Advanced Molecular Detection Clips Content (Published on 08/12/2021)
NEWS
-
Science Academies from G20 Nations Urge Their Governments to Promote Creation of Global Surveillance Network to Detect Early Signs of Potential Future Pandemics
NASEM, Aug 6, 2021. -
The Delta Variant Isn't As Contagious As Chickenpox. But It's Still Highly Contagious
Doucleff N. NPR, Aug 11, 2021. -
The U.K.'s Delta Surge Is Collapsing. Will Ours?
Wallace-Wells D. New York Magazine, Aug 1, 2021. -
How the pandemic now ends
Yong E. Atlantic, Aug 12, 2021.
EVENTS / TRAINING / WEB RESOURCES
-
Ten simple rules for teaching applied programming in an authentic and immersive online environment.
Hooley Frances et al. PLoS computational biology 2021 8 (8) e1009184 -
sandbox.bio: Interactive bioinformatics tutorials
Aboukhalil R.
CONCEPTS / COMMENTS
-
Preventing zoonotic pandemics--are we there yet?
Gruber K. Lancet Microbe, Aug 3, 2021. -
The Relevance of Genomic Epidemiology for Control of Tuberculosis in West Africa.
Asare Prince et al. Frontiers in public health 2021 8 706651 -
Genomic surveillance to combat COVID-19: challenges and opportunities
Robishaw JD, et al. Lancet Microbe, Jul 27, 2021. -
Jumping a Moving Train: SARS-CoV-2 Evolution in Real Time.
Moustafa Ahmed M et al. Journal of the Pediatric Infectious Diseases Society 2021 8 -
Key variables affecting genetic distance calculations in genomic epidemiology
Coll F. Lancet Microbe, Aug 6, 2021.
METHODS / TOOLS
-
A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes.
VanOeffelen Margo et al. Briefings in bioinformatics 2021 8 -
INGOT-DR: an interpretable classifier for predicting drug resistance in M. tuberculosis.
Zabeti Hooman et al. Algorithms for molecular biology : AMB 2021 8 (1) 17 -
ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.
Dovrolis Nikolas et al. PLoS computational biology 2021 8 (8) e1009304 -
Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool
O'Toole A, et al. Virus Evol, Jul 30, 2021. -
A deep learning model for predicting next-generation sequencing depth from DNA sequence.
Zhang Jinny X et al. Nature communications 2021 7 (1) 4387 -
Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing.
Stüder François et al. Scientific reports 2021 8 (1) 15869 -
Development of a reproducible method for monitoring SARS-CoV-2 in wastewater.
Palmer Emma J et al. The Science of the total environment 2021 8 149405 -
Sars-CoV-2 Genome Sequencing Methods Differ In Their Ability To Detect Variants From Low Viral Load Samples.
Lam C et al. Journal of clinical microbiology 2021 8 JCM0104621 -
Human Papillomavirus Detection by Whole-Genome Next-Generation Sequencing: Importance of Validation and Quality Assurance Procedures.
Mühr Laila Sara Arroyo et al. Viruses 2021 8 (7)
EVOLUTION / ECOLOGY / POPULATIONS
-
Changing epidemiology of vancomycin-resistant Enterococcus faecium: Results of a genome-based study at a regional neurological acute hospital with intensive care and early rehabilitation treatment.
Falgenhauer Linda et al. Infection prevention in practice 2021 8 (2) 100138 -
Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021.
Franceschi Vinícius Bonetti et al. Virus research 2021 8 198532 -
Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database
Zelenova M, et al. bioRxiv, Aug 4, 2021. -
SARS-CoV-2 Variants in Immunocompromised Patient Given Antibody Monotherapy.
Truffot Aurélie et al. Emerging infectious diseases 2021 8 (10) -
The emergence of highly fit SARS-CoV-2 variants accelerated by recombination
Garvin MR, et al. bioRxiv, Aug 8, 2021. -
Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York.
Anthony P West et al. Nat Commun 2021 8 (1) 4886 -
Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2.
