varVAMP

varVAMP designs pan-specific PCR primers from viral multiple sequence alignments to enable tiled amplicon sequencing and qPCR-based genomic surveillance of highly variable viruses such as SARS-CoV-2, Hepatitis E virus, rat Hepatitis E virus, Hepatitis A virus, Borna-disease-virus-1, and Poliovirus.

Key Features:

• Pan-Specific Primer Design: Automates design of pan-specific primers tailored for qPCR and whole-genome sequencing via tiled amplicon approaches.
• Multiple Sequence Alignment Input: Leverages multiple sequence alignments of highly variable viral sequences to identify optimal primer-binding regions.
• Conserved Region Identification: Identifies regions with minimal sequence variability within alignments as targets for primer placement.
• Degenerate Nucleotide Integration: Incorporates degenerate nucleotides into primer sequences to accommodate common strain-specific variations.
• Cross-Virus Applicability: Has been applied to design primer schemes for SARS-CoV-2, Hepatitis E virus, rat Hepatitis E virus, Hepatitis A virus, Borna-disease-virus-1, and Poliovirus.
• Surveillance-Grade Assay Development: Enables design of primers that support highly sensitive and specific qPCR assays for viral surveillance, including Poliovirus monitoring.

Scientific Applications:

• Tiled Amplicon Sequencing: Generates primer schemes for amplifying genomes as overlapping PCR amplicons for tiled sequencing approaches.
• qPCR Assay Design: Produces primers for quantitative PCR assays with broad strain coverage via degenerate bases.
• Genomic Surveillance: Supports time- and cost-efficient surveillance of viral genomes across genetically diverse virus populations.
• Virus-Specific Primer Schemes: Facilitates whole-genome and targeted sequencing projects across multiple viral pathogens listed above.

Methodology:

Analyzes viral multiple sequence alignments to identify regions of minimal variation and designs primers that incorporate degenerate nucleotides for tiled amplicon sequencing and qPCR assays.