Co-sponsored by APHL and CDC Influenza Division (ID)
DESCRIPTION
This hands-on workshop provides a comprehensive overview of influenza virus sequencing for the laboratory professional who works on library preparation at the bench. The workshop combines lectures, laboratory work and practical bioinformatics training. Participants will learn to implement standardized CDC laboratory protocols for sequencing influenza viruses from respiratory specimens using the Illumina MiSeq or other Illumina platforms.
The course includes instruction on the use of the MIRA bioinformatics pipeline for processing raw sequencing data into high-quality consensus genomes, with a focus on quality control procedures. Additionally, participants will gain experience in basic influenza genome assembly, data curation, sequence analysis and uploading sequences to public databases.
OBJECTIVES
At the conclusion of the program, the participant will be able to:
- Discuss the goals of performing influenza sequencing to contribute to national surveillance
- Perform influenza sequencing from respiratory specimens using standardized CDC protocols with Illumina sequencing instrumentation
- Identify and troubleshoot challenges that may be encountered in laboratory protocols for influenza sequencing
- Apply the MIRA bioinformatics pipeline to process raw sequencing reads into consensus genomes
- Identify key aspects of quality control in sequence data curation and analysis
SPEAKERS
Juliana DaSilva, Biologist, Genomics and Diagnostics Team
Julia Frederick, Biologist, Genomics and Diagnostics Team
Lisa Keong, Biologist, Genomics and Diagnostics Team
Marie Kirby, PhD, Team Lead, Genomics and Diagnostics Team
Ben Rambo-Martin, PhD, Team Lead, Bioinformatics Infrastructure Activity
Malania Wilson, Biologist, Genomics and Diagnostics Team
AUDIENCE
This course is intended for public health laboratorians who are currently conducting wet-lab influenza sequencing procedures in their laboratory, using Illumina instrumentation.
Applicants’ laboratories should currently have implemented or be establishing sequencing for influenza surveillance in their jurisdiction, with intent and a plan for sustainable continuation of influenza sequencing in future seasons. However, applicants whose laboratories participate as Influenza Sequencing Centers (ISCs) or National Influenza References Centers (NIRCs) will NOT be accepted for this workshop. PLEASE NOTE there is no federal funding support expressly provided or implied beyond this workshop for influenza sequencing by applicants’ laboratories.
CONTINUING EDUCATION
The Association of Public Health Laboratories (APHL) is approved as a provider of continuing education programs in the clinical laboratory sciences by the ASCLS P.A.C.E.® Program. P.A.C.E.® is accepted by all licensure states except Florida. This workshop will provide 26.0 contact hour for participants who successfully complete this training.
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