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: 

Connecting the dots: Translating the vaginal microbiome into a drug.

The Journal of infectious diseases

Lagenaur LA, Hemmerling A, Chiu C, Miller S, Lee PP, Cohen CR, Parks TP

Timely Intervention and Control of a Novel Coronavirus (COVID-19) Outbreak at a Large Skilled Nursing Facility - San Francisco, California, 2020.

Infection control and hospital epidemiology

Karmarkar E, Blanco I, Amornkul P, DuBois A, Deng X, Moonan PK, Rubenstein BL, Miller DA, Kennedy I, Yu J, Dauterman J, Ongpin M, Hathaway W, Hoo L, Trammell S, Ememu E, Yu G, Khwaja Z, Lu W, Talai N, Jain S, Louie J, Philip S, Federman S, Masinde G, Wadford DA, Bobba N, Stoltey J, Smith A, Epson E, Chiu C, Bennett A, Vasquez AM, Williams T

Fatal Case of Chronic Jamestown Canyon Virus Encephalitis Diagnosed by Metagenomic Sequencing in Patient Receiving Rituximab.

Emerging infectious diseases

Solomon IH, Ganesh VS, Yu G, Deng XD, Wilson MR, Miller S, Milligan TA, Mukerji SS, Mathewson A, Linxweiler J, Morse D, Ritter JM, Staples JE, Hughes H, Gould CV, Sabeti PC, Chiu CY, Piantadosi A

Two sides of a coin: a Zika virus mutation selected in pregnant rhesus macaques promotes fetal infection in mice but at a cost of reduced fitness in nonpregnant macaques and diminished transmissibility by vectors.

Journal of virology

Lemos D, Stuart JB, Louie W, Singapuri A, Ramírez AL, Watanabe J, Usachenko J, Keesler RI, Martin CS, Li T, Martyn C, Oliveira G, Saraf S, Grubaugh ND, Andersen KG, Thissen J, Allen J, Borucki M, Tsetsarkin KA, Pletnev AG, Chiu CY, Van Rompay KKA, Coffey LL

Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids.

Nature medicine

Gu W, Deng X, Lee M, Sucu YD, Arevalo S, Stryke D, Federman S, Gopez A, Reyes K, Zorn K, Sample H, Yu G, Ishpuniani G, Briggs B, Chow ED, Berger A, Wilson MR, Wang C, Hsu E, Miller S, DeRisi JL, Chiu CY