Research in the Chiu laboratory focuses on detection of known and novel viral agents in acute diseases suspected to have an infectious etiology. We use the ViroChip microarray, a viral microarray with 60,000 probes designed to detect all viruses, both known and novel, on the basis of sequence homology. In parallel, we employ next-generation sequencing methods to identify viruses that are even more divergent and would elude detection by all other methods, including the ViroChip. We are also developing automated computational pipelines to rapidly analyze vast amounts of sequence data within minutes to hours via highly efficient bioinformatics algorithms and cloud computing.

We are actively validating ViroChip / FluChip / BloodChip microarrays and unbiased “deep” sequencing for use in pathogen discovery, clinical diagnostics, and outbreak investigation. Current projects include (1) identification and discovery of novel hemorrhagic fever viruses in Africa, (2) design and development of improved diagnostics for Lyme disease, (3) investigating the cause of STARI (Southern Tick-Associated Rash Illness), (4) comparative whole-genome sequencing and quasispecies analysis of hantaviruses and filoviruses in the wild, and (6) screening of transfusion-transmissible agents in deferred blood donors and patients with hepatitis.

In support of our research efforts, we gratefully acknowledge the National Institutes of Health (NIH R01 grants HL105701-01 and A10935500), Abbott Laboratories, Metabiota , the National Research Fund for Tick-Borne Diseases (NRFTD), the University of California Discovery Grant Program, UCSF QB3, and the Rogers Family Foundation.