Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Apr 9, 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
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• How sewage could reveal true scale of coronavirus outbreak
  Mallapaty S. Nature, Apr 3, 2020.
• Reanalysis of Flu-Like Illnesses in Wuhan Suggests Coronavirus Community Transmission in January
  GenomeWeb, Apr 7, 2020.
• Fast, portable tests come online to curb coronavirus pandemic
  Nat Biotech, Mar 23, updated Apr 7, 2020.
• Most New York Coronavirus Cases Came From Europe, Genomes Show
  Zimmer C. New York Times, Apr 9, 2020.

EVENTS / TRAINING / WEB RESOURCES

• Next-Generation Sequencing Technologies to Advance Global Infectious Disease Research / Public Health / Clinical Medicine
  (journal supplement) J Infect Dis, Apr 15, 2020.

CONCEPTS / COMMENTS

• Precision Medicine and Precision Public Health in the Era of Pathogen Next-Generation Sequencing.
  Leguia Mariana et al. The Journal of infectious diseases 2020 Mar (Supplement_3) S289-S291 
• Considering mutational meltdown as a potential SARS-CoV-2 treatment strategy.
  Jensen Jeffrey D et al. Heredity 2020 Apr
• Humanity tested
  (editorial) Nat Biomed Eng, Apr 8, 2020.
• The COVID-19 vaccine development landscape
  Le TT, et al. Nat rev Drug Disc, Apr 9, 2020.

METHODS / TOOLS

• Molecular diagnostics in South Africa and challenges in the establishment of a molecular laboratory in developing countries.
  Singh-Moodley Ashika et al. Journal of infection in developing countries 2020 Mar (3) 236-243 
• Specialist laboratory networks as preparedness and response tool - the Emerging Viral Diseases-Expert Laboratory Network and the Chikungunya outbreak, Thailand, 2019.
  Venturi Giulietta et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2020 Apr (13) 
• Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes.
  Lal Gupta Chhedi et al. Environment international 2020 May 105667
• pyrpipe: a python package for RNA-Seq workflows
  Singh U, et al. bioRxiv, Apr 8, 2020.
• Accelerating surveillance and research of antimicrobial resistance - an online repository for sharing of antimicrobial susceptibility data associated with whole-genome sequences.
  Matamoros Sébastien et al. Microbial genomics 2020 Apr 
• Accurate Identification of SARS-CoV-2 from Viral Genome Sequences using Deep Learning
  Lopez-Rincon A, et al. bioRxiv, Apr 6, 2020.
• Efficient sample pooling strategies for COVID-19 data gathering
  Szapudi I. medRxiv, Apr 7, 2020.
• SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases
  Wu F, et al. medRxiv, Apr 7, 2020.
• Analysis and Applications of Non-Adaptive and Adaptive Group Testing Methods for COVID-19
  Mentus C, et al. bioRxiv, Apr 7, 2020.
• One-step RNA extraction for RT-qPCR detection of 2019-nCoV
  Sentmanat M, et al. bioRxiv, Apr 5, 2020.
• A snapshot of SARS-CoV-2 genome availability up to 30th March, 2020 and its implications
  Mavian C, et al. bioRxiv, Apr 5, 2020. 
• Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing.
  Byrd Doratha A et al. mSphere 2020 Feb (1)

EVOLUTION / ECOLOGY / POPULATIONS

• Temporal Dynamics of Salmonella enterica subsp. enterica Serovar Agona Isolates From a Recurrent Multistate Outbreak.
  Hoffmann Maria et al. Frontiers in microbiology 2020 478
• Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1.
  Zhang Chengxin et al. Journal of proteome research 2020 04 (4) 1351-1360
• Serological and molecular findings during SARS-CoV-2 infection: the first case study in Finland, January to February 2020.
  Haveri Anu et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2020 03 (11)
• Zoonotic origins of human coronaviruses.
  Ye Zi-Wei et al. International journal of biological sciences 2020 (10) 1686-1697

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• New Mutations Involved in Colistin Resistance in Acinetobacter baumannii.
  Sun Bingbing et al. mSphere 2020 Apr (2)
• Multispecies Outbreak of Verona Integron-Encoded Metallo-ß-Lactamase-Producing Multidrugresistant Bacteria Driven by a Promiscuous Incompatibility Group A/C2.
  de Man Tom J B et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Apr
• Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses
  Auslander N, et al. bioRxiv, Apr 8, 2020.
• Virological assessment of hospitalized patients with COVID-2019.
  Wölfel Roman et al. Nature 2020 Apr

