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Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Pathogen Genomics and Health Database|AMD Clips|PHGKB
Publication Date: Aug 4, 2022
NEWS

Deadly Bacteria in U.S. Soil Not Tied to Lab Leak, Aromatherapy
Fiore K. MedPage Today, Aug 1, 2022.

Inside the super-secure Swiss lab trying to stop the next pandemic
Rigsby J. Reuters, Aug 1, 2022.

FDA accelerates booster campaign to September, emphasizes new formula
McGinley L, Diamond D. Washington Post, Jul 29, 2022.

Heart disease after COVID: what the data say
Sidik SM. Nature, Aug 2, 2022.

Animal Reservoirs—Where the Next SARS-CoV-2 Variant Could Arise
Madhusoodanan J. JAMA, Aug 3, 2022.

How the U.S. Let 20 Million Doses of Monkeypox Vaccine Expire
Goldstein J. New York Times, Aug 1, 2022.

The campaign to rename monkeypox gets complicated
Branswell H. STAT, Aug 1, 2022.

There’s a Monkeypox Testing Bottleneck
Mullin E. Wired, Aug 1, 2022.

U.S. polio case tied to viruses detected in U.K., Israel, suggesting silent spread
Branswell H. STAT, Jul 29, 2022.

‘The entire protein universe’: AI predicts shape of nearly every known protein
Callaway E. Nature, Jul 28, 2022.


EVENTS / TRAINING / WEB RESOURCES

Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses.
Bacon Wendi et al. PLoS computational biology 2022 7 (7) e1010220

The United States COVID-19 Forecast Hub dataset.
Cramer Estee Y et al. Scientific data 2022 8 (1) 462

SARS-ANI: a global open access dataset of reported SARS-CoV-2 events in animals.
Nerpel Afra et al. Scientific data 2022 7 (1) 438


CONCEPTS / COMMENTS

Host genomics beyond the pandemic Turner H. PHG Foundation, Jul 8, 2022.


METHODS / TOOLS

PanExplorer: A web-based tool for exploratory analysis and visualization of bacterial pan-genomes. Dereeper Alexis et al. Bioinformatics (Oxford, England) 2022 8

SARS-CoV-2 genomic epidemiology: data and sequencing infrastructure. Merhi Georgi et al. Future microbiology 2022 7

Namco: a microbiome explorer. Dietrich Alexander et al. Microbial genomics 2022 8 (8)



PATHOGENICITY / ANTIMICROBIAL RESISTANCE

Salmonella Yoruba: a rare serotype revealed through genomic sequencing along the farm-to-fork continuum of an intensive poultry farm in KwaZulu-Natal, South Africa. Ramtahal Melissa A et al. Acta tropica 2022 7 106620

A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella. Malaka De Silva P et al. Proceedings. Biological sciences 2022 8 (1980) 20220581

Molecular characterisation of Neisseria gonorrhoeae associated with disseminated gonococcal infections in Queensland, Australia: a retrospective surveillance study. Guglielmino Christine J D et al. BMJ open 2022 8 (8) e061040

Development of Resistance-Associated Mutations After Sotrovimab Administration in High-risk Individuals Infected With the SARS-CoV-2 Omicron Variant. Birnie Emma et al. JAMA 2022 8


DETECTION / DIAGNOSIS

Early Detection of SARS-CoV-2 Omicron BA.4/5 in German wastewater Wilhelm A, et al. medRxiv, Aug 1, 2022.

Progression of LAMP as a Result of the COVID-19 Pandemic: Is PCR Finally Rivaled? Mannier Cassidy et al. Biosensors 2022 7 (7)

Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform Stanhope BJ, et al. medRxiv, Aug 2, 2022.

Temporal dynamics of SARS-CoV-2 genome and detection of variants of concern in wastewater influent from two metropolitan areas in Arkansas. Silva Camila S et al. The Science of the total environment 2022 8 157546

Detection of SARS-CoV-2 in exhaled air using non-invasive embedded strips in masks. Gallichotte Emily N et al. American journal of infection control 2022 7 (8) 890-897

An analysis of 45 large-scale wastewater sites in England to estimate SARS-CoV-2 community prevalence. Morvan Mario et al. Nature communications 2022 7 (1) 4313

Rapid Adaptation of Established High-Throughput Molecular Testing Infrastructure for Monkeypox Virus Detection. Nörz Dominik et al. Emerging infectious diseases 2022 7 (9)

Detection of monkeypox viral DNA in a routine wastewater monitoring program Wolfe MK, et al. medRxiv, Jul 26, 2022.

Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa Lyimo BM, et al. Front Cell Infect Microbiol. 2022 Jul 13;12:757844.


EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

A Hierarchical Framework for Assessing Transmission Causality of Respiratory Viruses. Jefferson Tom et al. Viruses 2022 7 (8)

Reconstruction of transmission chains of SARS-CoV-2 amidst multiple outbreaks in a geriatric acute-care hospital: a combined retrospective epidemiological and genomic study. Abbas Mohamed et al. eLife 2022 7

Investigation of healthcare-associated COVID-19 in a large French hospital group by whole-genome sequencing. Leducq Valentin et al. Microbiological research 2022 7 127133

Risk of BA.5 infection in individuals exposed to prior SARS-CoV-2 variants Malato J, et al. medRxiv, Jul 28, 2022.

Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada. McLaughlin Angela et al. eLife 2022 8

Phylogenetic prioritization of HIV-1 transmission clusters with viral lineage-level diversification rates. Miller Rachel L et al. Evolution, medicine, and public health 2022 7 (1) 305-315


HOST-MICROBE INTERACTIONS

Plasma proteomics of SARS-CoV-2 infection and severity reveals impact on Alzheimer and coronary disease pathways Wang L, et al. medRxiv, Jul 25, 2022.

Microbiota succession throughout life from the cradle to the grave. Martino Cameron et al. Nature reviews. Microbiology 2022 7

Metabolic control by the microbiome. Cox Timothy O et al. Genome medicine 2022 7 (1) 80


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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