Advanced Molecular Detection Clips Content (Published on 03/10/2022)
NEWS
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Public health experts sketch a roadmap to get from the Covid pandemic to the "next normal"
Branswell H. STAT, Mar 7, 2022. -
Monitoring chronic coronavirus infections may help forecast new variant threats, study suggests
Pelley L. CBC News, Mar 5, 2022. -
Health groups press for more wildlife SARS-CoV-2 tracking
Schnirring L. CIDRAP, Mar 7, 2022. -
Why Do Some People Never Get Covid?
Lamas DJ. New York Times, March 8, 2022. -
Wide-ranging genetic study of severe COVID finds common risk factors
Kreier F. Nature, Mar 10, 2022.
EVENTS / TRAINING / WEB RESOURCES
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Visualization types
(website) Data Visualization Standards, US Census Bureau.
CONCEPTS / COMMENTS
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Molecular mechanisms and drivers of pathogen emergence.
Balasubramanian Deepak et al. Trends in microbiology 2022 3 -
Editorial: The Transition Era to New Sequencing Technologies and Their Application to Integrative Omics in Molecular Surveillance.
Hölzer Martin et al. Frontiers in genetics 2022 3 840782 -
25 years of surveillance of drug-resistant tuberculosis: achievements, challenges, and way forward.
Dean Anna S et al. The Lancet. Infectious diseases 2022 3
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The changing epidemiology of SARS-CoV-2
Koelle K, et al. Science, Mar 10, 2022. -
COVID-19--lessons for zoonotic disease
Holmes EC. Science, Mar 10, 2022.
METHODS / TOOLS
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Software testing in microbial bioinformatics: a call to action
van der Putten BC, et al. Microb Genom. 2022 Mar;8(3).
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GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids.
Ebmeyer Stefan et al. Bioinformatics (Oxford, England) 2021 12 -
Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads.
Bankevich Anton et al. Nature biotechnology 2022 3 -
BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies.
Chandrakumar Induja et al. Communications biology 2022 2 (1) 151 -
Rapid genome surveillance of SARS-CoV-2 and study of risk factors using shipping container laboratories and portable DNA sequencing technology
Bilooei SF, et al. medRxiv, Feb 26, 2022.
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Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank.
Underwood Beverly A et al. Database : the journal of biological databases and curation 2022 3
EVOLUTION / ECOLOGY / POPULATIONS
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Genome analysis of Legionella pneumophila ST23 from various countries reveals highly similar strains.
Ricci Maria Luisa et al. Life science alliance 2022 3 (6) -
Population structure of ocular Streptococcus pneumoniae is highly diverse and formed by lineages that escape current vaccines.
Andre Camille et al. Microbial genomics 2022 3 (3) -
The mutational steps of SARS-CoV-2 to become like Omicron within seven months: the story of immune escape in an immunocompromised patient
Sonnleitner ST, et al. medRxiv, Mar 7, 2022. -
Intragenomic rearrangements of SARS-CoV-2 and other beta-coronaviruses
Patarca R, Haseltine WA. bioRxiv, Mar 7, 2022. -
Distribution and phylogenetics of hepatitis E virus genotype 4 in humans and animals.
Li Bingzhe et al. Zoonoses and public health 2022 3 -
Investigation of cross-regional spread and evolution of equine influenza H3N8 at US and global scales using Bayesian phylogeography based on balanced subsampling.
Lee Kyuyoung et al. Transboundary and emerging diseases 2022 3 -
Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016-2018.
Agbla Jijoho Michel et al. Virus research 2022 3 198715
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A Retrospective Overview of Zika Virus Evolution in the Midwest of Brazil.
Giovanetti Marta et al. Microbiology spectrum 2022 3 e0015522 -
Genetic and hosts characterization of hantaviruses in port areas in Hainan Province, P. R. China.
Wang Qiu-Wei et al. PloS one 2022 3 (3) e0264859 -
Echinococcus spp. and genotypes infecting humans in Tibet Autonomous Region of China: a molecular investigation with near-complete/complete mitochondrial sequences.
Zhao Yanping et al. Parasites & vectors 2022 3 (1) 75
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Genomic Insights on Variation Underlying Capsule Expression in Meningococcal Carriage Isolates From University Students, United States, 2015-2016.
Whaley Melissa J et al. Frontiers in microbiology 2022 3 815044
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Characterization of a Clostridioides difficile outbreak caused by PCR ribotype 046, associated with increased mortality.
Magnusson Cecilia et al. Emerging microbes & infections 2022 3 1-31 -
Vancomycin-resistant enterococcus bacteraemia in an endemic region: clinical features and genomic analysis: a 12-year cohort.
Abu-Lybdeh O et al. The Journal of hospital infection 2021 12 105-113 -
Whole-genome sequencing for the characterization of resistance mechanisms and epidemiology of colistin-resistant Acinetobacter baumannii.
Hahm Chorong et al. PloS one 2022 3 (3) e0264335 -
Gonococcal Clinical Strains Bearing a Common gdhR Single Nucleotide Polymorphism That Results in Enhanced Expression of the Virulence Gene lctP Frequently Possess a mtrR Promoter Mutation That Decreases Antibiotic Susceptibility.
