Advanced Molecular Detection Clips Content (Published on 03/24/2022)
NEWS
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Scientists struggle to probe COVID's origins amid sparse data from China
Maxmen A. Nature, Mar 17, 2022. -
'Stealth' Omicron Is Stealthy No More: What's Known About the BA.2 Variant
Zimmer C. New York Times, Mar 18, 2022. -
Deltacron: what scientists know so far about this new hybrid coronavirus
O'Neill N. The Conversation, Mar 21, 2022. -
How Is the U.S. Watching for the Next COVID Variant? While sequencing efforts are better than before, experts say there's a long way to go
Putka S. MedPage Today, Mar 18, 2022. -
Poop surveillance proved its worth during pandemic, could become standard practice
Barry-Jester AM. Los Angeles Times, Mar 21, 2022.
CONCEPTS / COMMENTS
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Lessons from the COVID data wizards
Peeples L. Nature, Mar 23, 2022. -
This is no time to stop tracking COVID-19
(editorial) Nature, Mar 23, 2022. -
Antigenic evolution will lead to new SARS-CoV-2 variants with unpredictable severity.
Markov Peter V et al. Nature reviews. Microbiology 2022 3 -
Multi-omics in COVID-19: Seeing the unseen but overlooked in the clinic
Lu T, et al. Cell Rep Med, Mar 15, 2022.
METHODS / TOOLS
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Phycova - a tool for exploring covariates of pathogen spread.
Blokker Tim et al. Virus evolution 2022 3 (1) veac015 -
Benchmarking the topological accuracy of bacterial phylogenomic workflows using in silico evolution.
van der Putten Boas C L et al. Microbial genomics 2022 3 (3) -
HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.
Kalmar Lajos et al. PLoS genetics 2022 3 (3) e1009776 -
Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex.
Lam Margaret M C et al. Microbial genomics 2022 3 (3) -
Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages.
Mostefai Fatima et al. Frontiers in medicine 2022 3 826746 -
Cov2clusters: genomic clustering of SARS-CoV-2 sequences
Sobkowiak B, et al. medRxiv, Mar 15, 2022. -
Cloud-Based Influenza Surveillance System in Emergency Departments Using Molecular-Based Testing: Advances and Challenges.
Shaw-Saliba Kathryn et al. The western journal of emergency medicine 2022 3 (2) 115-123 -
Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data.
Gehrig Jeanette L et al. Microbial genomics 2022 3 (3)
EVOLUTION / ECOLOGY / POPULATIONS
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High Prevalence and Low Diversity of Rickettsia in Dermacentor reticulatus Ticks, Central Europe
Balazova A, et al. Emerg Infect Dis, Mar 8, 2022. -
Genomic Characteristics of Recently Recognized Vibrio cholerae El Tor Lineages Associated with Cholera in Bangladesh, 1991 to 2017.
Monir Md Mamun et al. Microbiology spectrum 2022 3 e0039122 -
Founder effect contributes to the unique pattern of SARS-CoV-2 variant B.1.1.519 emergence in Alaska
Haan TJ, et al. medRxiv, Mar 18, 2022. -
SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads
Bolze A, et al. Cell Rep Med, Mar 15, 2022. -
Identification of a Novel SARS-CoV-2 Delta-Omicron Recombinant Virus in the United States
Lacek KA, et al. bioRxiv, Mar 21, 2022. -
Rapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021.
Bbosa Nicholas et al. Emerging infectious diseases 2022 3 (5) -
Isolation of Heartland Virus from Lone Star Ticks, Georgia, USA, 2019
Romer Y, et al. Emerg Infect Dis, Mar 16, 2022. -
Whole-genome analysis to determine the rate and patterns of intra-subtype reassortment among influenza type-A viruses in Africa
Nabakooza G, et al. Virus Evol. 2022 Jan 29;8(1):veac005 -
RSV reemergence in Argentina since the SARS-CoV-2 pandemic.
Dolores Acuña et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2022 3 105126 -
Unprecedented outbreak of respiratory syncytial virus in Taiwan associated with ON1 variant emergence between 2010 and 2020.
Lin Wei-Hsuan et al. Emerging microbes & infections 2022 3 1-46
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Molecular characterisation and detection of macrolide and fluoroquinolone resistance determinants in Mycoplasma genitalium in South Africa, 2015-2018.
Mahlangu Mahlape P et al. Sexually transmitted diseases 2022 3 -
Global evolutionary dynamics and resistome analysis of Clostridioides difficile ribotype 017.
Imwattana Korakrit et al. Microbial genomics 2022 3 (3) -
Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex.
Ono Tomoyuki et al. Microbial genomics 2022 3 (3) -
Multiple secondary outbreaks of NDM-producing Enterobacter hormaechei in the context of endemic NDM-producing Klebsiella pneumoniae.
