Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Sep 24, 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

• Nothing Eats Viruses, Right? Meet Some Hungry Protists
  Wu KJ. New York Times, Sep 24, 2020.
• Center for Genomic Regulation's COVID-19 Viral Beacon Digs Into Thousands of SARS-CoV-2 Genomes
  Versel N. GenomeWeb, Sep 23, 2020.
• FDA Publishes First Batch of SARS-CoV-2 MDx Limit of Detection Comparison Results
  Johnson M. 360dx, Sep 16, 2020.
• Massive genetic study shows coronavirus mutating and potentially evolving amid rapid U.S. spread
  Mooney C, et al. Washington Post, Sep 23, 2020.
• COVID-19 likely spreading from people to animals--and vice versa
  Van Beusekom M. CIDRAP, Sep 18, 2020.
• Studies trace COVID-19 spread to international flights
  Van Beusekom M. CIDRAP, Sep 21, 2020.
• State-based genomic screening labs to be united in $3.3m project
  Mannix L. Sydney Morning Herald, Sep 15, 2020.

EVENTS / TRAINING / WEB RESOURCES

• SARS-CoV-2 Reference Panel Comparative Data
  (website) FDA, Sep 15, 2020.
• ARTIC Network: Real-time molecular epidemiology for outbreak response
  (website) ARTIC Network (funded by Wellcome Trust).
• CRG Viral Beacon
  (website) Center for Genomic Regulation, Sep 2020.

CONCEPTS / COMMENTS

• Recombination should not be an afterthought.
  Neches Russell Y et al. Nature reviews. Microbiology 2020 Sep
• Low genetic diversity may be an Achilles heel of SARS-CoV-2.
  Rausch Jason W et al. Proceedings of the National Academy of Sciences of the United States of America 2020 Sep
• Informed consent for HIV phylogenetic research: A case study of urban individuals living with HIV approached for enrollment in an HIV study.
  Rudolph Abby E et al. EHQUIDAD (14) 129-143
• What Should Health Departments Do with HIV Sequence Data?
  Romero-Severson Ethan et al. Viruses 2020 Sep (9)

METHODS / TOOLS

• Genome sequence-based curation of PubMLST data challenges interspecies recombination in the Burkholderia cepacia complex.
  Peeters Charlotte et al. Future microbiology 2020 Aug 1091-1093
• Similarity Studies of Corona Viruses through Chaos Game Representation.
  Sengupta Dipendra C et al. Computational molecular bioscience 2020 Sep (3) 61-72
• An analysis of clinical and geographical metadata of over 75,000 records in the GISAID COVID-19 database
  Velazquez A, et al. medRxiv, Sep 23, 2020.
• Semiparametric Bayesian inference for the transmission dynamics of COVID-19 with a state-space model.
  Zhou Tianjian et al. Contemporary clinical trials 2020 Sep 106146
• Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization.
  Zhao Zhengqiao et al. PLoS computational biology 2020 Sep (9) e1008269
• Leveraging pathogen sequence and contact tracing data to enhance vaccine trials in emerging epidemics
  Kahn R, et al. medRxiv, Sep 16, 2020.

EVOLUTION / ECOLOGY / POPULATIONS

• Digging metagenomic data of pangolins revealed SARS-CoV-2 related viruses and other significant viruses.
  Yang Shixing et al. Journal of medical virology 2020 Sep
• Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area
  Long SW, et al. medRxiv, Sep 23, 2020.
• Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity
  Volz EM, et al. medRxiv, Sep 1, 2020.
• Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America.
  Franco-Muñoz Carlos et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 Sep 104557
• Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data.
  Xu Xiaofeng et al. BMC genomics 2020 Sep (1) 641
• Expanded genome-wide comparisons give novel insights into population structure and genetic heterogeneity of Leishmania tropica complex.
  Salloum Tamara et al. PLoS neglected tropical diseases 2020 Sep (9) e0008684

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Clinical and molecular epidemiology of invasive Staphylococcus aureus infection in Utah children; continued dominance of MSSA over MRSA.
  Crandall Hillary et al. PloS one 2020 (9) e0238991
• Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniae
  David S, et al. Proc Natl Acad Sci USA. 2020 Sep 23;202003407.
• Prevalence of integrase strand transfer inhibitor resistance mutations in antiretroviral-naive HIV-1-infected individuals in Cameroon.
  Wenk Benjamin M et al. The Journal of antimicrobial chemotherapy 2020 Sep
• Complex genetic encoding of the hepatitis B virus on-drug persistence
  Thai H, et al. Sci Rep 2020 Sep 23;10(1):15574. 

