Advanced Molecular Detection Clips Content (Published on 06/30/2022)
NEWS
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A bacterium that is not a microbe
Levin PA. Science, Jun 23, 2022. -
Each SARS-CoV-2 reinfection causes more severe disease
Mathur N. News-Medical, Jun 20, 2022. -
SARS-CoV-2 Spike: A Potential Biomarker For Long Covid
Haseltine WA. Forbes, Jun 23, 2022. -
First reported case of a person getting COVID from a cat
Mallapaty S. Nature, Jun 29, 2022. -
Fast-evolving COVID variants complicate vaccine updates
Callaway E. Nature, Jun 27, 2022. -
Scientists Zero In on Origins of the Monkeypox Outbreak
Mandavilli A. New York Times, Jun 23, 2022. -
U.S. monkeypox response mirrors early coronavirus missteps, experts say
Sun LH, et al. Washington Post, Jun 23, 2022. -
Monkeypox Outbreak Strain Has Far More Mutations Than Expected
Fiore K. MedPage Today, Jun 24, 2022. -
Traces of monkeypox virus found in San Francisco wastewater
KTVU, Jun 24, 2022. -
Monkeypox Genome Analysis Points to Single Origin of Recent Outbreak
GenomeWeb, Jun 24, 2022. -
Non-Sputum CRISPR-Based Tuberculosis Test Shows High Sensitivity in HIV-Infected Children
Johnson M. GenomeWeb, Jun 24, 2022.
CONCEPTS / COMMENTS
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One Health: A new definition for a sustainable and healthy future.
et al. PLoS pathogens 2022 6 (6) e1010537
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Detection of Ancient Viruses and Long-Term Viral Evolution.
Nishimura Luca et al. Viruses 2022 6 (6) -
Vaccines, Variants, and Vigilance: Strengthening the COVID-19 Public Health Response through Partnerships and Collaborations.
Kutty Preeta K et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 6
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Monkeypox Virus Emerges from The Shadow of Its More Infamous Cousin: Family Biology Matters
Xiang Y, White A. Emerg Microbes Infect, Jun 24, 2022.
METHODS / TOOLS
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PIMGAVir and Vir-MinION: Two Viral Metagenomic Pipelines for Complete Baseline Analysis of 2nd and 3rd Generation Data.
Mastriani Emilio et al. Viruses 2022 6 (6) -
The Dataharmonizer: a Tool for Faster Data Harmonization, Validation, Aggregation, and Analysis of Pathogen Genomics Contextual Information
Gill I, et al. Preprints.org, Jun 23, 2022. -
Virus finding tools: current solutions and limitations.
Privitera Grete Francesca et al. Briefings in bioinformatics 2022 6 -
Catwalk: identifying closely related sequences in large microbial sequence databases
Volk D, et al. Microb Genom. 2022 Jun;8(6). -
High throughput SARS-CoV-2 variant analysis using molecular barcodes coupled with next generation sequencing.
Cohen-Aharonov Lyora A et al. PloS one 2022 6 (6) e0253404
EVOLUTION / ECOLOGY / POPULATIONS
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Population genomics of pneumococcal carriage in South Africa following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) immunization.
Javaid Nida et al. Microbial genomics 2022 6 (6)
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Origin and Global Expansion of Mycobacterium tuberculosis Complex Lineage 3.
Shuaib Yassir A et al. Genes 2022 6 (6) -
Draft Genome Sequence of Clostridium botulinum Subtype bont/A5(B2').
Kruemmel Ana Rafaela et al. Microbiology resource announcements 2022 6 e0034822
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A critical evaluation of Mycobacterium bovis pangenomics, with reference to its utility in outbreak investigation.
Ceres Kristina M et al. Microbial genomics 2022 6 (6) -
Genetic background of Cambodian pneumococcal carriage isolates following pneumococcal conjugate vaccine 13.
Belman Sophie et al. Microbial genomics 2022 6 (6)
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Whole genome sequence analysis of Salmonella Typhi provides evidence of phylogenetic linkage between cases of typhoid fever in Santiago, Chile in the 1980s and 2010-2016.
Maes Mailis et al. PLoS neglected tropical diseases 2022 6 (6) e0010178 -
Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.