Izdebski R et al. The Journal of antimicrobial chemotherapy 2022 3 -
Metagenomic Approaches Reveal Strain Profiling and Genotyping of Klebsiella pneumoniae from Hospitalized Patients in China.
Liu Jiao et al. Microbiology spectrum 2022 3 e0219021 -
Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia.
Darboe Saffiatou et al. Microbial genomics 2022 3 (3) -
High prevalence of pre-treatment HIV drug resistance in Papua New Guinea: findings from the first nationally representative pre-treatment HIV drug resistance study.
Gare Janet et al. BMC infectious diseases 2022 3 (1) 266 -
De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report
Gandhi S, et al. Nat Commun. 2022 Mar 17;13(1):1547.
DETECTION / DIAGNOSIS
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Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks.
Cherchame Emeline et al. BMC genomics 2022 3 (1) 217 -
Biosafety materials: ushering in a new era of infectious disease diagnosis and treatment with the CRISPR/Cas system.
Zhang Yuquan et al. Biosafety and health 2022 3 -
Integrating CRISPR/Cas within isothermal amplification for point-of-Care Assay of nucleic acid.
Zhang Limei et al. Talanta 2022 3 123388 -
Direct Real-Time PCR for the Detection and Serotyping of Haemophilus influenzae without DNA Extraction.
Marasini Daya et al. Journal of clinical microbiology 2022 3 e0211121 -
Early detection of SARS-CoV-2 variants using traveler-based genomic surveillance at four US airports, September 2021- January 2022
Wegrzyn RD, et al. medRxiv, Mar 22, 2022. -
Highly Sensitive Lineage Discrimination of SARS-CoV-2 Variants through Allele-Specific Probe PCR
Ratcliff J, et al. J Clin Microbiol. 2022 Mar 24;e0228321. -
Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection.
Dezordi Filipe Zimmer et al. Microbial genomics 2022 3 (3) -
End-point RT-PCR based on a conservation landscape for SARS-COV-2 detection.
Cruz-Rangel Armando et al. Scientific reports 2022 3 (1) 4759 -
A multiplexed Cas13-based assay with point-of-care attributes for simultaneous COVID-19 diagnosis and variant surveillance
Patchsung M, et al. medRxiv, Mar 18, 2022. -
SARS-CoV-2 Lineage Tracking, and Evolving Trends Seen during Three Consecutive Peaks of Infection in Delhi, India: a Clinico-Genomic Study.
Gautam Pramod et al. Microbiology spectrum 2022 3 e0272921 -
Study of the SARS-CoV-2 genomic data generation to evaluate the introduction of genomics in epidemiological surveillance and public health decision making
Souho T, et al. Pan Afr Med J. 2022 Jan 20;41:55. -
Quantitative differential analysis of norovirus outbreak samples using RT-ddPCR.
Song Miok et al. Letters in applied microbiology 2022 3 -
Detection of multiple mycetoma pathogens using fungal metabarcoding analysis of soil DNA in an endemic area of Sudan.
Hashizume Hiroki et al. PLoS neglected tropical diseases 2022 3 (3) e0010274 -
Comparison between Two Molecular Techniques: Nested and Real-Time Polymerase Chain Reaction Targeting 100-kDa Hc Protein for Detection of Histoplasma capsulatum in Environmental Samples.
Gómez Luisa F et al. The American journal of tropical medicine and hygiene 2022 3 -
Development and Introduction of the Filariasis Test Strip: A New Diagnostic Test for the Global Program to Eliminate Lymphatic Filariasis.
Pantelias Anastasia et al. The American journal of tropical medicine and hygiene 2022 3 -
A novel metabarcoded deep amplicon sequencing tool for disease surveillance and determining the species composition of Trypanosoma in cattle and other farm animals
Yasein G, et al. Acta Trop. 2022 Mar 19;106416.
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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A Cluster-based Method to Quantify Individual Heterogeneity in Tuberculosis Transmission.
Smith Jonathan P et al. Epidemiology (Cambridge, Mass.) 2021 12 (2) 217-227 -
Simultaneous Hospital Outbreaks of New Delhi Metallo-β-Lactamase-Producing Enterobacterales Unraveled Using Whole-Genome Sequencing.
Lo Stéphane et al. Microbiology spectrum 2022 3 e0228721 -
Prolonged silent carriage, genomic virulence potential and transmission between staff and patients characterize a neonatal intensive care unit (NICU) outbreak of methicillin-resistant Staphylococcus aureus (MRSA).
Madera Sharline et al. Infection control and hospital epidemiology 2022 3 1-7 -
Rectal Colonization and Nosocomial Transmission of Carbapenem-Resistant Acinetobacter baumannii in an Intensive Care Unit, Southwest Nigeria
Odih EE, et al. Front Med (Lausanne). 2022 Mar 7;9:846051. -
Genomic Investigation Reveals a Community Typhoid Outbreak Caused by Contaminated Drinking Water in China, 2016.
