Advanced Molecular Detection Clips Content (Published on 02/03/2022)
NEWS
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The staggering death toll of drug-resistant bacteria
Thompson T. Nature, Jan 31, 2022. -
Sudden rise of more transmissible form of Omicron catches scientists by surprise
Wadman M. Science, Jan 31, 2022. -
Where did Omicron come from? Three key theories
Mallapaty S. Nature, Jan 28, 2022. -
The Clues to the Next Variant Surge Are All Around Us
Bright R. New York Times, Feb 2, 2022. -
In New York City Sewage, a Mysterious Coronavirus Signal
Anthes E. New York Times, Feb 3, 2022. -
Cheap, Rapid 'Flurona' Test Developed by UCSB Solves Problems With LAMP Sensitivity
Ketchum K. GenomeWeb, Feb 1, 2022. -
How well can Omicron evade immunity from COVID vaccines?
Reardon S. Nature, Feb 2, 2022. -
Does the world need an Omicron vaccine? What researchers say
Waltz E. Nature, Jan 28, 2022. -
Long COVID: Researchers Find Antibody Signature to Identify High-Risk Patients; Two Vaccine Shots Could Stop the Syndrome
Hoffman M. Health Policy Watch, Jan 31, 2022. -
What We Can Learn From How the 1918 Pandemic Ended
Barry JM. New York Times, Jan 31, 2022.
EVENTS / TRAINING / WEB RESOURCES
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The Power of Genomics to Understand the COVID-19 Pandemic
(online course) Wellcome Connecting Science, Feb 7-28, 2022.
CONCEPTS / COMMENTS
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Applied Bioinformatics and Public Health Microbiology: challenges, discoveries and innovations during a pandemic.
Cunningham-Oakes Edward et al. Microbial genomics 2022 1 (1)
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When viruses become more virulent
Wertheim J. Science, Feb 3, 2022. -
Challenges in Inferring Intrinsic Severity of the SARS-CoV-2 Omicron Variant.
Bhattacharyya Roby P et al. The New England journal of medicine 2022 2
METHODS / TOOLS
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Polypolish: Short-read polishing of long-read bacterial genome assemblies.
Wick Ryan R et al. PLoS computational biology 2022 1 (1) e1009802 -
A mixture model for determining SARS-Cov-2 variant composition in pooled samples.
Valieris Renan et al. Bioinformatics (Oxford, England) 2022 2 -
HiSpike Method for High-Throughput Cost Effective Sequencing of the SARS-CoV-2 Spike Gene.
Fass Ephraim et al. Frontiers in medicine 2022 1 798130 -
Fast and accurate influenza forecasting in the United States with Inferno.
Osthus Dave et al. PLoS computational biology 2022 1 (1) e1008651
EVOLUTION / ECOLOGY / POPULATIONS
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Whole-genome single nucleotide variant phylogenetic analysis of Mycobacterium tuberculosis Lineage 1 in endemic regions of Asia and Africa.
Netikul Thidarat et al. Scientific reports 2022 1 (1) 1565 -
Whole Genome Sequencing Reveals Biopesticidal Origin of Bacillus thuringiensis in Foods.
Biggel Michael et al. Frontiers in microbiology 2022 1 775669 -
Large-Scale Phylogenetic Analysis Reveals a New Genetic Clade among Escherichia coli O26 Strains.
Long Jinzhao et al. Microbiology spectrum 2022 2 e0252521 -
WGS analysis of Listeria monocytogenes from rural, urban, and farm environments in Norway: Genetic diversity, persistence, and relation to clinical and food isolates.
Fagerlund Annette et al. Applied and environmental microbiology 2022 2 aem0213621 -
Salmonella enterica serovar Typhimurium from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type.
Fu Yezhi et al. Applied and environmental microbiology 2022 2 AEM0197921 -
Pathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care?
Dias Diana et al. The Science of the total environment 2021 12 152324 -
EARLY INTRODUCTION, DISPERSAL AND EVOLUTION OF DELTA SARS-CoV-2 IN SOUTHERN BRAZIL, LATE PREDOMINANCE OF AY.99.2 AND AY.101 RELATED LINEAGES.
Gularte Juliana Schons et al. Virus research 2022 2 198702 -
Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway.
Zhou Jie et al. Cell reports 2022 1 110344 -
Genome surveillance of SARS-CoV-2 variants and their role in pathogenesis focusing on second wave of COVID-19 in India
Sarkar P, et al. medRxiv, Jan 31, 2022. -
A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands.
