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Impact of Viral Intra-Host Diversity on Transmission Dynamics and Antiviral Resistance
Influenza virus is a highly contagious virus that is typically transmitted person-to-person through sneezing and coughing. Critical gaps remain in our understanding of the evolutionary dynamics of IAV on both a global scale and at the level of intra-host dynamics and inter-host transmission. Similarly, resistance to the NA protein inhibitor, Oseltamivir, can be wide-spread among various subtypes of influenza viruses and has been reported for some highly pathogenic H5N1 influenza viruses....
Influenza: Host-Virus-Microbiome Interactions
Influenza is a leading cause of death in the United States and worldwide, resulting in approximately 40,000 deaths annually due to seasonal epidemics alone. A major complication of influenza infections resulting in lethality, particularly during pandemics, is secondary bacterial infections of the lung (pneumonia). Streptococcus pneumoniae, Staphylococcus aureus (especially methicillin-resistant S. aureus or MRSA), and Hemophilus influenzae are the most common pathogens associated with...
Genetic Diversity and Evolutionary Dynamics of Influenza A and B Viruses
Influenza viruses are members of the Orthomyxoviridae family whose genomes consist of 8 segments of single-stranded negative-sense RNA. Influenza A virus (IAV) and influenza B virus (IBV) are responsible for seasonal epidemics of respiratory illness among humans. While IBV circulates only among humans, IAV circulates among many mammalian and avian hosts. Global surveillance of these viruses is necessary for maintaining a well-matched annual influenza vaccine, as well as for detecting the...
TIGRFAMS
TIGRFAMs is a database of protein family definitions. Each entry features a seed alignment of trusted representative sequences, a hidden Markov model (HMM) built from that alignment, cutoff scores that let automated annotation pipelines decide which proteins are members, and annotations for transfer onto member proteins. Most TIGRFAMs models are designated equivalog, meaning they assign a specific name to proteins conserved in function from a common ancestral sequence. Models describing...
PROVEAN
After many years of supporting PROVEAN beyond grant funding the web-based version has been retired. While unsupported, it may still be downloaded. PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. PROVEAN is useful for filtering sequence variants to identify nonsynonymous or indel variants that are predicted to be functionally important. The performance...
Human Hair Microbiota
Human hair samples are an important trace evidence type for providing leads in forensic investigations. They are used to determine the race, gender, and identity of the individual responsible for a criminal act. Hair also supports its own microbial habitat that is intra- and inter-personal variable, and as such, this little explored substrate has significant potential in forensics microbiome research due to the unique signatures that are available on an individual. We explored...
Resolving the Bottleneck in Antibiotic Discovery
The goal of this multicomponent project is to develop an efficient transcriptomic approach to dereplicate antibacterial extracts of pure isolates of uncultured soil bacteria, revealing which are chemically identical to known antibiotics. Leveraging our expertise in transcriptomics at JCVI and in collaboration with Dr. Kim Lewis (Northeastern University) and Dr. Amy Spoering (NovoBiotic), we will develop an effective discovery program based on exploiting uncultured bacteria to resolve the...
New Pathogen Discovery in Travelers’ Diarrhea by Metagenomic Sequencing
Diarrheal disease affects one billion people per year worldwide, yet >80% of these cases are of unknown etiology. Travelers’ diarrhea or TD, affects between 20 to 60% of those who travel from developed to low-income countries and impacts 20-40 million travelers worldwide each year. Bouts of travelers’ diarrhea can predispose to development of post-infectious irritable bowel disease (IBD). The travelers are often immunologically naïve to the pathogens that they encounter in the...
Novel Diversity of Bacterial Communities Associated with Bottlenose Dolphin Upper Respiratory Tracts
Respiratory illness is thought to be most the common cause of death in both wild and captive populations of bottlenose dolphins (Tursiops truncatus). The suspected pathogens that have been isolated from diseased animals have also been isolated from healthy individuals, suggesting they may be part of the normal flora. Our current understanding of the bacteria associated with the upper respiratory tract (URT) of bottlenose dolphins is based exclusively upon culture-based isolation and...
Virus Pathogen Resource (ViPR)
In order to support research focused on newly emerging pathogens, the Division of Microbiology and Infectious Diseases (DMID) of the National Institute of Allergy and Infectious Diseases (NIAID), at the US National Institutes of Health (NIH), is supporting a variety of resources for researchers including: the Genomic Sequencing Centers for Infectious Diseases, Structural Genomics Centers for Infectious Diseases, Systems Biology for Infectious Diseases Research, and BEI Resources...