Hu Bing et al. Frontiers in medicine 2022 3 753085 -
Prospective epidemiological, molecular, and genetic characterization of a novel coronavirus disease in the Val Venosta/Vinschgau: the CHRIS COVID-19 study protocol.
Pattaro Cristian et al. Pathogens and global health 2021 10 (2) 128-136 -
SARS-CoV-2 Outbreak among Malayan Tigers and Humans, Tennessee, USA, 2020.
Grome Heather N et al. Emerging infectious diseases 2022 3 (4) 833-836 -
Genomic Epidemiology of Early SARS-CoV-2 Transmission Dynamics, Gujarat, India.
Raghwani Jayna et al. Emerging infectious diseases 2022 2 (4) 751-758 -
Regional importation and asymmetric within-country spread of SARS-CoV-2 variants of concern in the Netherlands
Han Ax, medRxiv, Mar 22, 2022. -
Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020-2021
Morobe JM, et al. medRxiv, Mar 21, 2022. -
Unrecognized introductions of SARS-CoV-2 into the US state of Georgia shaped the early epidemic
Babiker A, et al. Virus Evol. 2022 Feb 15;8(1):veac011. -
Minimal SARS-CoV-2 classroom transmission at a large urban university experiencing repeated into campus introduction.
Kuhfeldt Kayla et al. medRxiv : the preprint server for health sciences 2022 3 -
Phylogenetic Analysis of Spread of Hepatitis C Virus Identified during HIV Outbreak Investigation, Unnao, India.
Mane Arati et al. Emerging infectious diseases 2022 3 (4) 725-733 -
Zika Virus Infection During Research Vaccine Development: Investigation of the Laboratory-Acquired Infection via Nanopore Whole-Genome Sequencing
Bang E, et al. Front Cell Infect Microbiol. 2022 Mar 7;12:819829. -
Cluster of human Puumala orthohantavirus infections due to indoor exposure?-An interdisciplinary outbreak investigation.
Princk Christina et al. Zoonoses and public health 2022 3
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Effectiveness of 2-Dose BNT162b2 (Pfizer BioNTech) mRNA Vaccine in Preventing SARS-CoV-2 Infection Among Children Aged 5-11 Years and Adolescents Aged 12-15 Years - PROTECT Cohort, July 2021-February 2022.
Fowlkes Ashley L et al. MMWR. Morbidity and mortality weekly report 2022 3 (11) 422-428 -
Effectiveness of mRNA Vaccination in Preventing COVID-19-Associated Invasive Mechanical Ventilation and Death--United States, March 2021-January 2022
Tenforde MW, et al. MMWR, Mar 18, 2022. -
Protection of prior natural infection compared to mRNA vaccination against SARS-CoV-2 infection and severe COVID-19 in Qatar
Chemaitelly H, et al. medRxiv, Mar 18, 2022. -
Vaccine effectiveness of two and three doses of BNT162b2 and CoronaVac against COVID-19 in Hong Kong
McMenamin ME, et al. medRxiv, Mar 22, 2022. -
Safety and Efficacy of a Third Dose of BNT162b2 Covid-19 Vaccine.
Moreira Edson D et al. The New England journal of medicine 2022 3 -
Efficacy of a Fourth Dose of Covid-19 mRNA Vaccine against Omicron.
Regev-Yochay Gili et al. The New England journal of medicine 2022 3 -
Vaccine-Associated Measles Encephalitis in Immunocompromised Child, California, USA
Costales C, et al. Emerg Infect Dis, Mar 11, 2022. -
Defective Interfering Viral Particle Treatment Reduces Clinical Signs and Protects Hamsters from Lethal Nipah Virus Disease.
Welch Stephen R et al. mBio 2022 3 e0329421 -
Identification of novel genetic variants in the malaria vaccine candidate PfRh5: structure-guided insights into potential function
Mangou K, et al. medRxiv, Mar 20, 2022. -
Effective Oral RNA Interference (RNAi) Administration to Adult Anopheles gambiae Mosquitoes.
Taracena Mabel et al. Journal of visualized experiments : JoVE 2022 3 (181)
HOST-MICROBE INTERACTIONS
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Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants
Servellita V, et al. Cell, Mar 17, 2022. -
Integrative transcriptomic, evolutionary, and causal inference framework for region-level analysis: Application to COVID-19.
Zhou Dan et al. NPJ genomic medicine 2022 3 (1) 24 -
Human genetic and immunological determinants of critical COVID-19 pneumonia.
Zhang Qian et al. Nature 2022 1 -
Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities.
Russell Magdalena L et al. eLife 2022 3 -
High-Content Screening and Computational Prediction Reveal Viral Genes That Suppress the Innate Immune Response.
Ng Tai L et al. mSystems 2022 3 e0146621
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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- Page last updated:Apr 25, 2024
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