Charles Chiu, MD, PhD

Director, UCSF-Abbott Viral Diagnostics and Discovery Center (VDDC)
Associate Director, UCSF Clinical Microbiology Laboratory
Professor
Department of Laboratory Medicine
Department of Medicine - Infectious Disease
+1 415 514-8219
Research Overview: 

I am an infectious diseases physician and microbiologist and lead a translational research laboratory focusing on (i) metagenomic next-generation sequencing (mNGS) assay development for infectious disease diagnostics, (ii) discovery and characterization of emerging viral pathogens, and (iii) development of new bioinformatic tools and cutting-edge genomic technologies for clinical and public health applications. Current projects in my laboratory include (i) pathogen discovery in tickborne infections, acute febrile illness, and blood screening, (ii) investigating links between enterovirus infection and acute flaccid myelitis, and (iii) cell culture, human, and animal studies of Zika virus infection in acutely infected patients and pregnant women. We are also actively leveraging nanopore sequencing for diagnosis and surveillance of febrile illnesses in remote locations, including point-of-care outbreak settings and aboard the International Space Station, and developing bioinformatic pipelines for pathogen identification and host response characterization. Finally, we are investigating the use of machine-learning based methods for generation of models that can predict the cause of infection on the basis of RNA-Seq transcriptomic data.

Primary Thematic Area: 
Virology & Microbial Pathogenesis
Secondary Thematic Area: 
Immunology
Research Summary: 
Metagenomics-Based Technologies for Virus Detection and Discovery

Websites

Publications: 

Severe Non-Donor-Derived Lymphocytic Choriomeningitis Virus Infection in Two Solid Organ Transplant Recipients.

Open forum infectious diseases

Leanna E Sayyad, Kami L Smith, Katrin S Sadigh, Caitlin M Cossaboom, Mary J Choi, Shannon Whitmer, Debi Cannon, Inna Krapiunaya, Maria Morales-Betoulle, Pallavi Annambhotla, Sridhar V Basavaraju, Irene Ruberto, Melissa Kretschmer, Nalleli Gutierrez, Karen Zabel, Connie Austin, Edith Sandoval, Venice Servellita, Abiodun Foresythe, Nanami Sumimoto, Bashar A Aqel, Hasan A Khamash, Carrie C Jadlowiec, Thomas E Grys, Andres Jaramillo, Marie F Grill, Joel M Montgomery, Trevor Shoemaker, John D Klena, Charles Y Chiu, Holenarasipur R Vikram

Clinical impact of metagenomic next-generation sequencing testing on cerebrospinal fluid in a pediatric cohort with suspected central nervous system infections.

Journal of the Pediatric Infectious Diseases Society

Mikaël de Lorenzi-Tognon, Patrick Benoit, Noah Brazer, Venice Servellita, Miriam Oseguera, Jessica Streithorst, Melissa Hillberg, Danielle Ingebrigtsen, Kelsey Zorn, Michael Wilson, Timothy M Blicharz, Amy P Wong, Brian O’Donovan, Brad Murray, Steve Miller, Charles Y Chiu

Diagnosis and management of invasive fungal diseases by next-generation sequencing: are we there yet?

Expert review of molecular diagnostics

Babady NE, Chiu CY, Craney A, Gaston DC, Hicklen RS, Hogan CA, John TM, Stewart AG

Comparison of Plasma Metagenomic Next-generation Sequencing and PCR Methods for Epstein-Barr Virus Viral Load Monitoring in Nasopharyngeal Carcinoma.

Anticancer research

Vasudevan HN, Lazar AA, Reyes K, Rong DA, Arevalo S, Federman S, Chan JW, Chiu CY, Miller S, Yom SS

Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery.

Nature communications

Tan JK, Servellita V, Stryke D, Kelly E, Streithorst J, Sumimoto N, Foresythe A, Huh HJ, Nguyen J, Oseguera M, Brazer N, Tang J, Ingebrigtsen D, Fung B, Reyes H, Hillberg M, Chen A, Guevara H, Yagi S, Morales C, Wadford DA, Mourani PM, Langelier CR, de Lorenzi-Tognon M, Benoit P, Chiu CY