Advanced Molecular Detection Clips Content (Published on 02/17/2022)
NEWS
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Public call for whole genome sequencing and phenotypic data from clinical isolates of M. tuberculosis complex
WHO, Feb 14, 2022. -
Why does the Omicron sub-variant spread faster than the original?
Callaway E. Nature, Feb 16, 2022. -
Was a 19th Century Global Pandemic a Case of COVID 1.0?
Dotinga R. MedPage Today, Feb 15, 2022. -
BA.2 May Not Disrupt U.S. COVID Case Declines
Fiore K. MedPage Today, Feb 15, 2022. -
Covid-19: What do we know about omicron sublineages?
Mahase E. BMJ. 2022:376. -
COVID reinfections surge during Omicron onslaught
Mallapaty S. Nature, Feb 16, 2022. -
Omicron-targeted vaccines do no better than original jabs in early tests
Waltz E. Nature, Feb 14, 2022. -
SARS-CoV-2-Related Coronaviruses From Bats in Laotian Caves Can Infect Human Cells
GenomeWeb, Feb 16, 2022. -
Unlocking the mystery of the "never COVID" cohort
O'Reilly ED. Axios, Feb 13, 2022. -
HIV variant causes concern
O'Leary K. Nature, Feb 14, 2022.
EVENTS / TRAINING / WEB RESOURCES
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Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing.
Runtuwene Lucky R et al. BMC research notes 2022 2 (1) 44 -
COVID-19: OIE's Response
(website) OIE-World Organisation for Animal Health. Accessed Feb 16, 2022.
CONCEPTS / COMMENTS
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Infection prevention and control insights from a decade of pathogen whole-genome sequencing.
Eyre David W et al. The Journal of hospital infection 2022 2
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Application and Challenge of 3rd Generation Sequencing for Clinical Bacterial Studies.
Ben Khedher Mariem et al. International journal of molecular sciences 2022 2 (3)
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THE CARBON FOOTPRINT OF BIOINFORMATICS.
Grealey Jason et al. Molecular biology and evolution 2022 2
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The next pandemic could start with a terrorist attack
Webb A. The Atlantic, Feb 14, 2022.
METHODS / TOOLS
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No one tool to rule them all: Prokaryotic gene prediction tool annotations are highly dependent on the organism of study.
Dimonaco Nicholas J et al. Bioinformatics (Oxford, England) 2021 12 -
Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in Bordetella pertussis and Mycobacterium tuberculosis.
Abrahams Jonathan S et al. Microbial genomics 2022 2 (2) -
A computationally tractable birth-death model that combines phylogenetic and epidemiological data.
Zarebski Alexander Eugene et al. PLoS computational biology 2022 2 (2) e1009805 -
Phylodynamic inference of bacterial outbreak parameters using nanopore sequencing.
Steinig Eike et al. Molecular biology and evolution 2022 2 -
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.
Griffiths Emma J et al. GigaScience 2022 2
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Virtifier: A deep learning-based identifier for viral sequences from metagenomes.
Miao Yan et al. Bioinformatics (Oxford, England) 2021 12 -
A curated dataset of peste des petits ruminants virus sequences for molecular epidemiological analyses.
Baron Michael D et al. PloS one 2022 2 (2) e0263616
EVOLUTION / ECOLOGY / POPULATIONS
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The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis.
van Hal Sebastiaan J et al. The Lancet. Microbe 2022 2 (2) e133-e141 -
Emergence of Neisseria meningitidis W South American sublineage strain variant in Brazil: disease and carriage.
Lemos Ana Paula Silva de et al. Journal of medical microbiology 2022 2 (2) -
Bat coronaviruses related to SARS-CoV-2 and infectious for human cells.
Temmam Sarah et al. Nature 2022 2 -
Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil.
Wink Priscila Lamb et al. Microbiology spectrum 2022 2 e0151121 -
Worldwide SARS-CoV-2 haplotype distribution in early pandemic.
Cairo Andrea et al. PloS one 2022 2 (2) e0263705 -
The genetic evolution and codon usage pattern of severe fever with thrombocytopenia syndrome virus.
Zu Zhipeng et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2022 2 105238 -
Bluetongue Research at a Crossroads: Modern Genomics Tools Can Pave the Way to New Insights.
Kopanke Jennifer et al. Annual review of animal biosciences 2022 2 303-324
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Genotyping of foot-and-mouth disease viruses collected in Sudan between 2009 and 2018.
