Advanced Molecular Detection Clips Content (Published on 10/21/2021)
NEWS
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Computational Biologists Seek Continuous Benchmarking of Bioinformatics Technology
Versel N. GenomeWeb, Oct 18, 2021. -
Tuberculosis, Like Covid, Spreads by Breathing, Scientists Report
Mandavilli A. New York Times, Oct 19, 2021. -
Largest ever global study of tuberculosis identifies genetic causes of drug resistance
(press release) Univ of Oxford, Oct 19, 2021. -
What We Know About Covid, the Flu and the Air We Breathe
Marr L. New York Times, Oct 19, 2021. -
COVID reinfections likely within one or two years, models propose
Peeples L. Nature, Oct 19, 2021. -
Delta sub-variant: what is AY.4.2 and is it contributing to a surge in cases?
Newey S. Telegraph, Oct 20, 2021. -
COVID vaccine makers brace for a variant worse than Delta
Waltz E. Nature, Oct 20, 2021. -
Moderna won't share its vaccine recipe. WHO has hired an African startup to crack it
Aizenman N. NPR, Oct 19, 2021. -
A cancer survivor had the longest documented COVID-19 infection. Here's what scientists learned
Couzin-Frankel J. Science, Oct 19, 2021. -
COVID super-immunity: one of the pandemic's great puzzles
Callaway E. Nature, Oct 14, 2021. -
Scientists Search for Cause of Mysterious Covid-Related Inflammation in Children
Szabo L. KHN, Oct 20, 2021. -
COG-UK Welcomes New "COG-Train" Global COVID-19 Genomics Training Programme Team
(blog COG-UK, Oct 19, 2021.
EVENTS / TRAINING / WEB RESOURCES
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COVID-19 Genomics (COG)-Train
(website) COG-UK, accessed Oct 21, 2021.
CONCEPTS / COMMENTS
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Infectious disease in an era of global change
Baker RE, et al. Nat Microbiol, Oct 13, 2021. -
SARS-CoV-2 and NIAID-supported Bat Coronavirus Research
(web page) NIAID/NIH, Oct 20, 2021.
METHODS / TOOLS
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Recommended reporting items for epidemic forecasting and prediction research: The EPIFORGE 2020 guidelines.
Pollett Simon et al. PLoS medicine 2021 10 (10) e1003793 -
Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes
Hunt M, et al. bioRxiv, Sep 27, 2021.
EVOLUTION / ECOLOGY / POPULATIONS
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Complete Genome Sequence of Neisseria gonorrhoeae Multilocus Sequence Type ST7363 Isolated from Thailand.
Cherdtrakulkiat Thitima et al. Microbiology resource announcements 2021 10 (41) e0057321 -
Genetic diversity of Salmonella Paratyphi A isolated from enteric fever patients in Bangladesh from 2008 to 2018.
Rahman Sadia Isfat Ara et al. PLoS neglected tropical diseases 2021 10 (10) e0009748 -
Detailed molecular characterization of Neisseria meningitidis isolates by whole genome sequencing (WGS), Czech Republic, 2010-2019.
Honskus M et al. Epidemiologie, mikrobiologie, imunologie : casopis Spolecnosti pro epidemiologii a mikrobiologii Ceske lekarske spolecnosti J.E. Purkyne 2021 10 (3) 168-177 -
Genome Sequence Analysis of Clostridium chauvoei Strains of European Origin and Evaluation of Typing Options for Outbreak Investigations.
Thomas Prasad et al. Frontiers in microbiology 2021 10 732106 -
Genome and Methylome analysis of a phylogenetic novel Campylobacter coli cluster with C. jejuni introgression.
Dieckmann Anastasia-Lisa et al. Microbial genomics 2021 10 (10) -
Emergence of Vibrio cholerae O1 Sequence Type 75, South Africa, 2018-2020
Smith AM, et al. Emerg Infect Dis, Oct 7, 2021. -
Mutations Associated with SARS-CoV-2 Variants of Concern, Benin, Early 2021.
Sander Anna-Lena et al. Emerging infectious diseases 2021 9 (11) 2889-2903 -
Intra-host evolution during SARS-CoV-2 prolonged infection.
Voloch Carolina M et al. Virus evolution 2021 10 (2) veab078 -
Comparative Genomics of Mycobacterium avium Complex Reveals Signatures of Environment-Specific Adaptation and Community Acquisition.
Keen Eric C et al. mSystems 2021 10 e0119421 -
Evaluation of global evolutionary variations in the early stage of SARS-CoV-2 pandemic.
Lee Sanghyun et al. Heliyon 2021 10 e08170 -
Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes.
Xia Xuhua et al. Viruses 2021 9 (9) -
Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution
Nunes DR, et al. medRxiv, Oct 14, 2021. -
Genomic reconstruction of the SARS-CoV-2 epidemic in England.