Patiño-Galindo Juan Ángel et al. Genome medicine 2021 8 (1) 124 -
Genomic analysis reveals a rapid spread and predominance of Lambda (C.37) SARS-COV-2 lineage in Peru despite circulation of variants of concern.
Padilla-Rojas Carlos et al. Journal of medical virology 2021 8 -
A novel SARS-CoV-2 related coronavirus with complex recombination isolated from bats in Yunnan province, China.
Li Li-Li et al. Emerging microbes & infections 2021 8 1-22 -
An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic.
Kumar Sudhir et al. Molecular biology and evolution 2021 5 (8) 3046-3059 -
Dominance of alpha and Iota variants in SARS-CoV-2 vaccine breakthrough infections in New York City.
Duerr Ralf et al. The Journal of clinical investigation 2021 8 -
Phylogenetic analysis of SARS-CoV-2 lineage development across the first and second waves in Eastern Germany in 2020: insights into the cause of the second wave.
Yi Buqing et al. Epidemiology and infection 2021 7 e177 -
Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-CoV-2 variants.
Tchesnokova Veronika et al. Journal of clinical microbiology 2021 8 JCM0092121 -
Transient transmission of Chikungunya virus in Singapore exemplifies successful mitigation of severe epidemics in a vulnerable population.
Hapuarachchi Hapuarachchige Chanditha et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 8 -
Characterizing genetic and antigenic divergence from vaccine strain of influenza A and B viruses circulating in Thailand, 2017-2020.
Suntronwong Nungruthai et al. Scientific reports 2021 1 (1) 735 -
Elucidation of Early Evolution of HIV-1 Group M in the Congo Basin Using Computational Methods.
Tongo Marcel et al. Genes 2021 5 (4) -
Viral intra-host evolution in immunocompetent children contributes to human norovirus diversification at the global scale.
Tohma Kentaro et al. Emerging microbes & infections 2021 8 1-56 -
Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade.
Guzmán-Solís Axel A et al. eLife 2021 8 -
West Nile Virus in Brazil.
Costa Érica Azevedo et al. Pathogens (Basel, Switzerland) 2021 8 (7) -
Identification, Genetic Characterization and Validation of Highly Diverse HIV-1 Viruses for Reference Panel Development.
Zhao Jiangqin et al. Viruses 2021 8 (7) -
Epidemiological and phylogenetic analysis for non-B subtypes of human immunodeficiency virus type 1 in Busan, Korea.
Lee Jeong Eun et al. Scientific reports 2021 8 (1) 16000 -
Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration.
Berger Duncan J et al. Nature communications 2021 8 (1) 4776 -
Comparative Genomic and Transcriptomic Analysis of Naegleria fowleri Clinical and Environmental Isolates.
Joseph Sandeep J et al. mSphere 2021 8 e0063721
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
-
The Resistome and Mobilome of Multidrug-Resistant Staphylococcus sciuri C2865 Unveil a Transferable Trimethoprim Resistance Gene, Designated dfrE, Spread Unnoticed.
Gómez-Sanz Elena et al. mSystems 2021 8 e0051121 -
Population Genomics of emm4 Group A Streptococcus Reveals Progressive Replacement with a Hypervirulent Clone in North America.
DebRoy Sruti et al. mSystems 2021 8 e0049521 -
Imipenem-Relebactam Susceptibility and Genotypic Characteristics of Carbapenem-Resistant Enterobacterales (CRE) Identified during Population-Based Surveillance.
Horwich-Scholefield Sam et al. Antimicrobial agents and chemotherapy 2021 8 AAC0228820 -
Whole Genome Analysis of Three Multi-Drug Resistant Listeria innocua and Genomic Insights Into Their Relatedness With Resistant Listeria monocytogenes.
Li Menghan et al. Frontiers in microbiology 2021 8 694361 -
Emergence and Clonal Spread of CTX-M-65-Producing Escherichia coli From Retail Meat in Portugal.
Leão Célia et al. Frontiers in microbiology 2021 8 653595 -
The Epistatic Landscape of Antibiotic Resistance of Different Clades of Mycobacterium tuberculosis.
