Publication Date: Aug 20, 2020
Advanced Molecular Detection Clips Content
NEWS
- Medieval DNA suggests Columbus didn't trigger syphilis epidemic in Europe
Hartley C. Science, Aug 13, 2020. - FDA, partners to expand NARMS antibiotic resistance efforts
Dall C. CIDRAP, Aug 19, 2020. - Israeli hospital trials super-quick saliva test for COVID-19
Reuters, Aug 13, 2020. - Coronavirus invaded the District and Maryland multiple times in March, genetic analysis shows
Achenbach J. Washington Post, Aug 17, 2020. - Coronavirus (COVID-19) Update: FDA Issues Emergency Use Authorization to Yale School of Public Health for SalivaDirect, Which Uses a New Method of Saliva Sample Processing
(news release) FDA, Aug 15, 2020.
CONCEPTS / COMMENTS
- On the evolutionary epidemiology of SARS-CoV-2.
Day Troy et al. Current biology : CB 2020 08 (15) R849-R857 - Legal and ethical implications of wastewater monitoring of SARS-CoV-2 for COVID-19 surveillance.
Gable Lance et al. Journal of law and the biosciences (1) lsaa039 - Bias at Warp Speed: How AI may Contribute to the Disparities Gap in the Time of COVID-19.
Röösli Eliane et al. Journal of the American Medical Informatics Association : JAMIA 2020 Aug - Accelerating genomics-based surveillance for COVID-19 response in Africa
Tessema SK, et al. Lancet Microbe, Aug 18, 2020. - Development of Microbiome Biobanks - Challenges and Opportunities.
Ryan M J et al. Trends in microbiology 2020 Jul
METHODS / TOOLS
- minMLST: machine-learning for optimization of bacterial strain typing.
Cohen Shani et al. Bioinformatics (Oxford, England) 2020 Aug - Going back to the roots: Evaluating Bayesian phylogeographic models with discrete trait uncertainty.
Vaiente Matteo A et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 Aug 104501 - Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination.
Berbers Bas et al. Antibiotics (Basel, Switzerland) 2020 Aug (8) - Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices.
Ott Isabel M et al. medRxiv : the preprint server for health sciences 2020 Aug
EVOLUTION / ECOLOGY / POPULATIONS
- Upsurge of conjugate vaccine serotype 4 invasive pneumococcal disease clusters among adults experiencing homelessness in California, Colorado, and New Mexico.
Beall Bernard et al. The Journal of infectious diseases 2020 Aug
- Molecular characterization of Staphylococcus aureus complex from fomites in Nigeria.
Shittu Adebayo Osagie et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 Aug 104504 - Phenotypic and genotypic characterization of Salmonella Typhimurium isolates from humans and foods in Brazil.
Seribelli Amanda Aparecida et al. PloS one 2020 (8) e0237886 - Genetic tracing of HCoV-19 for the re-emerging outbreak of COVID-19 in Beijing, China.
Yang Jing et al. Protein & cell 2020 Aug - Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020.
Alm Erik et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2020 Aug (32) - Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region
Thielen P, medRxiv, Aug 15, 2020. - Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity
Islam MR, et al. Sci Rep, Aug 19, 2020. - Molecular Characterization of Chikungunya Virus during the 2019 Outbreak in the Democratic Republic of the Congo.
Selhorst Philippe et al. Emerging microbes & infections 2020 Aug 1-25 - Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities.
Jia Na et al. Cell 2020 Aug
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Genomic background of the Klebsiella pneumoniae NDM-1 outbreak in Poland, 2012-18.
Izdebski R et al. The Journal of antimicrobial chemotherapy 2020 Aug - Comparative genomic analysis of a Shiga toxin-producing Escherichia coli (STEC) O145:H25 associated with a severe pediatric case of hemolytic uremic syndrome in Davidson County, Tennessee, US
Guerra JA, et al. BMC Genomics, Aug 17, 2020. - Population-level emergence of bedaquiline and clofazimine resistance-associated variants among patients with drug-resistant tuberculosis in southern Africa: a phenotypic and phylogenetic analysis.
Nimmo Camus et al. The Lancet. Microbe 2020 Aug (4) e165-e174 - Whole genome sequencing for antimicrobial resistance mechanisms, virulence factors and clonality in invasive Streptococcus agalactiae blood culture isolates recovered in Australia.
Stewart Adam G et al. Pathology 2020 Aug - Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study
Young BE, et al. Lancet, Aug 18, 2020. - Hepatitis A Virus Survival on Drug Paraphernalia.
Medrzycki Magdalena et al. Journal of viral hepatitis 2020 Aug - Assessment of molecular markers of anti-malarial drug resistance among children participating in a therapeutic efficacy study in western Kenya.
