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Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Pathogen Genomics and Health Database|AMD Clips|PHGKB
Publication Date: May 19, 2022
NEWS

What the current spike in Covid-19 cases could say about the coronavirus’ future
Joseph A. STAT, May 12, 2022.

How Often Can You Be Infected With the Coronavirus?
Mandavilli A. New York Times, May 16, 2022.

The U.S. Is About to Make a Big Gamble on Our Next COVID Winter
Wu KJ. Atlantic, May 13, 2022.

Trained scent dogs detect airline travelers with COVID-19
Van Beusekom M. CIDRAP, May 17, 2022.

Traveling in the U.S. soon? Get tested before your trip, CDC says.
Diller N. Washington Post, May 18, 2022.

Flu vaccine could cut COVID risk
Callaway E. Nature, May 16, 2022.

On-campus COVID-19 measures couldn't contain Omicron
Van Beusekom M. CIDRAP, May 18, 2022.

Coronavirus ‘ghosts’ found lingering in the gut
Ledford H. Nature, May 11, 2022.

U.S. monkeypox case reported, as Spain, Portugal report infections in growing outbreak
Branswell H. STAT, May 18, 2022.

Mozambique declares polio outbreak linked to Pakistan
AP, May 18, 2022.


POLICY

How climate law can help to prevent the next pandemic. Phelan Alexandra L et al. Nature 2022 5 (7910) 397


CONCEPTS / COMMENTS

How Public Health Failed America Varma J. Atlantic, May 15, 2022. Brand

Want to prevent pandemics? Stop spillovers Vora NM, et al. Nature, May 12, 2022.

Genomic outbreak surveillance in resource-poor settings. Musila Lillian et al. Nature reviews. Genetics 2022 5 1

Are Countries Becoming Better at SARS-CoV-2 Genomic Surveillance? Mahanta Utkarsha et al. Frontiers in public health 2022 5 887955

Developing a Rapid Response Single IRB Model for Conducting Research During a Public Health Emergency. Lowe Abigail E et al. Health security 2022 5


METHODS / TOOLS

TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. Caraballo-Ortiz Marcos A et al. Bioinformatics (Oxford, England) 2022 5 (10) 2719-2726

RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures. Zhang Hao et al. Bioinformatics (Oxford, England) 2022 5 (10) 2932-2933

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts. Lo Chien-Chi et al. Bioinformatics (Oxford, England) 2022 5 (10) 2700-2704

SASpector: analysis of missing genomic regions in draft genomes of prokaryotes. Lood Cédric et al. Bioinformatics (Oxford, England) 2022 5 (10) 2920-2921

B-assembler: a circular bacterial genome assembler. Huang Fengyuan et al. BMC genomics 2022 5 (Suppl 4) 361

Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks. Bertelli Claire et al. Microbial genomics 2022 5 (5)

Fragment Size-Based Enrichment of Viral Sequences in Plasma Cell-Free DNA. Phung Quynh et al. The Journal of molecular diagnostics : JMD 2022 5 (5) 476-484


EVOLUTION / ECOLOGY / POPULATIONS

Dissecting Listeria monocytogenes Persistent Contamination in a Retail Market Using Whole-Genome Sequencing. Wang Yan et al. Microbiology spectrum 2022 5 e0018522

Core-, pan- and accessory genome analyses of Clostridium neonatale: insights into genetic diversity. Mesa Victoria et al. Microbial genomics 2022 5 (5)

Diverse lineages of pathogenic Leptospira species are widespread in the environment in Puerto Rico, USA. Stone Nathan E et al. PLoS neglected tropical diseases 2022 5 (5) e0009959 Brand

Phylogenetic and amino acid signature analysis of the SARS-CoV-2s lineages circulating in Tunisia. Sassi Mouna Ben et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2022 5 105300

SARS-CoV-2 Delta-Omicron Recombinant Viruses, United States. Lacek Kristine A et al. Emerging infectious diseases 2022 5 (7) Brand

