Publication Date: Apr 2, 2020
Advanced Molecular Detection Clips Content
NEWS
- UK Government Invests $28M in FIND to Support SARS-CoV-2 Test Development
GenomeWeb, Mar 27, 2020. - Oxford University Developing Molecular Point-of-Care Coronavirus Test
O'Connor L. GenomeWeb, Mar 26, 2020. - SARS-CoV-2 Serology Testing Ramping Up to Address Next Stages of Pandemic
Bonislawski A. GenomeWeb, Mar 26, 2020. - Covid-19 spreads too fast for traditional contact tracing. New digital tools could help
Begley S. STAT, Apr 2, 2020. - Africa Contributes SARS-CoV-2 Sequencing to COVID-19 Tracking
Makoni M. The Scientist, Mar 30, 2020. - COVID-19 Vaccine Developers Gain Enhanced Access to Supercomputers
Winter L. The Scientist, Mar 27, 2020. - Scientists, under pressure, try to balance speed and safety on coronavirus vaccine research
Chow D. NBC News, Mar 26, 2020. - How sick will the coronavirus make you? The answer may be in your genes
Kaiser J. Science, Mar 27, 2020.
EVENTS / TRAINING / WEB RESOURCES
- NextTrace
(announcement) - Announcing NCBI Datasets -- try it out!
(announcement) NCBI Insights, Mar 30, 2020. - Manipulating the Human Microbiome for Precision Public Health: Prospects and Challenges
(blog post) Haile M, et al. CDC, Office of Genomics and Precision Public Health, Mar 31, 2020.
CONCEPTS / COMMENTS
- On the responsible use of digital data to tackle the COVID-19 pandemic
Ienca M, Vayena E. Nat Med, Mar 27, 2020. - Digital technology and COVID-19
Ting DS, et al. Nat Med, Mar 27, 2020. - Using whole genome sequencing to help combat COVID-19
Janus J. PHG Foundation, Mar 27, 2020. - Immunoproteomics Methods and Techniques.
Fulton Kelly M et al. Methods in molecular biology (Clifton, N.J.) 2019 25-58 - Developing Covid-19 Vaccines at Pandemic Speed
Lurie N, et al. New Engl J Med, Mar 30, 2020. - Forty years with coronaviruses.
Weiss Susan R et al. The Journal of experimental medicine 2020 May (5) - Publishing in the time of COVID-19.
Eisen Michael B et al. eLife 2020 03 - Do preprints improve with peer review? A little, one study suggests
Brainard J. Science, Mar 26, 2020. - Experts' Perspectives on Key Ethical Issues Associated With HIV Phylogenetics as Applied in HIV Transmission Dynamics Research.
Mutenherwa Farirai et al. Journal of empirical research on human research ethics : JERHRE 2019 02 (1) 61-77 - Ten simple rules for providing effective bioinformatics research support.
Kumuthini Judit et al. PLoS computational biology 2020 Mar (3) e1007531
METHODS / TOOLS
- Deciphering the role of insertion sequences in the evolution of bacterial epidemic pathogens with panISa software.
Couchoud Charlotte et al. Microbial genomics 2020 Mar - TiTUS: Sampling and Summarizing Transmission Trees with Multi-strain Infections
Sashittal P, El-Kebir M. bioRxiv, Mar 26, 2020. - Defining metrics for whole-genome sequence analysis of MRSA in clinical practice.
Raven Kathy E et al. Microbial genomics 2020 Mar - Meta-SourceTracker: application of Bayesian source tracking to shotgun metagenomics.
McGhee Jordan J et al. PeerJ 2020 e8783 - A model of tuberculosis clustering in low incidence countries reveals more transmission in the United Kingdom than the Netherlands between 2010 and 2015.
Brooks-Pollock Ellen et al. PLoS computational biology 2020 Mar (3) e1007687 - Prediction of SARS-CoV-2 epitopes across 9360 HLA class I alleles
Campbell KM, et al. bioRxiv, Apr 1, 2020. - PAIVS: prediction of avian influenza virus subtype.
Park Hyeon-Chun et al. Genomics & informatics 2020 Mar (1) e5 - Optimization of parasite DNA enrichment approaches to generate whole genome sequencing data for Plasmodium falciparum from low parasitaemia samples.