Joel O Wertheim et al. Nat Commun 2022 6 (1) 3645 -
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Tegally H. Nat Med, Jun 27, 2022. -
Ongoing positive selection drives the evolution of SARS-CoV-2 genomes.
Hou Yali et al. Genomics, proteomics & bioinformatics 2022 6 -
The past, current and future epidemiological dynamic of SARS-CoV-2
Balloux F, et al. Oxford Open Immunol, Jun 20, 2022. -
Genomic diversity of SARS-CoV-2 in Pakistan during the fourth wave of pandemic
Umair M, et al. J Med Virol. 2022 Jun 26 -
Sequential Appearance and Isolation of a SARS-CoV-2 Recombinant between Two Major SARS-CoV-2 Variants in a Chronically Infected Immunocompromised Patient.
Burel Emilie et al. Viruses 2022 6 (6) -
Omicron Sub-Lineages (BA.1.1.529 + BA.*) Current Status in Ecuador.
Carrazco-Montalvo Andrés et al. Viruses 2022 6 (6) -
Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico.
Taboada Blanca et al. Viruses 2022 6 (6) -
Evolutionary and Mutational Characterization of the First H5N8 Subtype Influenza A Virus in Humans.
Ding Lin et al. Pathogens (Basel, Switzerland) 2022 6 (6) -
The Clinical and Genomic Epidemiology of Rhinovirus in Homeless Shelters-King County, Washington.
Chow Eric J et al. The Journal of infectious diseases 2022 6
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Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus.
Isidro Joana et al. Nature medicine 2022 6 -
Epidemiological and virological surveillance of influenza viruses in China during 2020-2021.
Huang Wei-Juan et al. Infectious diseases of poverty 2022 6 (1) 74 -
Viral Hyperparasitism in Bat Ectoparasites: Implications for Pathogen Maintenance and Transmission.
Tendu Alexander et al. Microorganisms 2022 6 (6)
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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The international and intercontinental spread and expansion of antimicrobial-resistant Salmonella Typhi: a genomic epidemiology study.
da Silva Kesia Esther et al. The Lancet. Microbe 2022 6 -
Changes in the Genotypic Characteristics of Community-Acquired Methicillin-Resistant Staphylococcus aureus Collected in 244 Medical Facilities in Japan between 2010 and 2018: a Nationwide Surveillance.
Yamaguchi Tetsuo et al. Microbiology spectrum 2022 6 e0227221
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Whole genome sequencing analysis to evaluate the influence of T2DM on polymorphisms associated with drug resistance in M. tuberculosis.
Bermudez-Hernández Gustavo Adolfo et al. BMC genomics 2022 6 (1) 465
DETECTION / DIAGNOSIS
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Diagnostic challenges with accurate identification of Listeria monocytogenes isolates from food and environmental samples in South Africa.
Thomas Teena S M et al. African journal of laboratory medicine 2022 6 (1) 1482 -
Sequencing-Based Genotyping of Pakistani Burkholderia mallei Strains: A Useful Way for Investigating Glanders Outbreaks.
Brangsch Hanka et al. Pathogens (Basel, Switzerland) 2022 6 (6) -
Phylogenomic Analysis of Salmonella enterica subsp. enterica Serovar Bovismorbificans from Clinical and Food Samples Using Whole Genome Wide Core Genes and kmer Binning Methods to Identify Two Distinct Polyphyletic Genome Pathotypes.
Gopinath Gopal R et al. Microorganisms 2022 6 (6) -
Detection of M. tuberculosis in the environment as a tool for identifying high-risk locations for tuberculosis transmission.
Verma Renu et al. The Science of the total environment 2022 6 156970 -
Virulence plasmid pINV as a genetic signature for Shigella flexneri phylogeny.
Pilla Giulia et al. Microbial genomics 2022 6 (6) -
Absolute Quantification of Viable but Nonculturable Vibrio cholerae Using Droplet Digital PCR with Oil-Enveloped Bacterial Cells.
Zhao Shuo et al. Microbiology spectrum 2022 6 e0070422 -
Evaluation of a Wastewater-Based Epidemiological Approach to Estimate the Prevalence of SARS-CoV-2 Infections and the Detection of Viral Variants in Disparate Oregon Communities at City and Neighborhood Scales.