Molecular epidemiology of Crimean-Congo hemorrhagic fever virus in Russia. Volynkina Anna et al. PloS one 2022 5 (5) e0266177

Australia as a global sink for the genetic diversity of avian influenza A virus. Wille Michelle et al. PLoS pathogens 2022 5 (5) e1010150



DETECTION / DIAGNOSIS

Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality. Paruch Lisa et al. International journal of environmental research and public health 2022 5 (9) Brand

Rapid Identification of Bacillus anthracis In Silico and On-Site Using Novel Single-Nucleotide Polymorphisms. Lyu Yufei et al. Microbiology spectrum 2022 5 e0228521

Use of Nucleic Acid Amplification Testing for Rapid Detection of Mycobacterium tuberculosis Complex Among US Tuberculosis Patients, 2011‒2017. Kumar Varsha et al. Open forum infectious diseases 2022 5 (11) ofab528 Brand Brand

Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance. Rockett Rebecca J et al. Nature communications 2022 5 (1) 2745

Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1. Rodino Kyle G et al. Journal of clinical microbiology 2022 5 e0060022

Routine Surveillance and Vaccination on a University Campus During the Spread of the SARS-CoV-2 Omicron Variant. Meredith Genevive R et al. JAMA network open 2022 5 (5) e2212906

Detection Of SARS-COV-2 Variants Of Concern In Wastewater Of Leuven, Belgium Bloemen M, et al. medRxiv, May 12, 2022.

Prion protein gene mutation detection using long-read Nanopore sequencing. Kroll François et al. Scientific reports 2022 5 (1) 8284

Determining the lower limit of detection required for HCV viral load assay for test of cure following direct-acting antiviral-based treatment regimens: Evidence from a global data set. Morgan Jake R et al. Journal of viral hepatitis 2022 3 (6) 474-486 Brand


EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

Matching Clostridioides difficile strains obtained from shoe soles of healthcare workers epidemiologically linked to patients and confirmed by whole genome sequencing. Büchler Andrea C et al. The Journal of hospital infection 2022 5

Carriage prevalence and genomic epidemiology of Staphylococcus aureus among Native American children and adults in the Southwestern USA. Cella Eleonora et al. Microbial genomics 2022 5 (5)

Human-to-dog transmission of SARS-CoV-2, Colombia. Rivero Ricardo et al. Scientific reports 2022 5 (1) 7880

Repeated transmission of SARS-CoV-2 in an overcrowded Irish emergency department elucidated by whole genome sequencing. Hare Daniel et al. The Journal of hospital infection 2022 5

HIV-1-Transmitted Drug Resistance and Transmission Clusters in Newly Diagnosed Patients in Portugal Between 2014 and 2019. Pingarilho Marta et al. Frontiers in microbiology 2022 5 823208

Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017-2019. Neto Zoraima et al. PLoS neglected tropical diseases 2022 5 (5) e0010255



HOST-MICROBE INTERACTIONS

Identification of shared and disease-specific host gene-microbiome associations across human diseases using multi-omic integration. Priya Sambhawa et al. Nature microbiology 2022 5

Cross-tissue immune cell analysis reveals tissue-specific features in humans. Domínguez Conde C et al. Science (New York, N.Y.) 2022 5 (6594) eabl5197

Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies. Lebeaux Rebecca M et al. Pediatric research 2022 5

Super Dominant Pathobiontic Bacteria in the Nasopharyngeal Microbiota Cause Secondary Bacterial Infection in COVID-19 Patients. Qin Tian et al. Microbiology spectrum 2022 5 e0195621

In Silico Analysis Predicts a Limited Impact of SARS-CoV-2 Variants on CD8 T Cell Recognition. Isaeva Olga I et al. Frontiers in immunology 2022 5 891524

An Artificial Intelligence-guided signature reveals the shared host immune response in MIS-C and Kawasaki disease. Ghosh Pradipta et al. Nature communications 2022 5 (1) 2687

Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination. Suryawanshi Rahul K et al. Nature 2022 5


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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