Shah Zalak et al. Malaria journal 2020 Mar (1) 135
EVOLUTION / ECOLOGY / POPULATIONS
- Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones.
Ludden Catherine et al. Microbial genomics 2020 Mar - Toxigenic Vibrio cholerae evolution and establishment of reservoirs in aquatic ecosystems
Mavian C, et al. Proc Natl Acad Sci, Mar 30, 2020. - Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins.
Lam Tommy Tsan-Yuk et al. Nature 2020 Mar - Sequence variation among SARS-CoV-2 isolates in Taiwan
Gong YN, et al. bioRxiv, Mar 31, 2020. - SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies
Karamitros T, et al. bioRxiv, Mar 28, 2020. - Codon usage and evolutionary rates of the 2019-nCoV genes
Dilucca M, et al. bioRxiv, Mar 29, 2020. - GENOMIC CHARACTERISATION AND PHYLOGENETIC ANALYSIS OF SARS-COV-2 IN ITALY.
Zehender Gianguglielmo et al. Journal of medical virology 2020 Mar - Survey on Non-Human Primates and Mosquitoes Does not Provide Evidences of Spillover/Spillback between the Urban and Sylvatic Cycles of Yellow Fever and Zika Viruses Following Severe Outbreaks in Southeast Brazil.
Abreu Filipe Vieira Santos de et al. Viruses 2020 Mar (4)
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Contributions of insertion sequences conferring colistin resistance in Klebsiella pneumoniae.
Yang Tsung-Ying et al. International journal of antimicrobial agents 2020 Mar (3) 105894 - Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium (VREfm) in Latin America: Revisiting The Global VRE Population Structure.
Rios Rafael et al. Scientific reports 2020 Mar (1) 5636 - Acquisition of plasmids conferring carbapenem and aminoglycoside resistance and loss of surface-exposed macromolecule structures as strategies for the adaptation of Acinetobacter baumannii CC104 O /CC15 P strains to the clinical setting.
Cameranesi María M et al. Microbial genomics 2020 Mar - Environmental Methicillin-resistant Staphylococcus aureus Contamination, Persistent Colonization, and Subsequent Skin and Soft Tissue Infection.
Hogan Patrick G et al. JAMA pediatrics 2020 Mar - Virological assessment of hospitalized patients with COVID-2019
Wolfel R, et al. Nature, Apr 1, 2020. - Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: An in silico analysis.
Ortega Joseph Thomas et al. EXCLI journal 2020 410-417 - Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study.
To Kelvin Kai-Wang et al. The Lancet. Infectious diseases 2020 Mar - Transmission Potential of SARS-CoV-2 in Viral Shedding Observed at the University of Nebraska Medical Center
Santarpia JL, et al. medRxiv, Mar 26, 2020. - Machine Learning Methods for Predicting Human-Adaptive Influenza A Viruses Based on Viral Nucleotide Compositions.
Li Jing et al. Molecular biology and evolution 2020 Apr (4) 1224-1236
DETECTION / DIAGNOSIS
- Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture.
Cummings Lisa A et al. Scientific reports 2020 Mar (1) 5446 - Diagnosing COVID-19: The Disease and Tools for Detection.
Udugama Buddhisha et al. ACS nano 2020 Mar - Analytical sensitivity and efficiency comparisons of SARS-COV-2 qRT-PCR assays
Vogels CB, et al. medRxiv, Apr 1, 2020. - SARS-CoV-2 detection using digital PCR for COVID-19 diagnosis, treatment monitoring and criteria for discharge
Lu R, et al. medRxiv, Mar 30, 2020. - Evaluation of Group Testing for SARS-CoV-2 RNA
Sinnott-Armstrong N, et al. medRxiv, Mar 30, 2020. - Failed detection of the full-length genome of SARS-CoV-2 by ultra-deep sequencing from the recovered and discharged patients retested viral PCR positive
Hu F, et al. medRxiv, Mar 30, 2020. - Comparative performance of four nucleic acid amplification tests for SARS-CoV-2 virus
Xiong Y, et al. Mar 29, 2020. - Evaluation of COVID-19 RT-qPCR test in multi-sample pools
Yelin I, et al. medRxiv, Mar 27, 2020. - Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients.
Yu Fengting et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Mar - Epidemiological Surveillance of Norovirus and Rotavirus in Sewage (2016-2017) in Valencia (Spain).
