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Sequencing of the Genome of the Mosquito, Aedes Aegypti
On June 14th, 2006, the NIAID Microbial Sequencing Centers announced annotation Release 1.0 of the Aedes aegypti genome sequence. This annotation was produced jointly by The Institute for Genomic Research and VectorBase with support from The Broad Institute of Harvard/MIT. Release 1.0 was deposited at GenBank under the accession version AAGE00000000. Long-term curation of the genome sequence and subsequent annotation updates will be the responsibility of VectorBase. Release...
Molecular Epidemiology of Enteric Calici Viruses
Enteric caliciviruses (norovirus – NoV and sapovirus – SaV), are responsible for most food-borne gastroenteritis outbreaks worldwide. Human norovirus (NoV), is the leading cause of foodborne illness in the US, accounting for 58% of all case. In the U.S., human NoVs are listed as Category B biodefense pathogens by NIH, and are on the EPA “candidate contaminant list” for the regulation of drinking water. NoVs are highly contagious and the infectious dose is low, with an estimated medium...
Sequencing of Human Adenovirus Clinical Isolates From Recent and Reference Genomes
Human adenoviruses (HAdV) are pathogens causing a range of human infectious diseases, including respiratory, ocular, gastrointestinal, renal and metabolic. HAdV infections can be highly contagious, causing high morbidity rate and mortality rates and result in outbreaks. They are also a model organism in the research laboratory for cell and molecular biology. The goal of this project is to understand HAdV biology, especially the evolution and emergence of new and highly pathogenic...
GCID Outreach: Training the Next Generation of Genomic Scientists
The J. Craig Venter Institute (JCVI) Genomic Center for Infectious Diseases (GCID) was established by the National Institute of Allergy and Infectious Disease (NIAID) to explore disease biology through the application of nucleic acid sequencing and bioinformatics analysis tools. Throughout the history of the program, which is in its third iteration, GCID has been focused on expanding access to these technological platforms through education and outreach. To that end, we have devoted resources...
Exploiting Viral Genomics to Understand Disease
Viruses are global pathogens that cause substantial morbidity and mortality in humans. Novel viruses jump into humans from animal host reservoirs, and these zoonotic events can lead to outbreaks, epidemics, and/or pandemics. Thus, the viral GCID projects are focused on significant endemic viral pathogens of humans, as well as viruses from animal hosts that have strong zoonotic potential. High-throughput whole-genome next-generation sequencing (NGS) and bioinformatics analyses will be performed...
Scientist Spotlight: Brett Pickett, PhD
The son of a dentist, Brett Pickett grew up in Salt Lake City, Utah focused initially on a career in the family business (his siblings are hygienists and an oral surgeon). Brett believed from an early age that he would follow in his father’s footsteps. He enrolled in Brigham Young University committed to dental school. It was not until Brett’s zoology major was canceled that he became a student of microbiology, where he began researching antibiotic resistance genes in gut...
DNA Synthesis and Biosecurity: <br>Lessons Learned and Options for the Future
Synthetic biology promises great scientific advances, but it also has the potential to pose unique biosecurity threats. It now is easier than ever to synthesize very long pieces of DNA from chemicals, potentially enabling a bioterrorist to build a toxin gene or an entire pathogenic virus. In 2007, the JCVI Policy Team released a report titled, “Synthetic Genomics: Options for Governance,” in which we proposed and evaluated a variety of options to address this biosecurity threat. A modified...
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 food and...
Forensics Microbiome Database
The Forensic Microbiome Database (FMD) is a unique resource that enables the visualization and comparison of 16S rRNA human microbiome data obtained from multiple body sites with metadata as it relates to forensics. The goal of the FMD is to predict the geographical location of subjects using human microbiome data. As part of this award, we actively continue to update the database with publicly available 16S rRNA microbiome data and we are expanding the dataset through the inclusion of...
Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen
A combination of Sanger and 454 sequences of small subunit rRNA loci were used to interrogate microbial diversity in the bovine rumen of 12 cows consuming a forage diet. Observed bacterial species richness, based on the V1-V3 region of the 16S rRNA gene, was between 1,903 to 2,432 species-level operational taxonomic units (OTUs) when 5,520 reads were sampled per animal. Eighty percent of species-level OTUs were dominated by members of the order Clostridiales, Bacteroidales, Erysipelotrichales...