genome medicine 2021 12 (1) 188 -
Microbiota composition is moderately associated with greenspace composition in a UK cohort of twins.
Bowyer Ruth C E et al. The Science of the total environment 2021 12 152321 -
Alterations of human skin microbiome and expansion of antimicrobial resistance after systemic antibiotics.
Jo Jay-Hyun et al. Science translational medicine 2021 12 (625) eabd8077 -
Evolutionary pathways to SARS-CoV-2 resistance are opened and closed by epistasis acting on ACE2.
Castiglione Gianni M et al. PLoS biology 2021 12 (12) e3001510 -
Discovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers
Vanshylla K, et al. Cell Host Microbe, Dec 18, 2021.
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.
- Page last reviewed:Oct 1, 2023
- Page last updated:Nov 16, 2023
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