Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Aug 27, 2020

Advanced Molecular Detection Clips Content

• News
• Policy
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• A Plan to Use Modern Data Tools to Fight Foodborne Illness
  Jaklevic MC. JAMA, Aug 18, 2020.
• First Case of COVID-19 Reinfection Confirmed - Viral sequence disparity indicates Hong Kong case not simply prolonged infection
  Walker M. MedPage Today, Aug 24, 2020.
• For Quick Coronavirus Testing, Israel Turns to a Clever Algorithm
  Halbfinger DM. New York Times, Aug 21, 2020.
• Genetic data show how a single superspreading event sent coronavirus across Massachusetts--and the nation
  Kaplan S, Mooney C. Washington Post, Aug 25, 2020.
• FDA and Lab-Developed Tests: The Saga Continues
  Walker M. MedPage Today, Aug 25, 2020.
• Russia vaccine roll-out plan prompts virus mutation worries
  Kelland K. Reuters, Aug 21, 2020.
• A Woman May Have Been Cured of H.I.V. Without Medical Treatment
  Mandavilli A. New York Times, Aug 26, 2020.
• Florida releasing genetically modified mosquitoes to prevent diseases like Zika
  Lanese N. Live Science, Aug 21, 2020.

POLICY

• Rescission of Guidances and Other Informal Issuances Concerning Premarket Review of Laboratory Developed Tests
  HHS, Aug 19, 2020. 

CONCEPTS / COMMENTS

• Application of Next Generation Sequencing in Laboratory Medicine.
  Zhong Yiming et al. Annals of laboratory medicine 2021 Jan (1) 25-43

METHODS / TOOLS

• Protoblock - A biological standard for formalin fixed samples.
  Flores Bueso Yensi et al. Microbiome 2020 Aug (1) 122
• Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes.
  Petit Robert A et al. mSystems 2020 Aug (4)
• FLAVi: An Enhanced Annotator for Viral Genomes of Flaviviridae .
  de Bernadi Schneider Adriano et al. Viruses 2020 Aug (8)
• Temporal signal and the phylodynamic threshold of SARS-CoV-2
  Duchene S. Virus Evol, Aug 19, 2020.
• Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic.
  Pillay Sureshnee et al. Genes 2020 08 (8) 
• A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture.
  Nasir Jalees A et al. Viruses 2020 08 (8) 
• Real-time public health communication of local SARS-CoV-2 genomic epidemiology.
  Kalinich Chaney C et al. PLoS biology 2020 Aug (8) e3000869 
• Employing Molecular Phylodynamic Methods to Identify and Forecast HIV Transmission Clusters in Public Health Settings: A Qualitative Study.
  Rich Shannan N et al. Viruses 2020 Aug (9)  

EVOLUTION / ECOLOGY / POPULATIONS

• Virulence genes and previously unexplored gene clusters in four commensal Neisseria spp. isolated from the human throat expand the neisserial gene repertoire.
  Calder Alan et al. Microbial genomics 2020 Aug
• SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies.
  Karamitros Timokratis et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2020 Aug 104585
• Genetic diversity and evolution of Hantaan virus in China and its neighbors.
  Li Naizhe et al. PLoS neglected tropical diseases 2020 Aug (8) e0008090
• Molecular characterisation of Influenza C viruses from outbreaks in Hong Kong SAR, China.
  Daniels Rodney S et al. Journal of virology 2020 Aug
• Species-Specific Evolution of Ebola Virus during Replication in Human and Bat Cells.
  Whitfield Zachary J et al. Cell reports 2020 Aug (7) 108028
• Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates.
  Damas Joana et al. Proceedings of the National Academy of Sciences of the United States of America 2020 Aug

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Emergence of Transferable mcr-9 Gene-Carrying Colistin-Resistant Salmonella enterica Dessau ST14 Isolated from Retail Chicken Meat in Korea.
  Cha Min-Hyeok et al. Foodborne pathogens and disease 2020 Aug
• Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria.
  Botelho João et al. Microbial genomics 2020 Aug
• Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study.
  Young Barnaby E et al. Lancet (London, England) 2020 Aug

