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Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Pathogen Genomics and Health Database|AMD Clips|PHGKB
Publication Date: Nov 17, 2022
CONCEPTS / COMMENTS

Ten simple rules for developing visualization tools in genomics.
Durant Eloi et al. PLoS computational biology 2022 11 (11) e1010622

Integrated pneumonia surveillance: pandemics and beyond.
Ginsburg Amy Sarah et al. The Lancet. Global health 2022 11

Toward a New Paradigm of North-South and South-South Partnerships for Pandemic Preparedness: Lessons Learned from COVID-19 and Other Outbreaks.
Nsanzimana Sabin et al. The American journal of tropical medicine and hygiene 2022 11

The landscape of mRNA nanomedicine.
Huang Xiangang et al. Nature medicine 2022 11


METHODS / TOOLS

MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens.
Kaur Sandeep et al. Database : the journal of biological databases and curation 2022 11

Taxonium, a web-based tool for exploring large phylogenetic trees.
Sanderson Theo et al. eLife 2022 11

MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing.
Bonin Nathalie et al. Nucleic acids research 2022 11

Benchmarking second and third-generation sequencing platforms for microbial metagenomics.
Meslier Victoria et al. Scientific data 2022 11 (1) 694

AvP: A software package for automatic phylogenetic detection of candidate horizontal gene transfers.
Koutsovoulos Georgios D et al. PLoS computational biology 2022 11 (11) e1010686

Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance
Connor R, et al. bioRxiv, Nov 3, 2022.

A Custom Hepatitis A Virus Assay for Whole-Genome Sequencing.
Cleary Nora G et al. Journal of virological methods 2022 11 114649


EVOLUTION / ECOLOGY / POPULATIONS

Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission.
Pickering Bradley et al. Nature microbiology 2022 11

Genetic Variability of the Monkeypox Virus Clade IIb B.1.
Scarpa Fabio et al. Journal of clinical medicine 2022 11 (21)

ORF-Interrupting Mutations in Monkeypox Virus Genomes from Washington and Ohio, 2022.
Sereewit Jaydee et al. Viruses 2022 11 (11)

Genetic Diversity and Possible Origins of the Hepatitis B Virus in Siberian Natives.
Manuylov Victor et al. Viruses 2022 11 (11)

African swine fever virus - variants on the rise.
Forth Jan H et al. Emerging microbes & infections 2022 11 1-57

Indian sewage microbiome has unique community characteristics and potential for population-level disease predictions.
Singh Kumar Siddharth et al. The Science of the total environment 2022 11 160178



DETECTION / DIAGNOSIS

Antibiotic resistance surveillance of Klebsiella pneumoniae complex is affected by refined MALDI-TOF identification, Swiss data, 2017 to 2022.
Voellmy Irene Katharina et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2022 11 (45) Brand

Tracing Foodborne Botulism Events Caused by Clostridium botulinum in Xinjiang Province, China, Using a Core Genome Sequence Typing Scheme.
Ma Xin et al. Microbiology spectrum 2022 11 e0116422

Global disparities in SARS-CoV-2 genomic surveillance
Brito AF, et al. Nat Commun. 2022 Nov 16;13(1):7003.

Using Genome Sequence Data to Predict SARS-CoV-2 Detection Cycle Threshold Values
Duesterwald L, et al. medRxiv, Nov 15, 2022.

City-wide wastewater genomic surveillance through the successive emergence of SARS-CoV-2 Alpha and Delta variants.
Brunner F S et al. Water research 2022 11 119306

One-year surveillance of SARS-CoV-2 in wastewater from vulnerable urban communities in metropolitan São Paulo, Brazil.
Barbosa Mikaela Renata Funada et al. Journal of water and health 2022 11 (2) 471-490

SARS-CoV-2 variant detection from wastewater: rapid spread of B.1.1.7 lineage in Hungary.
Róka Eszter et al. Journal of water and health 2022 11 (2) 277-286

Identification of a rare SARS-CoV-2 XL hybrid variant in wastewater and the subsequent discovery of two infected individuals in Nevada.
Vo Van et al. The Science of the total environment 2022 11 (Pt 3) 160024

Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation.
Wallace Zachary S et al. Frontiers in bioinformatics 2022 11 1020189

Exploration of wastewater surveillance for Monkeypox virus
Mejia EM, et al. medRxiv, Nov 14, 2022.


EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

Bi-national Outbreak of Salmonella Newport Infections Linked to Onions: the United States Experience.
McCormic Z D et al. Epidemiology and infection 2022 11 1-23 Brand Brand

Tracking the progressive spread of the SARS-CoV-2 Omicron variant in Italy, December 2021 to January 2022.
Stefanelli Paola et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2022 11 (45)

SARS-CoV-2 Genomic Diversity in Households Highlights the Challenges of Sequence-Based Transmission Inference
Bendall EE, et al. mSphere. 2022 Nov 15;e0040022.

Impact of molecular sequence data completeness on HIV cluster detection and a network science approach to enhance detection.
Mazrouee Sepideh et al. Scientific reports 2022 11 (1) 19230

Transmission network and phylogenetic analysis reveal older male-centered transmission of CRF01_AE and CRF07_BC in Guangxi, China.
Zhang Fei et al. Emerging microbes & infections 2022 11 1-48



HOST-MICROBE INTERACTIONS

The population genomic legacy of the second plague pandemic.
Gopalakrishnan Shyam et al. Current biology : CB 2022 10 (21) 4743-4751.e6

Gene set predictor for post-treatment Lyme disease
Clarke DJ, et al. Cell Rep, Nov 15, 2022.

Novel genes and sex differences in COVID-19 severity.
Cruz Raquel et al. Human molecular genetics 2022 6 (22) 3789-3806


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.

About Weekly AMD Clips

Clips are selected weekly 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. CDC-authored articles are flagged. Items marked I&E address aspects of implementation or evaluation in clinical or public health practice.


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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