Muzondiwa Dillon et al. Antibiotics (Basel, Switzerland) 2021 8 (7) -
Evaluation of Virulence Determinants Using Whole-Genome Sequencing and Phenotypic Biofilm Analysis of Outbreak-Linked Staphylococcus aureus Isolates.
Hait Jennifer M et al. Frontiers in microbiology 2021 8 687625 -
A Comparative Transcriptome Between Anti-drug Sensitive and Resistant Candida auris in China.
Zhou Wenkai et al. Frontiers in microbiology 2021 8 708009 -
Genomic Diversity of Azole-Resistant Aspergillus fumigatus in the United States.
Etienne Kizee A et al. mBio 2021 8 e0180321
DETECTION / DIAGNOSIS
-
Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination.
Jacob Christopher G et al. eLife 2021 8 -
Prediction of species composition ratios in pooled specimens of the Anopheles Hyrcanus group using quantitative sequencing.
Lee Do Eun et al. Malaria journal 2021 8 (1) 338 -
Centre-specific bacterial pathogen typing affects infection-control decision making.
Coolen Jordy P M et al. Microbial genomics 2021 8 (8) -
Spatially resolved qualified sewage spot sampling to track SARS-CoV-2 dynamics in Munich - One year of experience.
Rubio-Acero Raquel et al. The Science of the total environment 2021 8 149031 -
Development and evaluation of an outbreak surveillance system integrating whole genome sequencing data for non-typhoidal Salmonella in London and South East of England, 2016-17.
Paranthaman Karthik et al. Epidemiology and infection 2021 7 e164 -
Environmental Surveillance for Risk Assessment in the Context of a Phase 2 Clinical Trial of Type 2 Novel Oral Polio Vaccine in Panama.
Rojas-Bonilla Magda et al. Viruses 2021 8 (7) -
Detection of SARS-CoV-2 on Surfaces in Households of Persons with COVID-19.
Perrine Marcenac et al. Int J Environ Res Public Health 2021 8 (15) -
Lessons learned from SARS-CoV-2 measurements in wastewater.
Sharkey Mark E et al. The Science of the total environment 2021 8 149177 -
Variant Analysis of SARS-CoV-2 Genomes from Belgian Military Personnel Engaged in Overseas Missions and Operations.
Pirnay Jean-Paul et al. Viruses 2021 8 (7) -
Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance.
Zelyas Nathan et al. Microbiology spectrum 2021 8 e0031521 -
Key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria: a systematic analysis
Gorrie CL, et al. Lancet Microbe, Aug 6, 2021. -
Machine learning detects SARS-CoV-2 and variants rapidly on DNA aptamer metasurfaces
Torun H, et al. medRxiv, Aug 8, 2021. -
Population normalisation in wastewater-based epidemiology for improved understanding of SARS-CoV-2 prevalence: A multi-site study
Sweetapple C, et al. medRxiv, Aug 5, 2021. -
Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants.
de Puig Helena et al. Science advances 2021 8 (32) -
Quantitative SARS-CoV-2 tracking of variants Delta, Delta plus, Kappa and Beta in wastewater by allele-specific RT-qPCR
Lee WL, et al. medRxiv, Aug 6, 2021. -
Impact of COVID-19 pre-test probability on positive predictive value of high cycle threshold SARS-CoV-2 real-time reverse transcription PCR test results.
Gubbay Jonathan B et al. Infection control and hospital epidemiology 2021 8 1-18 -
Global patterns of submicroscopic Plasmodium falciparum malaria infection: insights from a systematic review and meta-analysis of population surveys
Whittaker C, et al. Lancet Microbe, May 25, 2021.
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
-
Ongoing diphtheria outbreak in Yemen: a cross-sectional and genomic epidemiology study
Badell E, et al. Lancet Microbe, May 26, 2021. -
Uncovering the novel Enterobacter cloacae complex species responsible for septic shock deaths in newborns: a cohort study
Girlich D, et al. Lancet Microbe, Jul 23, 2021. -
The First Reported Outbreak of an Undetermined Species of Human Infection with Spotted Fever Group Rickettsia in Lu'an, China.
