Advanced Molecular Detection Clips Content (Published on 01/06/2022)
NEWS
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Tech-Boosted Genome Assembly Helps Resolve Closely Related Microbes in Metagenomic Sample
Han AP. GenomeWeb, Jan 3, 2022. -
Forecasting the Omicron winter: Experts envision various scenarios, from bad to worse
Molteni M. STAT, Dec 27, 2021. -
Omicron cases are exploding. Scientists still don't know how bad the wave will be
Kupferschmidt K, Vogel G. Science, Jan 4, 2022. -
Omicron's feeble attack on the lungs could make it less dangerous
Kozlov M. Nature, Jan 5, 2022. -
Diagnostic Developers Pursue SARS-CoV-2 Omicron Assays for Surveillance, Potential Clinical Use
Johnson M. GenomeWeb, Dec 17, 2021. -
Study raises doubts about rapid Covid tests' reliability in early days after infection
Herper M. STAT, Jan 5, 2022. -
Are we testing for omicron wrong?
Gever J. MedPage Today, Dec 27, 2021. -
Israel begins studying the effectiveness of a 4th vaccine dose.
Kershner I. New York Times, Dec 27, 2021. -
A new coronavirus vaccine heading to India was developed by a small team in Texas. It expects nothing in return.
Taylor A. Washington Post, Dec 30, 2021.
EVENTS / TRAINING / WEB RESOURCES
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Resource Profile: The Regenstrief Institute COVID-19 Research Data Commons (CoRDaCo)
Allen KS, et al. medRxiv, Dec 18, 2021. -
Genomic sequencing: Here's how researchers identify omicron and other COVID-19 variants
Hudson A, Wadsworth C. The Conversation, Dec 20, 2021.
CONCEPTS / COMMENTS
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Of variants and vaccines.
Grubaugh Nathan D et al. Cell 2021 12 (26) 6222-6223 -
Vaccinomics: a future avenue for vaccine development against emerging pathogens.
de la Fuente José et al. Expert review of vaccines 2021 9 (12) 1561-1569 -
The SARS-CoV-2 pandemic: remaining uncertainties in our understanding of the epidemiology and transmission dynamics of the virus, and challenges to be overcome.
Anderson Roy M et al. Interface focus 2021 12 (6) 20210008 -
Metagenomic Next-Generation Sequencing (mNGS): SARS-CoV-2 as an Example of the Technology's Potential Pediatric Infectious Disease Applications.
Handel Andrew S et al. Journal of the Pediatric Infectious Diseases Society 2021 12 (Supplement_4) S69-S70 -
A new tool to probe SARS-CoV-2 variants.
Johnson Bryan A et al. Science (New York, N.Y.) 2021 12 (6575) 1557-1558 -
Influenza viruses and coronaviruses: Knowns, unknowns, and common research challenges.
Terrier Olivier et al. PLoS pathogens 2021 12 (12) e1010106 -
Eroding norms over release of self-spreading viruses
Lentzos F, et al. Science, Jan 6, 2022.
METHODS / TOOLS
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Simplified Point-of-Care Full SARS-CoV-2 Genome Sequencing Using Nanopore Technology.
Pembaur Anton et al. Microorganisms 2021 12 (12) -
InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses.
Ferguson James M et al. Bioinformatics (Oxford, England) 2021 12 -
Interpretable and Predictive Deep Modeling of the SARS-CoV-2 Spike Protein Sequence
Sokhansanj B, et al. medRxiv, Dec 27, 2021. -
Early Computational Detection of Potential High Risk SARS-CoV-2 Variants
Beguir K, et al. bioRxiv, Dec 27, 2021. -
Tutorial: Investigating SARS-CoV-2 evolution and phylogeny using MNHN-Tree-Tools
Haschka T. bioRxiv, Dec 23, 2021. -
CalmBelt: Rapid SARS-CoV-2 Genome Characterization for Outbreak Tracking.
Yingtaweesittikul Hatairat et al. Frontiers in medicine 2021 12 790662
EVOLUTION / ECOLOGY / POPULATIONS
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Genetic diversity of Leptospira isolates in Lao PDR and genome analysis of an outbreak strain.
Grillová Linda et al. PLoS neglected tropical diseases 2021 12 (12) e0010076 -
Global emergence and dissemination of Neisseria gonorrhoeae ST-9363 isolates with reduced susceptibility to azithromycin.
