Advanced Molecular Detection Clips Content (Published on 09/01/2022)
NEWS
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New Sequencing Method Tackles Environmental DNA Contamination for Cell-Free DNA Samples
Zhang H. GenomeWeb, Aug 24, 2022. -
FDA Authorizes Omicron-Targeted Booster Shots
Hein I. MedPage Today, Aug 31, 2022. -
COVID vaccines slash risk of spreading Omicron — and so does previous infection
Scully RP. Nature, Aug 26, 2022. -
Omicron booster shots are coming—with lots of questions
Vogel G. Science, Aug 30, 2022. -
Coronavirus boosters targeting omicron get FDA blessing for fall push
McGinley L. Washington Post, Aug 31, 2022. -
10 key questions about monkeypox the world needs to answer
Molteni M, et al. STAT, Aug 30, 2022. -
How Long Has Polio Been Circulating in the U.S.?
DePeau-Wilson M. MedPage Today, Aug 25, 2022. -
After the Genome—A Brief History of Proteomics
Suran M. JAMA, Aug 31, 2022.
EVENTS / TRAINING / WEB RESOURCES
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Monkeypox vs. COVID-19
(explainer) Barron M. ASM, Aug 19, 2022. -
Ten simple rules for organizing a special session at a scientific conference.
Chicco Davide et al. PLoS computational biology 2022 8 (8) e1010395
CONCEPTS / COMMENTS
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Advancing microfluidic diagnostic chips into clinical use: a review of current challenges and opportunities.
Iyer Vasant et al. Lab on a chip 2022 6 (17) 3110-3121 -
Integrating genomic and epidemiologic data to accelerate progress toward schistosomiasis elimination.
Lund Andrea J et al. eLife 2022 8 -
Modelling infectious disease to support human health.
Tobin David M et al. Disease models & mechanisms 2022 8 (8) -
Modeling infection from SARS-CoV-2 wastewater concentrations: promise, limitations, and future directions.
Soller Jeffrey et al. Journal of water and health 2022 8 (8) 1197-1211
METHODS / TOOLS
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A metagenomic DNA sequencing assay that is robust against environmental DNA contamination.
Mzava Omary et al. Nature communications 2022 7 (1) 4197 -
Finding Asymptomatic Spreaders in a COVID-19 Transmission Network by Graph Attention Networks.
Liu Zeyi et al. Viruses 2022 8 (8) -
VGsim: Scalable viral genealogy simulator for global pandemic.
Shchur Vladimir et al. PLoS computational biology 2022 8 (8) e1010409 -
Empowering SARS-CoV-2 Genomics Surveillance in Missouri with Data Analytics and Integration Portals.
Zhen Lyu et al. Mo Med 2022 8 (3) 185-187 -
Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches.
Mugnier Nathalie et al. Viruses 2022 8 (8) -
Statistical Challenges in Tracking the Evolution of SARS-CoV-2.
Cappello Lorenzo et al. Statistical science : a review journal of the Institute of Mathematical Statistics 2022 8 (2) 162-182
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Current status and capacity of pathogen laboratories in centers for disease control and prevention in China during the COVID-19 pandemic: A nationwide cross-sectional survey.
Wang Ji et al. Frontiers in public health 2022 8 927318
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Intrahost SARS-CoV-2 k-mer identification method (iSKIM) for rapid detection of mutations of concern reveals emergence of global mutation patterns.
Thommana Ashley et al. bioRxiv : the preprint server for biology 2022 8 -
From Clinical Specimen to Whole Genome Sequencing of A(H3N2) Influenza Viruses: A Fast and Reliable High-Throughput Protocol.
Galli Cristina et al. Vaccines 2022 8 (8) -
Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification.
Lundgren Erik et al. PLoS computational biology 2022 8 (8) e1009741
EVOLUTION / ECOLOGY / POPULATIONS
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Population structure of Mycobacterium tuberculosis from referral clinics in Western Siberia, Russia: Before and during the Covid-19 pandemic.
Vyazovaya Anna et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2022 7 105343 -
Molecular characterization of circulating Salmonella Typhi strains in an urban informal settlement in Kenya.
Ochieng Caroline et al. PLoS neglected tropical diseases 2022 8 (8) e0010704 -
Genome Sequences of 18 Salmonella enterica Serotype Hadar Strains Collected from Patients in the United States.
Webb Hattie E et al. Microbiology resource announcements 2022 8 e0052222
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The emergence, spread and vanishing of a French SARS-CoV-2 variant exemplifies the fate of RNA virus epidemics and obeys the Mistigri rule.
Colson Philippe et al. Journal of medical virology 2022 8 -
Genomic characterization of SARS-CoV-2 from vaccine breakthrough cases in Allegheny County, Pennsylvania.
