Viral RNA Genome Replication Strategies
📌 Viruses discussed are categorized into Baltimore groups: Group 3 (dsRNA), Group 5 (negative-strand RNA), and Group 4 (positive-strand RNA).
🦠 RNA-dependent RNA polymerase (RdRp) activity was first detected in cells infected with poliovirus, demonstrating RNA could be copied from RNA.
🧬 The GDD (Gly-Asp-Asp) motif is a conserved signature for the active site in many polymerases, involved in coordinating catalytic metals (usually Magnesium).

RNA Polymerase Structure and Catalysis
🛠️ All nucleic acid polymerases (DdDp, DdRp, RT, RdRp) structurally resemble a right hand, with the active site located in the palm.
⚙️ RNA synthesis proceeds via a two-metal mechanism of catalysis involving two coordinating aspartate residues (Asp) that facilitate nucleophilic attacks to link nucleotides in the 5' to 3' direction.
🔝 RdRp activity can either initiate de novo (without a primer) or require a primer (protein or capped RNA piece).

Positive-Strand RNA Virus Replication (e.g., Poliovirus)
🧬 Poliovirus (+)RNA genome acts directly as mRNA upon entry, translated into a polyprotein which includes proteases and the RdRp (3Dpol).
🔗 Poliovirus RNA synthesis requires a protein primer (VPg), which is primed with two U's at a *cis*-acting element (CRE) on the genome.
🔄 Replication involves circularization of the template via interaction between the 3' poly(A) tail and the 5' cloverleaf structure, mediated by cellular proteins.

Coronavirus Replication Strategy
👑 Coronaviruses (large (+)RNA genomes, up to 30–40 kb) exist as nucleocapsids in the particle.
📜 They utilize a complex system of subgenomic mRNAs (sgmRNAs), nested transcripts generated via a discontinuous mechanism initiated at the 3' end, which allows access to downstream coding regions.
📈 High recombination rates in coronaviruses are linked to the polymerase jumping between templates during sgRNA synthesis, facilitated by the polymerase’s movement across transcriptional regulatory sequences (TRSs).

Negative-Strand RNA Virus Replication (e.g., VSV, Influenza)
⚙️ These viruses carry RdRp within the particle because the negative-strand genome cannot be directly translated.
🔄 A crucial switch occurs from synthesizing short mRNAs to synthesizing full-length (+)RNA strands, which is mediated by high levels of the nucleocapsid (N) protein causing RdRp anti-termination.
🤧 For Influenza, mRNA synthesis uses a host cell capped RNA fragment as a primer (cap-snatching), resulting in viral mRNAs that are shorter than the genome and possess a cellular sequence at the 5' end.

Double-Stranded RNA Virus Replication (e.g., Reovirus)
🧱 The dsRNA genome never leaves the viral core particle after entry via endocytosis; the core remains intact in the cytoplasm.
🔬 An RdRp located at the 12 five-fold axes (turrets) synthesizes mRNA from the dsRNA template, which then exits the particle for translation.
💡 The switch to genome replication (synthesis of the second strand) occurs when the core produces the full double-stranded RNA genome.

Fidelity and Diversity in RNA Viruses
📉 RNA polymerases typically lack proofreading mechanisms, leading to high error rates (e.g., one mistake per $10^4$ bases polymerized), driving viral diversity.
🔬 In poliovirus, fidelity is controlled by conformational changes upon correct NTP base-pairing; mutations remote from the active site (like residue 64 in the fingers domain) can increase fidelity by slowing this process.
🔁 RNA recombination is a high-frequency event in positive-strand viruses like poliovirus (up to 20% of molecules), where the polymerase switches templates, distinct from genome reassortment.

Key Points & Insights
➡️ The GDD motif is central to catalysis for RNA-dependent RNA polymerases, coordinating the divalent cations essential for phosphate bond formation.
➡️ Poliovirus achieves genome replication via a circularized template mechanism utilizing its VPg protein as a specialized primer.
➡️ The N protein in negative-strand viruses controls the shift from early gene expression (mRNA synthesis) to genome replication by inducing anti-termination in the polymerase.
➡️ Coronaviruses maintain large genomes by employing an exonuclease (ExoN) for error correction, a feature likely required due to their genome size.

📸 Video summarized with SummaryTube.com on Nov 27, 2025, 04:36 UTC