Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Aug 13, 2020

Advanced Molecular Detection Clips Content

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

NEWS

• How genomics will help us track Covid-19
  Daalder M. Newsroom (New Zealand), Aug 12, 2020.
• The pandemic appears to have spared Africa so far. Scientists are struggling to explain why
  Nordling L. Science, Aug 11, 2020.
• Inspired by llamas' unique antibodies, scientists create a potent anti-coronavirus molecule
  McFarling U. STAT, Aug 11, 2020.
• Many Initiatives Turning to RT-LAMP as an Alternative to PCR for Rapid COVID-19 Screening Assays
  Johnson M. GenomeWeb, Aug 13, 2020.
• Antimicrobial Resistance Test Makers Maneuver to Compete for Nesta's L10M Longitude Prize
  Petrone J. 360dx, Aug 5, 2020.

EVENTS / TRAINING / WEB RESOURCES

• Coronavirus: indexed data speed up solutions.
  Ohno-Machado Lucila et al. Nature 2020 08 (7820) 192
• COVID-19 Data Index: Search for Covid-19 datasets
  (website)
• Integrative illustration for coronavirus outreach.
  Goodsell David S et al. PLoS biology 2020 Aug (8) e3000815
• SARS-CoV-2 contextual data specification for open genomic epidemiology
  (podcast) Micro Binfie (Microbial Bioinformatics), Aug 12, 2020.
• Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2
  (report) NASEM, Aug 2020.

POLICY

• Regulatory, safety, and privacy concerns of home monitoring technologies during COVID-19.
  Gerke Sara et al. Nature medicine 2020 Aug (8) 1176-1182

CONCEPTS / COMMENTS

• SARS-CoV-2 in wastewater: State of the knowledge and research needs.
  Kitajima Masaaki et al. The Science of the total environment 2020 Apr 139076
• Precision Public Health as a Key Tool in the COVID-19 Response
  Rasmussen SA, et al. JAMA, Aug 12, 2020.

METHODS / TOOLS

• STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies.
  Bharucha Tehmina et al. The Lancet. Infectious diseases 2020 Aug  
• The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country.
  Nouws Stéphanie et al. Foods (Basel, Switzerland) 2020 Aug (8) 
• Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study.
  Saltykova Assia et al. International journal of molecular sciences 2020 Aug (16)
• EUAdb: a resource for COVID-19 test development.
  Woronik Alyssa et al. bioRxiv : the preprint server for biology 2020 Jul
• The PHA4GE SARS-CoV-2 Contextual Data Specification for Open Genomic Epidemiology
  Griffiths EJ, et al. preprints.org, Aug 7, 2020.  
• A Public Website for the Automated Assessment and Validation of SARS-CoV-2 Diagnostic PCR Assays.
  Li Po-E et al. Bioinformatics (Oxford, England) 2020 Aug
• VIDHOP, viral host prediction with Deep Learning.
  Mock Florian et al. Bioinformatics (Oxford, England) 2020 Aug
• An optimized reverse genetics system suitable for efficient recovery of simian, human and murine-like rotaviruses.
  Sánchez-Tacuba Liliana et al. Journal of virology 2020 Aug 

EVOLUTION / ECOLOGY / POPULATIONS

• Diversification in immunogenicity genes caused by selective pressures in invasive meningococci.
  Kremer Philip H C et al. Microbial genomics 2020 Aug 
• Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014.
  Huong Nguyen Quynh et al. PloS one 2020 (8) e0237129
• COVID-19: Time to exonerate the pangolin from the transmission of SARS-CoV-2 to humans.
  Frutos Roger et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 Aug 104493
• Whole genome and in-silico analyses of G1P[8] rotavirus strains from pre- and post-vaccination periods in Rwanda.
  Rasebotsa Sebotsana et al. Scientific reports 2020 Aug (1) 13460  
• Yellow fever transmission in non-human primates, Bahia, Northeastern Brazil.
  Goes de Jesus Jaqueline et al. PLoS neglected tropical diseases 2020 Aug (8) e0008405
• Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018.
  Hill Sarah C et al. PLoS pathogens 2020 Aug (8) e1008699 

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• Carbapenemase-Producing Klebsiella pneumoniae From Transplanted Patients in Brazil: Phylogeny, Resistome, Virulome and Mobile Genetic Elements Harboring bla KPC- 2 or bla NDM- 1 .
  Raro Otávio Hallal Ferreira et al. Frontiers in microbiology 2020 1563
• An alarming high prevalence of resistance-associated mutations to macrolides and fluoroquinolones in Mycoplasma genitalium in Belgium: results from samples collected between 2015 and 2018.
  De Baetselier Irith et al. Sexually transmitted infections 2020 Aug
• Fatal respiratory diphtheria caused by β-lactam-resistant Corynebacterium diphtheriae.
  Forde Brian M et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Aug
• Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon.
  Pascoe Ben et al. PLoS neglected tropical diseases 2020 Aug (8) e0008533
• Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis
  Ferrarini MG, et al. bioRxiv, Aug 5, 2020.
• Natural Polymorphisms Are Present in the Furin Cleavage Site of the SARS-CoV-2 Spike Glycoprotein.
  Xing Yue et al. Frontiers in genetics 2020 783
• Genetic Features of HIV-1 Integrase Sub-Subtype A6 Predominant in Russia and Predicted Susceptibility to INSTIs.
  Kirichenko Alina et al. Viruses 2020 Jul (8)

