Viral Genomics and Surveillance
One-Sentence Definition
Viral genomics and surveillance sequence viral genomes at scale to track variants, transmission, and resistance in near real time.
Simple Explanation
Sequence viruses continuously so you can see new variants appear and spread while it still matters.
Detailed Scientific Explanation
Distinct features vs bacterial genomics:
- Tiny genomes, very high mutation rates (RNA viruses) → strong temporal signal for Phylodynamics
- Amplicon tiling (e.g., ARTIC protocols) rather than whole-shotgun for low-titer clinical samples
- Consensus genome + intra-host variant frequencies (quasispecies)
- Lineage nomenclature systems (Pango for SARS-CoV-2, clades for influenza) and platforms (Nextstrain, GISAID)
- Wastewater sequencing for population-level, individual-independent surveillance
Antiviral resistance: HIV genotypic resistance testing is a mature, guideline-embedded example; influenza NA mutations; SARS-CoV-2 antiviral resistance monitoring.
Mechanism
Reference-based assembly of amplicon reads → consensus calling with depth/frequency thresholds → lineage assignment → time-scaled phylogeny.
Clinical Importance
- HIV/HBV/HCV resistance genotyping directly guides therapy
- Variant identification informs vaccine and monoclonal antibody effectiveness
Research Importance
- Real-time evolutionary biology at pandemic scale; immune escape mapping (Antigenic Variation)
Diagnostic Relevance
- Detects primer-site mutations that cause PCR dropout (PCR)
AMR Relevance
- Antiviral resistance is the viral analogue of AMR (Antimicrobial Resistance)
Related MOCs
Active Recall Questions
- Why use amplicon tiling for clinical viral genomes?
- What is a quasispecies?
- How can genomics explain a sudden drop in PCR sensitivity?