A5016711537- SARS-CoV-2 and COVID-19 Research
- Animal Virus Infections Studies
- Evolution and Genetic Dynamics
- Viral gastroenteritis research and epidemiology
- Evolutionary Game Theory and Cooperation
- COVID-19 Clinical Research Studies
- SARS-CoV-2 detection and testing
- Monoclonal and Polyclonal Antibodies Research
- Immune Cell Function and Interaction
- Mathematical and Theoretical Epidemiology and Ecology Models
- Plant Virus Research Studies
- T-cell and B-cell Immunology
- Genomic variations and chromosomal abnormalities
- Gene Regulatory Network Analysis
- Pharmacogenetics and Drug Metabolism
- HIV Research and Treatment
- Influenza Virus Research Studies
- Long-Term Effects of COVID-19
- Respiratory viral infections research
- Atherosclerosis and Cardiovascular Diseases
- Drug Transport and Resistance Mechanisms
- Platelet Disorders and Treatments
- Blood groups and transfusion
- Virus-based gene therapy research
- Infectious Encephalopathies and Encephalitis
Helix (United States)
2021-2025
Fujian Agriculture and Forestry University
2024
Pfizer (United States)
2024
University of California, Berkeley
2015-2019
Los Alamos National Laboratory
2014-2015
Government of the United States of America
2014
Duke University
2012-2013
Acetaminophen (N-acetyl-para-aminophenol) is the most widely used over-the-counter or prescription painkiller in world. metabolized liver where a toxic byproduct produced that can be removed by conjugation with glutathione. overdoses, either accidental intentional, are leading cause of acute failure United States, accounting for 56,000 emergency room visits per year. The standard treatment overdose N-acetyl-cysteine (NAC), which given to stimulate production glutathione.We have created...
Significance Broadly neutralizing antibodies against HIV have recently been discovered, but their highly mutated nature and late emergence in infection make it difficult to infer how they arose. As a step understanding development, we investigate antibody–virus coevolution, using mathematical model. Here find that broadly principle may arise earlier be less mutated, competition between broad responses initial autologous antibody delays emergence. It possible reduce this elicit than...
This study reports on the displacement of Alpha (B.1.1.7) by Delta (B.1.617.2 and its substrains AY.1, AY.2, AY.3) in United States. By analyzing RT-qPCR testing results viral sequencing samples collected across States, we show that percentage SARS-CoV-2 positive cases caused dropped from 67% May 2021 to less than 3.0% just 10 weeks. We also variant has outcompeted Iota (B.1.526) interest Gamma (P.1) concern. An analysis mean quantification cycles (Cq) values tests over time reveal...
Abstract Between November 2021 and February 2022, SARS-CoV-2 Delta Omicron variants co-circulated in the United States, allowing for co-infections possible recombination events. We sequenced 29,719 positive samples during this period analyzed presence fraction of reads supporting mutations specific to either or variant. identified 18 co-infections, one which displayed evidence a low Delta-Omicron recombinant viral population. also two independent cases infection by virus, where 100% RNA came...
As part of a multi-state viral genomic surveillance program, we conducted case-only analysis to evaluate the effectiveness XBB.1.5-adapated mRNA vaccines in preventing severe illness among individuals with medically attended SARS-CoV-2 infection. We compared prior receipt an XBB.1.5-adapted vaccine between SARS-CoV-2-infected adults inpatient or emergency department (ED) visits (as proxy for illness) vs those outpatient mild illness). Among 6,551 patients September 2023 and January 2024,...
The immunoglobulin heavy variable (IGHV) and T cell beta (TRBV) loci are among the most complex regions in human genome. Generated through a process of gene duplication/deletion diversification, these can vary extensively between individuals copy number contain genes that highly similar, making their analysis technically challenging. Here, we present comprehensive study functional segments IGHV TRBV loci, quantifying single-nucleotide variation globally diverse sample 109 286 humans from...
ABSTRACT Within a multi-state viral genomic surveillance program, we conducted case-control analysis comparing prior receipt of XBB.1.5-adapted mRNA vaccination between SARS-CoV-2-infected adults with inpatient/ED visits (proxy for severe illness) vs outpatient visits. Among 6,551 patients from September 2023-January 2024, 6.1% 12.0% had received XBB.1.5 (aOR=0.41; 95%CI:0.32-0.53). This protective association was weaker among JN.1 (aOR=0.62; 95%CI:0.40-0.96) XBB-lineage (aOR=0.28;...
