Publication Date: Sep 17, 2020
Advanced Molecular Detection Clips Content
NEWS
- Genome Data Help to Track COVID-19 Superspreading Event
(blog post) Collins F. NIH Director's Blog, Sep 8, 2020. - Real-time gene sequencing can help control - and may someday prevent - pandemics
Quick J. STAT, Sep 11, 2020. - FDA Publishes First Batch of SARS-CoV-2 MDx Limit of Detection Comparison Results
Johnson M. GenomeWeb, Sep 16, 2020. - Fast coronavirus tests: what they can and can't do
Guglielmi G. Nature, Sep 16, 2020. - New York City Opening Dedicated COVID-19 Testing Laboratory
GenomeWeb, Sep 17, 2020. - NIST Creating Reference Material for SARS-CoV-2 Diagnostic Assay Developers
Rizk C. GenomeWeb, Sep 11, 2020. - The Coronavirus Is Mutating, and That's Fine (So Far)
Holmes E. New York Times, Sep 11, 2020. - Early research from 23andMe strengthens link between blood types and Covid-19
Sheridan K. STAT, Sep 14, 2020. - Investigating Whether Blood Type Is Linked to COVID-19 Risk
Rubin R. JAMA, Sep 16, 2020.
EVENTS / TRAINING / WEB RESOURCES
- Landscape of Emerging Infectious Disease Research and Development: Preventing the Next Pandemic
(link to report) Policy Cures Research (Australia), Sep 17, 2020. - Biological Collections: Ensuring Critical Research and Education for the 21st Century
(report) NASEM, Sep 2020. - How to make your research jump off the page: Co-creation to broaden public engagement in medical research.
Finley Nina et al. PLoS medicine 2020 Sep (9) e1003246
CONCEPTS / COMMENTS
- Array programming with NumPy
Harris CR, et al. Nature, Sep 16, 2020. - Coinfections in wildlife: Focus on a neglected aspect of infectious disease epidemiology.
Hoarau Axel O G et al. PLoS pathogens 2020 Sep (9) e1008790 - COVID-19 and the Path to Immunity.
Stephens David S et al. JAMA 2020 Sep - Bringing the path toward an HIV-1 vaccine into focus.
Lopez Angel Cesar J et al. PLoS pathogens 2020 Sep (9) e1008663
METHODS / TOOLS
- Adaptive preferential sampling in phylodynamics.
Cappello Lorenzo et al. ArXiv 2020 Sep - MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets.
Choi Meena et al. Nature methods 2020 Sep - Potential applications of human viral metagenomics and reference materials: considerations for current and future viruses.
Santiago-Rodriguez Tasha M et al. Applied and environmental microbiology 2020 Sep - Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore.
Tyson John R et al. bioRxiv : the preprint server for biology 2020 Sep - The UCSC SARS-CoV-2 Genome Browser.
Fernandes Jason D et al. Nature genetics 2020 Sep - Exploring the coronavirus pandemic with the WashU Virus Genome Browser.
Flynn Jennifer A et al. Nature genetics 2020 Sep - Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource.
Portelli Stephanie et al. Nature genetics 2020 Sep - Evaluating the performance of malaria genetics for inferring changes in transmission intensity using transmission modelling.
Watson Oliver J et al. Molecular biology and evolution 2020 Sep
EVOLUTION / ECOLOGY / POPULATIONS
- Analysis of SARS-CoV-2 genomes from across Africa reveals potentially clinically relevant mutations
Iweriebor EC, et al. bioRxiv, Sep 8, 2020. - Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus.
Banerjee Arinjay et al. The Journal of general virology 2020 Sep - Where Did SARS-CoV-2 Come From?
Leitner Thomas et al. Molecular biology and evolution 2020 09 (9) 2463-2464 - Emerging HxNy Influenza A Viruses.
Liu William J et al. Cold Spring Harbor perspectives in medicine 2020 Sep - Sequence Analysis of Egyptian Foot-and-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus.
Abd El Rahman Sahar et al. Viruses 2020 09 (9) - Molecular epidemiology of mumps viruses in the Netherlands, 2017-2019.
Bodewes Rogier et al. PloS one 2020 (9) e0233143 - Molecular Analysis of the Bloodmeals of Culex spp. Mosquitoes at Natural Habitats in Singapore to Investigate the Potential Risk of Japanese Encephalitis Virus and West Nile Virus Transmission.
Yeo Gladys et al. Vector borne and zoonotic diseases (Larchmont, N.Y.) 2020 Sep (9) 703-714 - Beyond Infection: Integrating Competence into Reservoir Host Prediction.
Becker Daniel J et al. Trends in ecology & evolution 2020 Sep
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Cross-border emergence of clonal lineages of ST38 Escherichia coli producing the OXA-48-like carbapenemase OXA-244 in Germany and Switzerland.
Falgenhauer Linda et al. International journal of antimicrobial agents 2020 Sep 106157 - Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources.
