Abstract

Modern molecular, DNA and RNA-based methods have seen ever increasing use, over the last decades, in the detection and analysis of viral pathogens. Most of these methods rely on PCR for amplification of viral DNA/RNA and are, thus, dependent on primers that recognize viral targets reliably and selectively. Designing such primers can be challenging if the diversity of viral genotypes that need to be recognized by the primers is high.

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• What are pan-specific primers and primer schemes and why are they important?
• How to capture viral species diversity in the form of a multiple sequence alignment?
• How to design primers that will be mostly unaffected by differences between viral genotypes?
• How to avoid generating primers with off-target binding sites?

Learning Objectives

• Reproduce published qPCR primers and primer schemes for polio virus using MAFFT and varVAMP
• Gain the knowledge and confidence to create your own primers and primer schemes