DETECTION / DIAGNOSIS

• Molecular diagnosis of polymicrobial brain abscesses with 16S rDNA-based next generation sequencing.
  Stebner Alexander et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2020 Mar
• Expanded sequential quadriplex real-time polymerase chain reaction (PCR) for identifying pneumococcal serotypes, penicillin susceptibility, and resistance markers
  Velusamy S, et al. Diagn Microbiol Infect Dis, Mar 12, 2020.
• Molecular detection of Rickettsia species in ticks collected in the Mexico-USA transboundary region.
  Merino O et al. Experimental & applied acarology 2020 Apr
• Does antiretroviral therapy use affect the accuracy of HIV rapid diagnostic assays? Experience from a demographic health and surveillance site in rural South Africa.
  Siedner Mark J et al. Diagnostic microbiology and infectious disease 2020 Mar 115031 
• Development of an RNA strand-specific hybridization assay to differentiate replicating versus non-replicating influenza A virus.
  Yang Genyan et al. Journal of clinical microbiology 2020 Apr 
• The Laboratory Diagnosis of COVID-19 Infection: Current Issues and Challenges.
  Tang Yi-Wei et al. Journal of clinical microbiology 2020 Apr 
• Pooling RT-PCR or NGS samples has the potential to cost-effectively generate estimates of COVID-19 prevalence in resource limited environments
  Narayanan K, et al. medRxiv, Apr 6, 2020.
• Patient-collected tongue, nasal, and mid-turbinate swabs for SARS-CoV-2 yield equivalent sensitivity to health care worker collected nasopharyngeal swabs
  Tu YP, et al. medRxiv, Apr 6, 2020.
• Detecting SARS-CoV-2 at point of care: Preliminary data comparing Loop-mediated isothermal amplification (LAMP) to PCR
  Osterdahl MF, et al. medRxiv, Apr 4, 2020.
• Potential false-negative nucleic acid testing results for Severe Acute Respiratory Syndrome Coronavirus 2 from thermal inactivation of samples with low viral loads.
  Pan Yang et al. Clinical chemistry 2020 Apr
• Assessment of Specimen Pooling to Conserve SARS CoV-2 Testing Resources
  Abdalhamid B, et al. medRxiv, Apr 6, 2020.
• Efficient and Practical Sample Pooling High-Throughput PCR Diagnosis of COVID-19
  Shani-Narkiss H, et al. medRxiv, Apr 7, 2020.
• Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-Co2 virus detection
  Gonzalez-Gonzalez E, et al. medRxiv, Apr 7, 2020.
• Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR
  Wikramaratna P, et al. medRxiv, Apr 7, 2020.
• SARS-CoV-2 detection in patients with influenza-like illness
  Kong WH, et al. Nat Microbiol, Apr 7, 2020.
• LAMP-Seq: Population-Scale COVID-19 Diagnostics Using a Compressed Barcode Space
  Schmid-Burgk JL, et al. bioRxiv, Apr 8, 2020.
• Extraction-free COVID-19 (SARS-CoV-2) diagnosis by RT-PCR to increase capacity for national testing programmes during a pandemic
  Grant PR, et al. bioRxiv, Apr 9, 2020.

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Novel Insights Into the Spread of Enteric Pathogens Using Genomics.
  Domman Daryl et al. The Journal of infectious diseases 2020 Mar (Supplement_3) S319-S330 
• Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital.
  Perdigão João et al. Microbial genomics 2020 Apr
• Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants.
  Sobkowiak Benjamin et al. Microbial genomics 2020 Apr
• Modeling Missing Cases and Transmission Links in Networks of Extensively Drug-Resistant Tuberculosis in KwaZulu-Natal, South Africa.
  Nelson Kristin N et al. American journal of epidemiology 2020 Apr 
• High Prevalence of Sequences Included in Transmission Clusters Within Newly Diagnosed HIV-1 Patients in Southern Spain (2004-2015).
  González-Domenech Carmen M et al. Microbial drug resistance (Larchmont, N.Y.) 2020 Mar
• Multiple Respiratory Syncytial Virus Introductions Into a Neonatal Intensive Care Unit.
  Rose Erica Billig et al. Journal of the Pediatric Infectious Diseases Society 2020 Apr
• Whole genome and phylogenetic analysis of two SARS-CoV-2 strains isolated in Italy in January and February 2020: additional clues on multiple introductions and further circulation in Europe.
  Stefanelli Paola et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2020 Apr (13)
• Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China
  Lu J, et al. medRxiv, Apr 4, 2020.
• Cryptic transmission of SARS-CoV-2 in Washington State
  Bedford T, et al. medRxiv, Apr 6, 2020.

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Using Next Generation Sequencing to Study the Genetic Diversity of Candidate Live Attenuated Zika Vaccines.
  Collins Natalie D et al. Vaccines 2020 Apr (2)
• Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus.
  Robson B et al. Computers in biology and medicine 2020 04 103670
• Sequence-based prediction of vaccine targets for inducing T cell responses to SARS-CoV-2 utilizing the bioinformatics predictor RECON
  Poran A, et al. bioRxiv, Apr 8, 2020.
• Respiratory virus shedding in exhaled breath and efficacy of face masks
  Leung NH, et al. Nat Med, Apr 3, 2020.

HOST-MICROBE INTERACTIONS

• The protein expression profile of ACE2 in human tissues
  Hikmet F, et al. medRxiv, Apr 3, 2020.
• Virus-host interactome and proteomic survey of PMBCs from COVID-19 patients reveal potential virulence factors influencing SARS-CoV-2 pathogenesis
  Li J, et al. bioRxiv, Apr 2, 2020.
• Dual RNA-Seq characterization of host and pathogen gene expression in liver cells infected with Crimean-Congo Hemorrhagic Fever Virus.
  Kozak Robert A et al. PLoS neglected tropical diseases 2020 Apr (4) e0008105
• Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response.
  de Vries Dylan H et al. PLoS pathogens 2020 Apr (4) e1008408
• Metagenomic evidence for a polymicrobial signature of sepsis
  Tan CC, et al. bioRxiv, Apr 7, 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.