Monte Daniel F M et al. Food microbiology 2021 Feb 103601 - Clinical and molecular epidemiology of vancomycin-resistant Enterococcus faecium bacteremia from an Indian tertiary hospital.
Rao Chandrabhan et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2020 Sep - Genomic serotyping, clinical manifestations, and antimicrobial resistance of non-typhoidal Salmonella gastroenteritis in hospitalized children in Ho Chi Minh City, Vietnam.
Thuy Duong Vu et al. Journal of clinical microbiology 2020 Sep - Prevalence and Distribution Characteristics of bla and bla Genes in Klebsiella pneumoniae .
Zhang Xiufeng et al. Infection and drug resistance 2020 2901-2910 - WGS-Based Prediction and Analysis of Antimicrobial Resistance in Campylobacter jejuni Isolates From Israel.
Rokney Assaf et al. Frontiers in cellular and infection microbiology 2020 365 - Antimicrobial Resistance of Campylobacter spp. Causing Human Infection in Australia: An International Comparison.
Wallace Rhiannon L et al. Microbial drug resistance (Larchmont, N.Y.) 2020 Sep - Genomic epidemiology of emerging ESBL-producing Salmonella Kentucky bla CTX-M-14b in Europe.
Coipan Claudia E et al. Emerging microbes & infections 2020 Sep 1-252 - Characterization of genomic variants associated with resistance to bedaquiline and delamanid in naïve Mycobacterium tuberculosis clinical strains.
Battaglia S et al. Journal of clinical microbiology 2020 Sep - D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization.
Weissman D, et al. medRxiv, Sep 12, 2020. - High levels of HIV drug resistance among adults failing second-line antiretroviral therapy in Namibia.
Jordan Michael R et al. Medicine 2020 Sep (37) e21661
- Infection with multiple HIV-1 founder variants is associated with lower viral replicative capacity, faster CD4+ T cell decline and increased immune activation during acute infection.
Macharia Gladys N et al. PLoS pathogens 2020 Sep (9) e1008853 - Continued Evolution of H5Nx Avian Influenza Viruses in Bangladeshi Live Poultry Markets: Pathogenic Potential in Poultry and Mammalian Models.
El-Shesheny Rabeh et al. Journal of virology 2020 Sep - Rare/cryptic Aspergillus species infections and importance of antifungal susceptibility testing.
Tsang Chi-Ching et al. Mycoses 2020 Sep
DETECTION / DIAGNOSIS
- Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory.
Church Deirdre L et al. Clinical microbiology reviews 2020 Sep (4) - Occurrence of Listeria and Escherichia coli in frozen fruit and vegetables collected from retail and catering premises in England 2018-2019.
Willis Caroline et al. International journal of food microbiology 2020 Aug 108849 - Risk factors associated with carbapenemase-producing Enterobacterales (CPE) positivity in the hospital wastewater environment.
Park Stacy C et al. Applied and environmental microbiology 2020 Sep - Understanding and predicting ciprofloxacin minimum inhibitory concentration in Escherichia coli with machine learning.
Pataki Bálint Ármin et al. Scientific reports 2020 Sep (1) 15026 - Genomic Prediction of Antimicrobial Resistance: Ready or Not, Here It Comes!
Ransom Eric M et al. Clinical chemistry 2020 Sep - Full Molecular Typing of Neisseria meningitidis Directly from Clinical Specimens for Outbreak Investigation
Itsko M, et al. J Clin Microbiol, Sep 16, 2020. - Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: A guide and case study in setting up an emergency-use, laboratory-developed molecular assay.
Anahtar Melis N et al. medRxiv : the preprint server for health sciences 2020 Sep - Detection and quantification of SARS-CoV-2 by droplet digital PCR in real-time PCR negative nasopharyngeal swabs from suspected COVID-19 patients.
Alteri Claudia et al. PloS one 2020 (9) e0236311 - Pooled Testing for Surveillance of SARS-CoV-2 in Asymptomatic Individuals.
Das Sanchita et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2020 Sep 104619 - Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants
Crit-Christoph A, et al. medRxiv, Sep 14, 2020. - Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing.
Joung Julia et al. The New England journal of medicine 2020 Sep - Metagenomic sequencing to detect respiratory viruses in persons under investigation for COVID-19
Babiker A, et al. medRxiv, Sep 10, 2020. - Analysis of partial sequences of the RNA-dependent RNA polymerase gene as a tool for genus and subgenus classification of coronaviruses.
Wilkinson David A et al. The Journal of general virology 2020 Sep - Development of a New Internally Controlled One-Step Real-Time RT-PCR for the Molecular Detection of Enterovirus A71 in Africa and Madagascar.