Ayala Julio C et al. mBio 2022 3 e0027622
DETECTION / DIAGNOSIS
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Discovering disease-causing pathogens in resource-scarce Southeast Asia using a global metagenomic pathogen monitoring system.
Bohl Jennifer A et al. Proceedings of the National Academy of Sciences of the United States of America 2022 3 (11) e2115285119
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Utility of the Whole Genome Sequencing based methodologies in routine European tuberculosis reference laboratory network setting.
Holicka Yen et al. Tuberculosis (Edinburgh, Scotland) 2022 3 102185
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Mortality from drug-resistant tuberculosis in high-burden countries comparing routine drug susceptibility testing with whole-genome sequencing: a multicentre cohort study.
Zürcher Kathrin et al. The Lancet. Microbe 2022 3 (7) e320-e330
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The Use of Whole-Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States.
Stevens Eric L et al. Journal of food protection 2022 3
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Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites.
Ham Rachel E et al. medRxiv : the preprint server for health sciences 2022 3 -
Detection of the novel SARS-CoV-2 European lineage B.1.177 in Ontario, Canada.
Guthrie Jennifer L et al. Journal of clinical virology plus 2022 3 (1) 100010
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RespiCoV: Simultaneous identification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and 46 respiratory tract viruses and bacteria by amplicon-based Oxford-Nanopore MinION sequencing.
Brinkmann Annika et al. PloS one 2022 3 (3) e0264855 -
Emergence and Spread of the SARS-CoV-2 Omicron Variant in Alberta Communities Revealed by Wastewater Monitoring
Hubert CR, et al. medRxiv, Mar 10, 2022.
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Implementation of a COVID-19 Genomic Surveillance Regional Network for Latin America and Caribbean region.
Leite Juliana Almeida et al. PloS one 2022 3 (3) e0252526
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Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance.
Chung Hsing-Yi et al. Microbiology spectrum 2022 2 (1) e0251321 -
Detection of Chikungunya virus in bodily fluids: The INOVACHIK cohort study.
Martins Ezequias B et al. PLoS neglected tropical diseases 2022 3 (3) e0010242 -
Diagnostic Accuracy of Dried Plasma Spot Specimens for HIV-1 Viral Load Testing: A Systematic Review and Meta-analysis.
Fong Youyi et al. Journal of acquired immune deficiency syndromes (1999) 2021 11 (3) 261-273
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Improving Taxonomic Delimitation of Fungal Species in the Age of Genomics and Phenomics.
Stengel Ashley et al. Frontiers in microbiology 2022 3 847067 -
Investigation of Plasmodium falciparum pfhrp2 and pfhrp3 gene deletions and performance of a rapid diagnostic test for identifying asymptomatic malaria infection in northern Ethiopia, 2015.
Leonard Colleen M et al. Malaria journal 2022 3 (1) 70
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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The use of core genome multilocus sequence typing to determine the duration of vancomycin-resistant Enterococcus faecium outbreaks.
Søndergaard Knudsen Maja et al. APMIS : acta pathologica, microbiologica, et immunologica Scandinavica 2022 3
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A Whole-Genome Sequencing-Based Study to Delineate the Risk and Characteristics of Tuberculosis Transmission in an Insular Population Over 10 Years in Shanghai.
Wang Min et al. Frontiers in microbiology 2022 3 768659 -
COVID-19: Integrating genomic and epidemiological data to inform public health interventions and policy in Tasmania, Australia.
Stephens Nicola et al. Western Pacific surveillance and response journal : WPSAR 2022 3 (4) 1-9 -
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters.
Gallego-García Pilar et al. Virus evolution 2022 3 (1) veac008
HOST-MICROBE INTERACTIONS
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Gastrointestinal Microbiome Disruption and Antibiotic-Associated Diarrhea in Children Receiving Antibiotic Therapy for Community-Acquired Pneumonia.
Kwon J et al. The Journal of infectious diseases 2022 3 -
Genetic Loci Associated With COVID-19 Positivity and Hospitalization in White, Black, and Hispanic Veterans of the VA Million Veteran Program.
Peloso Gina M et al. Frontiers in genetics 2022 2 777076 -
Whole genome sequencing reveals host factors underlying critical Covid-19
Kousathanas A, et al. Nature, Mar 7, 2022. -
Proteome-wide Mendelian randomization identifies causal links between blood proteins and severe COVID-19.
Palmos Alish B et al. PLoS genetics 2022 3 (3) e1010042 -
Age-related changes in the nasopharyngeal microbiome are associated with SARS-CoV-2 infection and symptoms among children, adolescents, and young adults.
Hurst Jillian H et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 3 -
Dissecting the Role of the Human Microbiome in COVID-19 via Metagenome-assembled Genomes
Ke S, et al. bioRxiv, Mar 10, 2022. -
Homotypic protection against influenza in a pediatric cohort in Managua, Nicaragua.
Wraith Steph et al. Nature communications 2022 3 (1) 1190
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.
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- Page last updated:Sep 21, 2023
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