A5001182619- Influenza Virus Research Studies
- Cancer Immunotherapy and Biomarkers
- Respiratory viral infections research
- Cytokine Signaling Pathways and Interactions
- Animal Disease Management and Epidemiology
- Lung Cancer Treatments and Mutations
- Viral gastroenteritis research and epidemiology
- Animal Virus Infections Studies
- Viral Infections and Vectors
- Tuberculosis Research and Epidemiology
- SARS-CoV-2 and COVID-19 Research
- Viral Infections and Immunology Research
- RNA and protein synthesis mechanisms
- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Immune cells in cancer
- Mosquito-borne diseases and control
- Ferroptosis and cancer prognosis
- Gut microbiota and health
- COVID-19 epidemiological studies
- Plant Virus Research Studies
- interferon and immune responses
- Tracheal and airway disorders
- Immune Cell Function and Interaction
- Virus-based gene therapy research
J. Craig Venter Institute
2015-2024
United States Courts
2023
AstraZeneca (United States)
2019-2022
AstraZeneca (Brazil)
2021
Vanderbilt University Medical Center
2017-2018
University of California, Davis
2014-2017
University of Alaska Fairbanks
2017
United States Geological Survey
2017
Massachusetts Institute of Technology
2017
United States Naval Medical Research Unit SOUTH
2015
Most RNA viruses lack the mechanisms to recognize and correct mutations that arise during genome replication, resulting in quasispecies diversity is required for pathogenesis adaptation. However, it not known how encoding large viral genomes such as Coronaviridae (26 32 kb) balance requirements stability diversity. Further, limits of replication infidelity decreased fidelity impacts virus fitness over time are known. Our previous work demonstrated genetic inactivation coronavirus...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other in Rickettsiales order. spp. display a unique large expansion immunodominant outer membrane proteins facilitating antigenic variation. All have diminished ability synthesize amino acids compared their...
Most emerging health threats are of zoonotic origin. For the overwhelming majority, their causative agents RNA viruses which include but not limited to HIV, Influenza, SARS, Ebola, Dengue, and Hantavirus. Of increasing importance therefore is a better understanding global viral diversity enable surveillance prediction pandemic threats; this will require rapid flexible methods for complete genome sequencing. We have adapted SISPA methodology [1–3] sequencing DNA viruses. demonstrated utility...
A complex interplay of viral, host, and ecological factors shapes the spatio-temporal incidence evolution human influenza viruses. Although considerable attention has been paid to viruses, a lack equivalent data means that an integrated evolutionary epidemiological framework until now not available for B despite their significant disease burden. Through analysis over 900 full genomes from collection more than 26,000 strains Australia New Zealand, we reveal fundamental differences in...
Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight bean. In this study, we report on genome sequence P. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp 51,711 bp). Comparative analyses with phylogenetically divergent pathovar, tomato DC3000, revealed strong degree conservation at gene levels. total, 4,133 ORFs were identified as...
Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus important primary producers in both types of ecosystems. We have found that genome a coastal cyanobacterium, sp. strain CC9311, has significant differences an strain, WH8102, consistent with between their respective environments. CC9311 greater capacity to sense respond changes its (coastal) environment. It much larger...
Lyme disease is the most common tick-borne human illness in North America. In order to understand molecular pathogenesis, natural diversity, population structure and epizootic spread of American agent, Borrelia burgdorferi sensu stricto, a much better understanding diversity its genome will be required. Towards this end we present comparative analysis nucleotide sequences numerous plasmids B. isolates B31, N40, JD1 297. These strains were chosen because they include three commonly studied...
Coronaviruses are well known for their potential to change host or tissue tropism, resulting in unpredictable new diseases and changes pathogenicity; severe acute respiratory syndrome feline coronaviruses, respectively, the most recognized examples. Feline coronaviruses occur as 2 pathotypes: nonvirulent enteric (FECVs), which replicate intestinal epithelium cells, lethal infectious peritonitis viruses (FIPVs), macrophages. Evidence indicates that FIPV originates from FECV by mutation, but...
Populations of seasonal influenza virus experience strong annual bottlenecks that pose a considerable extinction risk. It has been suggested an source population located in tropical Southeast or East Asia seeds temperate epidemics. Here we investigate the dynamics and migration patterns A H3N2 by analysis samples obtained from 2003 to 2006 Australia, Europe, Japan, New York, Zealand, Asia, newly sequenced viruses Hong Kong. In contrast epidemics, relatively low levels relative genetic...
