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Advanced Molecular Detection Clips Database|AMD Clips|Public Health Genomics and Precision Health Knowledge Base (PHGKB) PHGKB Horizon Scan > Advanced Molecular Detection Clips


Update Date: Apr 25, 2024

NEWS

The pandemic cost 7 million lives, but talks to prevent a repeat stall
Sellers FS. Post, Apr 21, 2024.

The H5N1 Outbreak Is Not a Test Run, It's a Warning Shot
Bhadelia N. MedPage Today, Apr 16, 2024.

USDA shares recent H5N1 avian flu sequences amid more dairy herd outbreaks
Schnirring L. CIDRAP, Apr 22, 2024.

Scientists find clues in early analysis of newly shared US H5N1 avian flu sequences
Schnirring L. CIDRAP, Apr 23, 2024.

Bird Flu Outbreak in Cattle May Have Begun Months Earlier Than Thought
Mandavilli A. New York Times, Apr 24, 2024.

Massive amounts of H5N1 vaccine would be needed if there’s a bird flu pandemic. Can we make enough?
Branswell H. STAT, Apr 24, 2024.

Are We FLiRTing With A New Covid Wave?
(blog post) Topol E. Ground Truths, Apr 18, 2024.

What toilets can reveal about COVID, cancer and other health threats
Ladyzhets B. Nature, Apr 17, 2024.


CONCEPTS / COMMENTS

Ten years of high-consequence pathogens-research gains, readiness gaps, and future goals
McQuiston, J. H., et al. Emerg Infect Dis 2024 30 (4) 800-802 Brand Brand

Community Voices and Whole-Genome Sequencing for Tuberculosis: Storytelling and the Importance of Listening.
Justin T Denholm et al. Public Health Genomics 2024 3 (1) 68-73

Emergence of SARS and COVID-19 and preparedness for the next emerging disease X.
Ben Hu et al. Front Med 2024 4 (1) 1-18 Brand


METHODS / TOOLS

Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes.
Mathieu Gand et al. Front Microbiol 2024 4 1336532

Construction of the ETECFinder database for the characterization of enterotoxigenic Escherichia coli (ETEC) and revision of the VirulenceFinder web tool at the CGE website.
Flemming Scheutz et al. J Clin Microbiol 2024 4 e0057023

INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance.
João Dourado Santos et al. Genome Med 2024 4 (1) 61

Data-driven recombination detection in viral genomes.
Tommaso Alfonsi et al. Nat Commun 2024 4 (1) 3313

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics.
Xavier Fernandez-Cassi et al. Food Environ Virol 2024 4

Development of a non-infectious control for viral hemorrhagic fever PCR assays.
Matthew A Knox et al. PLoS Negl Trop Dis 2024 4 (4) e0011390


EVOLUTION / ECOLOGY / POPULATIONS

Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections.
David VanInsberghe et al. PLoS Pathog 2024 4 (4) e1012131 Brand

How fast are viruses spreading in the wild?
Simon Dellicour et al. bioRxiv 2024 4



DETECTION / DIAGNOSIS

Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline.
Dan Lu et al. bioRxiv 2024 4

Simultaneous detection and characterization of common respiratory pathogens in wastewater through genomic sequencing.
Rachel C Williams et al. Water Res 2024 4 121612

Emergence of OXA-48-producing Klebsiella pneumoniae in Lithuania, 2023: a multi-cluster, multi-hospital outbreak.
Paulius Greicius et al. Euro Surveill 2024 4 (16) Brand

Literature Review of Pathogen Agnostic Molecular Testing of Clinical Specimens From Difficult-to-Diagnose Patients: Implications for Public Health.
Diane L Downie et al. Health Secur 2024 4 (2) 93-107 Brand Brand

A novel cgMLST for genomic surveillance of Yersinia enterocolitica infections in France allowed the detection and investigation of outbreaks in 2017-2021.
Anne-Sophie Le Guern et al. Microbiol Spectr 2024 e0050424 Brand

Bacterial discrimination by Fourier transform infrared spectroscopy, MALDI-mass spectrometry and whole-genome sequencing.
Rachel McGalliard et al. Future Microbiol 2024