Layton Blythe A et al. Environmental health perspectives 2022 6 (6) 67010 -
COVID-19 Variant Detection with a High-Fidelity CRISPR-Cas12 Enzyme.
Fasching Clare L et al. Journal of clinical microbiology 2022 6 e0026122 -
Wastewater-based epidemiology in countries with poor wastewater treatment - Epidemiological indicator function of SARS-CoV-2 RNA in surface waters.
Kolarevic Stoimir et al. The Science of the total environment 2022 6 156964 -
National Scale Real-Time Surveillance of SARS-CoV-2 Variants Dynamics by Wastewater Monitoring in Israel.
Bar-Or Itay et al. Viruses 2022 6 (6) -
Coupling Wastewater-Based Epidemiological Surveillance and Modelling of SARS-COV-2/COVID-19: Practical Applications at the Public Health Agency of Canada
Joung MJ, et al. medRxiv, Jun 27, 2022. -
Capturing the SARS-CoV-2 infection pyramid within the municipality of Rotterdam using longitudinal sewage surveillance
de Graaf M, et al. medRxiv, Jun 27, 2022. -
Wastewater-based epidemiological surveillance to monitor the prevalence of SARS-CoV-2 in developing countries with onsite sanitation facilities.
Jakariya Md et al. Environmental pollution (Barking, Essex : 1987) 2022 6 119679 -
A Rapid, Whole Genome Sequencing Assay for Detection and Characterization of Novel Coronavirus (SARS-CoV-2) Clinical Specimens Using Nanopore Sequencing.
Arévalo Maria T et al. Frontiers in microbiology 2022 6 910955 -
SARS-CoV-2 wastewater monitoring using a novel PCR-based method rapidly captured the Delta-to-Omicron ΒΑ.1 transition patterns in the absence of conventional surveillance evidence.
Chassalevris Taxiarchis et al. The Science of the total environment 2022 6 156932 -
Advancing Precision Vaccinology by Molecular and Genomic Surveillance of SARS-CoV-2 in Germany, 2021.
Oh Djin-Ye et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 6 -
Evaluation of a commercial SARS-CoV-2 multiplex PCR genotyping assay for variant identification in resource-scarce settings.
Umunnakwe Chijioke N et al. PloS one 2022 6 (6) e0269071 -
Redesign and Validation of a Real-Time RT-PCR to Improve Surveillance for Avian Influenza Viruses of the H9 Subtype.
Panzarin Valentina et al. Viruses 2022 6 (6) -
Molecular typing of enteroviruses: comparing 5'UTR, VP1 and whole genome sequencing methods.
Gulholm T et al. Pathology 2022 6 -
Current RT-qPCR to detect SARS-CoV-2 may give positive results for related coronaviruses.
Martínez-Murcia Antonio et al. Archives of microbiology 2022 6 (7) 415 -
Molecular Epidemiology of Enterovirus A71 in Surveillance of Acute Flaccid Paralysis Cases in Senegal, 2013-2020.
Ndiaye Ndack et al. Vaccines 2022 6 (6) -
Technologies for HIV-1 drug resistance testing: inventory and needs.
Metzner Karin J et al. Current opinion in HIV and AIDS 2022 6 (4) 222-228 -
Detection of Marburg Virus Disease in Guinea.
Koundouno Fara R et al. The New England journal of medicine 2022 6 (26) 2528-2530 -
Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic.
Vandenbogaert Mathias et al. Scientific reports 2022 6 (1) 10768 -
First experience of implementing Candida auris Real Time PCR for surveillance in the UK: detection of multiple introductions with two international clades and improved patient outcomes.
Taori Surabhi K et al. The Journal of hospital infection 2022 6 -
Screening strategies and laboratory assays to support Plasmodium falciparum histidine-rich protein deletion surveillance: where we are and what is needed.
Beshir Khalid B et al. Malaria journal 2022 6 (1) 201
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Assembly of a Large Collection of Maxicircle Sequences and Their Usefulness for Leishmania Taxonomy and Strain Typing.
