A5066795130- SARS-CoV-2 and COVID-19 Research
- SARS-CoV-2 detection and testing
- Bacteriophages and microbial interactions
- Viral gastroenteritis research and epidemiology
- COVID-19 epidemiological studies
- COVID-19 Clinical Research Studies
- Vaccine Coverage and Hesitancy
- Poxvirus research and outbreaks
- HIV, TB, and STIs Epidemiology
- Plant Virus Research Studies
- Reproductive tract infections research
- Respiratory viral infections research
- Data-Driven Disease Surveillance
- COVID-19 diagnosis using AI
- Viral Infections and Outbreaks Research
- Bacillus and Francisella bacterial research
- Viral Infections and Immunology Research
- Syphilis Diagnosis and Treatment
- Herpesvirus Infections and Treatments
- Animal Virus Infections Studies
- vaccines and immunoinformatics approaches
- Congenital Diaphragmatic Hernia Studies
University of Washington
2021-2024
University of Washington Medical Center
2021-2023
Fred Hutch Cancer Center
2022
The coronavirus disease 2019 (COVID-19) pandemic is dominated by variant viruses; the resulting impact on severity remains unclear. Using a retrospective cohort study, we assessed hospitalization risk following infection with 7 severe acute respiratory syndrome 2 (SARS-CoV-2) variants.Our study includes individuals positive SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) in Washington Disease Reporting System available viral genome data, from 1 December 2020 to 14 January...
Abstract Across 20 vaccine breakthrough cases detected at our institution, all (100%) infections were due to variants of concern (VOCs) and had a median Ct 20.2 (IQR, 17.1–23.3). When compared with 5174 contemporaneous samples sequenced in laboratory, VOCs significantly enriched among (P < .05).
Monkeypox virus, the causative agent of 2022 monkeypox outbreak, is a double-stranded DNA virus in Orthopoxvirus genus Poxviridae family. Genes terminal regions genomes mostly code for host-pathogen interaction proteins and are prone to selective pressure modification events. Using viral whole genome sequencing, we identified twenty-five total clinical samples with ORF-disrupting mutations, including twenty encoding nonsense mutations MPXVgp001/191 (OPG001), MPXVgp004/188 (OPG015), MPXVgp010...
SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving health departments to design interventions with limited information. We analyzed genomes sampled between February 2020 and March 2022 jointly epidemiological cell phone mobility data investigate fine scale spatiotemporal in King County, Washington, diverse, metropolitan US county. applied an approximate structured coalescent approach model within North County South alongside the rate of outside...
Abstract Across 20 vaccine breakthrough cases detected at our institution, all (100%) infections were due to variants of concern (VOC) and had a median Ct 20.2 (IQR=17.1-23.3). When compared 5174 contemporaneous samples sequenced in laboratory, VOC significantly enriched among (p < .05).
Abstract Background The COVID-19 pandemic is dominated by variant viruses; the resulting impact on disease severity remains unclear. Using a retrospective cohort study, we assessed hospitalization risk following infection with seven SARS-CoV-2 variants. Methods Our study includes individuals positive RT-PCR in Washington Disease Reporting System available viral genome data, from December 1, 2020 to January 14, 2022. analysis was restricted cases specimens collected through sentinel...
The global spread of the SARS-CoV-2 virus has resulted in emergence lineages which impact effectiveness immunotherapies and vaccines that are based on early Wuhan isolate. All currently approved employ spike protein S, as it is target for neutralizing antibodies. Here we describe two isolates with unusually large deletions N-terminal domain (NTD) spike. Cryo-EM structural analysis shows result complete reshaping NTD supersite, an antigenically important region NTD. For both variants...
The sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this paper, we performed the whole-genome using nanopore Illumina to describe circulation virus lineages in Armenia. analysis 145 full genomes identified six clades (19A, 20A, 20B, 20I, 21J, 21K) considerable intra-clade PANGO lineage diversity. Phylodynamic transmission allowed attribute specific as well infer their importation routes. Thus, first two waves positive case...
Abstract SARS-CoV-2 remdesivir resistance mutations have been generated in vitro but not reported patients receiving treatment with the antiviral agent. We present a case of an immunocompromised patient acquired B-cell deficiency who developed indolent, protracted course infection. Remdesivir therapy alleviated symptoms and produced transient virologic response, her was complicated by recrudescence high-grade viral shedding. Whole genome sequencing identified mutation, E802D, nsp12...
Abstract SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving health departments to design interventions with limited information. We analyzed genomes sampled between February 2020 and March 2022 jointly epidemiological cell phone mobility data investigate fine scale spatiotemporal in King County, Washington, diverse, metropolitan US county. applied an approximate structured coalescent approach model within North County South alongside the rate of...
Abstract Mitigation measures against the COVID-19 pandemic affected RSV seasonality and led to an unexpectedly high number of cases in Washington State since October 2022. Here we describe genomic characteristics evolutionary relationship 2022 outbreak compared previous outbreaks region globally.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused one of the worst pandemics in recent history. Few reports have revealed that SARS-CoV-2 was spreading United States as early end January. In this study, we aimed to determine if had been circulating Los Angeles (LA) area at a time when access diagnostic testing for disease 2019 (COVID-19) severely limited.We used pooling strategy look remnant samples submitted regular pathogen from symptomatic patients November March...
Abstract Background Syphilis incidence continues to increase dramatically in the United States and yet little is known about Treponema pallidum (TP) genomic epidemiology within American metropolitan areas. Methods We performed whole genome sequencing tprK deep of 28 TP-containing specimens collected mostly from remnant Aptima swabs 24 individuals Seattle Sexual Health Clinic during 2021-2022. Results All 12 infected with Nichols lineage strains were MSM, while a specific SS14 cluster...
ABSTRACT Amplicon-based sequencing methods have been central in characterizing the diversity, transmission and evolution of SARS-CoV-2, but need to be rigorously assessed for clinical utility. Here, we validated Swift Biosciences’ SARS-CoV-2 Normalase Amplicon Panels using remnant specimens. High quality genomes meeting our established library sequence criteria were recovered from positive specimens with a 95% limit detection ≥ 40.08 copies/PCR reaction. Breadth genome recovery was evaluated...
Abstract The SARS-CoV-2 spike protein is the target of neutralizing antibodies and immunogen used in all currently approved vaccines. global spread virus has resulted emergence lineages which are concern for effectiveness immunotherapies vaccines based on early Wuhan isolate. Here we describe two isolates with large deletions N-terminal domain (NTD) spike. Cryo-EM structural analysis showed that result complete reshaping antigenic surface NTD supersite. remodeling affects binding tested...