SARS-CoV-2
One-Sentence Definition
SARS-CoV-2 is an enveloped positive-sense RNA coronavirus (Betacoronavirus) that causes COVID-19, entering cells mainly via spike–ACE2 interaction and evolving antigenically under immune and transmissibility selection.
Taxonomy & Structure
- Family Coronaviridae; related to SARS-CoV-1 and MERS-CoV (different epidemiology)
- ~30 kb (+)ssRNA — one of the largest RNA virus genomes; proofreading exonuclease reduces but does not eliminate mutation
- Structural proteins: Spike (S), Envelope (E), Membrane (M), Nucleocapsid (N)
- Variants of concern defined by lineage nomenclature (Pango) + phenotypic impact
Replication & Pathogenesis Highlights
- Respiratory (and other) epithelial infection; dysregulated inflammation in severe disease
- Multisystem involvement: thrombosis, anosmia, MIS-C (children), long COVID phenotypes
- Zoonotic origin narrative with ongoing animal reservoirs (mink, deer…) under One Health watch (One Health)
Clinical Syndromes
- Asymptomatic → mild URI → pneumonia/ARDS → critical illness
- Extra-pulmonary: cardiac, neuro, renal, thromboembolic events
- Reinfection possible as immunity and virus diverge
Diagnosis
- RT-PCR / qPCR on NP/OP/saliva — reference NAAT
- Rapid antigen — lower sensitivity, useful for infectiousness triage
- Syndromic Molecular Panels often include SARS-CoV-2
- Sequencing for lineage surveillance (Viral Genomics and Surveillance · Targeted Enrichment)
Treatment & Prevention (conceptual)
- Antivirals (e.g., nirmatrelvir/ritonavir, remdesivir — indication/timing dependent)
- Immunomodulators in severe hospitalized disease (steroids ± others per guidelines)
- Vaccines (mRNA, viral vector, protein) reduce severe outcomes; boosters as recommended (Vaccination)
- IPC: airborne/droplet strategies per setting; ventilation important
Genomics & Computational Notes
- Spike mutations affecting ACE2 affinity, antibody escape, diagnostics dropout
- Amplicon tiling NGS (ARTIC-style) for genomic epi (NGS Library Preparation)
- Phylodynamics of waves; wastewater sequencing as population signal
Related Notes
- Influenza Virus · RNA Extraction · RT-PCR · AI for Outbreak Detection
- MOCs: MOC - Virology · MOC - Public Health & Epidemiology · MOC - Bioinformatics in Microbiology
Active Recall
- What host receptor does spike primarily engage?
- Antigen vs PCR — which is more sensitive early?
- Why do primer dropouts appear in tiled SARS-CoV-2 genomes?