Solana Jose Carlos et al. Genes 2022 6 (6)
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Nosocomial Outbreak of Extensively Drug-Resistant (Polymyxin B and Carbapenem) Klebsiella pneumoniae in a Collapsed University Hospital Due to COVID-19 Pandemic.
Gaspar Gilberto G et al. Antibiotics (Basel, Switzerland) 2022 6 (6) -
Source Attribution of Human Campylobacteriosis Using Whole-Genome Sequencing Data and Network Analysis.
Wainaina Lynda et al. Pathogens (Basel, Switzerland) 2022 6 (6) -
Identification of domestic reservoirs and common exposures in an emerging lineage of Shiga toxin-producing Escherichia coli O157:H7 in England: a genomic epidemiological analysis.
Dallman Timothy J et al. The Lancet. Microbe 2022 6
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Plasma Virome Reveals Blooms and Transmission of Anellovirus in Intravenous Drug Users with HIV-1, HCV, and/or HBV Infections.
Li Yanpeng et al. Microbiology spectrum 2022 6 e0144722 -
Similar But Different: Integrated Phylogenetic Analysis of Austrian and Swiss HIV-1 Sequences Reveal Differences in Transmission Patterns of the Local HIV-1 Epidemics.
Kusejko Katharina et al. Journal of acquired immune deficiency syndromes (1999) 2022 3 (4) e4-e12 -
Suspected Cat-to-Human Transmission of SARS-CoV-2, Thailand, July-September 2021.
Sila Thanit et al. Emerging infectious diseases 2022 6 (7) 1485-1488 -
Within-hotel transmission of SARS-CoV-2 during on-arrival quarantine in Hong Kong
Adam DC, et al. medRxiv, Jun 27, 2022. -
A Whole Genome Sequencing-Based Epidemiological Investigation of a Pregnancy-Related Invasive Listeriosis Case in Central Italy.
Russini Valeria et al. Pathogens (Basel, Switzerland) 2022 6 (6)
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SARS-CoV-2: Two Years in the Pandemic: What Have We Observed from Genome Sequencing Results in Lithuania?
Zemaitis Lukas et al. Microorganisms 2022 6 (6) -
Two Separate Clusters of SARS-CoV-2 Delta Variant Infections in a Group of 41 Students Travelling from India: An Illustration of the Need for Rigorous Testing and Quarantine.
Van Elslande Jan et al. Viruses 2022 6 (6)
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Effectiveness of Coronavirus Disease 2019 (COVID-19) mRNA Vaccines Against Infection During an Outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Beta (B.1.351) Variant in a Skilled Nursing Facility: Virginia, March-April 2021.
Heidi L Moline et al. Clin Infect Dis 2022 6 (Suppl 2) S155-S158
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An Immunoinformatics Prediction of Novel Multi-Epitope Vaccines Candidate Against Surface Antigens of Nipah Virus.
Rahman Md Mahfuzur et al. International journal of peptide research and therapeutics 2022 6 (4) 123
HOST-MICROBE INTERACTIONS
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Whole-Genome Sequencing Reveals Age-Specific Changes in the Human Blood Microbiota.
Lee Eun-Ju et al. Journal of personalized medicine 2022 6 (6) -
Persistent circulating SARS-CoV-2 spike is associated with post-acute COVID-19 sequelae
Swank Z, et al. medRxiv, Jun 16, 2022. -
Epigenetic profiling linked to multisystem inflammatory syndrome in children (MIS-C): A multicenter, retrospective study
Davalos V, et al. eClin Med, Jun 25, 2022. -
SARS-CoV-2 ORF1abA1061S potentiate autoreactive T cell responses via epitope mimicry: an explanation to hepatitis of unknown cause
Wang Y, Liu Y. bioRxiv, May 23, 2022. -
The genetic and evolutionary determinants of COVID-19 susceptibility.
Kerner Gaspard et al. European journal of human genetics : EJHG 2022 6 -
Presence of rare potential pathogenic variants in subjects under 65 years old with very severe or fatal COVID-19.
López-Rodríguez Rosario et al. Scientific reports 2022 6 (1) 10369 -
PARIS and SPARTA: Finding the Achilles’ Heel of SARS-CoV-2
Simon V, et al. mSphere, May 19, 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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