Advanced Molecular Detection Clips Content (Published on 08/05/2021)
NEWS
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Unraveling the Mysterious Mutations That Make Delta the Most Transmissible COVID Virus Yet
Szabo L. Medscape, Jul 28, 2021. -
More Variants Are Coming. The U.S. Isn't Ready
Koons C. Bloomberg, Jul 24, 2021. -
The coronavirus is rife in common US deer
Mallapaty S. Nature, Aug 2, 2021. -
Those Virus Sequences That Were Suddenly Deleted? They're Back
Zimmer C. New York Times, Jul 30, 2021. -
Singapore-MIT Alliance Shows Benefits of Wastewater SARS-CoV-2 Variant Test
Johnson M. GenomeWeb, Jul 30, 2021. -
The overlooked superpower of mRNA vaccines
Wadman M. Science, Jul 30, 2021. -
Vaccination Alone Won't Counter Rise of Resistant Variants: Study
Lewis R. Medscape, Jul 30, 2021. -
No shortcuts to SARS-CoV-2 antivirals
Edwards A, Hartung IV. Science, Jul 30, 2021. -
Hundreds of AI tools have been built to catch covid. None of them helped.
Heaven WD. MIT Tech Review, Jul 30, 2021.
EVENTS / TRAINING / WEB RESOURCES
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Protocols for SARS-CoV-2 detection from wastewater
protocols.io, accessed Aug 5, 2021.
CONCEPTS / COMMENTS
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An implementation science approach to evaluating pathogen whole genome sequencing in public health.
Ferdinand Angeline S et al. Genome medicine 2021 7 (1) 121
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Can Science Help Resolve the Controversy on the Origins of the SARS-CoV-2 Pandemic?
Casadevall Arturo et al. mBio 2021 8 e0194821 -
Genomic surveillance to combat COVID-19: challenges and opportunities.
Robishaw Janet D et al. The Lancet. Microbe 2021 8
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Improving Pandemic Response: Employing Mathematical Modeling to Confront COVID-19.
Biggerstaff Matthew et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 8
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Understanding why superspreading drives the COVID-19 pandemic but not the H1N1 pandemic
Chen PZ, et al. Lancet Infect Dis, Aug 2, 2021. -
COVID-19, the first pandemic in the post-genomic era
van Dorp L, et al. Current Opinion in Virology. 2021;50:40-48.
METHODS / TOOLS
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COPLA, a taxonomic classifier of plasmids.
Redondo-Salvo Santiago et al. BMC bioinformatics 2021 8 (1) 390
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STRONG: metagenomics strain resolution on assembly graphs.
Quince Christopher et al. Genome biology 2021 7 (1) 214 -
Generalizable characteristics of false-positive bacterial variant calls.
Bush Stephen J et al. Microbial genomics 2021 8 (8)
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An alternative approach for bioanalytical assay optimization for wastewater-based epidemiology of SARS-CoV-2.
Boogaerts Tim et al. The Science of the total environment 2021 7 148043 -
Assessment of SARS-CoV-2 genome sequencing: quality criteria and low frequency variants.
Jacot Damien et al. Journal of clinical microbiology 2021 7 JCM0094421
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poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing
Brandt C, et al. Front Genet, Jul 28, 2021. -
Prevalence of COVID-19 genomic variation in Africa: a living systematic review protocol.
Adjei George et al. JBI evidence synthesis 2021 8
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Chainchecker: An application to visualise and explore transmission chains for Ebola virus disease.
Gaythorpe Katy et al. PloS one 2021 2 (2) e0247002
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Skin Metagenomic Sequence Analysis of Early Candida auris Outbreaks in U.S. Nursing Homes.
Huang Xin et al. mSphere 2021 8 e0028721
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An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples.
et al. Wellcome open research 2021 7 42
EVOLUTION / ECOLOGY / POPULATIONS
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Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction.
Senghore Madikay et al. Microbial genomics 2021 7 (7)
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Whole-Genome Comparative Analysis Reveals Association Between Salmonella Genomic Variation and Egg Production Systems.
Sodagari Hamid Reza et al. Frontiers in veterinary science 2021 7 666767 -
SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts.
