Publication Date: Jun 18, 2020
Advanced Molecular Detection Clips Content
NEWS
- With every flush, a stream of data for these coronavirus trackers
Kossakovski F. PBS, Jun 16, 2020. - Coronavirus Pathogenicity Clues Uncovered Using Machine-Learning Approach
GenomeWeb, Jun 11, 2020.
EVENTS / TRAINING / WEB RESOURCES
- A statistical transmission model for COVID-19 outbreak with adjustment of external factors
(webinar) Yifan Zhu, Fred Hutchinson Cancer Research Center. 11:00 am EDT, Jun 19, 2020. - NIH launches analytics platform to harness nationwide COVID-19 patient data to speed treatments
(press release) NIH, Jun 15, 2020. - The impact of genomics on precision public health
(call for papers) Genome Medicine (guest editors Muin Khoury and Kat Holt), submission deadline Jul 15, 2020.
POLICY
- Addressing ethical challenges in US-based HIV phylogenetic research.
Dawson Liza et al. The Journal of infectious diseases 2020 Jun
CONCEPTS / COMMENTS
- COVID-19 vaccine design: the Janus face of immune enhancement.
Hotez Peter J et al. Nature reviews. Immunology 2020 06 (6) 347-348 - How Data Became One of the Most Powerful Tools to Fight an Epidemic
Johnson S. New York Times Magazine, Jun 10, 2020. - Machine Learning Maps Research Needs in COVID-19 Literature
Doanvo A, et al. bioRxiv, Jun 12, 2020. - Artificial-intelligence tools aim to tame the coronavirus literature
Hutson M, et al. Nature, Jun 9, 2020.
METHODS / TOOLS
- Ten recommendations for supporting open pathogen genomic analysis in public health.
Black Allison et al. Nature medicine 2020 Jun 
- V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data
Posada-Cespedes S, et al. bioRxiv, Jun 11, 2020. - bigPint: A Bioconductor visualization package that makes big data pint-sized.
Rutter Lindsay et al. PLoS computational biology 2020 Jun (6) e1007912 - LabxDB: Versatile databases for genomic sequencing and lab management.
Vejnar Charles E et al. Bioinformatics (Oxford, England) 2020 Jun - Higher order Markov models for metagenomic sequence classification.
Burks David J et al. Bioinformatics (Oxford, England) 2020 Jun - A decade of advances in transposon-insertion sequencing.
Cain Amy K et al. Nature reviews. Genetics 2020 Jun - Broad-Range Virus Detection and Discovery Using Microfluidic PCR Coupled with High-throughput Sequencing
Tao Y, et al. bioRxiv, Jun 12, 2020. - Whole Genome Sequencing of Hepatitis A Virus Using a PCR-Free Single-Molecule Nanopore Sequencing Approach.
Batista Frederico M et al. Frontiers in microbiology 2020 874 - Genotyping SARS-CoV-2 through an interactive web application
Maan H, et al. Lancet Digit Health, Jun 12, 2020. - Development and Application of Performance Assessment Criteria for Next-Generation Sequencing-Based HIV Drug Resistance Assays.
Becker Michael G et al. Viruses 2020 Jun (6) - Elimination of "kitome" and "splashome" contamination results in lack of detection of a unique placental microbiome.
Olomu Isoken Nicholas et al. BMC microbiology 2020 Jun (1) 157
EVOLUTION / ECOLOGY / POPULATIONS
- Genome-scale approach to study the genetic relatedness among Brucella melitensis strains.
Pelerito Ana et al. PloS one 2020 (3) e0229863 - Emergence of genomic diversity and recurrent mutations in SARS-CoV-2.
van Dorp Lucy et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 Sep 104351 - Transmission and evolutionary dynamics of human coronavirus OC43 strains in coastal Kenya investigated by partial spike sequence analysis, 2015-16.
Abidha Carol A et al. Virus evolution 2020 Jan (1) veaa031 - Genomic Sequencing and Analysis of Eight Camel-Derived Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Isolates in Saudi Arabia.
Al-Shomrani Badr M et al. Viruses 2020 06 (6) - International Expansion of a Novel SARS-CoV-2 Mutant.
