flu2009
Chiu Lab Viral Discovery
The purpose of this project is to analyze clinical specimens associated with human acute or chronic illness for the presence of novel to unusual viral pathogens by Virochip microarray (Wang and DeRisi, et al., PNAS, 2002; Greninger and Chiu, et al., PloS ONE, 2010) and high-throughput sequencing technologies (Sorber, Chiu, and DeRisi, PloS ONE, 2008; Greninger and Chiu, et al., PloS ONE, 2010).  Follow-up phylogenetic characterization and epidemiological association studies are performed subsequently to link these candidate pathogens to the disease.  The specimen types that will be analyzed include but are not limited to respiratory secretions, cerebrospinal fluid, serum / plasma, stool, and tissue.  The spectrum of diseases that will be studied includes but is not limited to respiratory illness, gastroenteritis, encephalitis, fever of unknown etiology, hepatitis, influenza-like illness, cancer, and autoimmune disease.    Briefly, we are using high throughput sequencing technology to identify novel viruses that may be causing different types of illness in patients who have undergone thorough medical evaluation, are suspected of infectious disease by their physicians, but whose tests have not yielded a source of infection.  These samples have been screened with our Virochip which may or may not have identified a possible source.  These samples were obtained through UCSF and/or as referrals from other institutions across the globe.  This project includes short Illumina reads of various depths sequenced from metagenomic RNA of sputum, blood, CSF, and diarrheal samples of patients with suspected infectious diseases unable to be confirmed by standard clinical tests.