Vöhringer Harald S et al. Nature 2021 10 -
The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil.
Bittar Cíntia et al. Frontiers in public health 2021 10 745310 -
Clinical and Molecular Epidemiology of Crimean-Congo Hemorrhagic Fever in Humans in Uganda, 2013-2019.
Balinandi Stephen et al. The American journal of tropical medicine and hygiene 2021 10 -
Genetically Divergent Highly Pathogenic Avian Influenza A(H5N8) Viruses in Wild Birds, Eastern China
He G, et al. Emerg Infect Dis, Oct 8, 2021. -
Tracing the Origin, Spread, and Molecular Evolution of Zika Virus in Puerto Rico, 2016-2017.
Santiago Gilberto A et al. Emerging infectious diseases 2021 10 (11) 2971-2973 -
Red foxes harbor two genetically distinct, spatially separated Echinococcus multilocularis clusters in Brandenburg, Germany.
Herzig Mandy et al. Parasites & vectors 2021 10 (1) 535
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Clinical Molecular and Genomic Epidemiology of Morganella morganii in China.
Xiang Guoxiu et al. Frontiers in microbiology 2021 10 744291 -
Molecular characterization of rpoB gene mutations in isolates from tuberculosis patients in Cubal, Republic of Angola.
Rando-Segura Ariadna et al. BMC infectious diseases 2021 10 (1) 1056 -
Linear regression equations to predict β-lactam, macrolide, lincosamide and fluoroquinolone minimum inhibitory concentrations from molecular antimicrobial resistance determinants in Streptococcus pneumoniae.
Demczuk Walter et al. Antimicrobial agents and chemotherapy 2021 10 AAC0137021 -
Genomic Profiling of Mycobacterium tuberculosis Strains, Myanmar
Aung H, et al. Emerg Infect Dis, Sep 28, 2021. -
Genome-wide association studies of global Mycobacterium tuberculosis resistance to thirteen antimicrobials in 10,228 genomes
CRyPTIC Consortium, et al. bioRxiv, Sep 16, 2021. -
Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach
CRyPTIC Consortium, et al. bioRxiv, Sep 21, 2021. -
Deciphering Bedaquiline and Clofazimine Resistance in Tuberculosis: An Evolutionary Medicine Approach
Sonnenkalb L, et al. bioRxiv, Aug 13, 2021. -
A generalisable approach to drug susceptibility prediction for M. Tuberculosis using machine learning and whole-genome sequencing
CRyPTIC Consortium, Sep 16, 2021. -
A data compendium of Mycobacterium tuberculosis antibiotic resistance
Brankin A, et al. bioRxiv, Sep 16, 2021. -
The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A new global standard for molecular diagnostics
Walker TM, et al. Lancet (preprint), 2021. -
Comparison of Symptoms and RNA Levels in Children and Adults With SARS-CoV-2 Infection in the Community Setting.
Chung Erin et al. JAMA pediatrics 2021 6 (10) e212025 -
Acquired HIV drug resistance and virologic monitoring in a HIV hyper-endemic setting in KwaZulu-Natal Province, South Africa.
Chimukangara Benjamin et al. AIDS research and therapy 2021 10 (1) 74 -
Encephalitis and Death in Wild Mammals at a Rehabilitation Center after Infection with Highly Pathogenic Avian Influenza A(H5N8) Virus, United Kingdom
Floyd T, et al. Emerg Infect Dis, Oct 13, 2021.
DETECTION / DIAGNOSIS
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Modification of the multiplex plasmid PCR assay for Borrelia miyamotoi strain LB-2001 based on the complete genome sequence reflecting genomic rearrangements differing from strain CT13-2396.
Gilmore Robert D et al. Ticks and tick-borne diseases 2021 10 (1) 101843 -
Screening patients at admission to Copenhagen hospitals for carriage of resistant bacteria after contact with health care systems abroad, 2016-2019.
Westerholt Marc et al. International journal of antimicrobial agents 2021 10 106452 -
Co-Infection with 4 Species of Mycobacteria Identified by Using Next-Generation Sequencing
Wang L, et al. Emerg Infect Dis, Oct 8, 2021. -
CoWWAn: Model-based assessment of COVID-19 epidemic dynamics by wastewater analysis
Proverbio D, et al. medRxiv, Oct 18, 2021. -
Evaluation of viral loads in patients with SARS-CoV-2 Delta variant infection: Higher loads do not translate into different testing scenarios
Marti JLG, et al. medRxiv, Oct 18, 2021. -
Assessing Multiplex Tiling PCR Sequencing Approaches for Detecting Genomic Variants of SARS-CoV-2 in Municipal Wastewater.
Lin Xuan et al. mSystems 2021 10 e0106821 -
Virologic features of SARS-CoV-2 infection in children
Yonker LM, et al. J Infect Dis, Oct 14, 2021. -
Normalization of SARS-CoV-2 viral load via RT-qPCR provides higher-resolution data for comparison across time and between patients.
