Advanced Molecular Detection Clips Content (Published on 04/15/2021)
NEWS
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Variant Hunters Race to Find New Strains Where Testing Lags
Barber G. Wired, Apr 9, 2021. -
Labs Craft SARS-CoV-2 Variant Genotyping Assays for Screening, Surveillance
Johnson M. GenomeWeb, Apr 13, 2021. -
As variants surge, efforts in a patchwork of surveillance have ramped up to detect them
Cox E, Portnoy J. Washington Post, Apr 11, 2021. -
Know Thine Enemy: Why Genetic Sequencing Is Key to Tracking COVID-19
Dance A. Medscape, Apr 14, 2021. -
How the Coronavirus Variants Are Spreading in New York City
Goldstein J, et al. New York Times, Apr 13, 2021. -
Why would a Covid vaccine cause rare blood clots? Researchers have found clues
Herper M. STAT, Apr 13, 2021. -
How to develop vaccines faster before the next pandemic
Piper K. Vox, Apr 14, 2021. -
Enterobacteriaceae Pangenomes Offer Look at Antimicrobial Resistance Reservoirs in Natural Populations
GenomeWeb, Apr 9, 2021.
CONCEPTS / COMMENTS
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Combining natural language processing and metabarcoding to reveal pathogen-environment associations.
Molik David C et al. PLoS neglected tropical diseases 2021 4 (4) e0008755 -
The evolving role of preprints in the dissemination of COVID-19 research and their impact on the science communication landscape.
Fraser Nicholas et al. PLoS biology 2021 4 (4) e3000959 -
Next-Generation Sequencing Reveals the Progression of COVID-19.
Chen Xiaomin et al. Frontiers in cellular and infection microbiology 2021 3 632490 -
Through the gut, down the drain.
Beresford-Jones Benjamin S et al. Nature reviews. Microbiology 2021 4
METHODS / TOOLS
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A Highly Automated Mobile Laboratory for On-site Molecular Diagnostics in the COVID-19 Pandemic.
Xing Wanli et al. Clinical chemistry 2021 4 (4) 672-683
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ACoRE: Accurate SARS-CoV-2 genome reconstruction for the characterization of intra-host and inter-host viral diversity in clinical samples and for the evaluation of re-infections.
Marcolungo Luca et al. Genomics 2021 4 -
K-SEIR-Sim: A simple customized software for simulating the spread of infectious diseases.
Wang Hongzhi et al. Computational and structural biotechnology journal 2021 4 -
Determination of antimicrobial resistance profiles and mechanisms of
Ma Luyao et al. Applied and environmental microbiology 2021 4 -
Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark.
Cheng Brianna et al. The Lancet. Microbe 2021 4 (3) e115-e129
EVOLUTION / ECOLOGY / POPULATIONS
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Urban foci of murine typhus involving cat fleas (Ctenocephalides felis felis) collected from opossums in Mexico City.
Santoyo-Colín Verónica et al. Zoonoses and public health 2020 12 (1) 1-7 -
Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae.
Shaw Liam P et al. Science advances 2021 4 (15) -
Examining horizontal gene transfer in microbial communities.
Brito Ilana Lauren et al. Nature reviews. Microbiology 2021 4 -
Emergence and Autochthonous Transmission of Dengue Virus Type I in a Low-Epidemic Region in Southeast China.
Zhang Yi et al. Frontiers in cellular and infection microbiology 2021 4 638785 -
Molecular Evolution of Human Norovirus GII.2 Clusters.
Li Xingguang et al. Frontiers in microbiology 2021 4 655567 -
The Origin and Molecular Epidemiology of Dengue Fever in Hainan Province, China, 2019.
Liu Lin et al. Frontiers in microbiology 2021 4 657966 -
Profiles of mutations in hepatitis B virus surface and polymerase genes isolated from treatment-naïve Nigerians infected with genotype E.
Olusola Babatunde A et al. Journal of medical microbiology 2021 3 (3) -
Advances and opportunities in malaria population genomics.
