Advanced Molecular Detection Clips Content (Published on 04/08/2021)
NEWS
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NIH, CDC Launch Program to Provide Free Coronavirus Self-Testing
360dx, Mar 31, 2021. -
Why US coronavirus tracking can't keep up with concerning variants
Maxmen A. Nature, Apr 7, 2021. -
B117 now most common COVID-19 variant in the US
Soucheray S. CIDRAP, Apr 7, 2021. -
Covid-19 reinfections are rare--but without better data, we don?t how rare
Joseph A. STAT, Apr 7, 2021. -
Common Hospital PCR Test Affected by Viral Variant
Fiore K. MedPage Today, Apr 5, 2021. -
The CDC's $1.75 billion sequencing boom may be throwing money at the wrong problem
Ferguson C. MIT Technology Review, Apr 5, 2021. -
Researchers Are Hatching a Low-Cost Coronavirus Vaccine
Zimmer C. New York Times, Apr 5, 2021. -
As Variants Have Spread, Progress Against the Virus in U.S. Has Stalled
Leatherby L. New York Times, Apr 6, 2021.
EVENTS / TRAINING / WEB RESOURCES
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The Impact of Novel Variants of Sars-Cov-2 on Diagnostic Testing
(report, image) PHG Foundation, Mar 2021. -
Genomic surveillance in the roll out of vaccines
(blog post) Cook S. PHG Foundation, Mar 31, 2021.
CONCEPTS / COMMENTS
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Concerns about SARS-CoV-2 evolution should not hold back efforts to expand vaccination.
Cobey Sarah et al. Nature reviews. Immunology 2021 4 -
The story behind COVID-19 vaccines
Fauci AS. Science, Apr 9, 2021. -
The world must learn from COVID before diving into a pandemic treaty
(editorial) Nature, Apr 6, 2021.
METHODS / TOOLS
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Detection of plasmid contigs in draft genome assemblies using customized Kraken databases.
Gomi Ryota et al. Microbial genomics 2021 4 (4) -
Simplitigs as an efficient and scalable representation of de Bruijn graphs.
Brinda Karel et al. Genome biology 2021 4 (1) 96 -
Complete Whole Genome Sequences of Escherichia coli Surrogate Strains and Comparison of Sequence Methods with Application to the Food Industry
Therrien DA, et al. Microorganisms. 2021 Mar 16;9(3):608. -
covid19.Explorer: A web application and R package to explore United States COVID-19 data
Revell LJ. medRxiv, Apr 4, 2021. -
Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing.
Tourancheau Alan et al. Nature methods 2021 4
EVOLUTION / ECOLOGY / POPULATIONS
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Population structure, case clusters, and genetic lesions associated with Canadian Salmonella 4,[5],12:i:- isolates.
Clark Clifford G et al. PloS one 2021 4 (4) e0249079 -
Genomic diversity and molecular epidemiology of Pasteurella multocida.
Smith Emily et al. PloS one 2021 4 (4) e0249138 -
Dynamics of intestinal multidrug-resistant bacteria colonisation contracted by visitors to a high-endemic setting: a prospective, daily, real-time sampling study.
Kantele Anu et al. The Lancet. Microbe 2021 4 (4) e151-e158 -
Colonization dynamics of Klebsiella pneumoniae in the pet animals and human owners in a single household.
Chen Chih-Ming et al. Veterinary microbiology 2021 4 109050 -
Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts.
Valesano Andrew L et al. PLoS pathogens 2021 4 (4) e1009499 -
Emergence and outcome of the SARS-CoV-2 "Marseille-4" variant.
Fournier Pierre-Edouard et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 4 -
Genomic Feature Analysis of Betacoronavirus Provides Insights Into SARS and COVID-19 Pandemics.
Li Xin et al. Frontiers in microbiology 2021 4 614494 -
Co-circulation of SARS-CoV-2 variants B.1.1.7 and P.1
Stefanelli P, et al. medRxiv, Apr 7, 2021. -
Genomic Sequencing of SARS-COV-2 in Rwanda: evolution and regional dynamics
Butera Y, et al. Apr 7, 2021. -
Characterisation of a G2P[4] Rotavirus Outbreak in Western Australia, Predominantly Impacting Aboriginal Children.
Donato Celeste M et al. Pathogens (Basel, Switzerland) 2021 4 (3)
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Multiple Reassortants of H5N8 Clade 2.3.4.4b Highly Pathogenic Avian Influenza Viruses Detected in South Korea during the Winter of 2020-2021.
Baek Yoon-Gi et al. Viruses 2021 4 (3) -
Limited Genetic Diversity Detected in Middle East Respiratory Syndrome-Related Coronavirus Variants Circulating in Dromedary Camels in Jordan.
