A5003933891- Respiratory viral infections research
- Bacteriophages and microbial interactions
- Plant Virus Research Studies
- Animal Virus Infections Studies
- Virus-based gene therapy research
- Viral Infections and Vectors
- Cancer Genomics and Diagnostics
- Bacillus and Francisella bacterial research
- SARS-CoV-2 and COVID-19 Research
- Polyomavirus and related diseases
- Ethics in Clinical Research
- Poxvirus research and outbreaks
- Virology and Viral Diseases
- Genomics and Phylogenetic Studies
- Bacterial Identification and Susceptibility Testing
- Viral Infections and Outbreaks Research
- Parasitic Infections and Diagnostics
- Radiology practices and education
- Clinical Reasoning and Diagnostic Skills
- Vector-Borne Animal Diseases
- Fecal contamination and water quality
- Clinical Laboratory Practices and Quality Control
- Advanced Biosensing Techniques and Applications
- Cystic Fibrosis Research Advances
- Digital Imaging for Blood Diseases
ARUP Laboratories (United States)
2023-2025
University of Utah
2023-2025
University of Washington Medical Center
2021
University of Washington
2017-2021
Fred Hutch Cancer Center
2017-2019
Cancer Research Center
2017-2019
Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
2017-2019
A next-generation, broad-spectrum, orally efficacious influenza and B virus inhibitor is associated with a high genetic resistance barrier.
More than 2 months separated the initial description of SARS-CoV-2 and discovery its widespread dissemination in United States. Despite this lengthy interval, implementation specific quantitative reverse transcription (qRT)-PCR-based tests US has been slow, testing is still not widely available. Metagenomic sequencing offers promise unbiased detection emerging pathogens, without requiring prior knowledge identity responsible agent or genomic sequence.To evaluate metagenomic approaches...
Recent data suggest that human coronavirus (HCoV) pneumonia is associated with significant mortality in hematopoietic cell transplant (HCT) recipients. Investigation of risk factors for prolonged shedding and intrahost genome evolution may provide critical information development novel therapeutics.We retrospectively reviewed HCT recipients HCoV detected nasal samples by polymerase chain reaction (PCR). strains were identified using strain-specific PCR. Shedding duration was defined as time...
With sequencing technologies becoming cheaper and easier to use, more groups are able obtain whole genome sequences of viruses public health scientific importance. Submission genomic data NCBI GenBank is a requirement prior publication plays critical role in making publicly available. currently has automatic prokaryotic eukaryotic annotation pipelines but no viral pipeline beyond influenza virus. Annotation submission sequence non-trivial task, especially for that do not routinely interact...
IMPORTANCE Human parainfluenza virus 3 is an important cause of morbidity and mortality among infants, the immunocompromised, elderly. Using deep genomic sequencing HPIV-3-positive clinical material its subsequent viral isolate, we discover a number known novel coding mutations in main HPIV-3 attachment protein HN during brief exposure to immortalized cells. These significantly alter function fusion complex, increasing promotion by as well generally decreasing neuraminidase activity...
Systemic mastocytosis is a hematologic malignancy characterized by clonal expansion of neoplastic mast cells. Detection this variation critical for screening and diagnosis, with recent guidelines emphasizing the need high-sensitivity assays that identify variants at variant allele frequency below 0.05%. Our reference laboratory offers droplet digital polymerase chain reaction (ddPCR) detection KIT D816V limit 0.03% frequency-substantially higher sensitivity than next-generation sequencing...
The capacity of respiratory viruses to undergo evolution within the tract raises possibility under selective pressure host environment or drug treatment. Long-term infections in immunocompromised hosts are potential drivers viral and development infectious variants. We showed that intrahost chronic human parainfluenza virus 3 (HPIV3) infection individuals elicited mutations favored entry persistence, suggesting similar processes may operate across enveloped viruses. profiled longitudinal...
Abstract CrAssphages are a diverse group of related phages detected in human feces where they the most prevalent and abundant prokaryotic virus. CrAssphages’ cellular host has been identified as anaerobic Bacteroides intestinalis . CrAssphage also reported non-human primates environmental samples proposed marker fecal contamination. Here we describe crAssphage DNA feline sample. 95% ~ 100 Kb genome could be assembled classified genus 1 recently Alphacrassvirinae subfamily. The cat origin...
The mpox pandemic necessitated the rapid development of clinical assays for monkeypox virus detection. While majority specimens have high viral loads with corresponding early cycle threshold (CT) values, reports indicated some late CT values can represent false positive results. To mitigate this risk, Centers Disease Control and Prevention (CDC) published an advisory recommending repeat testing all ≥34. However, limited experimental data were available to support specific cutoff. In study,...
