Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Apr 23, 2020

Advanced Molecular Detection Clips Content

• News
• Events / Training / Web Resources
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Host-Microbe Interactions

NEWS

• Coronavirus Is Forcing Medical Research to Speed Up
  Tingley K. New York Times Magazine, Apr 21, 2020.
• Why Some People Get Sicker Than Others
  Hamblin J. The Atlantic, Apr 21, 2020.
• Could Curbing Runaway Immune Responses Treat COVID-19?
  Williams S. The Scientist, Apr 21, 2020.
• New York COVID-19 Genomics Research Network Coalesces to Battle Pandemic
  Karow J. GenomeWeb, Apr 21, 2020.
• Teams Scour ACE2 Sequence, Expression Data to Search For SARS-CoV-2 Infection Clues
  Anderson A. GenomeWeb, Apr 20, 2020.
• German Researchers Launch Study to Identify Genomic Variants Affecting COVID-19 Disease Response
  Petrone J. GenomeWeb, Apr 20, 2020.
• NIST and OSTP Launch Effort to Improve Search Engines for COVID-19 Research
  National Library of Medicine, NIH. Apr 20, 2020.
• Genetic tracing 'barcode' is rapidly revealing COVID-19's journey and evolution
  Faulstick B. phys.org, Apr 17, 2020.
• First US COVID-19 Deaths Happened Weeks Earlier than Thought
  Offord C. The Scientist, Apr 22, 2020.
• Home testing for Covid-19 will provide the combination to unlock the U.S.
  Millenson E. STAT, Apr 22, 2020.
• How FDA Plans to Tackle Coronavirus Serology Tests -- For Now
  Johnson M. 360dx, Apr 16, 2020.
• Study Raises Questions About False Negatives From Quick COVID-19 Test
  Stein R. NPR, Apr 21, 2020.
• Dozens of coronavirus antibody tests on the market were never vetted by the FDA, leading to accuracy concerns
  McGinley L. Washington Post, Apr 19, 2020.
• CRISPR And Spit Might Be Keys To Faster, Cheaper, Easier Tests For The Coronavirus
  Palca J. NPR, Apr 17, 2020.
• The researchers taking a gamble with antibody tests for coronavirus
  Maxmen A. Nature, Apr 21, 2020.
• Untapped potential: More US labs could be providing tests for coronavirus
  Maxmen A. Nature, Apr 21, 2020.

EVENTS / TRAINING / WEB RESOURCES

• COVID-19 Testing Directory
  (website) American Association for Clinical Chemistry (AACC)
• Outbreak Science: a non-profit to advance the science of outbreak response
  (website) See also @outbreaksci and @PREreview_ on Twitter
• Canadian Bioinformatics Workshop Series, Summer 2020
  (announcement, PDF) bioinformatics.ca, early-bird registration deadline May 14, 2020.
• COVID-19 Open Research Dataset (CORD-19)
  (data resource) Allen Institute for AI, et al.
• A New Resource for Genomics and Precision Health Information and Publications on the Investigation and Control of COVID-19 and other Coronaviruses
  Yu W, et al. bioRxiv, Apr 21, 2020.
• Call for papers: The impact of genomics on precision public health
  Khoury M, Holt K. Genome Med, deadline July 15, 2020.
• The Public Health Impact of COVID-19: Why Host Genomics?
  (blog post) Khoury M, et al. Office of Genomics and Precision Public Health, OS, CDC. Apr 21, 2020.
• How the UK is cracking the coronavirus code
  (blog post) Genomics Education Program (UK), Apr 17, 2020.

CONCEPTS / COMMENTS

• Prudently conduct the engineering and synthesis of the SARS-CoV-2 virus.
  Ma Shiwen et al. Synthetic and systems biotechnology 2020 Apr
• A "One-Health" approach for diagnosis and molecular characterization of SARS-CoV-2 in Italy.
  Lorusso Alessio et al. One health (Amsterdam, Netherlands) 2020 Apr 100135 
• Ten simple rules for innovative dissemination of research.
  Ross-Hellauer Tony et al. PLoS computational biology 2020 Apr (4) e1007704 

