A5090325143- SARS-CoV-2 and COVID-19 Research
- COVID-19 Clinical Research Studies
- Vaccine Coverage and Hesitancy
- vaccines and immunoinformatics approaches
- COVID-19 and healthcare impacts
- SARS-CoV-2 detection and testing
- Long-Term Effects of COVID-19
- Animal Virus Infections Studies
- Viral gastroenteritis research and epidemiology
- COVID-19 diagnosis using AI
- Single-cell and spatial transcriptomics
- Machine Learning in Healthcare
- Respiratory viral infections research
- COVID-19 epidemiological studies
- CRISPR and Genetic Engineering
- Heparin-Induced Thrombocytopenia and Thrombosis
- Traditional Chinese Medicine Studies
- Venous Thromboembolism Diagnosis and Management
- Immune responses and vaccinations
- Influenza Virus Research Studies
- Sepsis Diagnosis and Treatment
- Bacillus and Francisella bacterial research
- Topic Modeling
- Gene expression and cancer classification
- COVID-19 and Mental Health
Nference (United States)
2020-2024
Nference (India)
2020-2024
University of Minnesota Rochester
2022
Mayo Clinic in Florida
2021
Although clinical trials and real-world studies have affirmed the effectiveness safety of FDA-authorized COVID-19 vaccines, reports breakthrough infections persistent emergence new variants highlight need to vigilantly monitor these vaccines. Here we compare two full-length Spike protein-encoding mRNA vaccines from Moderna (mRNA-1273) Pfizer/BioNTech (BNT162b2) in Mayo Clinic Health System over time January July 2021, during which either Alpha or Delta variant was highly prevalent. We...
Molecular mimicry is an evolutionary strategy adopted by viruses to exploit the host cellular machinery. We report that SARS-CoV-2 has evolved a unique S1/S2 cleavage site, absent in any previous coronavirus sequenced, resulting striking of identical FURIN-cleavable peptide on human epithelial sodium channel α-subunit (ENaC-α). Genetic alteration ENaC-α causes aldosterone dysregulation patients, highlighting FURIN site critical for activation ENaC. Single cell RNA-seq from 66 studies shows...
Abstract Clinical studies are ongoing to assess whether existing vaccines may afford protection against SARS-CoV-2 infection through trained immunity. In this exploratory study, we analyze immunization records from 137,037 individuals who received PCR tests. We find that polio, Haemophilus influenzae type-B (HIB), measles-mumps-rubella (MMR), Varicella, pneumococcal conjugate (PCV13), Geriatric Flu, and hepatitis A/hepatitis B (HepA–HepB) administered in the past 1, 2, 5 years associated...
Understanding temporal dynamics of COVID-19 symptoms could provide fine-grained resolution to guide clinical decision-making. Here, we use deep neural networks over an institution-wide platform for the augmented curation notes from 77,167 patients subjected PCR testing. By contrasting Electronic Health Record (EHR)-derived COVID-19-positive (COVID pos ; n = 2,317) versus COVID-19-negative neg 74,850) week preceding testing date, identify anosmia/dysgeusia (27.1-fold), fever/chills...
Continuous assessment of the effectiveness and safety US Food Drug Administration-authorized SARS-CoV-2 vaccines is critical to amplify transparency, build public trust, ultimately improve overall health outcomes.To evaluate Johnson & Ad26.COV2.S vaccine for preventing infection.This comparative research study used large-scale longitudinal curation electronic records from multistate Mayo Clinic Health System (Minnesota, Arizona, Florida, Wisconsin, Iowa) identify vaccinated unvaccinated...
Although clinical trials and real-world studies have affirmed the effectiveness safety of FDA-authorized COVID-19 vaccines, reports breakthrough infections persistent emergence new variants highlight need to vigilantly monitor these vaccines. Here we compare two full-length Spike protein-encoding mRNA vaccines from Moderna (mRNA-1273) Pfizer/BioNTech (BNT162b2) in Mayo Clinic Health System over time January July 2021, during which either Alpha or Delta variant was highly prevalent. We...
The emergence of a heavily mutated SARS-CoV-2 variant (B.1.1.529, Omicron) and it’s spread to 6 continents within week initial discovery has set off global public health alarm. Characterizing the mutational profile Omicron is necessary interpret its shared or distinctive clinical phenotypes with other variants. We compared mutations prior variants concern (Alpha, Beta, Gamma, Delta), interest (Lambda, Mu, Eta, Iota Kappa), all 1523 lineages constituting 5.4 million genomes. Omicron’s Spike...
The COVID-19 pandemic demands assimilation of all biomedical knowledge to decode mechanisms pathogenesis. Despite the recent renaissance in neural networks, a platform for real-time synthesis exponentially growing literature and deep omics insights is unavailable. Here, we present nferX dynamic inference from over 45 quadrillion possible conceptual associations unstructured text, triangulation with single-cell RNA-sequencing, bulk RNA-seq proteomics diverse tissue types. A hypothesis-free...
Abstract Large Phase 3 clinical trials of the two FDA-authorized COVID-19 vaccines, mRNA-1273 (Moderna) and BNT162b2 (Pfizer/BioNTech), have demonstrated efficacies 94.1% (n = 30,420, 95% CI: 89.3-96.8) 43,448, 90.3-97.6) in preventing symptomatic COVID-19, respectively. Given ongoing vaccine rollout to healthcare personnel residents long-term care facilities, here we provide a preliminary assessment real-world vaccination efficacy 62,138 individuals from Mayo Clinic associated health system...
Abstract Intensive care unit (ICU) admissions and mortality in severe COVID-19 patients are driven by “cytokine storms” acute respiratory distress syndrome (ARDS). Interim clinical trial results suggest that the corticosteroid dexamethasone displays better 28-day survival requiring ventilation or oxygen. In this study, 10 out of 16 (62.5%) had an average plasma IL-6 value over pg/mL post administration corticosteroids also worse outcomes (i.e., ICU stay >15 days death), compared to 8 41...