Volle Romain et al. Frontiers in microbiology 2020 1907 - Evidence for missing HPV-45 and -59 positives with the SPF 10 -DEIA-LiPA 25 (version 1) platform compared to the type-specific qPCR assays and the impact on vaccine effectiveness estimates.
van Eer Kahren et al. Journal of clinical microbiology 2020 Sep - Metagenomic Analysis of the Virome of Mosquito Excreta.
Ramírez Ana L et al. mSphere 2020 Sep (5) - A Targeted Metagenomics Approach to Study the Diversity of Norovirus GII in Shellfish Implicated in Outbreaks.
Desdouits Marion et al. Viruses 2020 09 (9) - Pooling saliva to increase SARS-CoV-2 testing capacity.
Watkins Anne E et al. medRxiv : the preprint server for health sciences 2020 Sep - Primary resistance to integrase strand transfer inhibitors in Spain using ultrasensitive HIV-1 genotyping.
Casadellà M et al. The Journal of antimicrobial chemotherapy 2020 Sep
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Forensic genomics of a novel Klebsiella quasipneumoniae type from a neonatal intensive care unit in China reveals patterns of colonization, evolution and epidemiology.
Perlaza-Jiménez Laura et al. Microbial genomics 2020 Sep - Levels of genetic diversity of SARS-CoV-2 virus: reducing speculations about the genetic variability of the virus in South America
Filho CB, et al. bioRxiv, Sep 15, 2020. - The emergence of SARS-CoV-2 in Europe and North America.
Worobey Michael et al. Science (New York, N.Y.) 2020 Sep - Viral genomics to inform infection control response in occupational COVID-19 transmission.
Whyler Naomi C A et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Sep - SARS-CoV-2 in Quarantined Domestic Cats from COVID-19 Households or Close Contacts, Hong Kong, China
Barrs VR, et al. Emerg Infect Dis, Sep 16, 2020. - Investigation of SARS-CoV-2 outbreaks in six care homes in London, April 2020.
Ladhani Shamez N et al. EClinicalMedicine 2020 Sep 100533 - Estimates of outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data
Vaughan T, et al. medRxiv, Sep 14, 2020. - Cryptic transmission of SARS-CoV-2 in Washington state.
Bedford Trevor et al. Science (New York, N.Y.) 2020 Sep - Absence of SARS-CoV-2 infection in cats and dogs in close contact with a cluster of COVID-19 patients in a veterinary campus.
Temmam Sarah et al. One health (Amsterdam, Netherlands) 2020 Dec 100164 - Sindbis Virus Strains of Divergent Origin Isolated from Humans and Mosquitoes During a Recent Outbreak in Finland.
Korhonen Essi M et al. Vector borne and zoonotic diseases (Larchmont, N.Y.) 2020 Sep - Investigation Report of cVDPV2 Outbreak in Bokh Woreda of Dollo Zone, Somali Regional State, Ethiopia.
Sufa Diriba et al. Case reports in infectious diseases 2020 6917313 - Direct costs and clinical impact of adenovirus genotype 8 conjunctivitis outbreak in a neonatology unit.
Angueyra María Florencia et al. Infection control and hospital epidemiology 2020 Sep 1-7
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies.
Lee Wen Shi et al. Nature microbiology 2020 Sep - Reassessment of the risk of narcolepsy in children in England 8 years after receipt of the AS03-adjuvanted H1N1 pandemic vaccine: A case-coverage study.
Stowe Julia et al. PLoS medicine 2020 Sep (9) e1003225
HOST-MICROBE INTERACTIONS
- In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.
Lieberman Nicole A P et al. PLoS biology 2020 09 (9) e3000849 - Racial/Ethnic Variation in Nasal Gene Expression of Transmembrane Serine Protease 2 (TMPRSS2)
Bunyavanich S, et al. JAMA, Sep 10, 2020. - Analysis of ACE2 genetic variants in 131 Italian SARS-CoV-2-positive patients.
Novelli Antonio et al. Human genomics 2020 09 (1) 29 - Genetic variants of the human host influencing the coronavirus-associated phenotypes (SARS, MERS and COVID-19): rapid systematic review and field synopsis.
Di Maria Emilio et al. Human genomics 2020 09 (1) 30 - Trans-ethnic analysis reveals genetic and non-genetic associations with COVID-19 susceptibility and severity
Shelton JF, et al. medRxiv, Sep 7, 2020. - An assessment of toll-like receptor 7 and 8 gene polymorphisms with susceptibility to HIV-1 infection, AIDS development and response to antiretroviral therapy.
Zaidane Imane et al. Immunology letters 2020 Sep 88-95 - The effect of KIR and HLA polymorphisms on dengue infection and disease severity in northeastern Thais.
Chaisri Suwit et al. Medical microbiology and immunology 2020 Oct (5) 613-620 - The Microbiome Composition of a Man's Penis Predicts Incident Bacterial Vaginosis in His Female Sex Partner With High Accuracy.
Mehta Supriya D et al. Frontiers in cellular and infection microbiology 2020 433
Note:
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 Public Health Genomics 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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