METHODS / TOOLS

• A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology
  Rambaut A, et al. bioRxiv, Apr 19, 2020.
• A Scalable, Easy-to-Deploy, Protocol for Cas13-Based Detection of SARS-CoV-2 Genetic Material
  Rauch JN, et al. bioRxiv, Apr 21, 2020.
• prewas: data pre-processing for more informative bacterial GWAS.
  Saund Katie et al. Microbial genomics 2020 Apr
• Testing hypotheses about the microbiome using the linear decomposition model (LDM).
  Hu Yi-Juan et al. Bioinformatics (Oxford, England) 2020 Apr 

EVOLUTION / ECOLOGY / POPULATIONS

• Genomic analysis of pathogenic isolates of Vibrio cholerae from eastern Democratic Republic of the Congo (2014-2017).
  Irenge Leonid M et al. PLoS neglected tropical diseases 2020 Apr (4) e0007642
• Genomic analysis of an Irish population of Mycobacterium abscessus complex collected between 2006 and 2017.
  Redondo Natalia et al. Journal of clinical microbiology 2020 Apr
• An emergent clade of SARS-CoV-2 linked to returned travellers from Iran.
  Eden John-Sebastian et al. Virus evolution 2020 Jan (1) veaa027
• Phylodynamics of SARS-CoV-2 transmission in Spain
  Fuertes FD, et al. bioRxiv, Apr 20, 2020.
• Epidemiological and Genomic Analysis of SARS-CoV-2 in Ten Patients from a Mid-sized City outside of Hubei, China
  Chen J, et al. medRxiv, Apr 21, 2020.
• Synonymous mutations and the molecular evolution of SARS-Cov-2 origins
  Nielsen R, et al. bioRxiv, Apr 21, 2020.
• Limited SARS-CoV-2 diversity within hosts and following passage in cell culture
  Moreno GK, et al. bioRxiv, Apr 20, 2020.
• Identification of super-transmitters of SARS-CoV-2
  Yang X, et al. medRxiv, Apr 22, 2020.
• Population genomics insights into the recent evolution of SARS-CoV-2
  Vasilarou M, et al. bioRxiv, Apr 23, 2020.
• Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates
  Damas J, et al. bioRxiv, Apr 18, 2020.
• Bats reveal the true power of influenza A virus adaptability.
  Ciminski Kevin et al. PLoS pathogens 2020 Apr (4) e1008384
• Distribution of rotavirus genotypes in Japan from 2015 to 2018: Diversity in genotypes before and after introduction of rotavirus vaccines.
  Hoque Sheikh Ariful et al. Vaccine 2020 Apr 
• West Nile Virus in Farmed Crocodiles, Zambia, 2019.
  Simulundu Edgar et al. Emerging infectious diseases 2020 Apr (4) 811-814
• Human infections caused by clonally related African clade (clade III) strains of Candida auris in the greater Houston region.
  Long S Wesley et al. Journal of clinical microbiology 2020 Apr 
• Genotyping Echinococcus multilocularis in Human Alveolar Echinococcosis Patients: An EmsB Microsatellite Analysis.
  Knapp Jenny et al. Pathogens (Basel, Switzerland) 2020 Apr (4)

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Molecular epidemiology of carbapenemase-producing Enterobacterales in Finland, 2012-2018.
  Räisänen Kati et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2020 Apr
• Patient-derived mutations impact pathogenicity of SARS-CoV-2
  Yao H, et al. medRxiv, Apr 19, 2020.
• Evidence for both sequential mutations and recombination in the evolution of kdr alleles in Aedes aegypti.
  Fan Yinjun et al. PLoS neglected tropical diseases 2020 Apr (4) e0008154
• Evolution of kdr haplotypes in worldwide populations of Aedes aegypti: Independent origins of the F1534C kdr mutation.
  Cosme Luciano Veiga et al. PLoS neglected tropical diseases 2020 Apr (4) e0008219