Neafsey Daniel E et al. Nature reviews. Genetics 2021 4
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Under pressure: phenotypic divergence and convergence associated with microhabitat adaptations in Triatominae.
Abad-Franch Fernando et al. Parasites & vectors 2021 4 (1) 195
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n4 The utilisation of CytB and COI barcodes for the identification of bloodmeals and Culicoides species (Diptera: Ceratopogonidae) reveals a variety of novel wildlife hosts in South Africa.
Snyman Jumari et al. Acta tropica 2021 4 105913
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Virulence genes identification and characterization revealed the presence of the Yersinia High Pathogenicity Island (HPI) in Salmonella from Brazil.
Dos Santos Anamaria M P et al. Gene 2021 4 145646 -
Population genomics and antimicrobial resistance dynamics of Escherichia coli in wastewater and river environments.
Delgado-Blas Jose F et al. Communications biology 2021 4 (1) 457 -
Disputed rpoB mutations in Mycobacterium tuberculosis and tuberculosis treatment outcomes
Lin Wan-Hsuan et al. Antimicrobial agents and chemotherapy 2021 4 -
Detection, spread and phylogeny of meticillin-resistant Staphylococcus aureus sequence type 45 in Taiwan
Huang Yhu-Chering et al. Microbial genomics 2021 4 (4) -
Genome-wide analysis in Escherichia coli unravels a high level of genetic homoplasy associated with cefotaxime resistance
Coolen Jordy P M et al. Microbial genomics 2021 4 (4) -
Novel SARS-CoV-2 encoded small RNAs in the passage to humans.
Merino Gabriela A et al. Bioinformatics (Oxford, England) 2020 11 (24) 5571-5581 -
Taxonomy of the Trichophyton mentagrophytes/T. interdigitale Species Complex Harboring the Highly Virulent, Multiresistant Genotype T. indotineae.
Tang Chao et al. Mycopathologia 2021 4 -
Emergence and clonal expansion of in vitro artemisinin-resistant Plasmodium falciparum kelch13 R561H mutant parasites in Rwanda.
Uwimana Aline et al. Nature medicine 2020 8 (10) 1602-1608
DETECTION / DIAGNOSIS
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CRISPR-Cas systems for diagnosing infectious diseases.
Kostyusheva Anastasiya et al. Methods (San Diego, Calif.) 2021 4 -
Enhanced Throughput of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Real-Time RT-PCR Panel by Assay Multiplexing and Specimen Pooling.
Lu Xiaoyan et al. Journal of virological methods 2021 4 114149
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Imaging Enterobacterales infections in patients using pathogen-specific positron emission tomography
Ordonez AA, et al. Sci Transl Med, Apr 14, 2021. -
Using viral load and epidemic dynamics to optimize pooled testing in resource-constrained settings
Cleary B, et al. Sci Transl Med, Apr 14, 2021. -
Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests
Barak N, et al. Sci Transl Med, Apr 14, 2021.
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SARS-CoV-2 Detection from the Built Environment and Wastewater and Its Use for Hospital Surveillance
Hinz A, et al. medRxiv, Apr 13, 2021. -
N-protein presents early in blood, dried blood and saliva during asymptomatic and symptomatic SARS-CoV-2 infection.
Shan Dandan et al. Nature communications 2021 3 (1) 1931 -
Detection of coronavirus in environmental surveillance and risk monitoring for pandemic control.
Yao Linlin et al. Chemical Society reviews 2021 3 (6) 3656-3676 -
Rapid Detection of SARS-CoV-2 Virus Using Dual Reverse Transcriptional Colorimetric Loop-Mediated Isothermal Amplification.
Ji Chao et al. ACS omega 2021 4 (13) 8837-8849 -
S-Gene Target Failure as a Marker of Variant B.1.1.7 Among SARS-CoV-2 Isolates in the Greater Toronto Area, December 2020 to March 2021.