Joseph Sandeep J et al. Genome biology and evolution 2021 12 -
Epidemiology of COVID-19 after Emergence of SARS-CoV-2 Gamma Variant, Brazilian Amazon, 2020-2021
Nicolete VC, et al. Emerg Infect Dis. 2021 Dec 28;28(3). -
Genomic Epidemiology of SARS-CoV-2 Divulge B.1, B.1.36, and B.1.1.7 as the Most Dominant Lineages in First, Second, and Third Wave of SARS-CoV-2 Infections in Pakistan.
Basheer Atia et al. Microorganisms 2021 12 (12) -
Rapid longitudinal SARS-CoV-2 intra-host emergence of novel haplotypes regardless of immune deficiencies
Manuto L, et al. bioRxiv, Dec 23, 2021. -
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Viana R, et al. medRxiv, Dec 21, 2021. -
Context-specific emergence and growth of the SARS-CoV-2 Delta variant
McCrone JT, et al. medRxiv, Dec 21, 2021. -
Geographical Landscape and Transmission Dynamics of SARS-CoV-2 Variants Across India: A Longitudinal Perspective.
Jha Neha et al. Frontiers in genetics 2022 1 753648 -
The 2017 Dengue virus 1 outbreak in northern Vietnam was caused by a locally circulating virus group.
Takemura Taichiro et al. Tropical medicine and health 2022 1 (1) 3 -
Crossroads of highly pathogenic H5N1: overlap between wild and domestic birds in the Black Sea-Mediterranean impacts global transmission.
Hill Nichola J et al. Virus evolution 2021 12 (1) veaa093 -
Co-circulation of a Novel Dromedary Camel Parainfluenza Virus 3 and Middle East Respiratory Syndrome Coronavirus in a Dromedary Herd With Respiratory Tract Infections.
Teng Jade Lee Lee et al. Frontiers in microbiology 2021 12 739779 -
Genomic Evaluation of the Genus Coltivirus Indicates Genetic Diversity among Colorado Tick Fever Virus Strains and Demarcation of a New Species.
Hughes Holly R et al. Diseases (Basel, Switzerland) 2021 12 (4) -
Spatiotemporal Associations and Molecular Evolution of Highly Pathogenic Avian Influenza A H7N9 Virus in China from 2017 to 2021.
He Dongchang et al. Viruses 2021 12 (12) -
Whole Genome Sequencing and Phylogenetic Analysis of Rabies Viruses from Bats in Connecticut, USA, 2018-2019.
Hyeon Ji-Yeon et al. Viruses 2021 12 (12) -
Molecular Epidemiology of Rabies in Wild Canidae in Tunisia.
Bouslama Zied et al. Viruses 2021 12 (12) -
Distribution and Genetic Diversity of Hepatitis E Virus in Wild and Domestic Rabbits in Australia.
Jenckel Maria et al. Pathogens (Basel, Switzerland) 2021 12 (12) -
Cryptic Plasmodium inui and P. fieldi infections among symptomatic malaria patients in Thailand.
Putaporntip Chaturong et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 12 -
Morphological and genomic characterisation of the Schistosoma hybrid infecting humans in Europe reveals admixture between Schistosoma haematobium and Schistosoma bovis.
Kincaid-Smith Julien et al. PLoS neglected tropical diseases 2021 12 (12) e0010062 -
Detection of Babesia spp. in High Altitude Cattle in Ecuador, Possible Evidence of the Adaptation of Vectors and Diseases to New Climatic Conditions.
Chávez-Larrea María A et al. Pathogens (Basel, Switzerland) 2021 12 (12) -
First detection of human pathogenic variant of Anaplasma phagocytophilum in field-collected Haemaphysalis longicornis, Pennsylvania, USA.
Price Keith J et al. Zoonoses and public health 2021 12
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Genomic Characterization of Clinical Listeria monocytogenes Isolates in Beijing, China.
Zhang Xiaoai et al. Frontiers in microbiology 2021 12 751003 -
Comparative Genomics of Clinical and Environmental Isolates of Vibrio spp. of Colombia: Implications of Traits Associated with Virulence and Resistance.
Pérez-Duque Alejandra et al. Pathogens (Basel, Switzerland) 2021 12 (12) -
Combination therapy for Mycoplasma genitalium, and new insights into the utility of parC mutant detection to improve cure.