López-Causapé Carla et al. Frontiers in microbiology 2022 1 803827 -
Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens.
Naung Myo T et al. PLoS computational biology 2022 2 (2) e1009801 -
Genome-wide insights into adaptive hybridisation across the Schistosoma haematobium group in West and Central Africa.
Landeryou Toby et al. PLoS neglected tropical diseases 2022 1 (1) e0010088
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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First National Genomic Epidemiological Study of Neisseria gonorrhoeae Strains Spreading Across Sweden in 2016.
Hadad Ronza et al. Frontiers in microbiology 2022 1 820998 -
Whole-genome sequencing of Mycobacterium tuberculosis for prediction of drug resistance.
Wang Luqi et al. Epidemiology and infection 2022 1 e22 -
Emergence of colistin-resistant hypervirulent Klebsiella pneumoniae (CoR-HvKp) in China.
Liu Xiaoyu et al. Emerging microbes & infections 2022 1 1-36 -
Carbapenemase-producing Klebsiella pneumoniae strains in Switzerland: Human and non-human settings may share high-risk clones.
Campos-Madueno Edgar I et al. Journal of global antimicrobial resistance 2022 1 -
Nosocomial Outbreak of Carbapenemase-Producing Proteus mirabilis With Two Novel Salmonella Genomic Island 1 Variants Carrying Different bla Gene Copies in China.
Yang Lang et al. Frontiers in microbiology 2022 1 800938 -
Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs.
Bengtsson Rebecca J et al. Nature microbiology 2022 2 -
Dissemination Routes of Carbapenem and Pan-Aminoglycoside Resistance Mechanisms in Hospital and Urban Wastewater Canalizations of Ghana.
Delgado-Blas Jose F et al. mSystems 2022 2 e0101921 -
SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection.
Khateeb Dina et al. PLoS pathogens 2022 1 (1) e1010242 -
Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk.
Zhao Lue Ping et al. Scientific reports 2022 1 (1) 1206 -
Deep sequencing of HIV-1 reveals extensive subtype variation and drug resistance after failure of first-line antiretroviral regimens in Nigeria.
El Bouzidi Kate et al. The Journal of antimicrobial chemotherapy 2022 2 (2) 474-482 -
Azole Resistance in Aspergillus fumigatus. The first 2-year's Data from the Danish National Surveillance Study, 2018-2020.
Risum Malene et al. Mycoses 2022 2
DETECTION / DIAGNOSIS
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Optimising genomic approaches for identifying vancomycin-resistant Enterococcus faecium transmission in healthcare settings.
Higgs Charlie et al. Nature communications 2022 1 (1) 509 -
Development of a simple, rapid, and sensitive diagnostic assay for enterotoxigenic E. coli and Shigella spp applicable to endemic countries.
Chakraborty Subhra et al. PLoS neglected tropical diseases 2022 1 (1) e0010180 -
Toward accurate diagnosis and surveillance of bacterial infections using enhanced strain-level metagenomic next-generation sequencing of infected body fluids.
Ruan Zhi et al. Briefings in bioinformatics 2022 2 -
Genome Sequencing of Wastewater Confirms the Arrival of the SARS-CoV-2 Omicron Variant at Frankfurt Airport but Limited Spread in the City of Frankfurt, Germany, in November 2021
Agrawal S. Microbiol Resour Announc. 2022 Jan 27;e0122921.
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Wastewater surveillance for COVID-19 response at multiple geographic scales: Aligning wastewater and clinical results at the census-block level and addressing pervasiveness of qPCR non-detects
Safford H, et al. medRxiv, Jan 29, 2022. -
N Gene Target Failure (NGTF) for detection of Omicron: a way out for the "stealth" too?
Harankhedkar S, et al. medRxiv, Jan 30, 2022. -
Rapid, Large-Scale Wastewater Surveillance and Automated Reporting System Enable Early Detection of Nearly 85% of COVID-19 Cases on a University Campus.
Karthikeyan Smruthi et al. mSystems 2021 8 (4) e0079321
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SARS-CoV-2 Variant Surveillance Using Tandem Targeted RT-PCR-based Genotyping Assays and Whole Genome Sequencing
Pinkhover NP, et al. medRxiv, Feb 2, 2022. -
Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater
Smyth DS, et al. Nat Commun, Feb 3, 2022.
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Monoclonal antibodies to Cache Valley virus for serological diagnosis.