Tasakis Rafail Nikolaos et al. PloS one 2021 7 (7) e0255169 -
Occupational and environmental exposure to SARS-CoV-2 in and around infected mink farms.
de Rooij Myrna M T et al. Occupational and environmental medicine 2021 8
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Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2
Laiton-Donato K, et al. medRxiv, Aug 2, 2021. -
Molecular Phylogenesis and Spatiotemporal Spread of SARS-CoV-2 in Southeast Asia
Zhu M, et al. Front Pub Health, Jul 30, 2021. -
SARS-CoV-2 Variants in Patients with Immunosuppression.
Corey Lawrence et al. The New England journal of medicine 2021 8 (6) 562-566 -
Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains.
Rella Simon A et al. Scientific reports 2021 8 (1) 15729
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Emergence and spread of a B.1.1.28-derived P.6 lineage with Q675H and Q677H Spike mutations in Uruguay
Rego N, et al. medRxiv, Jul 31, 2021. -
Effects of SARS-CoV-2 P.1 introduction and the impact of COVID-19 vaccination on the epidemiological landscape of Sao Jose Do Rio Preto, Brazil
Banho CA, et al. medRxiv, Jul 31, 2021.
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Genomic epidemiology of SARS-CoV-2 divulge B.1, B.1.36, and B.1.1.7 as the most dominant lineages in first, second, and third wave of SARS-CoV-2 infections in Pakistan
Basheer A, Zahoor I. medRxiv, Jul 30, 2021. -
Molecular typing of human adenoviruses among hospitalized patients with respiratory tract infections in a tertiary Hospital in Guangzhou, China between 2017 and 2019.
Wang Xinye et al. BMC infectious diseases 2021 8 (1) 748
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Using a public database of Neisseria gonorrhoeae genomes to detect mutations associated with zoliflodacin resistance.
Adamson Paul C et al. The Journal of antimicrobial chemotherapy 2021 7 -
The genomic epidemiology of multi-drug resistant invasive non-typhoidal Salmonella in selected sub-Saharan African countries.
Park Se Eun et al. BMJ global health 2021 8 (8)
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Analysis of Virulence and Antimicrobial Resistance Gene Carriage in Staphylococcus aureus Infections in Equids Using Whole-Genome Sequencing.
Little Sara V et al. mSphere 2021 8 e0019620 -
Progressive Increase in Virulence of Novel SARS-CoV-2 Variants in Ontario, Canada
Fisman D, Tuite A. medRxiv, Aug 4, 2021. -
SARS-CoV-2 Lambda variant exhibits higher infectivity and immune resistance
Kimura I, et al. bioRxiv, Jul 28, 2021.
DETECTION / DIAGNOSIS
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Application of Whole-Genome Sequencing in the National Molecular Tracing Network for Foodborne Disease Surveillance in China.
Li Weiwei et al. Foodborne pathogens and disease 2021 8
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Identification of Streptococcus pseudopneumoniae and other mitis group streptococci using matrix assisted laser desorption/ionization - time of flight mass spectrometry.
Jensen Christian Salgård et al. Diagnostic microbiology and infectious disease 2021 8 (3) 115487 -
Genomic Epidemiology of Multidrug-Resistant Nontyphoidal Salmonella in Young Children Hospitalized for Gastroenteritis.
Woh Pei Yee et al. Microbiology spectrum 2021 8 e0024821 -
Monitoring COVID-19 spread in Prague local neighborhoods based on the presence of SARS-CoV-2 RNA in wastewater collected throughout the sewer network
Zdenkova K, et al. medRxiv, Jul 31, 2021. -
The Dual/Global Value of SARS-CoV-2 Genome Surveillance on Migrants Arriving to Europe via the Mediterranean Routes.
Marotta Claudia et al. Annals of global health 2021 7 (1) 71
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Rapid detection of SARS-CoV-2 with CRISPR-Cas12a.
Xiong Dan et al. PLoS biology 2020 12 (12) e3000978 -
Quantitative SARS-CoV-2 Alpha Variant B.1.1.7 Tracking in Wastewater by Allele-Specific RT-qPCR
Lee WL, et al. Environ Sci Technol Lett, Jul 18, 2021. -
Rabies virus in slaughtered dogs for meat consumption in Ghana: A potential risk for rabies transmission.
