Publication Date: Jun 4, 2020
Advanced Molecular Detection Clips Content
NEWS
- How countries are using genomics to help avoid a second coronavirus wave
Watson C. Nature, May 29, 2020. - SARS-CoV-2 Spike Protein Shares Sequence with a Human Protein
Olena A. The Scientist, Jun 1, 2020. - NIH-halted study unveils its massive analysis of bat coronaviruses
Kupferschmidt K, Cohen J. Science, Jun 1, 2020. - Just stop the super-spreading
Adam DC, Cowling BJ. New York Times, Jun 2, 2020. - Microbial matters: modelling the complex web of host-microbiome interactions
Eisenstein, Nature, May 26, 2020.
EVENTS / TRAINING / WEB RESOURCES
- gnomAD: genome aggregation database
(collection) Nature, May 27, 2020. - GenOMICC study on COVID-19 patients
(study registration) GenOMICC Consortium, NHS (UK).
POLICY
- Connecting data, tools and people across Europe: ELIXIR's response to the COVID-19 pandemic.
Blomberg Niklas et al. European journal of human genetics : EJHG 2020 06 (6) 719-723 - An integrated national scale SARS-CoV-2 genomic surveillance network
The COVID-19 Genomics UK (COG-UK)Consortium, Lancet Microbe, Jun 2, 2020.
CONCEPTS / COMMENTS
- Knowledge synthesis of 100 million biomedical documents augments the deep expression profiling of coronavirus receptors.
Venkatakrishnan A J et al. eLife 2020 May - Ratcheting Down the Virulence of SARS-CoV-2 in the COVID-19 Pandemic.
Brufsky Adam et al. Journal of medical virology 2020 May - SARS-CoV-2 and COVID-19: A genetic, epidemiological, and evolutionary perspective.
Sironi Manuela et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 May 104384 - Promoting best practice in nucleotide sequence data sharing.
et al. Scientific data 2020 May (1) 152 - Left-Handed DNA Has a Biological Role Within a Dynamic Genetic Code
Brazil R. The Scientist, Jun 1, 2020. - The Infant Gut Microbiome and Probiotics that Work
Smilowitz JT, Taft DH. The Scientist, Jun 1, 2020. - Wastewater surveillance for population-wide Covid-19: The present and future.
Daughton Christian G et al. The Science of the total environment 2020 May 139631 - The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic.
et al. European journal of human genetics : EJHG 2020 06 (6) 715-718 - Airborne Spread of SARS-CoV-2 and a Potential Role for Air Disinfection.
Nardell Edward A et al. JAMA 2020 Jun - COVID-19 and veterinarians for one health, zoonotic- and reverse-zoonotic transmissions.
Yoo Han Sang et al. Journal of veterinary science 2020 May (3) e51 - Opinion: Intercepting pandemics through genomics
Kress WJ, et al. Proc Nat Acad Sci, Jun 3, 2020. - Editorial: Pathogen Genomics: Empowering Infectious Disease Surveillance and Outbreak Investigations
Struelens MJ, Sintchenko V. Front Public Health, May 19, 2020.
METHODS / TOOLS
- Improving Quantitative Power in Digital PCR through Digital High-Resolution Melting.
Aralar April et al. Journal of clinical microbiology 2020 May (6) - PIQMEE: Bayesian phylodynamic method for analysis of large datasets with duplicate sequences.
Boskova Veronika et al. Molecular biology and evolution 2020 Jun - Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding
Freed NE, et al. bioRxiv, May 29, 2020. - Optimizing the molecular diagnosis of Covid-19 by combining RT-PCR and a pseudo-convolutional machine learning approach to characterize virus DNA sequences
Gomes JC, et al. bioRxiv, Jun 2, 2020. - Predicting host taxonomic information from viral genomes: A comparison of feature representations.
Young Francesca et al. PLoS computational biology 2020 May (5) e1007894
EVOLUTION / ECOLOGY / POPULATIONS
- Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica.
Gao Ruimin et al. BMC genomics 2020 May (1) 374 - Similar yet different: phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries.
Pilar Ana Victoria C et al. BMC genomics 2020 May (1) 377 - Population Genomics of Mycobacterium leprae Reveals a New Genotype in Madagascar and the Comoros.
Avanzi Charlotte et al. Frontiers in microbiology 2020 711 - Early phylodynamics analysis of the COVID-19 epidemics in France
Danesh G, et al. medRxiv, Jun 4, 2020. - Exhaled breath is a significant source of SARS-CoV-2 emission
Ma J, et al. medRxiv, Jun 2, 2020.
- Emergence of SARS-CoV-2 through recombination and strong purifying selection
Li X, et al. Sci Adv, May 29, 2020. - Early Phylogenetic Diversification of SARS-CoV-2: Determination of Variants and the Effect on Epidemiology, Immunology, and Diagnostics.
Kaden Rene et al. Journal of clinical medicine 2020 May (6) - Origin and cross-species transmission of bat coronaviruses in China
Latinne A, et al. bioRxiv, May 31, 2020. - Update: proposed reference sequences for subtypes of hepatitis E virus (species Orthohepevirus A ).
Smith Donald B et al. The Journal of general virology 2020 May
- DNA analysis reveals non-falciparum malaria in the Democratic Republic of the Congo.
Podgorski Rachel M et al. Acta tropica 2020 May 105557
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Evolutionary causes and consequences of bacterial antibiotic persistence.
