Illumina virology solutions
Detect low-frequency variants and subtypes within a viral population with Illumina
next-generation sequencing (NGS) solutions for virology. With NGS, you can see amore complete picture not only of viruses and host interaction, but also other phages
specific to microbes.
Determine the source of infection, route of transmission, and molecular pathway.
Perform drug resistance testing, molecular epidemiology of viral pathogens, vaccine
development, viral-host transcriptome interactions, viral surveillance, quality control/contamination of biologics, and virus discovery with our comprehensive solutions.

Workflow
Library preparation

Sequencing

Data analysis

Nextera® XT Kit

NextSeq® Series,HiSeq® Series

Cloud: BaseSpace® Sequence Hub,
Kraken Metagenomics,
MetaPhlan

Bioinformatics solutions
BaseSpace® Sequencing Hub is the Illumina cloud-based genomics computing environment for
NGS data management and analysis. Access BaseSpace Hub via the intuitive web-based interface
or linux-based command line tool for simple data storage and sharing.

Targeted Re-sequencing
Genotyping software which is an integrated sequencing solutions for HIV, HCV and HBV drug
resistance determination.

Whole RNA-Seq
Kraken software is aligning k-mers and then classifying with a bacterial, archaeal, and viraldatabase

For Research Use Only. Not for use in diagnostic procedures.

Recent virology articles using Illumina MiSeq technology:
da Silva F. R., Cibulski S. P., Daudt C., Weber M. N., Guimaraes L. L., et al. (2016) Novel Bovine Papillomavirus Type Discovered by
Rolling-Circle Amplification Coupled with Next-Generation Sequencing. PLoS One 11: e0162345
El-Shamy A., Pendleton M., Eng F. J., Doyle E. H., Bashir A., et al. (2016) Impact of HCV core gene quasispecies on hepatocellular
carcinoma risk among HALT-C trial patients. Sci Rep 6: 27025
Kok Y. L., Vongrad V., Shilaih M., Di Giallonardo F., Kuster H., et al. (2016) Monocyte-derived macrophages exhibit distinct and more
restricted HIV-1 integration site repertoire than CD4(+) T cells. Sci Rep 6: 24157
Lee H. K., Lee C. K., Tang J. W., Loh T. P. and Koay E. S. (2016) Contamination-controlled high-throughput whole genome sequencing
for influenza A viruses using the MiSeq sequencer. Sci Rep 6: 33318
Li Y., Wang H., Nie K., Zhang C., Zhang Y., et al. (2016) VIP: an integrated pipeline for metagenomics of virus identification anddiscovery. Sci Rep 6: 23774
Russier M., Yang G., Rehg J. E., Wong S. S., Mostafa H. H., et al. (2016) Molecular requirements for a pandemic influenza virus: An
acid-stable hemagglutinin protein. Proc Natl Acad Sci U S A 113: 1636-1641
Schobel S. A., Stucker K. M., Moore M. L., Anderson L. J., Larkin E. K., et al. (2016) Respiratory Syncytial Virus whole-genome
sequencing identifies convergent evolution of sequence duplication in the C-terminus of the G gene. Sci Rep 6: 26311
Stewart H., Bingham R. J., White S. J., Dykeman E. C., Zothner C., et al. (2016) Identification of novel RNA secondary structures within
the hepatitis C virus genome reveals a cooperative involvement in genome packaging. Sci Rep 6: 22952
van Diemen F. R., Kruse E. M., Hooykaas M. J., Bruggeling C. E., Schurch A. C., et al. (2016) CRISPR/Cas9-Mediated Genome Editingof Herpesviruses Limits Productive and Latent Infections. PLoS Pathog 12: e1005701
Wang Z., Pan Q., Gendron P., Zhu W., Guo F., et al. (2016) CRISPR/Cas9-Derived Mutations Both Inhibit HIV-1 Replication andAccelerate Viral Escape. Cell Rep 15: 481-489
Xu Y., Bailey E., Spackman E., Li T., Wang H., et al. (2016) Limited Antigenic Diversity in Contemporary H7 Avian-Origin Influenza A
Viruses from North America. Sci Rep 6: 20688
Zhao J., Liu J., Vemula S. V., Lin C., Tan J., et al. (2016) Sensitive Detection and Simultaneous Discrimination of Influenza A and B
Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics. PLoS One 11: e0163175
Dedkov V. G., Lukashev A. N., Deviatkin A. A., Kuleshov K. V., Safonova M. V., et al. (2016) Retrospective diagnosis of two rabies cases
in humans by high throughput sequencing. J Clin Virol 78: 74-81
Kolehmainen P., Siponen A., Smura T., Kallio-Kokko H., Vapalahti O., et al. (2017) Intertypic recombination of human parechovirus 4
isolated from infants with sepsis-like disease. J Clin Virol 88: 1-7
McGinnis J., Laplante J., Shudt M. and George K. S. (2016) Next generation sequencing for whole genome analysis and surveillance ofinfluenza A viruses. J Clin Virol 79: 44-50
Parker J. and Chen J. (2017) Application of next generation sequencing for the detection of human viral pathogens in clinical specimens.
J Clin Virol 86: 20-26
Sato M., Kuroda M., Kasai M., Matsui H., Fukuyama T., et al. (2016) Acute encephalopathy in an immunocompromised boy withastrovirus-MLB1 infection detected by next generation sequencing. J Clin Viro

Explore the exciting discoveries our NGS solutions are enabling.
Visit www.illumina.com/MicroStories and www.illumina.com/MicroWebinars.

www.illumina.com
For Research Use Only. Not for use in diagnostic procedures.
© 2017 Illumina, Inc. All rights reserved. Pub. No. 1270-2017-001