DETECTION / DIAGNOSIS

• Genetic Diversity of Non-O157 Shiga Toxin-Producing Escherichia coli Recovered From Patients in Michigan and Connecticut.
  Blankenship Heather M et al. Frontiers in microbiology 2020 529
• Proteome-wide analysis of differentially-expressed SARS-CoV-2 antibodies in early COVID-19 infection
  Zhang X, et al. medRxiv, Apr 20, 2020.
• Temporal detection and phylogenetic assessment of SARS-CoV-2 in municipal wastewater
  Nemudryi A, et al. medRxiv, Apr 20, 2020.
• Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients.
  Xiao Ai Tang et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Apr
• The duration of viral shedding of discharged patients with severe COVID-19.
  Zhou Bo et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Apr
• Triplex Real-Time RT-PCR for Severe Acute Respiratory Syndrome Coronavirus 2.
  Waggoner Jesse J et al. Emerging infectious diseases 2020 Apr (7)
• Triplex Real-Time RT-PCR for Severe Acute Respiratory Syndrome Coronavirus 2.
  Waggoner Jesse J et al. Emerging infectious diseases 2020 Apr (7)
• Aerosol and Surface Distribution of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospital Wards, Wuhan, China, 2020.
  Guo Zhen-Dong et al. Emerging infectious diseases 2020 Apr (7)
• Severe Acute Respiratory Syndrome Coronavirus 2 RNA Detected in Blood Donations.
  Chang Le et al. Emerging infectious diseases 2020 Apr (7) 
• Analysis of SARS-CoV-2 Antibodies in COVID-19 Convalescent Plasma using a Coronavirus Antigen Microarray
  de Assis RR, et al. bioRxiv, Apr 17, 2020.
• Efficient high throughput SARS-CoV-2 testing to detect asymptomatic carriers
  Shental N, et al. medRxiv, Apr 20, 2020.
• Rapid direct nucleic acid amplification test without RNA extraction for SARS-CoV-2 using a portable PCR thermocycler
  Wee SK, et al. bioRxiv, Apr 20, 2020.
• Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs
  Wyllie AL, et al. medRxiv, Apr 22, 2020.
• An alternative workflow for molecular detection of SARS-CoV-2 - escape from the NA extraction kit-shortage, Copenhagen, Denmark, March 2020.
  Fomsgaard Anna S et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2020 04 (14) 
• Development of a reverse transcription-loop-mediated isothermal amplification as a rapid early-detection method for novel SARS-CoV-2.
  Baek Yun Hee et al. Emerging microbes & infections 2020 Apr 1-31
• Detection of Influenza A(H3N2) Virus RNA in Donated Blood.
  Dos Santos Bezerra Rafael et al. Emerging infectious diseases 2020 Apr (7)

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Shigella sonnei Outbreak Investigation During a Municipal Water Crisis-Genesee and Saginaw Counties, Michigan, 2016.
  McClung R Paul et al. American journal of public health 2020 Apr e1-e8  
• Emergence of a Novel Salmonella enterica Serotype Reading Clonal Group Is Linked to Its Expansion in Commercial Turkey Production, Resulting in Unanticipated Human Illness in North America.
  Miller Elizabeth A et al. mSphere 2020 Apr (2)  
• Dissemination routes of the carbapenem resistance plasmid pOXA-48 in a hospital setting
  Leon-Sampedro R, et al. bioRxiv, Apr 22, 2020.
• Biphasic Outbreak of Invasive Group A Streptococcus Disease in Eldercare Facility, New Zealand.
  Worthing Kate A et al. Emerging infectious diseases 2020 May (5) 841-848 
• Sequencing analysis of the spread of SARS-CoV2 in the Greater New York City region
  Maurano MT, et al. medRxiv, Apr 21, 2020.
• Revealing COVID-19 transmission by SARS-CoV-2 genome sequencing and agent based modelling
  Rockett RJ, et al. bioRxiv, Apr 22, 2020.
• Phylogenetic Cluster Analysis Identifies Virological and Behavioral Drivers of HIV Transmission in MSM.
  Bachmann Nadine et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Apr
• Person-to-Person Transmission of Andes Virus in Hantavirus Pulmonary Syndrome, Argentina, 2014.
  Alonso Daniel O et al. Emerging infectious diseases 2020 Apr (4) 756-759

HOST-MICROBE INTERACTIONS

• Revealing variants in SARS-CoV-2 interaction domain of ACE2 and loss of function intolerance through analysis of >200,000 exomes
  Cirulli ET, et al. bioRxiv, Apr 17, 2020.
• Human leukocyte antigen susceptibility map for SARS-CoV-2.
  Nguyen Austin et al. Journal of virology 2020 Apr
• Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
  Butler DJ, et al. bioRxiv, Apr 21, 2020.
• Consumption of artificially sweetened beverages during pregnancy impacts infant gut microbiota and body mass index
  Laforest-Lapointe I, et al. bioRxiv, Apr 21, 2020.

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.