Vodstrcil Lenka A et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 1 -
High Rate of Asymptomatic Carriage Associated with Variant Strain Omicron
Garret N, et al. medRxiv, Dec 27, 2021. -
Early assessment of the clinical severity of the SARS-CoV-2 Omicron variant in South Africa
Wolter N, et al. medRxiv, Dec 21, 2021. -
HIV Pretreatment Drug Resistance Trends in Mexico City, 2017-2020.
García-Morales Claudia et al. Pathogens (Basel, Switzerland) 2021 12 (12)
DETECTION / DIAGNOSIS
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New Insight regarding Legionella Non-Pneumophila Species Identification: Comparison between the Traditional mip Gene Classification Scheme and a Newly Proposed Scheme Targeting the rpoB Gene.
Pascale Maria Rosaria et al. Microbiology spectrum 2021 12 (3) e0116121 -
Top-Down Mass Spectrometry for Trace Level Quantification of Staphylococcal Enterotoxin A Variants.
Lefebvre Donatien et al. Journal of proteome research 2021 12 -
A survey of current activities and technologies used to detect carbapenem resistance in bacteria isolated from companion animals at veterinary diagnostic laboratories-United States, 2020.
Waltenburg Michelle A et al. Journal of clinical microbiology 2022 1 JCM0215421 -
Sampling for SARS-CoV-2 Aerosols in Hospital Patient Rooms.
Lane Morgan A et al. Viruses 2021 12 (12) -
Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina.
Torres Carolina et al. Frontiers in medicine 2021 12 755463 -
SARS-CoV-2 in hospital air as revealed by comprehensive respiratory viral panel sequencing.
Habibi Nazima et al. Infection prevention in practice 2022 1 100199 -
Association of SARS-CoV-2 presence in sewage with public adherence to precautionary measures and reported COVID-19 prevalence in Tehran.
Amereh Fatemeh et al. The Science of the total environment 2021 12 152597 -
SARS-CoV-2 variant detection with ADSSpike.
Castañeda-Mogollón Daniel et al. Diagnostic microbiology and infectious disease 2021 12 (3) 115606 -
A Novel High-Throughput Nanopore-Sequencing-Based Strategy for Rapid and Automated S-Protein Typing of SARS-CoV-2 Variants.
Wagner Gabriel E et al. Viruses 2021 12 (12) -
Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results.
Lesbon Jéssika Cristina Chagas et al. Viruses 2021 12 (12) -
SARS-CoV-2 B.1.1.529 (Omicron) Variant - United States, December 1-8, 2021.
et al. MMWR. Morbidity and mortality weekly report 2021 12 (50) 1731-1734 -
Saliva swabs are the preferred sample for Omicron detection
Marais G, et al. medRxiv, Dec 24, 2021. -
Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission
Karthikeyan S, et al. medRxiv, Dec 27, 2021. -
National Scale Real-Time Surveillance of Sars-Cov-2 Variants Dynamics By Wastewater Monitoring in Israel
Bar-Or I, et al. medRxiv, Dec 27, 2021. -
Utilization of a SARS-CoV-2 Variant Assay for the Rapid Differentiation of Omicron and Delta
Barasch NJ, et al. medRxiv, Dec 27, 2021. -
Surveillance and correlation of SARS-CoV-2 viral RNA, antigen, virus isolation, and self-reported symptoms in a longitudinal study with daily sampling
Bonenfant G, et al. medRxiv, Dec 23, 2021. -
Quantitative detection of SARS-CoV-2 Omicron variant in wastewater through allele-specific RT-qPCR
Lee WL, et al. medRxiv, Dec 21, 2021. -
An Evaluation of Hepatitis E Virus Molecular Typing Methods.
Baylis Sally A et al. Clinical chemistry 2021 12 (1) 181-191 -
Exploration of a new hepatitis a surveillance system in Beijing, China: based on molecular epidemiology.
Wang Huai et al. BMC infectious diseases 2022 1 (1) 22 -
Universal Exponential Amplification Confers Multilocus Detection of Mutation-Prone Virus.
Zhao Yue et al. Analytical chemistry 2022 1 -
Detection of Norovirus Using Paper-Based Cell-Free Systems.