Abstract Diagnostically informative microbial cell-free DNA (cfDNA) can be detected from blood plasma during fulminant infections such as sepsis. However, the potential for airway pathogens to enter circulation of cystic fibrosis (CF) patients chronic infective states has not yet been evaluated. We assessed whether patient contained measurable quantities cfDNA CF respiratory microorganisms by sequencing 21 individuals with recruited outpatient clinics and 12 healthy controls. To account...
We report draft genome sequences of three novel bunyaviruses, two rhabdoviruses, and one nyamivirus identified metagenomically from 10 moths in Washington state.
Dairy farming involves frequent contact among animals, workers and farm environments. To explore the Staphylococcus spp. diversity that occurs on dairy farms, a pilot study sampled workers, cows environments from five two organic three conventional in Washington State. Samples were taken nares hands of consenting (n = 24), udders selected 25) representative environmental surfaces 96) each farm. increase characterized, distinct colonies sample for identification with 16S analysis. A total 198...
ABSTRACT Given the cost and unclear clinical impact of metagenomic next-generation sequencing (mNGS), laboratory stewardship may improve utilization. This retrospective observational study examines mNGS results from two academic medical centers employing different approaches. Eighty orders [54 cerebrospinal fluid (CSF) 26 plasma] were identified 2019 to 2021 at University Washington (UW), which requires director-level approval for orders, Utah (Utah), does not restrict ordering. The...
A wealth of viral data sits untapped in publicly available metagenomic sets when it might be extracted to create a usable index for the virological research community. We hypothesized that work this complexity and scale could done hackathon setting. Ten teams comprised over 40 participants from six countries, assembled crowd-sourced set analysis processing pipelines complex biological three-day event on San Diego State University campus starting 9 January 2019. Prior hackathon, 141,676...
Abstract With their small genomes, fast evolutionary rates, and clinical significance, viruses have long been fodder for studies of whole genome evolution. One common need in these is the analysis viral evolution over time through longitudinal sampling. However, there exists no simple tool to automate such analyses. We created a command-line visualization called LAVA (Longitudinal Analysis Viral Alleles). allows dynamic interactive across time. Results are easily shared via single HTML file...
Infectious pathogens are known for their rapid evolutionary rates with new mutations arising over days to weeks. The ability rapidly recover whole genome sequences and analyze the spread evolution of using genetic information pathogen collection dates has lead interest in real-time tracking infectious transmission outbreaks. However, level temporal resolution afforded by these analyses may conflict definitions what constitutes protected health (PHI) privacy requirements de-identification...
Metagenomic next-generation sequencing (mNGS) allows unbiased of all or nearly nucleic acid in a sample. As evidenced by the many excellent reviews on topic, there is much intere...
We report draft genome sequences of six novel Picornavirales members from different spider species found in Washington state. These viral distinctly clustered together phylogenetically with less than 35% amino acid identity to the closest reference genome.
We describe metagenomic next-generation sequencing (mNGS) of a human coronavirus 229E from patient with AML and persistent upper respiratory symptoms, who underwent hematopoietic cell transplantation (HCT). mNGS revealed 548-nucleotide deletion, which comprised the near entirety ORF4 gene, no minor allele variants were detected to suggest mixed infection. As part her pre-HCT conditioning regimen, received myeloablative treatment cyclophosphamide 12 Gy total body irradiation. Iterative RT-PCR...
Abstract Demographic and structural changes in the workforce are resulting ever smaller cohorts of laboratory medical professionals while advancements an aging population has increased demand for testing. Furthermore, inexorable our technologists resulted a with high variation experience. The need new tools to help bridge experience gap increase productivity readily apparent. Recently, large language models (LLMs) have emerged as powerful various industries, including healthcare. However,...
Background Given the cost and unclear clinical impact of metagenomic next-generation sequencing (mNGS), laboratory stewardship may improve utilization. This study examines mNGS results from two academic medical centers employing different approaches. Methods 80 orders (54 CSF 26 plasma) were identified 2019 to 2021 at University Washington (UW), which requires director-level approval for orders, Utah (Utah), does not restrict ordering. The relationship traditional microbiology...
Abstract Acute myeloid leukemia (AML) is a cancer of hematopoietic systems that poses high population burden, especially among pediatric populations. AML presents with molecular heterogeneity, complicating patient risk stratification and treatment planning. While cytogenetic subtypes are well described, significance subtype-specific gene expression patterns poorly understood effective modeling these individual algorithms challenging. Using novel consensus machine learning approach, we...
Abstract The global outbreak of mpox necessitated the rapid development clinical assays for monkeypox virus detection. While majority specimens have high viral loads with corresponding early CT values, reports indicated some late values can represent false positive results. To mitigate this risk, Centers Disease Control and Prevention (CDC) published an advisory recommending repeat testing all ≥34. However, limited experimental data was available to support specific cutoff. In study, we...