Waggle Kady D et al. PloS one 2022 8 (8) e0272954 -
Within-host genetic diversity of SARS-CoV-2 in the context of large-scale hospital-associated genomic surveillance.
Mushegian Alexandra et al. medRxiv : the preprint server for health sciences 2022 8 -
Circulation of hepatitis B virus genotype-E among outpatients in tertiary hospitals in the Niger-Delta region of Nigeria.
Umego Chinenye F et al. African health sciences 2022 8 (1) 511-520 -
Rotavirus Strain Trends in United States, 2009-2016: Results from the National Rotavirus Strain Surveillance System (NRSSS).
Mijatovic-Rustempasic Slavica et al. Viruses 2022 8 (8) -
Retrospective Genomic Surveillance of Chikungunya Transmission in Minas Gerais State, Southeast Brazil.
Fritsch Hegger et al. Microbiology spectrum 2022 8 e0128522 -
Genetic adaptations to SIV across chimpanzee populations.
Pawar Harvinder et al. PLoS genetics 2022 8 (8) e1010337 -
Phylogenomic Placement of American Southwest-Associated Clinical and Veterinary Isolates Expands Evidence for Distinct Cryptococcus gattii VGVI.
Juan Monroy-Nieto et al. Microorganisms 2022 8 (8) -
Independent Circulation of Leishmania major and Leishmania tropica in Their Respective Sandfly Vectors for Transmission of Zoonotic and Chronic Cutaneous Leishmaniasis Co-Existing in a Mixed Focus of Central Tunisia.
Abbas Mohammed Abdo Saghir et al. Pathogens (Basel, Switzerland) 2022 8 (8) -
Metagenomic profiles of Dermacentor tick pathogens from across Mongolia, using next generation sequencing.
Altantogtokh Doniddemberel et al. Frontiers in microbiology 2022 8 946631
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Pervasive Listeria monocytogenes Is Common in the Norwegian Food System and Is Associated with Increased Prevalence of Stress Survival and Resistance Determinants.
Fagerlund Annette et al. Applied and environmental microbiology 2022 8 e0086122 -
Genomic characterization of invasive typhoidal and non-typhoidal Salmonella in southwestern Nigeria.
Ikhimiukor Odion O et al. PLoS neglected tropical diseases 2022 8 (8) e0010716 -
Systematic Analysis of Mobile Genetic Elements Mediating β-Lactamase Gene Amplification in Noncarbapenemase-Producing Carbapenem-Resistant Enterobacterales Bloodstream Infections.
Shropshire W C et al. mSystems 2022 8 e0047622 -
Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis.
Merker Matthias et al. Nature communications 2022 8 (1) 5105 -
Clinical severity of Omicron SARS-CoV-2 variant relative to Delta in British Columbia, Canada: A retrospective analysis of whole genome sequenced cases.
Harrigan Sean P et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 8 -
HIV-1 Diversity and Drug Resistance in Treatment-Naïve Children and Adolescents from Rio de Janeiro, Brazil.
de Azevedo Suwellen Sardinha Dias et al. Viruses 2022 8 (8)
DETECTION / DIAGNOSIS
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Effect of Intragenomic Sequence Heterogeneity among Multiple 16S rRNA Genes on Species Identification of Elizabethkingia.
Lin Jiun-Nong et al. Microbiology spectrum 2022 8 e0133822
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Highly specific and sensitive detection of Burkholderia pseudomallei genomic DNA by CRISPR-Cas12a.
Wongpalee Somsakul Pop et al. PLoS neglected tropical diseases 2022 8 (8) e0010659 -
The first detection of SARS-CoV-2 RNA in urban wastewater in Giza, Egypt.
Shaheen Mohamed N F et al. Journal of water and health 2022 8 (8) 1212-1222 -
Biomarkers selection for population normalization in SARS-CoV-2 wastewater-based epidemiology.
Shu-Yu Hsu et al. Water Res 2022 8 118985 -
Time-of-Day Variation in SARS-CoV-2 RNA Levels during the Second Wave of COVID-19.
Zhuang Xiaodong et al. Viruses 2022 8 (8) -
Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy.
Amendola Antonella et al. Environmental research 2022 8 113979 -
Whole genome sequencing of SARS-CoV-2 from wastewater links to individual cases in catchments.
Levy Avram et al. The Science of the total environment 2022 8 158266 -
Delineating the spread and prevalence of SARS-CoV-2 Omicron sub-lineages (BA.1- BA.5) and Deltacron using wastewater in the Western Cape, South Africa.
Johnson Rabia et al. The Journal of infectious diseases 2022 8 -
Rapid Amplicon Nanopore Sequencing (RANS) for the Differential Diagnosis of Monkeypox Virus and Other Vesicle-Forming Pathogens.
Israeli Ofir et al. Viruses 2022 8 (8) -
A public health approach to monitoring HIV with resistance to HIV pre-exposure prophylaxis.