Brown Kevin A et al. JAMA 2021 4 -
Implementation of an in-house real-time reverse transcription-PCR assay for the rapid detection of the SARS-CoV-2 Marseille-4 variant.
Bedotto Marielle et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2021 4 104814 -
Novel opportunities for NGS-based one health surveillance of foodborne viruses.
Desdouits Marion et al. One health outlook 2021 4 14 -
Detection of malaria parasites in samples from returning US travelers using the Alethia® Malaria Plus LAMP assay.
Ljolje Dragan et al. BMC research notes 2021 4 (1) 128
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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A cross-border outbreak of Salmonella Bareilly cases confirmed by whole genome sequencing, Czech Republic and Slovakia, 2017 to 2018
Labsk? Kl?ra et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 4 (14)
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Evaluation of WGS-subtyping methods for epidemiological surveillance of foodborne salmonellosis.
Mohammed Manal et al. One health outlook 2021 4 13
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Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions.
Ragonnet-Cronin Manon et al. Nature communications 2021 4 (1) 2188
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Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study
Graham MS, et al. Lancet, Apr 12, 2021. -
Genomic characteristics and clinical effect of the emergent SARS-CoV-2 B.1.1.7 lineage in London, UK: a whole-genome sequencing and hospital-based cohort study
Frampton D, et al. Lancet Infect Dis, Apr 12, 2021. -
Transmission dynamics and molecular characterization of HIV-1 epidemic among therapeutic failure patients in Santa Catarina state, southern Brazil.
Fritsch Hegger M et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 4 104854 -
Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo.
Kinganda-Lusamaki Eddy et al. Nature medicine 2021 4
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Molecular analysis of cryptosporidiosis cases in Western Australia in 2019 and 2020 supports the occurrence of two swimming pool associated outbreaks and reveals the emergence of a rare C. hominis IbA12G3 subtype.
Braima Kamil et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 4 104859
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Structure-based identification of SARS-CoV-2 main protease inhibitors from anti-viral specific chemical libraries: an exhaustive computational screening approach.
Bhowmick Shovonlal et al. Molecular diversity 2021 4 -
Vaccine development for emerging infectious diseases.
Excler Jean-Louis et al. Nature medicine 2021 4
HOST-MICROBE INTERACTIONS
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A human coronavirus evolves antigenically to escape antibody immunity.
Eguia Rachel T et al. PLoS pathogens 2021 4 (4) e1009453 -
SARS-CoV-2 evolution in an immunocompromised host reveals shared neutralization escape mechanisms.
Clark Sarah A et al. Cell 2021 4 -
Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19.
Liu Can et al. Cell 2021 3 (7) 1836-1857.e22 -
A study of differential circRNA and lncRNA expressions in COVID-19-infected peripheral blood.
Wu Yingping et al. Scientific reports 2021 4 (1) 7991 -
Shared B cell memory to coronaviruses and other pathogens varies in human age groups and tissues.
Yang Fan et al. Science (New York, N.Y.) 2021 4 -
SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8+ T cell activation in COVID-19 patients
Saini SK, et al. Science Immunol, Apr 14, 2021. -
Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19.
Yeoh Yun Kit et al. Gut 2021 1 (4) 698-706 -
Mendelian randomisation identifies alternative splicing of the FAS death receptor as a mediator of severe COVID-19.
Klaric Lucija et al. medRxiv : the preprint server for health sciences 2021 4 -
Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV.
Stukalov Alexey et al. Nature 2021 4 -
The long-term genetic stability and individual specificity of the human gut microbiome.
Chen Lianmin et al. Cell 2021 4 -
Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity
Zuo T, et al. Microbiome. 2021 Apr 14;9(1):91 -
Genetic Variants in TNFSF4 and TNFSF8 Are Associated With the Risk of HCV Infection Among Chinese High-Risk Population
Fu Zuqiang et al. Frontiers in genetics 2021 4 630310 -
Peripheral spectrum neurological disorder after arbovirus infection is associated with HLA-F variants among Northeastern Brazilians.
Sonon Paulin et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 4 104855
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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