DETECTION / DIAGNOSIS

• A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine.
  Buytaers Florence E et al. Microorganisms 2020 Aug (8)
• Pentaplex real-time PCR for differential detection of Yersinia pestis and Y. pseudotuberculosis and application for testing fleas collected during plague epizootics.
  Bai Ying et al. MicrobiologyOpen 2020 Aug e1105 
• Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms.
  Yee Rebecca et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2020 Aug
• Genomic Surveillance of Streptococcus pyogenes Strains Causing Invasive Disease, United States, 2016-2017
  Li Y, et al. Front Microbiol, Jul 24, 2020. 
• A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples
  Thi VL, et al. Sci Transl Med, Aug 12, 2020.
• Rapid and extraction-free detection of SARS-CoV-2 from saliva with colorimetric LAMP
  Lalli MA, et al. medRxiv, Aug 6, 2020.
• Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP)
  Bokelmann L, et al. medRxiv, Aug 6, 2020.
• Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens
  Renuse S, et al. medRxiv, Aug 6, 2020.
• A Rapid, Simple, Inexpensive, and Mobile Colorimetric Assay COVID-19-LAMP for Mass On-Site Screening of COVID-19.
  Chow Franklin Wang-Ngai et al. International journal of molecular sciences 2020 Jul (15)
• Chikungunya virus Detection in Aedes aegypti and Culex quinquefasciatus during an Outbreak in the Amazon Region.
  Ribeiro Cruz Ana Cecília et al. Viruses 2020 Aug (8)
• Viruses in wastewater: occurrence, abundance and detection methods.
  Corpuz Mary Vermi Aizza et al. The Science of the total environment 2020 Jul 140910
• Impact of pretreatment low-abundance HIV-1 drug-resistant variants on virological failure among HIV-1/TB-co-infected individuals.
  Chimukangara Benjamin et al. The Journal of antimicrobial chemotherapy 2020 Aug
• Molecular epidemiology of astrovirus in children with gastroenteritis in southwestern Nigeria.
  Arowolo K O et al. Archives of virology 2020 Aug
• Rapid genotyping protocol to improve dengue virus serotype 2 survey in Lao PDR.
  Calvez Elodie et al. PloS one 2020 (8) e0237384
• Molecular evidence for local acquisition of human alveolar echinococcosis in Saskatchewan, Canada.
  Schurer Janna M et al. The Journal of infectious diseases 2020 Aug

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• Uncovering infant group B streptococcal (GBS) disease clusters in the UK and Ireland through genomic analysis: a population-based epidemiological study.
  Collin Simon M et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Aug
• Multidrug-Resistant Tuberculosis Among Workers at Two Food Processing Facilities -- Ohio, 2018-2019
  Talwar A, et al. MMWR, Aug 14, 2020.  
• An outbreak of Clostridioides difficile infections due to a 027-like PCR ribotype 181 in a rehabilitation centre: Epidemiological and microbiological characteristics.
  Kachrimanidou Melina et al. Anaerobe 2020 Aug 102252
• COVID-19 in Americans aboard the Diamond Princess cruise ship.
  Plucinski Mateusz M et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Aug  
• Using Virus Sequencing to Determine Source of SARS-CoV-2 Transmission for Healthcare Worker.
  Safdar Nasia et al. Emerging infectious diseases 2020 Aug (10) 
• Comprehensive Analyses of SARS-CoV-2 Transmission in a Public Health Virology Laboratory.
  Zuckerman Neta S et al. Viruses 2020 Aug (8)
• Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand
  Geoghegan JL, et al. medRxiv, Aug 7, 2020.
• Unique SARS-CoV-2 clusters causing a large COVID-19 outbreak in Hong Kong.
  To Kelvin Kai-Wang et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Aug

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• Engineered ACE2 receptor traps potently neutralize SARS-CoV-2.
  Glasgow Anum et al. bioRxiv : the preprint server for biology 2020 Aug

HOST-MICROBE INTERACTIONS

• Genetic variability in the expression of the SARS-CoV-2 host cell entry factors across populations.
  Ortiz-Fernández Lourdes et al. Genes and immunity 2020 Aug
• Management of epigenomic networks entailed in coronavirus infections and COVID-19.
  El Baba Ranim et al. Clinical epigenetics 2020 Aug (1) 118
• Evidence-Based Considerations Exploring Relations between SARS-CoV-2 Pandemic and Air Pollution: Involvement of PM2.5-Mediated Up-Regulation of the Viral Receptor ACE-2.
  Borro Marina et al. International journal of environmental research and public health 2020 08 (15)
• Genetic Susceptibility to Life-threatening Respiratory Syncytial Virus Infection in Previously Healthy Infants.
  López Eduardo Luis et al. The Pediatric infectious disease journal 2020 Jul
• Major Histocompatibility Complex Class I Chain-Related A and B (MICA and MICB) Gene, Allele, and Haplotype Associations With Dengue Infections in Ethnic Thais.
  Luangtrakool Panpimon et al. The Journal of infectious diseases 2020 Aug (5) 840-846
• Donor fecal microbiota transplantation ameliorates intestinal graft-versus-host disease in allogeneic hematopoietic cell transplant recipients
  van Lier YF, et al. Sci Transl Med, Aug 12, 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.