Bakkeren Erik et al. Nature reviews. Microbiology 2020 May - Sustained transmission of the ceftriaxone-resistant Neisseria gonorrhoeae FC428 clone in China.
Chen Shao-Chun et al. The Journal of antimicrobial chemotherapy 2020 May - Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes.
Iramiot Jacob Stanley et al. PloS one 2020 (5) e0231852 - Horizontal Gene Transfer of Antibiotic Resistance from Acinetobacter baylyi to Escherichia coli on Lettuce and Subsequent Antibiotic Resistance Transmission to the Gut Microbiome.
Maeusli Marlène et al. mSphere 2020 May (3) - Emerging Threat of Antimicrobial Resistance in β-Hemolytic Streptococci.
Oppegaard Oddvar et al. Frontiers in microbiology 2020 797 - Genomic signatures of drug resistance in highly resistant Mycobacterium tuberculosis strains of the early ancient sublineage of Beijing genotype in Russia.
Mokrousov Igor et al. International journal of antimicrobial agents 2020 May 106036 - Mutations strengthened SARS-CoV-2 infectivity
J Chen et al, arxiv, May 27, 2020. - Viral load dynamics in transmissible symptomatic patients with COVID-19
Kawasuji H, et al. medRxiv, Jun 4, 2020. - Impact of an Open Access Nationwide Treatment Model on Hepatitis C Virus Antiviral Drug Resistance.
Douglas Mark W et al. Hepatology communications 2020 Jun (6) 904-915 - Genomic and Phenotypic Heterogeneity of Clinical Isolates of the Human Pathogens Aspergillus fumigatus , Aspergillus lentulus , and Aspergillus fumigatiaffinis .
Dos Santos Renato A C et al. Frontiers in genetics 2020 459
DETECTION / DIAGNOSIS
- A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing.
Neuenschwander Stefan Moritz et al. Journal of clinical microbiology 2020 May (6) - Identification of Mycobacterium tuberculosis Peptides in Serum Extracellular Vesicles from Persons with Latent Tuberculosis Infection.
Mehaffy Carolina et al. Journal of clinical microbiology 2020 May (6) - Comparative Performance of SARS-CoV-2 Detection Assays Using Seven Different Primer-Probe Sets and One Assay Kit
Nalla AK, et al. J Clin Microbiol, May 26, 2020. - EasyCOV : LAMP based rapid detection of SARS-CoV-2 in saliva
L'Helgouach N, et al. medRxiv, May 30, 2020. - Implication of SARS-CoV-2 evolution in the sensitivity of RT-qPCR diagnostic assays.
Osório Nuno Sampaio et al. The Lancet. Infectious diseases 2020 May - Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay.
Yan C et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2020 Jun (6) 773-779 - Rapid detection of SARS-CoV-2 and other respiratory viruses by using LAMP method with Nanopore Flongle workflow
Li J, et al. bioRxiv, Jun 3, 2020. - Direct diagnostic testing of SARS-CoV-2 without the need for prior RNA extraction.
Wei S, et al. medRxiv, Jun 2, 2020. - Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients.
Chia Po Ying et al. Nature communications 2020 May (1) 2800 - SARS-CoV-2 RNA in wastewater anticipated COVID-19 occurrence in a low prevalence area.
Randazzo Walter et al. Water research 2020 May 115942
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Evidence for Limited Early Spread of COVID-19 Within the United States, January-February 2020
CDC COVID-19 Response Team, et al. MMWR, May 29, 2020. - SARS-CoV-2 transmission chains from genetic data: a Danish case study
Bluhm A, et al. bioRxiv, May 29, 2020. - Genomic analysis of early SARS-CoV-2 strains introduced in Mexico
Taboada B, et al. bioRxiv, May 29, 2020. - A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates
Banu S, et al. bioRxiv, May 29, 2020. - Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report
Giandhari J, et al. medRxiv, May 30, 2020. - Introductions and early spread of SARS-CoV-2 in the New York City area.
Gonzalez-Reiche Ana S et al. Science (New York, N.Y.) 2020 May - Seoul virus infection and spread in US home-based ratteries-rat and human testing results from a multistate outbreak investigation.
Knust Barbara et al. The Journal of infectious diseases 2020 Jun - Mapping of HIV-1C Transmission Networks Reveals Extensive Spread of Viral Lineages across Villages in Botswana Treatment-as-Prevention Trial.
Novitsky Vlad et al. The Journal of infectious diseases 2020 Jun - Origin of HAV strains responsible for 2016-2017 outbreak among MSM: Viral phylodynamics in Lazio region.
Minosse Claudia et al. PloS one 2020 (5) e0234010
HOST-MICROBE INTERACTIONS
- Human Genetic Susceptibility of Leprosy Recurrence.
Uaska Sartori Priscila Verchai et al. Scientific reports 2020 Jan (1) 1284 - Proteomic and Metabolomic Characterization of COVID-19 Patient Sera
Shen B, et al. Cell, May 27, 2020. - Targeted Immunosuppression Distinguishes COVID-19 from Influenza in Moderate and Severe Disease
Mudd PA, et al. medRxiv, May 30, 2020. - Clearance and Persistence of SARS-CoV-2 RNA in COVID-19 patients.
Carmo Anália et al. Journal of medical virology 2020 Jun - The stepwise assembly of the neonatal virome is modulated by breastfeeding.
Liang Guanxiang et al. Nature 2020 May (7809) 470-474 - Persistence and clearance of oral human papillomavirus infections: a prospective population-based cohort study.
Wong Martin Cs et al. Journal of medical virology 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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