DETECTION / DIAGNOSIS

• Optimizing direct RT-LAMP to detect transmissible SARS-CoV-2 from primary nasopharyngeal swab and saliva patient samples
  Dudley DM, et al. medRxiv, Sep 17, 2020.
• Assessing a novel, lab-free, point-of-care test for SARS-CoV-2 (CovidNudge): a diagnostic accuracy study
  Gibani MM, et al. Lancet Microbe, Sep 17, 2020.
• Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020
  Van Walle I, et al. medRxiv, Sep 18, 2020. 
• Sensitive fluorescence detection of SARS-CoV-2 RNA in clinical samples via one-pot isothermal ligation and transcription.
  Woo Chang Ha et al. Nature biomedical engineering 2020 Sep
• Viable SARS-CoV-2 in the air of a hospital room with COVID-19 patients.
  Lednicky John A et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2020 Sep
• Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing
  Izquierdo RW, et al. medRxiv, Sep 22, 2020.
• Metagenomic Insights into the Sewage RNA Virosphere of a Large City.
  Guajardo-Leiva Sergio et al. Viruses 2020 Sep (9)
• Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics.
  Peccia Jordan et al. Nature biotechnology 2020 Sep
• Update on MALDI-TOF MS Identification of Filamentous Fungi.
  Wilkendorf Laura S et al. Journal of clinical microbiology 2020 Sep
• Retrospective Review of Clinical Utility of Shotgun Metagenomic Sequencing Testing of Cerebrospinal Fluid at a U.S. Tertiary Care Medical Center.
  Rodino Kyle G et al. Journal of clinical microbiology 2020 Sep 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Risk factors associated with large clusters of tuberculosis patients determined by whole-genome sequencing in a high-tuberculosis-burden country.
  Miyahara Reiko et al. Tuberculosis (Edinburgh, Scotland) 2020 Sep 101991
• Tracking the COVID-19 pandemic in Australia using genomics.
  Seemann Torsten et al. Nature communications 2020 09 (1) 4376
• Genomic epidemiology of a densely sampled COVID19 outbreak in China
  Geidelberg L, et al. medRxiv, Sep 16, 2020.
• Genomic epidemiology of the Los Angeles COVID-19 outbreak
  Guo L, et al. medRxiv, Sep 18, 2020.
• Whole-genome sequencing to track SARS-CoV-2 transmission in nosocomial outbreaks.
  Lucey Mary et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Sep 
• Serial Testing for SARS-CoV-2 and Virus Whole Genome Sequencing Inform Infection Risk at Two Skilled Nursing Facilities with COVID-19 Outbreaks - Minnesota, April-June 2020.
  Taylor Joanne et al. MMWR. Morbidity and mortality weekly report 2020 Sep (37) 1288-1295  
• SARS-CoV-2 in Quarantined Domestic Cats from COVID-19 Households or Close Contacts, Hong Kong, China.
  Barrs Vanessa R et al. Emerging infectious diseases 2020 Sep (12)
• Jumping back and forth: anthropozoonotic and zoonotic transmission of SARS-CoV-2 on mink farms
  Munnink BB, et al. bioRxiv, Sep 1, 2020.
• In-Flight Transmission of Severe Acute Respiratory Syndrome Coronavirus 2.
  Choi Edward M et al. Emerging infectious diseases 2020 Sep (11) 
• Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 During Long Flight.
  Khanh Nguyen Cong et al. Emerging infectious diseases 2020 Sep (11) 
• Resurgence of an international hepatitis A outbreak linked to imported frozen strawberries, Germany, 2018 to 2020.
  Ruscher Claudia et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2020 Sep (37) 

HOST-MICROBE INTERACTIONS

• Battlefronts of evolutionary conflict between bacteria and animal hosts.
  Aleru Omoshola et al. PLoS pathogens 2020 Sep (9) e1008797
• Common genetic variation in humans impacts in vitro susceptibility to SARS-CoV-2 infection
  Dobrindt K, et al. bioRxiv, Sep 21, 2020.
• Genetic variants of PIEZO1 associate with COVID-19 fatality
  Cheng CW, et al. medRxiv, Sep 18, 2020.
• The COVID-19 immune landscape is dynamically and reversibly correlated with disease severity
  Bolouri H, et al. bioRxiv, Sep 21, 2020.
• Genetics and COVID-19: How to Protect the Susceptible.
  Field Robert I et al. Trends in genetics : TIG 2020 Aug
• Association of TLR3(rs3775291) and IL-10(rs1800871) gene polymorphisms with susceptibility to Hepatitis B infection: A meta-analysis.
  Ye Susu et al. Epidemiology and infection 2020 Sep 1-28 

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.