Advanced Molecular Detection Clips Content (Published on 04/14/2022)
NEWS
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Meningitis B Vaccine May Protect Against ... Gonorrhea?
Walker M. MedPage Today, Apr 12, 2022. -
FIND Project Aims to Accelerate Targeted NGS Solutions for Global Drug-Resistant TB Testing
Zhang H. GenomeWeb, Apr 8, 2022. -
New York State Department of Health Announces Emergence of Recently Identified, Highly Contagious Omicron Subvariants in New York and Urges Continued Vigilance Against COVID-19
(news release) New York State Dept of Health, Apr 13, 2022. -
Covid cases rise in Northeast as BA.2 omicron subvariant takes hold
Sellers FS, et al. Washington Post, Apr 12, 2022.
CONCEPTS / COMMENTS
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Critical Assessment of Metagenome Interpretation: the second round of challenges.
Meyer Fernando et al. Nature methods 2022 4 -
Unlocking capacities of genomics for the COVID-19 response and future pandemics.
Knyazev Sergey et al. Nature methods 2022 4 -
Addressing Privacy Concerns in Sharing Viral Sequences and Minimum Contextual Data in a Public Repository During the COVID-19 Pandemic.
Song Lingqiao et al. Frontiers in genetics 2022 4 716541 -
In pursuit of data immortality
Eisenstein M. Nature, Apr 4, 2022.
METHODS / TOOLS
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Mind your Ps: A probabilistic model to aid the interpretation of molecular epidemiology data.
Penedos Ana Raquel et al. EBioMedicine 2022 4 103989 -
Rapid in situ identification of biological specimens via DNA amplicon sequencing using miniaturized laboratory equipment.
Pomerantz Aaron et al. Nature protocols 2022 4 -
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes.
Ebler Jana et al. Nature genetics 2022 4 (4) 518-525 -
SAM-TB: a whole genome sequencing data analysis website for detection of Mycobacterium tuberculosis drug resistance and transmission.
Yang Tingting et al. Briefings in bioinformatics 2022 2 (2)
EVOLUTION / ECOLOGY / POPULATIONS
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Phylogenetic Structure and Comparative Genomics of Multi-National Invasive Haemophilus influenzae Serotype a Isolates.
Topaz Nadav et al. Frontiers in microbiology 2022 4 856884
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Recombinant BA.1/BA.2 SARS-CoV-2 Virus in Arriving Travelers, Hong Kong, February 2022.
Gu Haogao et al. Emerging infectious diseases 2022 4 (6) -
Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function.
Martin Darren P et al. Molecular biology and evolution 2022 3 (4) -
Molecular characterisation and tracking of the severe acute respiratory syndrome coronavirus 2, Thailand, 2020-2022
Puenpa J, et al. Research Square, Apr 12, 2022. -
Measuring How Recombination Re-shapes the Evolutionary History of PRRSV-2: A Genome-Based Phylodynamic Analysis of the Emergence of a Novel PRRSV-2 Variant.
Pamornchainavakul Nakarin et al. Frontiers in veterinary science 2022 4 846904 -
Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load.
Zhao Lele et al. Virus evolution 2022 4 (1) veac022 -
Host diversity and behavior determine patterns of interspecies transmission and geographic diffusion of avian influenza A subtypes among North American wild reservoir species.
Hicks Joseph T et al. PLoS pathogens 2022 4 (4) e1009973 -
Global Population Genomics of Two Subspecies of Cryptosporidium hominis during 500 Years of Evolution.
Tichkule Swapnil et al. Molecular biology and evolution 2022 3 (4)
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Genomic Screening of Antimicrobial Resistance Markers in UK and US Campylobacter Isolates Highlights Stability of Resistance over an 18-Year Period.
van Vliet Arnoud H M et al. Antimicrobial agents and chemotherapy 2022 4 e0168721
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Pathogenomes and variations in Shiga toxin production among geographically distinct clones of Escherichia coli O113:H21.
Allué-Guardia Anna et al. Microbial genomics 2022 4 (4) -
Comparative Genomic Analysis Reveals Potential Pathogenicity and Slow-Growth Characteristics of Genus Brevundimonas and Description of Brevundimonas pishanensis sp. nov.
Huang Zhenzhou et al. Microbiology spectrum 2022 4 e0246821 -
Litter Commensal Bacteria Can Limit the Horizontal Gene Transfer of Antimicrobial Resistance to Salmonella in Chickens.