ABSTRACT Influenza virus defective interfering (DI) particles are naturally occurring noninfectious virions typically generated during in vitro serial passages cell culture of the at a high multiplicity infection. DI recognized for role they play inhibiting viral replication and impact have on production infectious virions. To date, influenza been reported primarily as phenomenon experimentally infected embryonated chicken eggs. They also isolated from respiratory infection chickens. Using...
ABSTRACT Influenza A(H3N2) viruses became widespread in humans during the 1968 H3N2 virus pandemic and have been a major cause of influenza epidemics ever since. These evolve continuously by reassortment genomic evolution. Antigenic drift is for need to update vaccines frequently. Using two data sets that span entire period circulation human viruses, it was shown evolution can be mapped 13 antigenic clusters. Here we analyzed full genomes 286 from these investigate patterns. Numerous events...
Background Since its initial detection in April 2009, the A/H1N1pdm influenza virus has spread rapidly humans, with over 5,700 human deaths. However, little is known about evolutionary dynamics of H1N1pdm and geographic temporal diversification.Methods Phylogenetic analysis was conducted upon concatenated coding regions whole-genome sequences from 290 isolates sampled globally between 1 - July 9, including relatively large samples US states Wisconsin New York. Results At least 7...
Influenza A viruses are human and animal pathogens that cause morbidity mortality, which range from mild to severe. The 2009 H1N1 pandemic was caused by the emergence of a reassortant subtype (H1N1pdm) influenza virus containing gene segments originally circulated in human, avian, swine reservoirs. molecular determinants replication pathogenesis H1N1pdm humans other mammals poorly understood. Therefore, we set out elucidate viral critical this novel using mouse model. We found...
Abstract Background The 18-gene tumor inflammation signature (TIS) is a clinical research assay that enriches for benefit to immune checkpoint blockade. We evaluated its ability predict of immunotherapy in cancer patients treated with PD-1 inhibitors routine care. Methods CERTIM cohort prospective which includes receiving Cochin University hospital. RNA extracted from 58 archival formalin fixed paraffin embedded blocks (including 38 lung cancers, 5 melanomas, 10 renal carcinomas, 4...
ABSTRACT Knowledge of influenza virus evolution at the point transmission and intrahost level remains limited, particularly for human hosts. Here, we analyze a unique viral data set next-generation sequencing (NGS) samples generated from challenge study wherein 17 healthy subjects were inoculated with cell- egg-passaged virus. Nasal wash collected 7 these successfully deep sequenced. From these, characterized changes in subjects' populations during infection identified differences between...
Infection with influenza can be aggravated by bacterial co-infections, which often results in disease exacerbation. The effects of infection on the upper respiratory tract (URT) microbiome are largely unknown. Here, we report a longitudinal study to assess temporal dynamics URT microbiomes uninfected and virus-infected humans ferrets. Uninfected human patients ferret have stable healthy ecostate communities both within between individuals. In contrast, infected ferrets exhibit large changes...
ABSTRACT Wild ducks and gulls are the major reservoirs for avian influenza A viruses (AIVs). The mechanisms that drive AIV evolution complex at sites where various duck gull species from multiple flyways breed, winter, or stage. Republic of Georgia is located intersection three migratory flyways: Central Asian flyway, East Africa/West Asia Black Sea/Mediterranean flyway. For six complete study years (2010 to 2016), we collected samples migrate, overwinter in Georgia. We found a substantial...
ABSTRACT Although human influenza B virus (IBV) is a significant pathogen, its great genetic diversity has limited our ability to universally amplify the entire genome for subsequent sequencing or vaccine production. The generation of sequence data via next-generation approaches and rapid cloning viral genes are critical basic research, diagnostics, antiviral drugs, vaccines combat IBV. To overcome difficulty amplifying diverse ever-changing IBV genome, we developed optimized techniques that...
Respiratory viruses alter the nasopharyngeal microbiome and may be associated with a distinct microbial signature. To test this hypothesis, we compared of 135 previously healthy infants acute respiratory infection due to human rhinovirus (HRV; n = 52) or syncytial virus (RSV; 83). The was assessed by sequencing V4 region 16S ribosomal RNA. were identified quantitative reverse-transcription polymerase chain reaction. We found significant differences in overall taxonomic composition abundance...
Abstract Respiratory Syncytial Virus (RSV) is responsible for considerable morbidity and mortality worldwide the most important respiratory viral pathogen in infants. Extensive sequence variability within between RSV group A B viruses ability of multiple clades sub-clades to co-circulate are likely mechanisms contributing evasion herd immunity. Surveillance large-scale whole-genome sequencing currently limited but would help identify its evolutionary dynamics sites selective immune evasion....