Advanced Molecular Detection Clips Content (Published on 03/12/2020)
NEWS
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DIAMONDS Project Using New Classification Approach to Develop Rapid Infectious Disease Tests
Petrone J. GenomeWeb, Mar 12, 2020. -
In Coronavirus Assay Validation for Emergency Use, Labs Encounter Multiple Pain Points
Johnson M. GenomeWeb, Mar 11, 2020. -
CPT fast tracking code development for novel coronavirus test
AMA, Mar 10, 2020. -
Gates-funded program will soon offer home-testing kits for new coronavirus
Doughton S. Seattle Times, Mar 9, 2020. -
People shed high levels of coronavirus, study finds, but most are likely not infectious after recovery begins
Branswell H. STAT, Mar 9, 2020. -
Study: COVID-19 may spread in several different ways
van Beusekom M, CIDRAP, Mar 12, 2020. -
Scientist links 2 state outbreaks with genetic fingerprints
Johnson CK. ABC News, Mar 11, 2020. -
Mutations can reveal how the coronavirus moves but they're easy to overinterpret
Kupferschmidt K. Science, Mar 9, 2020. -
Coronavirus: Scientists use genetic code to track UK spread
Walsh F. BBC News, Mar 9, 2020. -
To develop a coronavirus vaccine, synthetic biologists try to outdo nature
Begley S. STAT, Mar 9, 2020.
CONCEPTS / COMMENTS
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New coronavirus outbreak: Framing questions for pandemic prevention
Layne SP, et al. Sci Transl Med, Mar 11, 2020.
METHODS / TOOLS
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grabseqs: Simple downloading of reads and metadata from multiple next-generation sequencing data repositories.
Taylor Louis J et al. Bioinformatics (Oxford, England) 2020 Mar -
Iroki: automatic customization and visualization of phylogenetic trees.
Moore Ryan M et al. PeerJ 2020 e8584 -
A minimum reporting standard for multiple sequence alignments
Wong TK, et al. bioRxiv, Mar 12, 2020. -
NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization
Yousif A, et al. bioRxiv, Mar 12, 2020. -
Long-read error correction: a survey and qualitative comparison
Morisse P, et al. bioRxiv, Mar 9, 2020. -
Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies
Lipworth S, et al. bioRxiv, Mar 6, 2020. -
Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens.
Hyun Jason C et al. PLoS computational biology 2020 Mar (3) e1007608 -
Optimization of sample preparation for culture-independent sequencing of Bordetella pertussis .
Fong Winkie et al. Microbial genomics 2020 Feb -
Closing Clostridium botulinum Group I Genomes Using a Combination of Short- and Long-Reads.
Gonzalez-Escalona Narjol et al. Frontiers in microbiology 2020 239 -
A scalable, efficient, and safe method to prepare high quality DNA from mycobacteria and other challenging cells.
Epperson L Elaine et al. Journal of clinical tuberculosis and other mycobacterial diseases 2020 May 100150 -
Modelling, Bayesian inference, and model assessment for nosocomial pathogens using whole-genome-sequence data.
Cassidy Rosanna et al. Statistics in medicine 2020 Mar -
DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing.
Mendes Catarina I et al. Microbial genomics 2020 Mar -
An analytical pipeline for identifying and mapping the integration sites of HIV and other retroviruses.
Wells Daria W et al. BMC genomics 2020 Mar (1) 216 -
Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities.
Beaulaurier John et al. Genome research 2020 Feb -
Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing.
Cinar Hediye Nese et al. Parasites & vectors 2020 Mar (1) 122
EVOLUTION / ECOLOGY / POPULATIONS
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Genetic Diversity of Listeria monocytogenes Isolates from Invasive Listeriosis in China.
Yin Yuelan et al. Foodborne pathogens and disease 2020 Mar (3) 215-227 -
First complete genome sequences of Streptococcus pyogenes NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus: 100% match in length and sequence identity between PacBio solo and Illumina plus Oxford Nanopore hybrid assemblies
Salva-Serra F, et al. bioRxiv, Mar 11, 2020. -
Evolutionary analysis of Mycobacterium bovis genotypes across Africa suggests co-evolution with livestock and humans.
Inlamea Osvaldo Frederico et al. PLoS neglected tropical diseases 2020 Mar (3) e0008081 -
Genomic epidemiological characteristics of dengue fever in Guangdong province, China from 2013 to 2017.
Sun Bangyao et al. PLoS neglected tropical diseases 2020 Mar (3) e0008049 -
Accounting for population structure reveals ambiguity in the Zaire Ebolavirus reservoir dynamics.
Vrancken Bram et al. PLoS neglected tropical diseases 2020 Mar (3) e0008117 -
Direct RNA sequencing and early evolution of SARS-CoV-2
Taiaroa G, et al. bioRxiv, Mar 8, 2020. -
Isolation and characterization of SARS-CoV-2 from the first US COVID-19 patient.