Chebore Winnie et al. Malaria journal 2020 Aug (1) 291 - Molecular and epidemiological characterization of imported malaria cases in Chile.
Escobar Daniel F et al. Malaria journal 2020 Aug (1) 289
DETECTION / DIAGNOSIS
- Comparison of Whole Genome (wg-) and Core Genome (cg-) MLST (BioNumerics TM ) Versus SNP Variant Calling for Epidemiological Investigation of Pseudomonas aeruginosa .
Blanc Dominique S et al. Frontiers in microbiology 2020 1729 - Clinical diagnostic application of metagenomic next-generation sequencing in children with severe nonresponding pneumonia.
Wang Heping et al. PloS one 2020 (6) e0232610 - Advances in Molecular Diagnosis of Tuberculosis.
MacLean Emily et al. Journal of clinical microbiology 2020 Aug - Epidemiology of Shigella infections and diarrhea in the first two years of life using culture-independent diagnostics in 8 low-resource settings.
Rogawski McQuade Elizabeth T et al. PLoS neglected tropical diseases 2020 Aug (8) e0008536 - Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020.
Singanayagam Anika et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2020 08 (32) - Extraction-free SARS-CoV-2 detection by rapid RT-qPCR universal for all primary respiratory materials.
Lübke Nadine et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2020 Aug 104579 - SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication
Alexanderson S, et al. medRxiv, Aug 16, 2020. - Genome sequencing and the diagnosis of novel coronavirus (SARS-COV-2) in Africa: how far are we?
Shey Muki et al. The Pan African medical journal 2020 80 - Pooling of SARS-CoV-2 samples to increase molecular testing throughput.
Perchetti Garrett A et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2020 Aug 104570 - Highly sensitive quantification of plasma SARS-CoV-2 RNA shelds light on its potential clinical value.
Veyer David et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Aug - Setting a baseline for global urban virome surveillance in sewage.
Nieuwenhuijse David F et al. Scientific reports 2020 Aug (1) 13748 - Herpes Simplex Virus Mistyping due to HSV-1 × HSV-2 Interspecies Recombination in Viral Gene Encoding Glycoprotein B.
Casto Amanda M et al. Viruses 2020 Aug (8) - Trypanosoma cruzi loop-mediated isothermal amplification (Trypanosoma cruzi Loopamp) kit for detection of congenital, acute and Chagas disease reactivation.
Besuschio Susana A et al. PLoS neglected tropical diseases 2020 Aug (8) e0008402
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Characterization and Source Investigation of Multidrug-Resistant Salmonella Anatum from a Sustained Outbreak, Taiwan
Feng Y, et al. Emerg Infect Dis, Aug 18, 2020. - Insights on COVID-19 epidemiology from a historic cruise ship quarantine.
Yamagishi Takuya et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Aug - Fatal multiple outbreaks of equine influenza H3N8 in Nigeria, 2019: the first introduction of Florida clade 1 to West Africa
Shittu I, et al. Vet Microbiol, Aug 13, 2020. - Microgeographic epidemiology of malaria parasites in an irrigated area of western Kenya by deep amplicon sequencing.
Hemming-Schroeder Elizabeth et al. The Journal of infectious diseases 2020 Aug
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- First insight into the whole-genome sequence variations in Mycobacterium bovis BCG-1 (Russia) vaccine seed lots and their progeny clinical isolates from children with BCG-induced adverse events.
Narvskaya Olga et al. BMC genomics 2020 Aug (1) 567 - Effect of an Inactivated Vaccine Against SARS-CoV-2 on Safety and Immunogenicity Outcomes Interim Analysis of 2 Randomized Clinical Trials
Shia S, et al. JAMA, Aug 13, 2020.
HOST-MICROBE INTERACTIONS
- Early Life Microbiota and Respiratory Tract Infections.
de Steenhuijsen Piters Wouter A A et al. Cell host & microbe 2020 Aug (2) 223-232 - The Impact of the Microbiome on Immunity to Vaccination in Humans.
de Jong Sanne E et al. Cell host & microbe 2020 Aug (2) 169-179 - Strain-level epidemiology of microbial communities and the human microbiome.
Yan Yan et al. Genome medicine 2020 Aug (1) 71 - Immuno-epidemiology and pathophysiology of coronavirus disease 2019 (COVID-19).
Olwenyi Omalla A et al. Journal of molecular medicine (Berlin, Germany) 2020 Aug - Host polymorphisms may impact SARS-CoV-2 infectivity
Brest P, et al. Trends Genet, Aug 10, 2020. - The Role of Host Genetic Factors in Coronavirus Susceptibility: Review of Animal and Systematic Review of Human Literature
LoPresti M, et al. Am J Hum Genet, Aug 10, 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.
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