Charles Chiu, MD, PhD

Associate Professor
Department of Laboratory Medicine
+1 415 514-8219

My research group focuses on the development of metagenomics-based technologies to identify viral etiologies of acute and chronic diseases in humans. This research consists of two major goals: (1) to explore the utility of pan-viral microarrays (Virochip) and high-throughput, “deep” sequencing in the detection and discovery of viruses associated with acute and chronic human illnesses, and (2) to characterize a novel human cardiovirus recently detected in clinical specimens by use of these technologies (Chiu, et al.PNAS, 2008).

  1. Viral etiologies of respiratory and gastrointestinal illness: In collaboration with the California Department of Public Health, we are using metagenomics to study viruses that cause influenza-like illness, currently focusing on genetic analysis of strains from the 2009 H1N1 influenza outbreak. We are also collaborating with groups in Mexico and Canada to investigate viral causes of gastroenteritis and respiratory infection in the setting of unexplained outbreaks. In addition, a major goal of the lab is to validate the Virochip as a clinical diagnostic test. In collaboration with Dr. Steve Miller and the CLIA-certified UCSF microbiology laboratory, we are initially focusing on using the Virochip to diagnose viruses associated with respiratory infections in immunocompromised transplant patients.
  2. Association between viral infection and chronic disease: We are actively investigating chronic diseases such as cancer and autoimmune disease for potential viral etiologies. We are collaborating with outside investigators on a number of studies in this area, including, among others, a study of non A-E viral etiologies of hepatocellular carcinoma and viral triggers of a rare sleep disorder called Kleine-Levin Syndrome.
  3. Prevalence and pathogenicity of a novel human cardiovirus: We previously identified a novel human cardiovirus in specimens from patients with influenza-like illness and gastroenteritis. Ongoing studies are aimed at culturing the cardiovirus, producing a molecular clone, and cloning and purifying its cellular receptor. We are also screening sera from blood bank donors to assess cardiovirus seroprevalence, as well as screening patients with encephalitis, multiple sclerosis, and myocarditis to determine if cardiovirus infection can be linked to any of these diseases. Findings from this work will likely define the prevalence and pathogenicity of this novel virus.
Primary Thematic Area: 
Virology & Microbial Pathogenesis
Secondary Thematic Area: 
Research Summary: 
Metagenomics-Based Technologies for Virus Detection and Discovery



Diagnosis of Fatal Human Case of St. Louis Encephalitis Virus Infection by Metagenomic Sequencing, California, 2016.

Emerging infectious diseases

Chiu CY, Coffey LL, Murkey J, Symmes K, Sample HA, Wilson MR, Naccache SN, Arevalo S, Somasekar S, Federman S, Stryke D, Vespa P, Schiller G, Messenger S, Humphries R, Miller S, Klausner JD

Upregulation of HERV-K is Linked to Immunity and Inflammation in Pulmonary Arterial Hypertension.


Saito T, Miyagawa K, Chen SY, Tamosiuniene R, Wang L, Sharp O, Samayoa E, Harada D, Moonen JAJ, Cao A, Chen PI, Hennigs JK, Gu M, Li CG, Leib RD, Li D, Adams CM, Del Rosario PA, Bill MA, Haddad F, Montoya JG, Robinson W, Fantl WJ, Nolan GP, Zamanian RT, Nicolls MR, Chiu CY, Ariza ME, Rabinovitch M

Correction: Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa.

PLoS pathogens

Grard G, Fair JN, Lee D, Slikas E, Steffen I, Muyembe JJ, Sittler T, Veeraraghavan N, Ruby JG, Wang C, Makuwa M, Mulembakani P, Tesh RB, Mazet J, Rimoin AW, Taylor T, Schneider BS, Simmons G, Delwart E, Wolfe ND, Chiu CY, Leroy EM

The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease.

Nature medicine

Legoff J, Resche-Rigon M, Bouquet J, Robin M, Naccache SN, Mercier-Delarue S, Federman S, Samayoa E, Rousseau C, Piron P, Kapel N, Simon F, Socié G, Chiu CY

Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients.

American journal of respiratory and critical care medicine

Langelier C, Zinter MS, Kalantar K, Yanik GA, Christenson S, O'Donovan B, White C, Wilson M, Sapru A, Dvorak CC, Miller S, Chiu CY, DeRisi JL