Next-generation sequencing survey of acute febrile illness in Senegal (2020-2022).
Gregory S Orf et al. Front Microbiol 2024 4 1362714 Brand

Genomic surveillance of SARS-CoV-2 in North Africa: 4 years of GISAID data sharing.
Zaineb Hamzaoui et al. IJID Reg 2024 4 100356 Brand

Implementation of point-of-care molecular testing for respiratory viruses in congregate living settings.
Charlie Tan et al. Infect Control Hosp Epidemiol 2024 4 1-5 Brand

High-resolution and real-time wastewater viral surveillance by Nanopore sequencing.
Xiaoqing Xu et al. Water Res 2024 4 121623

Evaluation of crAssphages as a potential marker of human viral contamination in environmental water and fresh leafy greens.
Soo Hwan Suh et al. Front Microbiol 2024 4 1374568 Brand

Genomic Analysis and Surveillance of Respiratory Syncytial Virus (RSV) Using Wastewater-Based Epidemiology (WBE).
Danielle M Allen et al. J Infect Dis 2024 4 Brand

Laboratory and field validation of the recombinase polymerase amplification assay targeting the Schistosoma mansoni mitochondrial minisatellite region (SmMIT-RPA) for snail xenomonitoring for schistosomiasis.
Silvia Gonçalves Mesquita et al. Int J Parasitol 2024 2 (5) 247-256

A next generation sequencing assay combining Ixodes species identification with pathogen detection to support tick surveillance efforts in the United States.
Lynn M Osikowicz et al. Ticks Tick Borne Dis 2024 4 (4) 102343 Brand


EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study.
Jada Hackman et al. Wellcome Open Res 2024 4 427

Overlapping Streptococcus pyogenes and Streptococcus dysgalactiae subspecies equisimilis household transmission and mobile genetic element exchange.
Ouli Xie et al. Nat Commun 2024 4 (1) 3477

A severe acute respiratory coronavirus virus 2 (SARS-CoV-2) nosocomial cluster with inter-facility spread: Lessons learned.
Aurora E Pop-Vicas et al. Infect Control Hosp Epidemiol 2024 1 (5) 635-643 Brand

Multiple introductions of monkeypox virus to Ireland during the international mpox outbreak, May 2022 to October 2023.
Gabriel Gonzalez et al. Euro Surveill 2024 4 (16)

Breakthrough Mpox outbreak investigation, the delicate balance between host immune response and viral immune escape.
Marco Moretti et al. Sex Transm Dis 2024 4

Rapid molecular epidemiology investigations into two recent measles outbreaks in Israel detected from October 2023 to January 2024.
Efrat Bucris et al. Euro Surveill 2024 4 (16) Brand


ANTIMICROBIALS / VACCINES / INTERVENTIONS

Overview of U.S. COVID-19 vaccine safety surveillance systems.
Julianne Gee et al. Vaccine 2024 4 Brand Brand

An Omicron-specific, self-amplifying mRNA booster vaccine for COVID-19: a phase 2/3 randomized trial.
Amit Saraf et al. Nat Med 2024 4


HOST-MICROBE INTERACTIONS

The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome
Su Q, et al. Cell Host Microbe, Apr 23, 2024.


Note: Brand indicates that at least one CDC-affiliated author; Brand indicates that the article addresses aspects of implementation or evaluation in clinical or public health practice.

Content Index

References

About AMD Clips

Clips are selected from a variety of sources, including PubMed, journal tables of contents, and online media. Special emphasis is given to the use of next-generation genetic sequencing in infectious disease public health surveillance, investigation, and development of new diagnostics and interventions. The collection is not comprehensive but aims to capture highlights, while surveying a wide range of topics.

Note:

  • Brand indicates that at least one CDC-affiliated author.
  • Brand indicates that the article addresses aspects of implementation or evaluation in clinical or public health practice.
  • Health Department: identifies articles having authors affiliated with U.S. public health departments, either at the indicated state or its sub-jurisdictions (city, county); health departments in U.S. territories are labeled Other.

Disclaimer: Articles listed in the Public Health Knowledge Base are selected by the CDC Office of Public Health Genomics to provide current awareness of the literature and news. Inclusion in the update 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 update, 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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