DETECTION / DIAGNOSIS

• Tracking of Antibiotic Resistance Transfer and Rapid Plasmid Evolution in a Hospital Setting by Nanopore Sequencing.
  Peter Silke et al. mSphere 2020 Aug (4) 
• Comparing serotyping with whole-genome sequencing for subtyping of non-typhoidal Salmonella enterica : a large-scale analysis of 37 serotypes with a public health impact in the USA.
  Elnekave Ehud et al. Microbial genomics 2020 Aug
• Comprehensive Surveillance of SARS-CoV-2 Spread Using Wastewater-based Epidemiology Studies
  Manupati H, et al. medRxiv, Aug 21, 2020.
• First study on surveillance of SARS-CoV-2 RNA in wastewater systems and related environments in Wuhan: Post-lockdown
  Zhao L, et al. medRxiv, Aug 21, 2020.
• Building the National SARS-CoV-2 Laboratory Diagnostic Capacity in Taiwan.
  Yang Ji-Rong et al. Health security 2020 Aug 
• SARS-CoV-2 has been circulating in northern Italy since December 2019: Evidence from environmental monitoring.
  La Rosa Giuseppina et al. The Science of the total environment 2020 Aug 141711
• Accelerating genomics-based surveillance for COVID-19 response in Africa.
  Tessema Sofonias K et al. The Lancet. Microbe 2020 Aug 
• Detection and Discovery of Coronaviruses in Wild Bird Populations.
  Snoeck Chantal J et al. Methods in molecular biology (Clifton, N.J.) 2020 41-53
• Monitoring COVID-19 transmission risks by RT-PCR tracing of droplets in hospital and living environments
  Piana A, et al. medRxiv, Aug 25, 2020.
• Outbreak of Trichophyton soudanense causing tinea capitis in an orphanage in Myanmar.
  Norrenberg S et al. Journal de mycologie medicale 2020 Jul 101013 
• Comparison of a Novel Rapid Lateral Flow Assay to Enzyme Immunoassay Results for Early Diagnosis of Coccidioidomycosis.
  Donovan Fariba M et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Aug

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• The distribution and spread of susceptible and resistant Neisseria gonorrhoeae across demographic groups in a major metropolitan center.
  Mortimer Tatum D et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Aug
• Polyclonal Burkholderia cepacia Complex Outbreak in Peritoneal Dialysis Patients Caused by Contaminated Aqueous Chlorhexidine.
  Wong Sally C Y et al. Emerging infectious diseases 2020 Sep (9) 1987-1997 
• Saprochaete clavata Outbreak Infecting Cancer Center through Dishwasher.
  Menu Estelle et al. Emerging infectious diseases 2020 Sep (9) 2031-2038 
• Clinical and Economic Outcomes of Genome Sequencing Availability on Containing a Hospital Outbreak of Resistant Escherichia coli in Australia.
  Lee Xing J et al. Value in health : the journal of the International Society for Pharmacoeconomics and Outcomes Research 2020 Aug (8) 994-1002 
• An outbreak of cutaneous abscesses caused by Panton-Valentine leukocidin-producing methicillin-susceptible Staphylococcus aureus among gold mine workers, South Africa, November 2017 to March 2018.
  Ismail Husna et al. BMC infectious diseases 2020 Aug (1) 621
• COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing.
  To Kelvin Kai-Wang et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Aug
• SARS-CoV-2 Community Transmission disproportionately affects Latinx population during Shelter-in-Place in San Francisco.
  Chamie Gabriel et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Aug
• Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events
  Lemieux J, et al. medRxiv, Aug 25, 2020.
• Geographical reconstruction of the SARS-CoV-2 outbreak in Lombardy (Italy) during the early phase.
  Micheli Valeria et al. Journal of medical virology 2020 Aug
• Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic.
  Surleac Marius et al. Life (Basel, Switzerland) 2020 Aug (8)
• Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate.
  Addetia Amin et al. Journal of clinical microbiology 2020 Aug

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• The Application of Single-Cell RNA Sequencing in Vaccinology.
  Noé Andrés et al. Journal of immunology research 2020 8624963
• RNA-Based COVID-19 Vaccine BNT162b2 Selected for a Pivotal Efficacy Study
  Walsh EE, et al. medRxiv, Aug 20, 2020.

HOST-MICROBE INTERACTIONS

• The current landscape of coronavirus-host protein-protein interactions.
  Perrin-Cocon Laure et al. Journal of translational medicine 2020 08 (1) 319
• Maternal bacteria to correct abnormal gut microbiota in babies born by C-section.
  Butler Éadaoin M et al. Medicine 2020 Jul (30) e21315
• Heritability jointly explained by host genotype and microbiome: will improve traits prediction?
  Awany Denis et al. Briefings in bioinformatics 2020 Aug
• Host genomics of the HIV-1 reservoir size and its decay rate during suppressive antiretroviral treatment.
  Thorball Christian W et al. Journal of acquired immune deficiency syndromes (1999) 2020 Aug
• A Genome-Wide Association Study Identifies SERPINB10, CRLF3, STX7, LAMP3, IFNG-AS1 and KRT80 As Risk Loci Contributing to Cutaneous Leishmaniasis In Brazil.
  Castellucci Léa C et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Aug

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.