Wu Kaiyue et al. Methods in molecular biology (Clifton, N.J.) 2022 1 375-390 -
Detection and genome characterization of Middelburg virus strains isolated from CSF and whole blood samples of humans with neurological manifestations in South Africa.
Fourie Isabel et al. PLoS neglected tropical diseases 2022 1 (1) e0010020 -
Tools for detecting a "superbug": updates on Candida auris testing.
Lockhart Shawn R et al. Journal of clinical microbiology 2022 1 jcm0080821 -
Identification of Rickettsia spp. and Babesia conradae in Dermacentor spp. Collected from Dogs and Cats Across the United States.
Duncan Kathryn T et al. Vector borne and zoonotic diseases (Larchmont, N.Y.) 2021 12 (12) 911-920 -
Technologies for Detection of Babesia microti: Advances and Challenges.
Meredith Scott et al. Pathogens (Basel, Switzerland) 2021 12 (12)
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology.
Greninger Alexander L et al. Journal of the Pediatric Infectious Diseases Society 2021 12 (Supplement_4) S88-S95 -
Investigation of a SARS-CoV-2 B.1.1.529 (Omicron) Variant Cluster--Nebraska, November-December 2021
Jansen L, et al. MMWR, Dec 28, 2021. -
Transmission of SARS-CoV-2 among children and staff in German daycare centers: results from the COALA study
Loss J, et al. medRxiv, Dec 27, 2021. -
The role of airborne transmission in a large single source outbreak of SARS-CoV-2 in a Belgian nursing home in 2020
Vuylsteke B, et al. medRxiv, Dec 21, 2021. -
An outbreak of SARS-CoV-2 on a transplant unit in the early vaccination era.
Roberts Scott C et al. Transplant infectious disease : an official journal of the Transplantation Society 2021 12 -
Airborne Transmission of SARS-CoV-2 Delta Variant within Tightly Monitored Isolation Facility, New Zealand (Aotearoa).
Fox-Lewis Andrew et al. Emerging infectious diseases 2021 12 (3) -
Genetic Analysis of the Measles Virus From the Outbreaks in South Korea, 2019.
Kim Jeong-Min et al. Frontiers in microbiology 2022 1 763107 -
Porcine Reproductive and Respiratory Syndrome (PRRS) Epidemiology in an Integrated Pig Company of Northern Italy: A Multilevel Threat Requiring Multilevel Interventions.
Franzo Giovanni et al. Viruses 2021 12 (12) -
Epidemiology and Molecular Transmission Characteristics of HIV in the Capital City of Anhui Province in China.
Zheng Shan et al. Pathogens (Basel, Switzerland) 2021 12 (12) -
Phylogeography reveals association between swine trade and the spread of porcine epidemic diarrhea virus in China and across the world.
He Wan-Ting et al. Molecular biology and evolution 2021 12
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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The Potential for a Released Autosomal X-Shredder Becoming a Driving-Y Chromosome and Invasively Suppressing Wild Populations of Malaria Mosquitoes.
Alcalay Yehonatan et al. Frontiers in bioengineering and biotechnology 2021 12 752253 -
Immunosequencing and epitope mapping reveal substantial preservation of the T cell immune response to Omicron generated by SARS-CoV-2 vaccines
May DH, et al. medRxiv, Dec 27, 2021. -
Effect of Covid-19 Vaccination on Transmission of Alpha and Delta Variants.
Eyre David W et al. The New England journal of medicine 2022 1 -
Waning Effectiveness of the BNT162b2 Vaccine Against Infection in Adolescents
Prunas O, et al. medRxiv, Jan 5, 2022.
HOST-MICROBE INTERACTIONS
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Bacterial and Parasitic Pathogens as Risk Factors for Cancers in the Gastrointestinal Tract: A Review of Current Epidemiological Knowledge.
Duijster Janneke W et al. Frontiers in microbiology 2021 12 790256 -
Influenza A H1N1 mediated pre-existing immunity to SARS-CoV-2 predicts COVID-19 outbreak dynamics
Almazan NM, et al. medRxiv, Dec 25, 2021. -
Minimal observed impact of HLA genotype on hospitalization and severity of SARS-CoV-2 infection
Nguyen A, et al. medRxiv, Dec 22, 2021. -
Human genetic polymorphism and Leishmaniasis
Bharati K. Infect Genet Evol, Jan 4, 2022.
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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