The study of genomic regions that contain gene copies and structural variation is a major challenge in modern genomics. Unlike involving single nucleotide changes, data on the copy number difficult to collect few tools exist for analyzing between individuals. immunoglobulin heavy variable (IGHV) locus, which plays an integral role adaptive immune response, example complex region varies number. Lack standard methods genotype this prevents it from being included association studies holding...
Antigenically evolving pathogens such as influenza viruses are difficult to control owing their ability evade host immunity by producing immune escape variants. Experimental studies have repeatedly demonstrated that viral variants emerge more often from immunized hosts than naive hosts. This empirical relationship between status and within-host is not fully understood theoretically, nor has its impact on antigenic evolution at the population level been evaluated. Here, we show this can be a...
Abstract Within a multistate viral genomic surveillance program, we evaluated whether proportions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections attributed to the JN.1 variant and XBB-lineage variants (including HV.1 EG.5) differed between inpatient outpatient care settings during periods cocirculation. Both were less likely than EG.5 account for among inpatients versus outpatients (adjusted odds ratio [aOR], 0.60 [95% confidence interval (CI), .43–.84; P = .003]...
The dynamics of a population undergoing selection is central topic in evolutionary biology. This question particularly intriguing the case where selective forces act opposing directions at two scales. For example, fast-replicating virus strain outcompetes slower-replicating strains within-host scale. However, if causes host morbidity and less frequently transmitted, it can be outcompeted by between-host Here we consider stochastic ball-and-urn process which models this type phenomenon. We...
In proposing his genetic feedback mechanism, David Pimentel was one of the first biologists to argue that reciprocal interplay ecological and evolutionary dynamics is an important process regulating population ultimately affecting community composition. Although past decade has seen increase in research activity on these so-called eco-evolutionary dynamics, there remains a conspicuous lack compelling natural examples such feedback. Here we this may be due inherent difficulty detecting...
Within a multistate clinical cohort, SARS-CoV-2 antiviral prescribing patterns were evaluated from April 2022-June 2023 among nonhospitalized patients with risk factors for severe COVID-19. Among 3247 adults, only 31.9% prescribed an agent (87.6% nirmatrelvir/ritonavir, 11.9% molnupiravir, 0.5% remdesivir), highlighting the need to identify and address treatment barriers.
In this study, we investigated how Radix pseudostellariae polysaccharide (RPP) enhances the immune response of inactivated porcine reproductive and respiratory syndrome virus (PRRSV) vaccine through interactions with microbiome metabolome. We pretreated sows 10 mg/kg body weight RPP via drinking water for 7 days prior to intramuscular injection PRRSV vaccine. This significantly increased concentrations GP5 protein antibody, interleukin (IL)-2, IL-4, IL-10, interferon (IFN)-γ. Oral...
ABSTRACT Within a multi-state viral genomic surveillance program, proportions of SARS-CoV-2 infections attributed to the JN.1 and HV.1 variants, compared EG.5, were each lower among inpatients versus outpatients (aOR=0.33 [95% CI: 0.20-0.55] aOR=0.62 0.44-0.86], respectively). variants may be associated with risk severe illness.
Genomic-guided pharmaceutical prescribing is increasingly recognized as an important clinical application of genetics. Accurate genotyping pharmacogenomic (PGx) genes can be difficult, owing to their complex genetic architecture involving combinations single-nucleotide polymorphisms and structural variation. Here, we introduce the Helix PGx database, open-source star allele, genotype, resulting metabolic phenotype frequency database for CYP2C9, CYP2C19, CYP2D6, CYP4F2, based on short-read...
Between November 2021 and February 2022, SARS-CoV-2 Delta Omicron variants co-circulated in the United States, allowing for co-infections possible recombination events. We sequenced 29,719 positive samples during this period analyzed presence fraction of reads supporting mutations specific to either or variant. identified 18 co-infections, one which displayed evidence a low Delta-Omicron recombinant viral population. also two independent cases infection by virus, where 100% RNA came from...
The sequencing of 74,348 SARS-CoV-2 positive samples collected across the United States showed that Delta variant was responsible for majority infections by July 1, 2021, and accounted >99.9% tests in September 2021. displaced Alpha, which dominant at time. also directly outcompeted Gamma concern as well Iota Mu variants interest. An analysis mean quantification cycles (Cq) values revealed lead to a higher viral load on average compared Alpha infections, but this increase only ~1.7x...