Santiso-Bellón Cristina et al. Microorganisms 2020 Mar (3) - Peptide arrays incubated with three collections of human sera from patients infected with mosquito-borne viruses.
Martinez Viedma Maria Del Pilar et al. F1000Research 2019 1875 - WHO malaria nucleic acid amplification test external quality assessment scheme: results of distribution programmes one to three.
Cunningham Jane A et al. Malaria journal 2020 Mar (1) 129
- Schistosoma species detection by environmental DNA assays in African freshwaters.
Alzaylaee Hind et al. PLoS neglected tropical diseases 2020 Mar (3) e0008129
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Genomic epidemiology and population structure of Neisseria gonorrhoeae in Norway, 2016-2017.
Alfsnes Kristian et al. Microbial genomics 2020 Mar - Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak
Sekizuka T, et al. Mar 27, 2020. - Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology
Fauver JR, et al. medRxiv, Mar 26, 2020. - A Territory-wide study of COVID-19 cases and clusters with unknown source in Hong Kong community: A clinical, epidemiological and phylogenomic investigation
Leung KS, et al. medRxiv, Mar 31, 2020. - Early Spread of SARS-Cov-2 in the Icelandic Population
Gudbjartsson DF, et al. medRxiv, Mar 31, 2020. - Using an Established Outbreak Response Plan and Molecular Epidemiology Methods in an HIV Transmission Cluster Investigation, Tennessee, January-June 2017.
Sizemore Lindsey et al. Public health reports (Washington, D.C. : 1974) 2020 Mar 33354920915445 - Investigation of an extensive outbreak of HIV infection among children in Sindh, Pakistan: protocol for a matched case - control study.
Siddiqui Amna R et al. BMJ open 2020 Mar (3) e036723 - Genotyping and Subtyping Cryptosporidium To Identify Risk Factors and Transmission Patterns - Nebraska, 2015-2017.
Loeck Brianna K et al. MMWR. Morbidity and mortality weekly report 2020 Mar (12) 335-338
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Anti-HCV, nucleotide inhibitors, repurposing against COVID-19.
Elfiky Abdo A et al. Life sciences 2020 May 117477 - Development of a new oral poliovirus vaccine for the eradication end game using codon deoptimization.
Konopka-Anstadt Jennifer L et al. NPJ vaccines 2020 26 - Influenza vaccine effectiveness by A(H3N2) phylogenetic sub-cluster and prior vaccination history: 2016-17 and 2017-18 epidemics in Canada.
Skowronski Danuta M et al. The Journal of infectious diseases 2020 Mar - Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design
Kames J, et al. bioRxiv, Mar 31, 2020.
HOST-MICROBE INTERACTIONS
- Site-specific molecular analysis of the bacteriota on worn spectacles.
Fritz Birgit et al. Scientific reports 2020 Mar (1) 5577 - Decreasing antibiotic use, the gut microbiota, and asthma incidence in children: evidence from population-based and prospective cohort studies.
Patrick David M et al. The Lancet. Respiratory medicine 2020 Mar - Cervicovaginal microbiome and natural history of HPV in a longitudinal study.
Usyk Mykhaylo et al. PLoS pathogens 2020 Mar (3) e1008376 - Immune-Microbiota Interplay and Colonization Resistance in Infection.
Leshem Avner et al. Molecular cell 2020 Mar - Recent advances in primary immunodeficiency: from molecular diagnosis to treatment.
Bucciol Giorgia et al. F1000Research 2020 - Structural analysis of SARS-CoV-2 and prediction of the human interactome
Vandelli A, et al. bioRxiv, Mar 31, 2020. - The host's angiotensin-converting enzyme polymorphism may explain epidemiological findings in COVID-19 infections.
Delanghe Joris R et al. Clinica chimica acta; international journal of clinical chemistry 2020 Mar - ACE2 Expression is Increased in the Lungs of Patients with Comorbidities Associated with Severe COVID-19
Bruna GG, et al. medRxiv, Mar 27, 2020. - Cigarette smoke triggers the expansion of a subpopulation of respiratory epithelial cells that express the SARS-CoV-2 receptor ACE2
Smith JC, Sheltzer JM. bioRxiv, Mar 31, 2020. - Is There an Association Between COVID-19 Mortality and the Renin-Angiotensin System-a Call for Epidemiologic Investigations.
Hanff Thomas C et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Mar
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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