Charles Chiu, MD, PhD

Director, UCSF-Abbott Viral Diagnostics and Discovery Center (VDDC)
Associate Director, UCSF Clinical Microbiology Laboratory
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: 
Research Summary: 
Metagenomics-Based Technologies for Virus Detection and Discovery



Viral load quantitation at the point-of-care with shaken digital droplet RT-LAMP.

Lab on a chip

Weisgerber DW, Langer K, Servellita V, Xu P, Chiu CY, Abate AR

Complement Factor I Gene Variant as a Treatable Cause of Recurrent Aseptic Neutrophilic Meningitis: A Case Report.

Neurology(R) neuroimmunology & neuroinflammation

Rolfes M, Harroud A, Zorn KC, Tubati A, Omura C, Kurtz K, Matloubian M, Berger A, Chiu CY, Wilson MR, Ramachandran PS

Association of culturable-virus detection and household transmission of SARS-CoV-2 - California and Tennessee, 2020-2022.

The Journal of infectious diseases

Deyoe JE, Kelly JD, Grijalva CG, Bonenfant G, Lu S, Anglin K, Garcia-Knight M, Pineda-Ramirez J, Briggs Hagen M, Saydah S, Abedi GR, Goldberg SA, Tassetto M, Zhang A, Donohue KC, Davidson MC, Diaz Sanchez R, Djomaleu M, Mathur S, Shak JR, Deeks SG, Peluso MJ, Chiu CY, Zhu Y, Halasa NB, Chappell JD, Mellis A, Reed C, Andino R, Martin JN, Zhou B, Talbot HK, Midgley CM, Rolfes MA

Phage diversity in cell-free DNA identifies bacterial pathogens in human sepsis cases.

Nature microbiology

Haddock NL, Barkal LJ, Ram-Mohan N, Kaber G, Chiu CY, Bhatt AS, Yang S, Bollyky PL

Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance.


Orf GS, Olivo A, Harris B, Weiss SL, Achari A, Yu G, Federman S, Mbanya D, James L, Mampunza S, Chiu CY, Rodgers MA, Cloherty GA, Berg MG