UCSF Viral Diagnostics and Discovery Center
Thank you for your interest in the UCSF Viral Diagnostics and Discovery Center (VDDC). We offer two
primary services here at the VDDC for viral detection / discovery: ViroChip microarray analysis(Chen et al., 2011;
Chiu et al., 2007; Chiu et al., 2008; Chiu et al., 2013) and Illumina MiSeq high-throughput sequencing (Chiu et
al., 2013; Grard et al., 2012; Greninger et al., 2010; Li et al., 2013; Swei et al., 2013; Yu et al., 2012). The current
iteration of the ViroChip microarray contains ~60,000 oligonucleotides, which represent the sequences of all
viruses in GenBank as of 2010. ViroChip analysis involves sample extraction, random primer amplification,
fluorescent dye labeling, hybridization to the ViroChip microarray, scanning and data analysis. As of 2012, we
also offer deep sequencing on our Illumina MiSeq instrument. This includes library preparation, library quality
confirmation, sequencing and data analysis utilizing our Sequence-Based Ultra Rapid Pathogen Identification
(SURPI) pipeline. This service yields approximately 15-20 million paired-end sequence reads per run.
The estimated limits of detection for both ViroChip and 2 million reads of a deep sequencing run are
approximately 102 – 103 viral copies / ml for RNA viruses and 103 – 104 viral copies / ml for DNA viruses.
Normally, we prefer primary samples for either of our services. A minimum starting volume of 500ul is
desirable, so that we can pre-treat as necessary to enrich for viral nucleic acids. We are able to perform various
sample pre-treatments and extraction protocols to selectively enrich for different viruses. We can also process
total nucleic acid extractions, but would need to know your extraction protocol before processing the samples.
Finally, matched negative controls are highly useful for the microarray data analysis, and can be processed at
reduced rates. These samples will be processed in exactly the same manner as your experimental samples.
If you are interested any of these services, please fill out our order form (available on our website) and the
sample questionnaire on the following page. We will also need a signed service contract, which we can send to
you by e-mail with instructions on filling it out. Once you are ready and have confirmed the project with us, ship
your samples to the following address and be sure send us your tracking number (shipping overnight with your
samples on dry ice is recommended).
If you have any other questions, please do not hesitate to contact us.
Shipping Information:
Attn: Erik Samayoa
UCSF China Basin Landing
185 Berry Street, Ste.290 Rm.2230
San Francisco, CA 94107
Direct: 415.353.4744
Fax: 415.514.6050
Erik.Samayoa@ucsfmedctr.org
Sincerely,
The UCSF VDDC Team http://vddc.ucsf.edu
Director: Dr. Charles Chiu, M.D./Ph.D., Charles.chiu@ucsf.edu, (415) 514-8219
Associate Director: Dr. Steve Miller, M.D./Ph.D., steve.miller@ucsfmedctr.org, (415) 353-9630
Staff Scientist: Erik Samayoa, CLS, erik.samayoa@ucsfmecdctr.org, (415) 353-4744
Project Questionnaire
1. What is the origin of your samples? (i.e human, animal, cell culture, environmental, etc.)
2. What is the source of your samples? (i.e. whole blood, serum, plasma, stool, respiratory, tissue, etc.)
3. Are your samples already extracted as nucleic acid or original material?
4. If you are sending extracted nucleic acid, please list or describe the protocol used to extract the
material.
5. What types of viruses are you most interested in? (i.e. RNA, DNA, intracellular or extracellular,
encapsidated or episomal / integrated)
6. Are you providing any control samples? If so, what are these samples?
7. In few sentences, please describe your project and list any goals that you may have for these samples.
8. Is there any additional information that may be useful when analyzing your data?
References
Chiu, C.Y., Alizadeh, A.A., Rouskin, S., Merker, J.D., Yeh, E., Yagi, S., Schnurr, D., Patterson, B.K., Ganem, D., and
DeRisi, J.L. (2007). Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a panvirus microarray. Journal of clinical microbiology 45, 2340-2343.
Chiu, C.Y., Greninger, A.L., Kanada, K., Kwok, T., Fischer, K.F., Runckel, C., Louie, J.K., Glaser, C.A., Yagi, S.,
Schnurr, D.P., et al. (2008). Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in
human infections. Proceedings of the National Academy of Sciences of the United States of America 105, 1412414129.
Greninger, A.L., Chen, E.C., Sittler, T., Scheinerman, A., Roubinian, N., Yu, G., Kim, E., Pillai, D.R., Guyard, C.,
Mazzulli, T., et al. (2010). A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients
from North America. PloS one 5, e13381.
Chen, E.C., Miller, S.A., DeRisi, J.L., and Chiu, C.Y. (2011). Using a pan-viral microarray assay (Virochip) to screen
clinical samples for viral pathogens. Journal of visualized experiments : JoVE.
Grard, G., Fair, J.N., Lee, D., Slikas, E., Steffen, I., Muyembe, J.J., Sittler, T., Veeraraghavan, N., Ruby, J.G., Wang,
C., et al. (2012). A novel rhabdovirus associated with acute hemorrhagic fever in central Africa. PLoS pathogens
8, e1002924.
Yu, G., Greninger, A.L., Isa, P., Phan, T.G., Martinez, M.A., de la Luz Sanchez, M., Contreras, J.F., Santos-Preciado,
J.I., Parsonnet, J., Miller, S., et al. (2012). Discovery of a novel polyomavirus in acute diarrheal samples from
children. PloS one 7, e49449.
Chiu, C.Y., Yagi, S., Lu, X., Yu, G., Chen, E.C., Liu, M., Dick, E.J., Jr., Carey, K.D., Erdman, D.D., Leland, M.M., et al.
(2013). A novel adenovirus species associated with an acute respiratory outbreak in a baboon colony and
evidence of coincident human infection. mBio 4.
Li, L., Pesavento, P.A., Leutenegger, C.M., Estrada, M., Coffey, L.L., Naccache, S.N., Samayoa, E., Chiu, C., Qiu, J.,
Wang, C., et al. (2013). A novel bocavirus in canine liver. Virology journal 10, 54.
Swei, A., Russell, B.J., Naccache, S.N., Kabre, B., Veeraraghavan, N., Pilgard, M.A., Johnson, B.J., and Chiu, C.Y.
(2013). The Genome Sequence of Lone Star Virus, a Highly Divergent Bunyavirus Found in the Amblyomma
americanum Tick. PloS one 8, e62083.