Skinner Benjamin et al. PLoS neglected tropical diseases 2022 1 (1) e0010156
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Characterising co-infections with Plasmodium spp., Mansonella perstans or Loa loa in asymptomatic children, adults and elderly people living on Bioko Island using nucleic acids extracted from malaria rapid diagnostic tests.
Yoboue Charlene Aya et al. PLoS neglected tropical diseases 2022 1 (1) e0009798 -
Development and evaluation of a molecular based protocol for detection and quantification of Cryptosporidium spp. In wastewater.
Mthethwa N P et al. Experimental parasitology 2022 2 108216
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Mutation of Mycobacterium tuberculosis and Implications for Using Whole-Genome Sequencing for Investigating Recent Tuberculosis Transmission.
Kristin N Nelson et al. Front Public Health 2022 1 790544
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Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults.
Siranosian Benjamin A et al. Nature communications 2022 2 (1) 586 -
Nosocomial transmission clusters and lineage diversity characterized by SARS-CoV-2 genomes from two large hospitals in Paris, France, in 2020.
Leducq Valentin et al. Scientific reports 2022 1 (1) 1094
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Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves
Lindsey BB, et al. Nat Commun, Feb 3, 2022.
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Transmission of SARS-CoV-2 Omicron VOC subvariants BA.1 and BA.2: Evidence from Danish Households
Lyngse FP, et al. medRxiv, Jan 30, 2022. -
Observed serial intervals of SARS-CoV-2 for the Omicron and Delta variants in Belgium based on contact tracing data, 19 November to 31 December 2021
Kremer C, et al. medRxiv, Jan 30, 2022. -
Phylogenomics of SARS-CoV-2 in Emergency Shelters for People Experiencing Homelessness.
Casto Amanda M et al. The Journal of infectious diseases 2022 1
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Comparing susceptibility and contagiousness in concurrent outbreaks with a non-VOC and the VOC SARS-CoV-2 variant B.1.1.7 in daycare centers in Hamburg, Germany.
Nakel Jacqueline et al. International journal of hygiene and environmental health 2022 1 113928 -
A2B-COVID: A tool for rapidly evaluating potential SARS-CoV-2 transmission events.
Illingworth Christopher J R et al. Molecular biology and evolution 2022 2 -
The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002-2020).
Brenner Bluma G et al. Viruses 2021 8 (8)
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Sociodemographic, Ecological, and Spatiotemporal Factors Associated with Human Immunodeficiency Virus Drug Resistance in Florida: A Retrospective Analysis.
Rich Shannan N et al. The Journal of infectious diseases 2020 7 (5) 866-875
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Effectiveness of COVID-19 vaccines among incarcerated people in California state prisons: retrospective cohort study.
Chin Elizabeth T et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 1
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Recent advances in nanotechnology-based COVID-19 vaccines and therapeutic antibodies.
Du Lanying et al. Nanoscale 2022 1 (4) 1054-1074 -
SARS-CoV-2 Infection and Hospitalization Among Adults Aged >=18 Years, by Vaccination Status, Before and During SARS-CoV-2 B.1.1.529 (Omicron) Variant Predominance--Los Angeles County, California, November 7, 2021-January 8, 2022
Danza P, et al. MMWR, Feb 1, 2022.
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Vaccination with BNT162b2 reduces transmission of SARS-CoV-2 to household contacts in Israel
Prunas O, et al. Science. 2022 Jan 27;eabl4292.
HOST-MICROBE INTERACTIONS
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Human genetic and immunological determinants of critical COVID-19 pneumonia
Zhang Q, et al. Nature. 2022 Jan 28. -
Association of HLA gene polymorphism with susceptibility, severity, and mortality of COVID-19: A systematic review.
Deb Paroma et al. HLA 2022 1 -
miRNAs, from Evolutionary Junk to Possible Prognostic Markers and Therapeutic Targets in COVID-19.
Bautista-Becerril Brandon et al. Viruses 2022 1 (1) -
Host methylation predicts SARS-CoV-2 infection and clinical outcome.
Konigsberg Iain R et al. Communications medicine 2022 1 (1) 42 -
Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19
Sahajpal NS, et al. iScience, Feb 18, 2022. -
Influenza Virus-Induced Novel miRNAs Regulate the STAT Pathway.
Othumpangat Sreekumar et al. Viruses 2021 6 (6)
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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- Page last updated:Nov 7, 2024