Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Jul 16, 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

• The pandemic virus is slowly mutating. But is it getting more dangerous?
  Kupferschmidt K. Science, Jul 14, 2020.
• First NGS-based COVID-19 diagnostic
  Nat Biotechnol, Jul 8, 2020.
• SARS-CoV-2 Pandemic May Promote Progress in Paper MDx
  Johnson M. 360dx, Jul 10, 2020.
• U.S. must spend $75 billion to fix flawed Covid-19 testing, report says
  Herper M. STAT, Jul 16, 2020.
• It's time to begin a national wastewater testing program for Covid-19
  Mehrotra A, et al. STAT, Jul 9, 2020.
• Mounting evidence suggests coronavirus is airborne - but health advice has not caught up
  Lewis D. Nature, Jul 8, 2020.
• Decades of research on an HIV vaccine boosts the bid for one against coronavirus
  Johnson CY, Bernstein L. Washington Post, Jul 14, 2020.
• Single-Cell Sequencing Reveals How Severe COVID-19 Exacerbated by Type I Interferons
  GenomeWeb, Jul 13, 2020.
• Researchers Home in on COVID-19 Severity Biomarkers
  Abbasi J. JAMA, Jul 14, 2020.

POLICY

• NIH-Wide Strategic Plan for COVID-19 Research
  NIH, Jul 13, 2020.
• New Era for Smarter Food Safety Blueprint
  FDA, Jul 13, 2020.

CONCEPTS / COMMENTS

• Rigorous wildlife disease surveillance
  Watsa M, Wildlife Disease Surveillance Focus Group. Science, Jul 10, 2020.
• The value of antimicrobial peptides in the age of resistance.
  Magana Maria et al. The Lancet. Infectious diseases 2020 Jul
• The Covid-19 Vaccine-Development Multiverse.
  Heaton Penny M et al. The New England journal of medicine 2020 Jul
• Proteomics and informatics for understanding phases and identifying biomarkers in COVID-19 disease.
  Whetton Anthony D et al. Journal of proteome research 2020 Jul
• Pre-existing immunity to SARS-CoV-2: the knowns and unknowns.
  Sette Alessandro et al. Nature reviews. Immunology 2020 Jul
• Rushing Science in the Face of a Pandemic Is Understandable but Risky
  Gleick P. Sci Am, Jul 16, 2020.

METHODS / TOOLS

• A dual-constriction biological nanopore resolves homonucleotide sequences with high fidelity.
  Van der Verren Sander E et al. Nature biotechnology 2020 Jul
• First results of a national external quality assessment scheme for the detection of SARS-CoV-2 genome sequences.
  Görzer I et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2020 Jul 104537 
• SARS-CoV-2 RNA extraction using magnetic beads for rapid large-scale testing by RT-qPCR and RT-LAMP
  Klein S, et al. medRxiv, Jul 11, 2020.
• Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation
  Charre C, et al. bioRxiv, Jul 15, 2020. 
• Alignment-free machine learning approaches for the lethality prediction of potential novel human-adapted coronavirus using genomic nucleotide
  bYin R, et al. bioRxiv, Jul 15, 2020.
• Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters.
  Liu Qi et al. Genomics, proteomics & bioinformatics 2020 Jul
• Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients.
  Bost Pierre et al. Cell 2020 06 (7) 1475-1488.e12
• GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies.
  Vetrovský Tomáš et al. Scientific data 2020 Jul (1) 228