Raouf Yazeed A et al. Transboundary and emerging diseases 2022 2
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Genome Informatics and Machine Learning-Based Identification of Antimicrobial Resistance-Encoding Features and Virulence Attributes in Escherichia coli Genomes Representing Globally Prevalent Lineages, Including High-Risk Clonal Complexes
Shaik S, et al. mBio. 2022 Feb 15;e0379621. -
Epidemiology of extended-spectrum β-lactamase-producing Enterobacterales in five US sites participating in the Emerging Infections Program, 2017.
Duffy Nadezhda et al. Infection control and hospital epidemiology 2022 2 1-9 -
Multiple phylogenetically-diverse, differentially-virulent Burkholderia pseudomallei isolated from a single soil sample collected in Thailand.
Roe Chandler et al. PLoS neglected tropical diseases 2022 2 (2) e0010172 -
Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations.
Williamson Charles Hall Davis et al. Microbial genomics 2022 2 (2) -
Molecular Characterization of Carbapenem-Resistant Enterobacterales Collected in the United States.
Karlsson Maria et al. Microbial drug resistance (Larchmont, N.Y.) 2022 2
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IS26 Veers Genomic Plasticity and Genetic Rearrangement toward Carbapenem Hyperresistance under Sublethal Antibiotics.
Wei Da-Wei et al. mBio 2022 2 e0334021 -
Drug-Resistant Characteristics, Genetic Diversity, and Transmission Dynamics of Rifampicin-Resistant Mycobacterium tuberculosis in Hunan, China, Revealed by Whole-Genome Sequencing.
He Wencong et al. Microbiology spectrum 2022 2 e0154321 -
Genomic and phenotypic analyses of diverse non-clinical Acinetobacter baumannii strains reveals strain-specific virulence and resistance capacity.
Hamidian Mohammad et al. Microbial genomics 2022 2 (2) -
Genomic Analysis of Multidrug-Resistant Enterococcus faecium Harboring vanA Gene from Wastewater Treatment Plants.
Farias Beatriz Oliveira de et al. Microbial drug resistance (Larchmont, N.Y.) 2022 2
DETECTION / DIAGNOSIS
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Whole genome sequencing-based classification of human-related Haemophilus species and detection of antimicrobial resistance genes.
Diricks Margo et al. Genome medicine 2022 2 (1) 13 -
Monitoring SARS-CoV-2 in wastewater during New York City's second wave of COVID-19: Sewershed-level trends and relationships to publicly available clinical testing data
Hoar C, et al. medRxiv, Feb 9, 2022.
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Development of a T cell-based immunodiagnostic system to effectively distinguish SARS-CoV-2 infection and COVID-19 vaccination status
Yu ED, et al. Cell Host Microbe, Feb 9, 2022. -
Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences.
O'Toole Áine et al. BMC genomics 2022 2 (1) 121 -
Co-infection with SARS-COV-2 Omicron and Delta Variants Revealed by Genomic Surveillance
Rockett RJ, et al. medRxiv, Feb 15, 2022. -
Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern.
Abdulnoor Mariana et al. Microbiology spectrum 2022 2 e0068121 -
Genomic Surveillance for SARS-CoV-2 Variants: Predominance of the Delta (B.1.617.2) and Omicron (B.1.1.529) Variants - United States, June 2021-January 2022.
Lambrou Anastasia S et al. MMWR. Morbidity and mortality weekly report 2022 2 (6) 206-211
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Epidemiological and clinical insights from SARS-CoV-2 RT-PCR crossing threshold values, France, January to November 2020.
Alizon Samuel et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2022 2 (6) -
Baseline HIV drug resistance testing: 12 U.S. jurisdictions, 2014-2019.
Hugueley Brandon et al. AIDS (London, England) 2022 2
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Collaborative Mining of Whole Genome Sequences for Intelligent HIV-1 Sub-Strain(s) Discovery.
Ekpenyong Moses E et al. Current HIV research 2022 2 -
Tracking ebolavirus genomic drift with a resequencing microarray.
Tiper Irina et al. PloS one 2022 2 (2) e0263732 -
Biennial surveillance of Plasmodium falciparum anti-malarial drug resistance markers in Democratic Republic of Congo, 2017 and 2019.
Yobi Doudou M et al. BMC infectious diseases 2022 2 (1) 145
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Shotgun metagenome sequencing of a Sudanese toombak snuff tobacco: genetic attributes of a high tobacco-specific nitrosamine containing smokeless tobacco product.
Tyx R E et al. Letters in applied microbiology 2021 12 (3) 444-451
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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First outbreak of multi-drug resistant tuberculosis (MDR-TB) in Denmark involving six Danish-born cases.