Tasiame William et al. Transboundary and emerging diseases 2021 8 -
Application of shotgun metagenomics sequencing and targeted sequence capture to detect circulating porcine viruses in the Dutch-German border region.
Schuele Leonard et al. Transboundary and emerging diseases 2021 8 -
First Case Report of an Unusual Fungus (Sporopachydermia lactativora) Associated with a Pulmonary Infection in a Drug Injection User.
Al Dallal Hiba A et al. Clinical pathology (Thousand Oaks, Ventura County, Calif.) 2021 8 2632010X211029970
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Smartphone-based DNA diagnostics for malaria detection using deep learning for local decision support and blockchain technology for security
Guo X, et al. Nat Electronics, Aug 2, 2021.
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Genomic Characterization of Strains From a Cluster of Infant Botulism Type A in a Small Town in Colorado, United States.
Gladney Lori et al. Frontiers in microbiology 2021 7 688240
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Human-to-Cattle Mycobacterium tuberculosis Complex Transmission in the United States.
Jason E Lombard et al. Front Vet Sci 2021 7 691192
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A Legionnaires' Disease Cluster in a Private Building in Italy.
Ricci Maria Luisa et al. International journal of environmental research and public health 2021 7 (13)
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Genetic source tracking of human plague cases in Inner Mongolia-Beijing, 2019.
Li Jianyun et al. PLoS neglected tropical diseases 2021 8 (8) e0009558 -
Outbreak of SARS-CoV-2 Infections, Including COVID-19 Vaccine Breakthrough Infections, Associated with Large Public Gatherings - Barnstable County, Massachusetts, July 2021.
Brown Catherine M et al. MMWR. Morbidity and mortality weekly report 2021 8 (31) 1059-1062
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Overlapping of Independent SARS-CoV-2 Nosocomial Transmissions in a Complex Outbreak.
Pérez-Lago Laura et al. mSphere 2021 8 e0038921
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Vaccine breakthrough infection and onward transmission of SARS-CoV-2 Beta (B.1.351) variant, Bavaria, Germany, February to March 2021.
Kroidl Inge et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 7 (30) -
Epidemiological data and genome sequencing reveals that nosocomial transmission of SARS-CoV-2 is underestimated and mostly mediated by a small number of highly infectious individuals.
Lumley Sheila F et al. The Journal of infection 2021 8 -
Genomic epidemiology and transmission dynamics of SARS-CoV-2 in congregate healthcare facilities in Santa Clara County, California.
MacCannell Tara et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 7
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Estimates of Single Dose and Full Dose BNT162b2 Vaccine Effectiveness among USAF Academy cadets, 1 Mar - 1 May 2021
Wickert DP, et al. medRxiv, Jul 31, 2021.
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Impact of B.1.351 (beta) SARS-CoV-2 variant on BNT162b2 mRNA vaccine effectiveness in long-term care facilities of eastern France: a retrospective cohort study
LeFevre B, et al. medRxiv, Jul 31, 2021.
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Assessment of genetic changes and neurovirulence of shed Sabin and novel type 2 oral polio vaccine viruses.
Wahid Rahnuma et al. NPJ vaccines 2021 7 (1) 94
HOST-MICROBE INTERACTIONS
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Ancient DNA Study in Medieval Europeans Shows an Association Between HLA-DRB1*03 and Paratyphoid Fever.
Haller Magdalena et al. Frontiers in immunology 2021 8 691475 -
The trans-omics landscape of COVID-19.
Wu Peng et al. Nature communications 2021 7 (1) 4543 -
Cross-reactive antibodies against human coronaviruses and the animal coronavirome suggest diagnostics for future zoonotic spillovers.
Klompus Shelley et al. Science immunology 2021 7 (61) -
Integrative genomic analyses identify susceptibility genes underlying COVID-19 hospitalization.
Pathak Gita A et al. Nature communications 2021 7 (1) 4569 -
Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine.
Heinken Almut et al. Annual review of microbiology 2021 7
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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