EVOLUTION / ECOLOGY / POPULATIONS

• Meningococcal carriage 7 years after introduction of a serogroup A meningococcal conjugate vaccine in Burkina Faso: results from four cross-sectional carriage surveys.
  Mbaeyi Sarah et al. The Lancet. Infectious diseases 2020 Jul  
• Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation.
  Chaguza Chrispin et al. Nature communications 2020 Jul (1) 3442 
• An update on the origin of SARS-CoV-2: Despite closest identity, bat (RaTG13) and pangolin derived coronaviruses varied in the critical binding site and O-linked glycan residues.
  Malaiyan Jeevan et al. Journal of medical virology 2020 Jul
• Evolving sequence mutations in the Middle East Respiratory Syndrome Coronavirus (MERS-CoV).
  AlBalwi Mohammed Ali et al. Journal of infection and public health 2020 Jul
• SARS-CoV-2 from faeces to wastewater treatment: What do we know? A review.
  Foladori Paola et al. The Science of the total environment 2020 Jun 140444
• Comparisons of the genome of SARS-CoV-2 and those of other betacoronaviruses
  Rodr?guez-Rom?n E, Gibbs AJ. bioRxiv, Jul 13, 2020.
• Worldwide Geographical and Temporal Analysis of SARS-CoV-2 Haplotypes shows Differential Distribution Patterns
  Arevalo SJ, et al. bioRxiv, Jul 13, 2020.
• Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018.
  Mwanga Mike J et al. BMC infectious diseases 2020 Jul (1) 504  
• Abundant and Diverse RNA Viruses in Insects Revealed by RNA-Seq Analysis: Ecological and Evolutionary Implications.
  Wu Haoming et al. mSystems 2020 Jul (4)
• Complete Genome Sequence of a Baboon Simian Foamy Virus Isolated from an Infected Human.
  Shankar Anupama et al. Microbiology resource announcements 2020 Jul (27) 
• Distribution and Occurrence of Amblyomma maculatum sensu lato (Acari: Ixodidae) and Rickettsia parkeri (Rickettsiales: Rickettsiaceae), Arizona and New Mexico, 2017-2019.
  Hecht Joy A et al. Journal of medical entomology 2020 Jul 

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Whole genome sequencing disproves two suspected transmission events of bla NDM between Pseudomonas aeruginosa and Enterobacteriaceae in hospitalized patients.
  Kocer Kaan et al. The Journal of hospital infection 2020 Jul
• The Salmonella enterica Plasmidome as a Reservoir of Antibiotic Resistance.
  Emond-Rheault Jean-Guillaume et al. Microorganisms 2020 Jul (7)
• Identification of Genetic Alterations Associated with Acquired Colistin Resistance in Klebsiella pneumoniae Isogenic Strains by Whole-Genome Sequencing.
  Choi Myeongjin et al. Antibiotics (Basel, Switzerland) 2020 Jul (7)
• Lateral Gene Transfer Shapes Diversity of Gardnerella spp.
  Bohr Lindsey L et al. Frontiers in cellular and infection microbiology 2020 293
• Genomic insights into evolution of extensive drug resistance in Stenotrophomonas maltophilia complex.
  Kumar Sanjeet et al. Genomics 2020 Jul
• Large-scale assessment of antimicrobial resistance marker databases for genetic phenotype prediction: a systematic review.
  Mahfouz Norhan et al. The Journal of antimicrobial chemotherapy 2020 Jul 
• Antimicrobial resistance, genetic characterization, and molecular epidemiology of Ureaplasma species in males with infertility.
  Zhao Lihong et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2020 Jul
• "Gene accordions" cause genotypic and phenotypic heterogeneity in clonal populations of Staphylococcus aureus.
  Belikova Darya et al. Nature communications 2020 Jul (1) 3526
• Dissemination and co-circulation of SARS-CoV2 subclades exhibiting enhanced transmission associated with increased mortality in Western Europe and the United States
  Hu Y, Riley LW. medRxiv, Jul 15, 2020.
• Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site.
  Jin Xi et al. Emerging microbes & infections 2020 Dec (1) 1474-1488
• A novel human acute encephalitis caused by pseudorabies virus variant strain.
  Liu Qingyun et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jul
• Characteristics of GII.4 Norovirus versus other Genotypes in Sporadic Pediatric Infections in Davidson County, Tennessee, USA.
  Haddadin Zaid et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jul 
• High multiple mutations of Plasmodium falciparum-resistant genotypes to sulphadoxine-pyrimethamine in Lagos, Nigeria.
  Quan Hong et al. Infectious diseases of poverty 2020 Jul (1) 91

