Many patients arrive at the hospital with unexplained acute febrile illness (also called ‘fevers of unknown origin’ ). In many cases, clinicians will suspect the presence of a limited subset of potential pathogens. However, in some cases, the pathogen may be undiscovered or the suspected pathogen is not the one causing the illness in the patient. Repetitive rounds of testing can follow, leading to delays in diagnosis and effective treatment, with potential serious consequences to the patient.
Utilizing state-of-the-art sequencing technologies and computational tools, the Pathogen Sequencing (PathSeq) study aims to provide a fast diagnostic platform that will allow testing for all currently known human pathogens and their antibiotic resistance profile with a single test. This will result in reduced costs, faster turnaround times for diagnosis, and improved efficiency with the goal of faster recovery and survival rates for patients. By developing new computational tools, researchers hope to significantly improve their ability to survey and detect known and unknown pathogens infecting humans.
Genomic Investigation of Disease Outbreaks
Recent infectious disease epidemics demonstrate how rapidly local outbreaks can escalate into global infectious threats. With the world growing increasing interconnected, health professionals are in need of better tools to tackle outbreaks of emerging diseases.
Scientists at STSI are using infectious disease genomics to investigate the outbreak dynamics and virus evolution of some of the most devastating human pathogens, such as Zika, Ebola, and Lassa. The goal of this research is to understand how these viruses emerge in new areas, evolve when transmitting in human populations, and spread across country borders.
Using a combination of computational biology, experimentation, and field work, researchers hope to change the way vaccines and therapeutics are developed for these and other emerging pathogens.
- Genomic epidemiology reveals multiple introductions of Zika virus into the United States, Nature 2017
- Establishment and cryptic transmission of Zika virus in Brazil and the Americas, Nature 2017
- Zika Virus Evolution and Spread in The Americas, Nature 2017
- Protocol Multiplex PCR Method for MinION and Illumina Sequencing of Zika and Other Virus Genomes Directly From Clinical Samples, Nature Protocols 2017
- Virus genomes reveal factors that spread and sustained the Ebola epidemic, Nature 2017
- Structures of Ebola virus GP and sGP in complex with therapeutic antibodies, Nature Microbiology 2016
- Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic, Cell 2016
- The Evolution Of Ebola Virus: Insights From The 2013-2016 Epidemic, Nature 2016
- Roots, Not Parachutes: Research Collaborations Combat Outbreaks, Cell 2016
- Comment on Mutation Rate And Genotype Variation of Ebola Virus From Mali Case Sequences, Science 2016
- Navigating the Zika panic, F1000Research 2016
- Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus, Cell 2015
- Ebola Virus Epidemiology, Transmission and Evolution during Seven Months in Sierra Leone, Cell 2015