Wang Minjin et al. Journal of virology 2020 06 (12) - Computational Inference of Selection Underlying the Evolution of the Novel Coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2.
Cagliani Rachele et al. Journal of virology 2020 06 (12) - Origin and evolution of dengue virus type 2 causing outbreaks in Kenya: Evidence of circulation of two cosmopolitan genotype lineages.
Langat Solomon K et al. Virus evolution 2020 Jan (1) veaa026 - Bat-borne virus diversity, spillover and emergence.
Letko Michael et al. Nature reviews. Microbiology 2020 Jun - Dynamic interactions of influenza viruses in Hong Kong during 1998-2018.
Yang Wan et al. PLoS computational biology 2020 Jun (6) e1007989
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Population genomic molecular epidemiological study of macrolide resistant Streptococcus pyogenes in Iceland, 1995-2016: Identification of a large clonal population with a pbp2x mutation conferring reduced in vitro β-lactam susceptibility.
Southon Sara B et al. Journal of clinical microbiology 2020 Jun - Emergence of multidrug-resistant Mycobacterium tuberculosis of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing.
Perdigão João et al. Emerging microbes & infections 2020 Dec (1) 1342-1353 - Combining Whole-Genome Sequencing and Multimodel Phenotyping To Identify Genetic Predictors of Salmonella Virulence.
Crouse Alanna et al. mSphere 2020 Jun (3) - Detection of Ciprofloxacin-Resistant, B-Lactamase-Producing Neisseria meningitidis Serogroup Y Isolates -- United States, 2019-2020
McNamara MA, et al. MMWR, Jun 19, 2020. - The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity
Zhang L, et al. bioRxiv, Jun 12, 2020. - Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses.
Gussow Ayal B et al. Proceedings of the National Academy of Sciences of the United States of America 2020 Jun - The importance of naturally attenuated SARS-CoV-2in the fight against COVID-19.
Armengaud Jean et al. Environmental microbiology 2020 06 (6) 1997-2000 - The Prediction of miRNAs in SARS-CoV-2 Genomes: hsa-miR Databases Identify 7 Key miRs Linked to Host Responses and Virus Pathogenicity-Related KEGG Pathways Significant for Comorbidities.
Arisan Elif Damla et al. Viruses 2020 06 (6) - The resistome and genomic reconnaissance in the age of malaria elimination.
Kümpornsin Krittikorn et al. Disease models & mechanisms 2019 12 (12)
DETECTION / DIAGNOSIS
- Environmental Bioaerosol Surveillance as an Early Warning System for Pathogen Detection in North Carolina Swine Farms: A Pilot Study.
Anderson Benjamin D et al. Transboundary and emerging diseases 2020 Jun - Development of a LAMP method for detection of carbapenem-resistant Acinetobacter baumannii during a hospital outbreak.
Garciglia Mercado Carolina et al. Journal of infection in developing countries 2020 May (5) 494-501 - A Vibrio cholerae Core Genome Multilocus Sequence Typing Scheme to Facilitate the Epidemiological Study of Cholera.
Liang Kevin Y H et al. Journal of bacteriology 2020 Jun - Bacteria encapsulation and rapid antibiotic susceptibility test using a microfluidic microwell device integrating surface-enhanced Raman scattering.
Huang Hsiu-Kang et al. Lab on a chip 2020 Jun - Next-generation sequencing of microbial cell-free DNA for rapid noninvasive diagnosis of infectious diseases in immunocompromised hosts.
Camargo Jose F et al. F1000Research 2019 1194 - The utility of MALDI-TOF MS for outbreak investigation in the neonatal intensive care unit.
Bar-Meir Maskit et al. European journal of pediatrics 2020 Jun - Microevolution and Gain or Loss of Mobile Genetic Elements of Outbreak-Related Listeria monocytogenes in Food Processing Environments Identified by Whole Genome Sequencing Analysis.
Yang Helen et al. Frontiers in microbiology 2020 866 - Amplicon-Based High-Throughput Sequencing Method Capable of Species-Level Identification of Coagulase-Negative Staphylococci in Diverse Communities.