DETECTION / DIAGNOSIS

• Optical maps of plasmids as a proxy for clonal spread of MDR bacteria: a case study of an outbreak in a rural Ethiopian hospital.
  Lin Yii-Lih et al. The Journal of antimicrobial chemotherapy 2020 Jul 
• Reconsidering Mycobacterium bovis as a proxy for zoonotic tuberculosis: a molecular epidemiological surveillance study.
  Duffy Shannon C et al. The Lancet. Microbe 2020 Jun (2) e66-e73 
• Genomic analyses of Staphylococcus aureus clonal complex 45 isolates does not distinguish nasal carriage from bacteraemia.
  Roe Chandler et al. Microbial genomics 2020 Jul
• Development and Validation of a Rapid, Single-Step Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) System Potentially to Be Used for Reliable and High-Throughput Screening of COVID-19.
  Jiang Minghua et al. Frontiers in cellular and infection microbiology 2020 331
• Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays.
  Fung Becky et al. Journal of clinical microbiology 2020 Jul 
• Smart Pooling: AI-powered COVID-19 testing
  Escobar M, et al. medRxiv, Jul 15, 2020.
• Detection of low-level HCV variants in DAA treated patients: comparison amongst three different NGS data analysis protocols.
  Caputo Valeria et al. Virology journal 2020 07 (1) 103 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Backtracking and forward checking of human listeriosis clusters identified a multiclonal outbreak linked to Listeria monocytogenes in meat products of a single producer.
  Lüth Stefanie et al. Emerging microbes & infections 2020 Dec (1) 1600-1608 
• Search and Contain: Impact of an integrated genomic and epidemiological surveillance and response program for control of carbapenemase-producing Enterobacterales.
  Lane Courtney R et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jul 
• Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study
  Meredith LW, et al. Lancet Infect Dis, Jul 14, 2020. 
• Detection and Genetic Characterization of Community-Based SARS-CoV-2 Infections - New York City, March 2020
  Bushman D, et al. MMWR, Jul 17, 2020. 
• Distinct patterns of SARS-CoV-2 transmission in two nearby communities in Wisconsin, USA
  Moreno GK, et al. medRxiv, Jul 10, 2020. 
• Introductions and early spread of SARS-CoV-2 in France, 24 January to 23 March 2020.
  Gámbaro Fabiana et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2020 07 (26)
• Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico.
  Taboada Blanca et al. Journal of virology 2020 Jul
• Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling.
  Rockett Rebecca J et al. Nature medicine 2020 Jul
• Probable Vertical Transmission of SARS-CoV-2 Infection.
  Demirjian Alicia et al. The Pediatric infectious disease journal 2020 Jul
• Successful containment of horizontal enterovirus infection in a neonatal unit in Singapore through diagnosis by polymerase chain reaction (PCR) and direct sequence analysis.
  Tan Yee Yin et al. Journal of infection and public health 2020 Jul 

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Vaccine-mediated protection against Campylobacter -associated enteric disease.
  Quintel Benjamin K et al. Science advances 2020 Jun (26) eaba4511
• An mRNA Vaccine against SARS-CoV-2 - Preliminary Report.
  Jackson Lisa A et al. The New England journal of medicine 2020 Jul

HOST-MICROBE INTERACTIONS

• Interactions between Borrelia burgdorferi and ticks.
  Kurokawa Cheyne et al. Nature reviews. Microbiology 2020 Jul
• Staphylococcus Agr virulence is critical for epidermal colonization and associates with atopic dermatitis development.
  Nakamura Yuumi et al. Science translational medicine 2020 Jul (551)
• COVID-19 outcomes and the human genome.
  Murray Michael F et al. Genetics in medicine : official journal of the American College of Medical Genetics 2020 07 (7) 1175-1177
• The role of host genetics in the immune response to SARS-CoV-2 and COVID-19 susceptibility and severity.
  Ovsyannikova Inna G et al. Immunological reviews 2020 Jul
• Assessment of risk conferred by coding and regulatory variations of TMPRSS2 and CD26 in susceptibility to SARS-CoV-2 infection in human.
  Senapati Sabyasachi et al. Journal of genetics 2020
• New insights into genetic susceptibility of COVID-19: an ACE2 and TMPRSS2 polymorphism analysis.
  Hou Yuan et al. BMC medicine 2020 Jul (1) 216
• Nasal microbiota dominated by Moraxella spp. is associated with respiratory health in the elderly population: a case control study.
  van den Munckhof Ellen H A et al. Respiratory research 2020 Jul (1) 181
• Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD.
  Hu Shixian et al. Gut 2020 Jul

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.