Advanced Molecular Detection Clips Content (Published on 07/14/2022)
NEWS
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New Method Optimizes Conversion of Illumina Libraries for Nanopore Sequencing
Zhang H. GenomeWeb, Jul 8, 2022. -
COVID variants found in sewage weeks before showing up in tests
Mallapaty S. Nature, Jul 8, 2022. -
Is BA.5 the ‘Reinfection Wave’?
Yong E. Atlantic, Jul 11, 2022. -
As BA.5 Spreads, White House Warns Covid Is Not Over
Stolberg SG. New York Times, Jul 12, 2022. -
RADx-Funded Team Develops Genotyping Panels for Monitoring SARS-CoV-2 Variants
Bonislawski A. GenomeWeb, Jul 13, 2022. -
Monkeypox cases continue to spike in UK
Soucheray S. CIDRAP, Jul 12, 2022. -
The U.S. May Be Losing the Fight Against Monkeypox, Scientists Say
Mandavilli A. New York Times, Jul 8, 2022. -
How Far Will Monkeypox Spread in the U.S.? — Testing and surveillance for both monkeypox and syphilis play a big role in the outcome
Swann J. MedPage Today, Jul 7, 2022. -
Ghana reports first-ever suspected cases of Marburg virus disease
WHO, Jul 7, 2022. -
Studies Probe Adenovirus Link to Childhood Hepatitis Cases
Anthes E. New York Times, Jul 13, 2022. -
NIAID initiates Phase I trial of Moderna’s Nipah virus vaccine
Clinical Trials Arena, Jul 12, 2022. -
Ex-Google chief’s venture aims to save neglected science software
Matthews D. Nature, Jul 13, 2022.
EVENTS / TRAINING / WEB RESOURCES
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A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data
(tutorial) Fang F, Zhou H. J Vis Exp, J Vis Exp. 2021 Sep 25;(175).
CONCEPTS / COMMENTS
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Genomic Sequencing Is Critical to Our Understanding of COVID
Karan A, et al. Scientific American, Jul 13, 2022. -
Monkeypox genomic surveillance will challenge lessons learned from SARS-CoV-2.
Pfaff Florian et al. Lancet (London, England) 2022 7 (10345) 22-23
METHODS / TOOLS
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Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes.
Hunt Martin et al. Genome biology 2022 7 (1) 147 -
Threshold-free genomic cluster detection to track transmission pathways in health-care settings: a genomic epidemiology analysis.
Hawken Shawn E et al. The Lancet. Microbe 2022 7 -
A Bottom-up Approach to Testing Hypotheses That Have a Branching Tree Dependence Structure, with Error Rate Control.
Li Yunxiao et al. Journal of the American Statistical Association 2022 7 (538) 664-677
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Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format (NAF).
Kryukov Kirill et al. Patterns (New York, N.Y.) 2022 7 100562 -
Identification of conserved regions from 230,163 SARS-CoV-2 genomes and their use in diagnostic PCR primer design.
Jeong Haeyoung et al. Genes & genomics 2022 6 (8) 899-912 -
VirusLab: A Tool for Customized SARS-CoV-2 Data Analysis.
Pinoli Pietro et al. Biotech (Basel (Switzerland)) 2022 7 (4) -
Rapid, in-field deployable, avian influenza virus haemagglutinin characterisation tool using MinION technology.
de Vries Ellen M et al. Scientific reports 2022 7 (1) 11886
EVOLUTION / ECOLOGY / POPULATIONS
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Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat.
Hannon William W et al. Virus evolution 2022 7 (2) veac052 -
Evolutionary insight into the emergence of SARS-CoV-2 variants of concern.
et al. Nature medicine 2022 7 -
Evolution, Transmission, and Pathogenicity of High Pathogenicity Avian Influenza Virus A (H5N8) Clade 2.3.4.4, South Korea, 2014-2016.
Baek Yoon-Gi et al. Frontiers in veterinary science 2022 7 906944 -
Replacement of Leishmania (Leishmania) infantum Populations in an Endemic Focus of Visceral Leishmaniasis in Brazil.
Valdivia Hugo O et al. Frontiers in cellular and infection microbiology 2022 7 900084 -
Estimating the genetic structure of Triatoma dimidiata (Hemiptera: Reduviidae) and the transmission dynamics of Trypanosoma cruzi in Boyacá, eastern Colombia.
Velásquez-Ortiz Natalia et al. PLoS neglected tropical diseases 2022 7 (7) e0010534 -
Origins of high latitude introductions of Aedes aegypti to Nebraska and Utah during 2019.
Andrea Gloria-Soria et al. Infect Genet Evol 2022 7 105333
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Use of Large-Scale Genomics to Identify the Role of Animals and Foods as Potential Sources of Extraintestinal Pathogenic Escherichia coli That Cause Human Illness.
Harrison Lucas et al. Foods (Basel, Switzerland) 2022 7 (13)
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Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections.
Serpa Paula Hayakawa et al. Genome medicine 2022 7 (1) 74 -
Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae.
David Sophia et al. PLoS pathogens 2022 7 (7) e1010334 -
Distinct Streptococcus pneumoniae cause invasive disease in Papua New Guinea.