Suppli Camilla Hiul et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2022 2 -
Model-based analysis of tuberculosis genotype clusters in the United States reveals high degree of heterogeneity in transmission, and state-level differences across California, Florida, New York, and Texas.
Shrestha Sourya et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 2
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Genomic Epidemiology Suggests Community Origins of Healthcare-Associated USA300 MRSA.
Thiede Stephanie N et al. The Journal of infectious diseases 2022 2 -
Transmission Of Tuberculosis Among illicit drug use Linkages (TOTAL): A cross-sectional observational study protocol using respondent driven sampling.
Carney Tara et al. PloS one 2022 2 (2) e0262440 -
A Community Outbreak of Legionnaires' Disease with Two Strains of L. pneumophila Serogroup 1 Linked to an Aquatic Therapy Centre.
Rousseau Cyril et al. International journal of environmental research and public health 2022 2 (3)
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Invasive pneumococcal disease clusters disproportionally impact persons experiencing homelessness, injecting drug users, and the western United States.
Beall Bernard et al. The Journal of infectious diseases 2022 2
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Household transmission of SARS-CoV-2 Alpha variant - United States, 2021.
Donnelly Marisa A P et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 2
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Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak.
Siddle Katherine J et al. Cell 2022 1 (3) 485-492.e10 -
Secondary attack rates in primary and secondary school bubbles following a confirmed case: Active, prospective national surveillance, November to December 2020, England.
Powell Annabel A et al. PloS one 2022 2 (2) e0262515 -
Generation time of the alpha and delta SARS-CoV-2 variants: an epidemiological analysis
Hart WS, et al. Lancet Infect Dis, Feb 14, 2022. -
Investigation of SARS-CoV-2 Transmission Associated With a Large Indoor Convention--New York City, November-December 2021
Sami S, et al. MMWR, Feb 18, 2022.
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Notes from the Field: Outbreak of COVID-19 Among a Highly Vaccinated Population Aboard a U.S. Navy Ship After a Port Visit--Reykjavik, Iceland, July 2021
Servies T, et al. MMWR, Feb 18, 2022.
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Linked nosocomial COVID-19 outbreak in three facilities for people with intellectual and developmental disabilities due to SARS-CoV-2 variant B.1.1.519 with spike mutation T478K in the Netherlands.
Gorgels Koen M F et al. BMC infectious diseases 2022 2 (1) 139
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Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study
Stirrup O, et al. medRxiv, Feb 13, 2022.
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Persistence of SARS-CoV-2 immunity, Omicron's footprints, and projections of epidemic resurgences in South African population cohorts
Sun K, et al. medRxiv, Feb 13, 2022.
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Initial analysis of viral dynamics and circulating viral variants during the mRNA-1273 Phase 3 COVE trial
Pajon R, et al. Nat Med. 2022 Feb 10. -
Waning 2-Dose and 3-Dose Effectiveness of mRNA Vaccines Against COVID-19-Associated Emergency Department and Urgent Care Encounters and Hospitalizations Among Adults During Periods of Delta and Omicron Variant Predominance--VISION Network, 10 States, August 2021-January 2022
Ferdinands JM, et al. MMWR, Feb 11, 2022.
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Effectiveness of BNT162b2 (Pfizer-BioNTech) mRNA Vaccination Against Multisystem Inflammatory Syndrome in Children Among Persons Aged 12-18 Years - United States, July-December 2021.
Zambrano Laura D et al. MMWR. Morbidity and mortality weekly report 2022 1 (2) 52-58
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Design of a mutation-integrated trimeric RBD with broad protection against SARS-CoV-2.
Liang Yu et al. Cell discovery 2022 2 (1) 17 -
Evaluating stability of attenuated Sabin and two novel type 2 oral poliovirus vaccines in children.
Wahid Rahnuma et al. NPJ vaccines 2022 2 (1) 19
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A multipathogen DNA vaccine elicits protective immune responses against two class A bioterrorism agents, anthrax and botulism.
Kim Na Young et al. Applied microbiology and biotechnology 2022 2
HOST-MICROBE INTERACTIONS
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Genome-scale CRISPR screens identify host factors that promote human coronavirus infection.
Grodzki Marco et al. Genome medicine 2022 1 (1) 10 -
Challenges and future directions for studying effects of host genetics on the gut microbiome.
Sanna Serena et al. Nature genetics 2022 2 (2) 100-106 -
Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2.
Foix Anna et al. PLoS computational biology 2022 2 (2) e1009726
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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