Harcourt Jennifer et al. bioRxiv : the preprint server for biology 2020 6
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Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients
Shen Z, et al. Clin Infect Dis, Mar 9, 2020. -
A novel bat coronavirus reveals natural insertions at the S1/S2 cleavage site of the Spike protein and a possible recombinant origin of HCoV-19
Zhou H, et al. bioRxiv, Mar 11, 2020. -
African swine fever virus-like integrated elements in a soft tick genome - an ancient virus vector arms race?
Forth JH, et al. bioRxiv, Mar 9, 2020.
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Molecular and clinical epidemiology of carbapenem-resistant Enterobacterales in the USA (CRACKLE-2): a prospective cohort study.
van Duin David et al. The Lancet. Infectious diseases 2020 Mar -
Phylogenetically informative mutations in genes implicated in antibiotic resistance in Mycobacterium tuberculosis complex.
Merker Matthias et al. Genome medicine 2020 Mar (1) 27 -
Pathogen to commensal? Longitudinal within-host population dynamics, evolution, and adaptation during a chronic >16-year Burkholderia pseudomallei infection.
Pearson Talima et al. PLoS pathogens 2020 Mar (3) e1008298 -
High Prevalence of Colistin-Resistant Escherichia coli with Chromosomally Carried mcr-1 in Healthy Residents in Vietnam.
Yamaguchi Takahiro et al. mSphere 2020 Mar (2)
DETECTION / DIAGNOSIS
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Rapid Next-Generation Sequencing-Based Diagnostics of Bacteremia in Septic Patients.
Grumaz Christian et al. The Journal of molecular diagnostics : JMD 2020 Mar (3) 405-418 -
Assessment of the Clinical Utility of Plasma Metagenomic Next-Generation Sequencing in a Pediatric Hospital Population
Lee RA, et al. bioRxiv, Mar 8, 2020.
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Comparative analysis of phenotypic and genotypic antibiotic susceptibility patterns in Mycobacterium avium complex.
Wetzstein Nils et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2020 Mar -
Recent advances in molecular diagnostics and understanding mechanisms of drug resistance in nontuberculous mycobacterial diseases.
Huh Hee Jae et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019 08 169-182 -
Diagnosis of Acute Respiratory Syndrome Coronavirus 2 Infection by Detection of Nucleocapsid Protein
Diao B, et al. medRxiv, Mar 10, 2020. -
Enabling animal rabies diagnostic in low-access areas: Sensitivity and specificity of a molecular diagnostic test from cerebral tissue dried on filter paper.
Rasolonjatovo Felana Suzah et al. PLoS neglected tropical diseases 2020 Mar (3) e0008116 -
Genomic and serologic characterization of enterovirus A71 brainstem encephalitis.
Leon Kristoffer E et al. Neurology(R) neuroimmunology & neuroinflammation 2020 May (3) -
The nucleic acid positive rate and genotype distribution of human cytomegalovirus in human milk banks in China.
Min Xiaoyu et al. Archives of virology 2020 Mar -
Aerodynamic Characteristics and RNA Concentration of SARS-CoV-2 Aerosol in Wuhan Hospitals during COVID-19 Outbreak
Liu Y, et al. bioRxiv, Mar 10, 2020. -
Targeted Sequencing of Genomic Repeat Regions Detects Circulating Cell-free Echinococcus DNA.
Wan Zhengqing et al. PLoS neglected tropical diseases 2020 Mar (3) e0008147 -
A LAMP-based colorimetric assay to expedite field surveillance of the invasive mosquito species Aedes aegypti and Aedes albopictus.
Huang Bixing et al. PLoS neglected tropical diseases 2020 Mar (3) e0008130
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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A prolonged multispecies outbreak of IMP-6 carbapenemase-producing Enterobacterales due to horizontal transmission of the IncN plasmid.
Yamagishi Takuya et al. Scientific reports 2020 Mar (1) 4139 -
Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis.
Gona Floriana et al. Microbial genomics 2020 Mar -
A Phylogenetic Analysis of HCV Transmission, Relapse, and Reinfection Among People Who Inject Drugs Receiving Opioid Agonist Therapy.
Akiyama M J et al. The Journal of infectious diseases 2020 Mar
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Investigation of Presumptive HIV Transmission Associated with Hospitalization Using Nucleotide Sequence Analysis - New York, 2017.
Anderson Bridget J et al. MMWR. Morbidity and mortality weekly report 2020 3 (10) 260-264
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Integrating epidemiological and genetic data with different sampling intensities into a dynamic model of respiratory syncytial virus (RSV) transmission.
Kombe IK, et al. medRxiv, Mar 10, 2020. -
Transmission of Cryptosporidium spp. among human and animal local contact networks in sub-Saharan Africa: a multi-country study.
Krumkamp Ralf et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Mar
HOST-MICROBE INTERACTIONS
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Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations.
Cao Yanan et al. Cell discovery 2020 11 -
Microbiome analyses of blood and tissues suggest cancer diagnostic approach
Poore GD, et al. Nature, Mar 11, 2020.
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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