Oladeinde Adelumola et al. Applied and environmental microbiology 2022 4 e0251721
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Large-Scale Genomic Epidemiology of Klebsiella pneumoniae Identified Clone Divergence with Hypervirulent Plus Antimicrobial-Resistant Characteristics Causing Within-Ward Strain Transmissions.
Pei Na et al. Microbiology spectrum 2022 4 e0269821 -
A nosocomial salmonellosis outbreak caused by bla-carrying extensively drug-resistant Salmonella enterica serovar Goldcoast in a hospital respiratory care ward in Taiwan.
Chen Chih-Ming et al. Journal of global antimicrobial resistance 2022 4 -
Genomic insights into the mechanism of carbapenem resistance dissemination in Enterobacterales from a tertiary public heath setting in South Asia.
Farzana Refath et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 4 -
Associations Between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants and Risk of Coronavirus Disease 2019 (COVID-19) Hospitalization Among Confirmed Cases in Washington State: A Retrospective Cohort Study.
Miguel I Paredes et al. Clin Infect Dis 2022 4 (1) e536-e544
DETECTION / DIAGNOSIS
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In silico analyses of penicillin binding proteins in Burkholderia pseudomallei uncovers SNPs with utility for phylogeography, species differentiation, and sequence typing.
McLaughlin Heather P et al. PLoS neglected tropical diseases 2022 4 (4) e0009882
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Fourteen mcr-1-Positive Salmonella enterica Isolates Recovered from Travelers Returning to the United States from the Dominican Republic.
Webb Hattie E et al. Microbiology resource announcements 2022 4 e0011822
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Diagnosis and Surveillance of Neonatal Infections by Metagenomic Next-Generation Sequencing.
Zhang Rong et al. Frontiers in microbiology 2022 4 855988 -
Evaluating the clinical impact of routine whole genome sequencing in tuberculosis treatment decisions and the issue of isoniazid mono-resistance.
Park Mirae et al. BMC infectious diseases 2022 4 (1) 349
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Quantifying the relationship between SARS-CoV-2 wastewater concentrations and building-level COVID-19 prevalence at an isolation residence using a passive sampling approach
Acer PT, et al. medRxiv, Apr 11, 2022. -
Second round of the interlaboratory comparison (ILC) exercise of SARS-CoV-2 molecular detection assays being used by 45 veterinary diagnostic laboratories in the US
Deng K, et al. medRxiv, Apr 10, 2022.
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SARS-CoV-2 infection in free roaming dogs from the Amazonian jungle.
Zambrano-Mila Marlon Steven et al. One health (Amsterdam, Netherlands) 2022 4 100387 -
Validation of a rapid, saliva-based, and ultra-sensitive SARS-CoV-2 screening system for pandemic-scale infection surveillance.
Dewhurst Robert E et al. Scientific reports 2022 4 (1) 5936 -
DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2.
Yermanos Alexander et al. BMC genomics 2022 4 (1) 289 -
Identification and Genomic Characterization of Parvovirus B19V Genotype 3 Viruses from Cases of Meningoencephalitis in West Bengal, India.
Pattabiraman Chitra et al. Microbiology spectrum 2022 4 e0225121
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Screening for Viral Nucleic Acids in the Cerebrospinal Fluid of Dogs With Central Nervous System Inflammation.
Barber Renee M et al. Frontiers in veterinary science 2022 4 850510
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Surveillance to Track Progress Toward Polio Eradication--Worldwide, 2020-2021
Wilkinson AL, et al. MMWR, Apr 15, 2022.
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission.
Smruthi Karthikeyan et al. medRxiv 2022 4 -
From elimination to suppression: genomic epidemiology of a large Delta SARS-CoV-2 outbreak in Aotearoa New Zealand
Jelley L, et al. medRxiv, Apr 12, 2022.
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Phylodynamic and phylogeographic reconstruction of porcine reproductive and respiratory syndrome virus (PRRSV) in Europe: patterns and determinants.
Franzo Giovanni et al. Transboundary and emerging diseases 2022 4
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Infectious viral load in unvaccinated and vaccinated individuals infected with ancestral, Delta or Omicron SARS-CoV-2.
Puhach Olha et al. Nature medicine 2022 4
HOST-MICROBE INTERACTIONS
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Understanding COVID-19 through genome-wide association studies.
Karlsen Tom H et al. Nature genetics 2022 4 (4) 368-369 -
Expanded COVID-19 phenotype definitions reveal distinct patterns of genetic association and protective effects.
Roberts Genevieve H L et al. Nature genetics 2022 4 (4) 374-381
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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