L10. Viral Replication Strategies

• Virus Replication Strategies
• Learning Objectives


  • Describe the replication strategies employed by different classes of virus (DNA, RNA and retroviruses)
• Reminder: Replication, translation, transcription in Eukaryotes
• Genome


  Each eukaryote cell contains a complete copy of the genome in paired, complementary DNA strands
• Cellular machinery


  All of the necessary cellular machinery is encoded in the genome to support replication, transcription (into messenger RNA) and translation
• Genomic DNA


  Genomic DNA is stable, the function is carried out by protein through mRNA intermediate
• Replication


  DNA -> DNA
• Transcription


  DNA -> mRNA
• Translation


  mRNA -> protein
• Virus


  Obligate intracellular parasites, in order to achieve propagation, the virus proteins/nucleic acid must be transported to location of required host cell enzymes
• Virus replication


  • The virus must replicate its genome, Use the host cell machinery, Encode viral genes / proteins provide specialised functions not provided by host cell (e.g., reverse transcriptase; RNA -> DNA)
• Nucleus


  The virus needs host enzymes for mRNA synthesis located in the nucleus
• Some viruses require virus entry / transport into nucleus (ex: Herpes virus, HIV)
• Some enzymes also accessible in mitochondria
• Some virus have a +ssRNA genomes
• Host cell translation machinery


  The virus must translate mRNA into protein using the host cell translation machinery
• Viruses do not encode the full range of proteins required for translation
• Viral Replication Strategies - Overview


  • The virus genome (genetic material) encodes information to support key replication stages: Entry into the host cell, Translation of viral genes into viral proteins (can be early or late), Replication of the viral genome, Virus assembly and release from the host cell, Virus must modify the structure and/or function of the host cell to support its lifecycle including anti-viral immune responses
• Viral Strategy


  Refers to the manner virus carries out these functions, Strategies are informed by viral genome and structure
• Virus Replication Cycle


  Attachment to host cell, Cell entry / penetration, Eclipse period – activation of viral machinery, Maturation period – production of new virus, Release
• Virus attachment to host cell

  • Viruses attach to host cell through surface proteins that bind receptors, Often members of the Ig superfamily (same as antibodies), Major determinant of host specificity: Determine virus host species & cell / tissue within host, HIV binds CD4 on immune T-cells, APCs, SARS-CoV-2 binds ACE2 on airway epithelial cells, Avian flu binds to α-2,3 sialic acid, human flu binds to α-2,6 sialic acid
• Virus entry strategies


  • Endocytosis, Fusion (enveloped viruses only)
• Endocytosis


  Invagination of the cell membrane after attachment (endosome), Hijacks host cell endocytosis machinery, Virus surrounded by host cell membrane
• Fusion


  F (fusion) protein directly fuses envelop with cell membrane, Viral proteins mediate direct fusion with host cell membrane, Virus enters into cytoplasm leaving envelope within host cell membrane
• Example of Respiratory Syncytial Virus (RSV): spread through cell syncytium formation
• Virus uncoating


  Upon entry into host cell the virion must be uncoated for virus genome to become available for transcription (genome release), Uncoating can occur in the endosome, cytoplasm or nucleus
• Enveloped viruses


  Nucleocapsid discharged into cytoplasm, uncoated by host or viral cell proteases, Viral nucleic acid remains associated with structure
• Non-enveloped viruses


  Structural changes (pH) (capsid disassembly): proteins are removed
• Early viral genes


  All genes expressed before replication of viral genome, Crucial for activation of virus functions and initiation of replication, Transcribed into messenger RNA -> protein translation, Shut down host cellular synthesis, Regulate expression of innate immunity
• Late viral genes


  Expressed after replication of viral genome, Replication of viral nucleic acids can still occurs at a low level, Transcribed into messenger RNA -> protein translation, Structural proteins for new virions, Proteins may be subject to post-translational modification (glycosylation, myristoylation, phosphorylation)
• Unlike eukaryotic/prokaryotic cells, viruses can have RNA or DNA-based genomes
• Unlike eukaryotic/prokaryotic cells viruses can have RNA or DNA-based genomes
• Overarching mechanisms


  • DNA transcribed to RNA (RNA -> DNA only when reverse transcriptase), Strands complementary to starting material (e.g. + RNA / - RNA), mRNA translated to protein
• Virus genome types


  • + RNA, - RNA, + DNA, - DNA, dsDNA, ssDNA, dsRNA
• Baltimore Classification (I-VII)


  Diversity in Virus Genomes
• Group 1 viruses – dsDNA


  • Replication mechanisms common to eukaryote biology: transcription of mRNA from dsDNA and DNA replication, Some viruses need to have their viral DNA transcribed in the nucleus by host cell polymerases (transcriptase) (Ex: Herpesviridae, Adenoviridae), Produce polycistronic mRNA (multiple mRNA transcripts in single molecule), Some viruses encode and package own DNA & RNA polymerase (eg: Poxviridae), Viral DNA is transcribed directly in the cytoplasm independent of host cell enzymes
• Examples families: Group 1 viruses


  • Herpesviridae, Papillomaviridae, Adenoviridae, Poxviridae
• Group 2 viruses – ssDNA


  • Family : Parvoviridae, ssDNA genome synthesized into dsDNA in the nucleus by cellular polymerase, Similar to DNA replication by host cell during mitosis, Viral dsDNA transcribed in the nucleus by cellular polymerase (transcriptase)
• Group 7 viruses – ss/dsDNA with reverse transcriptase

  • Hepadnaviridae (HBV) : Unique reverse transcription of an RNA intermediate to replicate the ss/dsDNA, ss/dsDNA is repaired by the host nucleus machinery : covalently closed circular DNA (cccDNA), cccDNA used to synthesise pregenomic RNA(PgRNA), PgRNA used as a template to generate genomic DNA using viral reverse transcriptase (RNA -> DNA)
• Viruses that replicate via RNA intermediates require RNA-dependent RNA-polymerases (RdRp) to replicate