Porter W Tanner et al. Virus research 2021 10 198604 -
Real-Time Genomic Surveillance for SARS-CoV-2 Variants of Concern, Uruguay.
Rego Natalia et al. Emerging infectious diseases 2021 8 (11) 2957-2960 -
Correlation of SARS-CoV-2 Subgenomic RNA with Antigen Detection in Nasal Midturbinate Swab Specimens.
Immergluck Katherine et al. Emerging infectious diseases 2021 8 (11) 2887-2891 -
Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexed RT-qPCR assay.
Boršová Kristína et al. Scientific reports 2021 10 (1) 20494 -
Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020.
Smith Maureen Rebecca et al. Nature communications 2021 10 (1) 6009 -
A deletion in the N gene may cause diagnostic escape in SARS-CoV-2 samples.
Zannoli Silvia et al. Diagnostic microbiology and infectious disease 2021 10 (1) 115540 -
Hepatitis A Virus Incidence Rates and Biomarker Dynamics for Plasma Donors, United States
Schoch S, et al. Emerg Infect Dis, Sep 27, 2021. -
Unraveling the Complexity of Imported Malaria Infections by Amplicon Deep Sequencing.
He Xi et al. Frontiers in cellular and infection microbiology 2021 10 725859
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Population Genomics and Inference of Mycobacterium avium Complex Clusters in Cystic Fibrosis Care Centers, United States
Hasan NA, et al. Emerg Infect Dis, Oct 7, 2021. -
Nonclonal Burkholderia pseudomallei Population in Melioidosis Case Cluster, Sri Lanka.
Jayasinghearachchi Himali S et al. Emerging infectious diseases 2021 8 (11) 2955-2957 -
Machine learning to predict the source of campylobacteriosis using whole genome data.
Arning Nicolas et al. PLoS genetics 2021 10 (10) e1009436 -
SARS-CoV-2 and wastewater: What does it mean for non-human primates?
Mathavarajah Sabateeshan et al. American journal of primatology 2021 10 e23340 -
Pneumonia Patients Caused by Co-infection With SARS-CoV-2 and Human Adenovirus in China.
Qiu Shaofu et al. Frontiers in medicine 2021 10 735779 -
The impact of global lineage dynamics, border restrictions, and emergence of the B.1.1.7 lineage on the SARS-CoV-2 epidemic in Norway.
Osnes Magnus N et al. Virus evolution 2021 10 (2) veab086 -
Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts
Siddle KJ, et al. medRxiv, Oct 20, 2021.
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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SARS-CoV-2 vaccine breakthrough infections with the alpha variant are asymptomatic or mildly symptomatic among health care workers.
Rovida Francesca et al. Nature communications 2021 10 (1) 6032 -
Coronavirus Disease 2019 Vaccine Impact on Rates of Severe Acute Respiratory Syndrome Coronavirus 2 Cases and Postvaccination Strain Sequences Among Health Care Workers at an Urban Academic Medical Center: A Prospective Cohort Study.
Bouton Tara C et al. Open forum infectious diseases 2021 10 (10) ofab465 -
Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India.
Gupta Nivedita et al. Viruses 2021 9 (9) -
Breakthrough Infections with Multiple Lineages of SARS-CoV-2 Variants Reveals Continued Risk of Severe Disease in Immunosuppressed Patients.
Deng Xufang et al. Viruses 2021 9 (9) -
Time-Varying Effectiveness of Three Covid-19 Vaccines in Puerto Rico
Robles-Fontan MM, et al. medRxiv, Oct 20, 2021. -
Duration of viral shedding and culture positivity with post-vaccination breakthrough delta variant infections
Siedner MJ, et al. medRxiv, Oct 17, 2021. -
Breakthrough SARS-CoV-2 infections in 620,000 U.S. Veterans, February 1, 2021 to August 13, 2021
Cohn BA, et al. medRxiv, Oct 14, 2021.
HOST-MICROBE INTERACTIONS
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Modulation of host epigenome by coronavirus infections and developing treatment modalities for COVID-19 beyond genetics.
Rabaan A A et al. European review for medical and pharmacological sciences 2021 10 (19) 5947-5964 -
A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection
Andreakos E, et al. Nat Immunol, Oct 19, 2021. -
Herpesvirus infections and Alzheimer's disease: a Mendelian randomization study.
Huang Shu-Yi et al. Alzheimer's research & therapy 2021 9 (1) 158 -
Maternal and Infant Immune Repertoire Sequencing Analysis Identifies Distinct Ig and TCR Development in Term and Preterm Infants.
Le Brian L et al. Journal of immunology (Baltimore, Md. : 1950) 2021 10 -
The gut microbiome in konzo.
Bramble Matthew S et al. Nature communications 2021 9 (1) 5371
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 18, 2024
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