Mellor Kate C et al. Microbial genomics 2022 7 (7) -
Data-driven platform for identifying variants of interest in COVID-19 virus.
Ramarao-Milne Priya et al. Computational and structural biotechnology journal 2022 6 2942-2950 -
Predictive model for severe COVID-19 using SARS-CoV-2 whole-genome sequencing and electronic health record data, March 2020-May 2021.
Zhu Lei et al. PloS one 2022 7 (7) e0271381 -
SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern.
Aggarwal A, et al. medRxiv, Jul 10, 2022.
DETECTION / DIAGNOSIS
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Genetic diversity and spatial distribution of Burkholderia mallei by core genome-based multilocus sequence typing analysis.
Appelt Sandra et al. PloS one 2022 7 (7) e0270499 -
Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon.
Fuesslin Valeria et al. Frontiers in microbiology 2022 7 909692 -
Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.
Smruthi Karthikeyan et al. Nature 2022 7 (7925) 101-108 -
Understanding the dynamic relation between wastewater SARS-CoV-2 signal and clinical metrics throughout the pandemic
Hegazy N, et al. medRxiv, Jul 7, 2022. -
SARS-CoV-2 molecular diagnosis at airports to minimize travel-related COVID-19 spread.
de La Vega Marc-Antoine et al. Scientific reports 2022 7 (1) 11753 -
Large-Scale SARS-CoV-2 Testing Utilizing Saliva and Transposition Sample Pooling.
Patterson Joseph R et al. Journal of visualized experiments : JoVE 2022 7 (184) -
Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand
Jelley L, et al. Nat Commun. 2022 Jul 12;13(1):4035. -
A Case Series of Children with Acute Hepatitis and Human Adenovirus Infection.
L Helena Gutierrez Sanchez et al. N Engl J Med 2022 7 (7) 620-630
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Monkeypox outbreak in Madrid (Spain): clinical and virological aspects.
Orviz Eva et al. The Journal of infection 2022 7 -
Rapid Diagnostic Testing for Response to the Monkeypox Outbreak — Laboratory Response Network, United States, May 17–June 30, 2022
Aden TA, et al. MMWR, Jul 8, 2022.
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Evidence of surface contamination in hospital rooms occupied by patients infected with monkeypox, Germany, June 2022.
Nörz Dominik et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2022 7 (26) -
A Straightforward HPV16 Lineage Classification Based on Machine Learning.
Asensio-Puig Laura et al. Frontiers in artificial intelligence 2022 7 851841 -
Diagnostic performance of loop-mediated isothermal amplification and ultra-sensitive rapid diagnostic tests for malaria screening among pregnant women in Kenya
Samuels AM, et al. J Infect Dis. 2022 Jul 11;jiac289.
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Prospective surveillance study to detect antimalarial drug resistance, gene deletions of diagnostic relevance and genetic diversity of Plasmodium falciparum in Mozambique: protocol
Mayor A, et al. BMJ Open. 2022 Jul 12;12(7):e063456.
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Listeria monocytogenes Illness and Deaths Associated With Ongoing Contamination of a Multiregional Brand of Ice Cream Products, United States, 2010-2015.
Amanda R Conrad et al. Clin Infect Dis 2022 7 (1) 89-95
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Outbreak of sexually transmitted, extensively drug-resistant Shigella sonnei in the UK, 2021-22: a descriptive epidemiological study.
Charles Hannah et al. The Lancet. Infectious diseases 2022 7
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Tuberculosis Outbreaks in State Prisons, United States, 2011-2019.
Stewart Rebekah J et al. American journal of public health 2022 7 (8) 1170-1179
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Genomic Surveillance Identifies SARS-CoV-2 Transmission Patterns in Local University Populations, Wisconsin, USA, 2020–2022
Ramaiah A, et al. medRxiv, Jul 8, 2022. -
Epidemiologic Features and Control Measures during Monkeypox Outbreak, Spain, June 2022.
Rodríguez Berta Suárez et al. Emerging infectious diseases 2022 7 (9)
HOST-MICROBE INTERACTIONS
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Infection With the US Neisseria meningitidis Urethritis Clade Does Not Lower Future Risk of Urethral Gonorrhea.
Turner Abigail Norris et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 9 (12) 2159-2165
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Analysis of the docking property of host variants of hACE2 for SARS-CoV-2 in a large cohort.
Paik Hyojung et al. PLoS computational biology 2022 7 (7) e1009834 -
The association of human leucocyte antigen (HLA) alleles with COVID-19 severity: A systematic review and meta-analysis.
Dobrijevic Zorana et al. Reviews in medical virology 2022 7 e2378 -
Genetic polymorphisms associated with susceptibility to COVID-19 disease and severity: A systematic review and meta-analysis.
Dieter Cristine et al. PloS one 2022 7 (7) e0270627 -
Genetic regulation of OAS1 nonsense-mediated decay underlies association with COVID-19 hospitalization in patients of European and African ancestries
Banday AR, et al. Nat Genet, Jul 14, 2022. -
SARS-CoV-2 Omicron sublineages exhibit distinct antibody escape patterns
Gruell H, et al. Cell Host Microbe, Jul 6, 2022.
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 Public Health Genomics Branch 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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