Buskin Susan E et al. PloS one 2022 8 (8) e0272958 -
Targeted NGS-Based Analysis of Pneumocystis jirovecii Reveals Novel Genotypes.
Pungan Dora et al. Journal of fungi (Basel, Switzerland) 2022 8 (8) -
Evaluation of Next-Generation Sequencing Applied to Cryptosporidium parvum and Cryptosporidium hominis Epidemiological Study.
Bailly Eloïse et al. Pathogens (Basel, Switzerland) 2022 8 (8)
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Free online genome analyses reveal multiple strains in the beginning of a hospital outbreak of Enterobacter hormaechei carrying bla carbapenemase gene.
Kemp Michael et al. Journal of infection prevention 2022 8 (5) 243-247
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Analyzing the impact of a real-life outbreak simulator on pandemic mitigation: An epidemiological modeling study.
Specht Ivan et al. Patterns (New York, N.Y.) 2022 8 (8) 100572
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SARS-CoV-2 variant dynamics across US states show consistent differences in effective reproduction numbers
Figgins MD, Bedford T. medRxiv, Aug 24, 2022. -
High Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Household Transmission Rates Detected by Dense Saliva Sampling.
Kolodziej Lisa M et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 4 (1) e10-e19 -
Increased transmissibility of SARS-CoV-2 alpha variant (B.1.1.7) in children: three large primary school outbreaks revealed by whole genome sequencing in the Netherlands.
Gorgels Koen M F et al. BMC infectious diseases 2022 8 (1) 713 -
The Role of Lebanon in the COVID-19 Butterfly Effect: The B.1.398 Example.
Nour Dalal et al. Viruses 2022 8 (8) -
Genomic epidemiology and emergence of SARS-CoV-2 variants of concern in the United Arab Emirates.
Alsafar Habiba et al. Scientific reports 2022 8 (1) 14669 -
Genomic and virologic characterization of samples from a shipboard outbreak of COVID-19 reveals distinct variants within limited temporospatial parameters.
Cer Regina Z et al. Frontiers in microbiology 2022 8 960932 -
Molecular Genetics and Epidemiological Characteristics of HIV-1 Epidemic Strains in Various Sexual Risk Behaviour Groups in Developed Eastern China, 2017-2020.
Fan Qin et al. Emerging microbes & infections 2022 8 1-28 -
Outbreak of Middle East Respiratory Syndrome Coronavirus in Camels and Probable Spillover Infection to Humans in Kenya.
Ngere Isaac et al. Viruses 2022 8 (8) -
Identifying HIV-1 Transmission Clusters in Uzbekistan through Analysis of Molecular Surveillance Data.
Lebedev Aleksey et al. Viruses 2022 8 (8) -
Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa.
Pujol-Hodge Emma et al. Viruses 2022 8 (8) -
Molecular Epidemiology of HIV-1 among Prisoners in Central Brazil and Evidence of Transmission Clusters.
Tanaka Tayana Serpa Ortiz et al. Viruses 2022 8 (8) -
Epidemiological and viral characteristics of undiagnosed HIV infections in Botswana.
Bhebhe Lynnette et al. BMC infectious diseases 2022 8 (1) 710
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Clustering of Cryptosporidium species infections among sheep and cattle but not children in remote highland communities of Madagascar.
Krumkamp Ralf et al. Parasites & vectors 2022 8 (1) 304
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Use of whole genome sequencing to estimate the contribution of immune evasion and waning immunity to decreasing COVID-19 vaccine effectiveness during alpha and delta variant waves
Lind ML, et al. medRxiv, Aug 26, 2022.
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A recombinant rabies vaccine that prevents viral shedding in rabid common vampire bats (Desmodus rotundus).
Cárdenas-Canales Elsa M et al. PLoS neglected tropical diseases 2022 8 (8) e0010699
HOST-MICROBE INTERACTIONS
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Variability in mRNA SARS-CoV-2 BNT162b2 vaccine immunogenicity is associated with differences in the gut microbiome and habitual dietary fibre intake
Healey GR, et al. medRxiv, Aug 25, 2022. -
Development of a multiomics model for identification of predictive biomarkers for COVID-19 severity: a retrospective cohort study.
Byeon Seul Kee et al. The Lancet. Digital health 2022 7 (9) e632-e645 -
Allelic Variations in the Human Genes TMPRSS2 and CCR5, and the Resistance to Viral Infection by SARS-CoV-2.
Vitello Girolamo Aurelio et al. International journal of molecular sciences 2022 8 (16) -
The GNB3 c.825C>T (rs5443) polymorphism and protection against fatal outcome of corona virus disease 2019 (COVID-19).
Möhlendick Birte et al. Frontiers in genetics 2022 8 960731 -
Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: a retrospective cohort study
Hay JA, et al. medRxiv, Aug 26, 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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- Page last updated:Jan 9, 2025