<h3>Importance</h3> Recent reports on waning of COVID-19 vaccine–induced immunity have led to the approval and rollout additional doses booster vaccinations. Individuals at increased risk SARS-CoV-2 infection are receiving vaccine in addition regimen that was tested clinical trials. Risks adverse event profiles associated with currently not well understood. <h3>Objective</h3> To evaluate safety third-dose vaccination US Food Drug Administration (FDA)–approved mRNA vaccines. <h3>Design,...
The hand of molecular mimicry in shaping SARS-CoV-2 evolution and immune evasion remains to be deciphered. Here, we report 33 distinct 8-mer/9-mer peptides that are identical between the human reference proteome. We benchmark this observation against other viral-human peptide identity, which suggests generally similar extents for many viruses. Interestingly, 20 novel mimicked by have not been observed any previous coronavirus strains (HCoV, SARS-CoV, MERS). Furthermore, four map onto...
Abstract Longitudinal characterization of SARS-CoV-2 PCR testing from COVID-19 patient’s nasopharynx and its juxtaposition with blood-based IgG-seroconversion diagnostic assays is critical to understanding infection durations. Here, we retrospectively analyze 851 SARS-CoV-2-positive patients at least two positive tests find that 99 these remain after 4 weeks their initial diagnosis date. For the 851-patient cohort, mean lower bound viral RNA shedding was 17.3 days (SD: 7.8), upper 668...
To assess the association of COVID-19 vaccines and non-COVID-19 with cerebral venous sinus thrombosis (CVST).We retrospectively analyzed a cohort 771,805 vaccination events across 266,094 patients in Mayo Clinic Health System between 01/01/2017 03/15/2021. The primary outcome was positive diagnosis CVST, identified either by presence corresponding ICD code or an NLP algorithm which detected CVST within free-text clinical notes. For each vaccine we calculated relative risk dividing incidence...
BackgroundCoagulopathies are a major class among COVID-19 associated complications. Although anticoagulants such as unfractionated Heparin and Enoxaparin both being used for therapeutic mitigation of COVID coagulopathy (CAC), differences in their clinical outcomes remain to be investigated.MethodsWe analyzed records 1,113 patients the Mayo Clinic Electronic Health Record (EHR) database who were admitted hospital between April 4, 2020 August 31, 2020, including 19 different sites Arizona,...
The presence of personally identifiable information (PII) in natural language portions electronic health records (EHRs) constrains their broad reuse. Despite continuous improvements automated detection PII, residual identifiers require manual validation and correction. Here, we describe an de-identification system that employs ensemble architecture, incorporating attention-based deep-learning models rule-based methods, supported by heuristics for detecting PII EHR data. Detected are then...
Case reports of patients infected with COVID-19 and influenza virus ("flurona") have raised questions around the prevalence severity coinfection. Using data from HHS Protect Public Data Hub, NCBI Virus, CDC FluView, we analyzed trends in SARS-CoV-2 hospitalized coinfection cases strain prevalences. We also characterized across Mayo Clinic Enterprise January 2020 to April 2022. compared expected observed case counts different waves pandemic assessed symptoms outcomes monoinfection after...
Early diagnosis of pulmonary hypertension (PH) is critical for effective treatment and management. We aimed to develop externally validate an artificial intelligence algorithm that could serve as a PH screening tool, based on analysis standard 12-lead ECG.
Understanding temporal dynamics of COVID-19 patient symptoms could provide fine-grained resolution to guide clinical decision-making. Here, we use deep neural networks over an institution-wide platform for the augmented curation notes from 77,167 patients subjected PCR testing. By contrasting Electronic Health Record (EHR)-derived COVID-19-positive (COVID pos ; n=2,317) versus COVID-19-negative neg n=74,850) week preceding testing date, identify anosmia/dysgeusia (27.1-fold), fever/chills...
Abstract Variants of SARS-CoV-2 are evolving under a combination immune selective pressure in infected hosts and natural genetic drift, raising global alarm regarding the durability COVID-19 vaccines. Here, we conducted longitudinal analysis over 1.8 million genomes from 183 countries or territories to capture vaccination-associated viral evolutionary patterns. To augment this macroscale analysis, performed genome sequencing 23 vaccine breakthrough patients 30 unvaccinated for whom also...
Abstract Understanding the relationships between pre-existing conditions and complications of COVID-19 infection is critical to identifying which patients will develop severe disease. Here, we leverage ~1.1 million clinical notes from 1803 hospitalized deep neural network models characterize associations 21 development 20 (e.g. respiratory, cardiovascular, renal, hematologic) throughout course (i.e. 0–30 days, 31–60 61–90 days). Pleural effusion was most frequent complication early (89/1803...
Abstract In light of the massive and rapid vaccination campaign against COVID-19, continuous real-world effectiveness safety assessment FDA-authorized vaccines is critical to amplify transparency, build public trust, ultimately improve overall health outcomes. this study, we leveraged large-scale longitudinal curation electronic records (EHRs) from multi-state Mayo Clinic system (MN, AZ, FL, WN, IA). We compared infection rate 2,195 individuals who received a single dose Ad26.COV2.S vaccine...
The highly contagious Delta variant of SARS-CoV-2 has become a prevalent strain globally and poses public health challenge around the world. While there been extensive focus on understanding amino acid mutations in variant's Spike protein, mutational landscape rest proteome (25 proteins) remains poorly understood. To this end, we performed systematic analysis all proteins from nearly 2 million genomes 176 countries/territories. Six missense viral life cycle-associated Membrane (I82T),...