Seifert Stephanie N et al. Viruses 2021 4 (4) -
Emergence of Indian lineage of ECSA chikungunya virus in Djibouti 2019.
Fourié Toscane et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 4 -
Rotavirus Genotype Trends and Gastrointestinal Pathogen Detection in the United States, 2014-16: Results from the New Vaccine Surveillance Network.
Esona Mathew D et al. The Journal of infectious diseases 2021 4
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Evolution of the complex transcription network controlling biofilm formation in Candida species
Mancera Eugenio et al. eLife 2021 4
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Shelter cats host infections with multiple Trypanosoma cruzi discrete typing units in southern Louisiana.
Dumonteil Eric et al. Veterinary research 2021 4 (1) 53
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Chimeric Zika viruses containing structural protein genes of insect-specific flaviviruses cannot replicate in vertebrate cells due to entry and post-translational restrictions.
Tangudu Chandra S et al. Virology 2021 4 30-39
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Novel Chromosome-Borne Accessory Genetic Elements Carrying Multiple Antibiotic Resistance Genes in
Yu Ting et al. Frontiers in cellular and infection microbiology 2021 4 638087 -
A Large Spatial Survey of Colistin-Resistant Gene
Teng Ching-Hao et al. Microorganisms 2021 4 (4) -
COVIDOUTCOME - Estimating COVID Severity Based on Mutation Signatures in the SARS-CoV-2 Genome
Nagy A, et al. bioRxiv, Apr 2, 2021. -
Molecular surveillance of drug resistance: Plasmodium falciparum artemisinin resistance single nucleotide polymorphisms in Kelch protein propeller (K13) domain from Southern Pakistan
Ghanchi NK, et al. Malar J. 2021 Apr 7;20(1):176.
DETECTION / DIAGNOSIS
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Distinguishing bla KPC -gene-containing IncF plasmids from epidemiologically related and unrelated Enterobacteriaceae based on short- and long-read sequence data
Stohr JJ, et al. Antimicrob Agents Chemother. 2021 Apr 5;AAC.00147-21. -
Cross-Contamination versus Outbreak: Pre-XDR Mycobacterial Strains Confirmed by Whole-Genome Sequencing.
Oh Jee Youn et al. Antibiotics (Basel, Switzerland) 2021 4 (3)
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Hidden Markov Model: a shortest unique representative approach to detect the protein toxins, virulence factors and antibiotic resistance genes.
Xie Gary et al. BMC research notes 2021 4 (1) 122 -
A whole genome-based gene-by-gene typing system for standardised high resolution strain typing of Bacillus anthracis
Abdel-Glil MY, et al. J Clin Microbiol. 2021 Apr 7;JCM.02889-20. -
Use of Real-Time PCR for Chlamydia psittaci Detection in Human Specimens During an Outbreak of Psittacosis - Georgia and Virginia, 2018.
McGovern Olivia L et al. MMWR. Morbidity and mortality weekly report 2021 4 (14) 505-509
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Detection of Mycobacterium tuberculosis complex DNA in CD34-positive peripheral blood mononuclear cells of asymptomatic tuberculosis contacts: an observational study
Belay M, et al. Lancet Microbe, Mar 31, 2021. -
A method for detection of SARS-CoV-2 RNA in healthy human stool: a validation study.
Coryell Michael P et al. The Lancet. Microbe 2021 4 -
Simultaneous Detection and Mutation Surveillance of SARS-CoV-2 and co-infections of multiple respiratory viruses by Rapid field-deployable sequencing.
Bi Chongwei et al. Med (New York, N.Y.) 2021 4 -
Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples.
Kubik Slawomir et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2021 4 -
Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 lineage (20H/501Y.V2) in Brazil
Slavov SN, et al. medRxiv, Apr 4, 2021. -
Fine-Scale Temporal Dynamics of SARS-CoV-2 RNA Abundance in Wastewater during A COVID-19 Lockdown.
Li Bo et al. Water research 2021 4 117093 -
Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene.
Hartley Paul D et al. Journal of genetics and genomics = Yi chuan xue bao 2021 4 -
Non-Polio Enteroviruses from Acute Flaccid Paralysis Surveillance in Korea, 2012-2019.
Yoon Youngsil et al. Viruses 2021 4 (3) -
Molecular Characterization of Coxsackievirus A24v from Feces and Conjunctiva Reveals Epidemiological Links.
Fonseca Magilé C et al. Microorganisms 2021 4 (3) -
Ultrasensitive point-of-care immunoassay for secreted glycoprotein detects Ebola infection earlier than PCR
Fontes CM, et al. Sci Transl Med. 2021 Apr 7;13(588):eabd9696. -
Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines.