Lyu Yong et al. Acta tropica 2021 8 106072 -
Notes from the Field: Recurrence of a Multistate Outbreak of Salmonella Typhimurium Infections Linked to Contact with Hedgehogs - United States and Canada, 2020.
Waltenburg Michelle A et al. MMWR. Morbidity and mortality weekly report 2021 8 (32) 1100-1102 -
Emergence of an early SARS-CoV-2 epidemic in the United States
Zeller M, et al. Cell, Jul 26, 2021. -
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters
Gallego-Garcia P, et al. medRxiv, Aug 9, 2021. -
Serial intervals in SARS-CoV-2 B.1.617.2 variant cases
Pung R, et al. Lancet, Aug 10, 2021. -
Transmission of SARS-CoV-2 Delta Variant Among Vaccinated Healthcare Workers, Vietnam
Chau NV, et al. SSRN, Aug 10, 2021. -
Rapid Increase in Circulation of the SARS-CoV-2 B.1.617.2 (Delta) Variant - Mesa County, Colorado, April-June 2021.
Herlihy Rachel et al. MMWR. Morbidity and mortality weekly report 2021 8 (32) 1084-1087 -
Outbreak or pseudo-outbreak? Integrating SARS-CoV-2 sequencing to validate infection control practices in a dialysis facility.
Pfaff Bridget L et al. American journal of infection control 2021 8 -
Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection Cases Corroborated by Sequencing.
Massachi Jonathan et al. The American journal of tropical medicine and hygiene 2021 8 -
Phylogenetic and Phylodynamic Analyses of HCV Strains Circulating among Patients Using Injectable Drugs in Central Italy.
Minosse Claudia et al. Microorganisms 2021 8 (7) -
Cuban history of CRF19 recombinant subtype of HIV-1.
Zhukova Anna et al. PLoS pathogens 2021 8 (8) e1009786 -
Norovirus Foodborne Outbreak Associated With the Consumption of Ice Pop, Southern Brazil, 2020.
Fumian Tulio Machado et al. Food and environmental virology 2021 8 -
Phylogenetic Analysis of the 2020 West Nile Virus (WNV) Outbreak in Andalusia (Spain).
Casimiro-Soriguer Carlos S et al. Viruses 2021 6 (5)
ANTIMICROBIALS / VACCINES / INTERVENTIONS
-
Phylogenomics and antimicrobial resistance of Salmonella Typhi and Paratyphi A, B and C in England, 2016-2019.
Chattaway Marie Anne et al. Microbial genomics 2021 8 (8) -
Effectiveness of Covid-19 Vaccines against the B.1.617.2 (Delta) Variant.
Lopez Bernal Jamie et al. The New England journal of medicine 2021 7 (7) 585-594 -
Comparison of two highly-effective mRNA vaccines for COVID-19 during periods of Alpha and Delta variant prevalence
Puranik A, et al. medRxiv, Aug 8, 2021. -
Effectiveness of COVID-19 Vaccines in Preventing Hospitalization Among Adults Aged ≥65 Years - COVID-NET, 13 States, February-April 2021.
Moline Heidi L et al. MMWR. Morbidity and mortality weekly report 2021 8 (32) 1088-1093 -
Genetic diversity in two leading Plasmodium vivax malaria vaccine candidates AMA1 and MSP119 at three sites in India.
Kale Sonal et al. PLoS neglected tropical diseases 2021 8 (8) e0009652
HOST-MICROBE INTERACTIONS
-
Deconvoluting complex correlates of COVID19 severity with local ancestry inference and viral phylodynamics: Results of a multiomic pandemic tracking strategy
Parikh VN, et al. medRxiv, Aug 8, 2021. -
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19.
Ziegler Carly G K et al. Cell 2021 8 -
The Molecular Evolution of Type 2 Vaccine-Derived Polioviruses in Individuals with Primary Immunodeficiency Diseases.
Kitamura Kouichi et al. Viruses 2021 8 (7)
![Brand](/GAPPKB/images/CDC_author.jpg)
![Brand](/GAPPKB/images/implementation.jpg)
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:Feb 1, 2024
- Page last updated:Jul 25, 2024