Van Reckem Emiel et al. Microorganisms 2020 Jun (6) - Detection of SARS-CoV-2 RNA by multiplex RT-qPCR
Kudo E, et al. bioRxiv, Jun 17, 2020. - Multiple assays in a real-time RT-PCR SARS-CoV-2 panel can mitigate the risk of loss of sensitivity by new genomic variants during the COVID-19 outbreak.
Penarrubia Authors Luis et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2020 Jun - Rapid point of care nucleic acid testing for SARS-CoV-2 in hospitalised patients: a clinical trial and implementation study
Collier DA, et al. medRxiv, Jun 11, 2020. - Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples.
Eis-Hübinger Anna M et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2020 06 104381 - Sentinel surveillance of SARS-CoV-2 in wastewater anticipates the occurrence of COVID-19 cases
Chavarria-Miro G, et al. medRxiv, Jun 13, 2020. - Previremic Identification of Ebola or Marburg Virus Infection Using Integrated Host-Transcriptome and Viral Genome Detection.
Speranza Emily et al. mBio 2020 Jun (3) - Quality Control of Next-Generation Sequencing-Based HIV-1 Drug Resistance Data in Clinical Laboratory Information Systems Framework.
Capina Rupert et al. Viruses 2020 Jun (6) - First international external quality assessment scheme of nucleic acid amplification tests for the detection of Schistosoma and soil-transmitted helminths, including Strongyloides: A pilot study.
Cools Piet et al. PLoS neglected tropical diseases 2020 Jun (6) e0008231 - High-throughput multiplex qPCRs for the surveillance of zoonotic species of canine hookworms.
Massetti Luca et al. PLoS neglected tropical diseases 2020 Jun (6) e0008392
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Nosocomial outbreak of COVID-19 pneumonia in Wuhan, China.
Wang Xiaorong et al. The European respiratory journal 2020 06 (6) - Evolution and epidemic spread of SARS-CoV-2 in Brazil
Candido DdS, et al. medRxiv, Jun 12, 2020. - Preliminary analysis of SARS-CoV-2 importation & establishment of UK transmission lineages
Pybus O, et al. virological, Jun 9, 2020. - SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East.
Gong Yu-Nong et al. Emerging microbes & infections 2020 Jun 1-37 - Candida auris outbreak involving liver transplant recipients in a Surgical Intensive Care Unit.
Theodoropoulos Nicole M et al. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2020 Jun
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Whole exome sequencing reveals the different responsiveness to Enterovirus 71 vaccination in Chinese children.
Zhang Li et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2020 Jun
HOST-MICROBE INTERACTIONS
- Initial Whole Genome Sequencing and Analysis of the Host Genetic Contribution to COVID-19 Severity and Susceptibility
Wang F, et al. medRxiv, Jun 13, 2020. - Genomewide Association Study of Severe Covid-19 with Respiratory Failure
Ellinghaus D, et al. New Engl J Med, Jun 17, 2020. - Why does COVID-19 disproportionately affect older people?
Mueller Amber L et al. Aging 2020 05 (10) 9959-9981 - Multi-level proteomics reveals host-perturbation strategies of SARS-CoV-2 and SARS-CoV
Stukalov A, et al. bioRxiv, Jun 17, 2020. - Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection
Wei J, et al. bioRxiv, Jun 17, 2020. - ACE2 receptor polymorphism: Susceptibility to SARS-CoV-2, hypertension, multi-organ failure, and COVID-19 disease outcome.
Devaux Christian A et al. Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi 2020 Jun (3) 425-435 - Human genetics of life-threatening influenza pneumonitis.
Zhang Qian et al. Human genetics 2020 Jun (6-7) 941-948 - Evolutionary and population (epi)genetics of immunity to infection.
Barreiro Luis B et al. Human genetics 2020 Jun (6-7) 723-732 - Exploring the interactions between the human and viral genomes.
Fellay Jacques et al. Human genetics 2020 Jun (6-7) 777-781 - Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study.
Clooney Adam G et al. Gut 2020 Jun
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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