Welsh Rory M et al. Journal of fungi (Basel, Switzerland) 2021 4 (3)
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Nonparametric Binary Classification to Distinguish Closely Related versus Unrelated P. Falciparum Parasites.
Plucinski Mateusz M et al. The American journal of tropical medicine and hygiene 2021 4
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Hidden Diversity within Common Protozoan Parasites as Revealed by a Novel Genomotyping Scheme.
Seabolt Matthew H et al. Applied and environmental microbiology 2021 1 (6)
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Mosquito Identification From Bulk Samples Using DNA Metabarcoding: a Protocol to Support Mosquito-Borne Disease Surveillance in Canada.
Mechai S et al. Journal of medical entomology 2021 4
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak
Buytaers Florence E et al. Microbial genomics 2021 4 (4) -
SARS-CoV-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions during the First Pandemic Wave.
Bousali Maria et al. Life (Basel, Switzerland) 2021 4 (3)
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Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level.
Sallam Malik et al. Pathogens (Basel, Switzerland) 2021 4 (3) -
Phylogenetic estimates of SARS-CoV-2 introductions into Washington State
Tordoff DM, et al. medRxiv, Apr 7, 2021. -
Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England
Davies NG< et al. Science, Apr 9, 2021. -
Estimation of secondary household attack rates for emergent spike L452R SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco.
Peng James et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 4 -
Epidemiologic Evidence for Airborne Transmission of SARS-CoV-2 during Church Singing, Australia, 2020.
Katelaris Anthea L et al. Emerging infectious diseases 2021 4 (6) -
Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions.
Radhakrishnan Chandni et al. Frontiers in genetics 2021 4 630542 -
Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa.
Engelbrecht Susan et al. Viruses 2021 4 (3) -
Analysis of SARS-CoV-2 genomic epidemiology reveals disease transmission coupled to variant emergence and allelic variation.
Bandoy D J Darwin R et al. Scientific reports 2021 4 (1) 7380 -
Rapid Spread of SARS-CoV-2 in a State Prison After Introduction by Newly Transferred Incarcerated Persons - Wisconsin, August 14-October 22, 2020.
Hershow Rebecca B et al. MMWR. Morbidity and mortality weekly report 2021 4 (13) 478-482
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Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area.
Thielen Peter M et al. JCI insight 2021 3 (6) -
Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador
Gutierrez B, et al. medRxiv, Apr 5, 2021. -
Increased household secondary attacks rates with Variant of Concern SARS-CoV-2 index cases
Buchan SA, et al. medRxiv, Apr 5, 2021. -
Ebola Virus Transmission Initiated by Relapse of Systemic Ebola Virus Disease.
Mbala-Kingebeni Placide et al. The New England journal of medicine 2021 4 (13) 1240-1247 -
Increasing Capacity to Detect Clusters of Rapid HIV Transmission in Varied Populations-United States.
Oster Alexandra M et al. Viruses 2021 4 (4)
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Assessing the uncertainty around age-mixing patterns in HIV transmission inferred from phylogenetic trees.
Niyukuri David et al. PloS one 2021 3 (3) e0249013 -
Genomic Epidemiology of Candida auris in Qatar Reveals Hospital Transmission Dynamics and a South Asian Origin
Salah H, et al. J Fungi (Basel. 2021 Mar 23;7(3):240.
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Preparing for the Future - Nanobodies for Covid-19?
Sasisekharan Ram et al. The New England journal of medicine 2021 4
HOST-MICROBE INTERACTIONS
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SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies.
Hoffmann Markus et al. Cell 2021 4 -
B.1.526 SARS-CoV-2 variants identified in New York City are neutralized by vaccine-elicited and therapeutic monoclonal antibodies.
Zhou Hao et al. bioRxiv : the preprint server for biology 2021 4 -
Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant.
Edara Venkata Viswanadh et al. Cell host & microbe 2021 4 -
Case Study: Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient.
Klein Jonathan et al. medRxiv : the preprint server for health sciences 2021 4 -
T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity.
Elyanow Rebecca et al. medRxiv : the preprint server for health sciences 2021 4 -
Phylogenomic Evidence of Reinfection and Persistence of SARS-CoV-2: First Report from Colombia.
Ramírez Juan David et al. Vaccines 2021 4 (3) -
Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19.
Ventero Maria Paz et al. Frontiers in microbiology 2021 4 637430 -
Association of Sociodemographic Factors and Blood Group Type With Risk of COVID-19 in a US Population.
Anderson Jeffrey L et al. JAMA network open 2021 4 (4) e217429 -
Plasmodium falciparum malaria drives epigenetic reprogramming of human monocytes toward a regulatory phenotype.
Guha Rajan et al. PLoS pathogens 2021 4 (4) e1009430
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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