Viral Genome Classification

Question 1

Classification of replication: Replication of viral genome vs. replication of a virus

Answer 1

Replication of viral genome: multiplication of the nuclei acid

Replication of a virus: multiplication of the viral particle

Question 2

Classification of translation

Answer 2

Viral mRNA uses host machinery (ribosomes) to translate their viral proteins

Question 3

The Baltimore classification: 7 classes of viruses

Answer 3

I. dsDNA viruses

II. (+) ssDNA viruses

III. dsRNA viruses

IV. (+) ssRNA viruses

V. (-) ssRNA viruses

VI. ssRNA-RT viruses: (+) RNA viruses that replicate through a DNA intermediate

VII. dsDNA-RT viruses: dsDNA viruses that replicate through an RNA intermediate

VI and VII requires reverse transcriptase

Question 4

Class I replication, transcription

Answer 4

dsDNA genome viruses

• Example: Herpesviruses

• Similar to replication of cellular DNA
- Viral proteins made in the cytoplasm
- Viral genome replicated in the nucleus

• Transcription: Viral dsDNA genome can be immediately transcribed into mRNA upon entry using host RNA polymerase
- Exception: Poxvirus (including smallpox virus) encodes their own DNA-dependent RNA polymerase and do not use the host machinery

• Replication: Use the host machinery to make more dsDNA

Question 5

Class II

Answer 5

ssDNA genome viruses

• Example: Parvoviruses

• Cells do not use ssDNA – rarely infect humans b/c of cell sensors

• Transcription: (+) or (-) ssDNA —> dsDNA —> mRNAs (transcription machinery)

• Replication: Most of these viruses have circular genomes that are replicated within the nucleus via a dsDNA intermediate. (host DNA polymerase)
to generate the complementary strand, later separate by enzyme, the preferred ssDNA go into new particle

• Some viral ssDNA strand folds back on itself to form dsDNA, which is replicated by cellular DNA polymerase
• Newly replicated strand is released as ssDNA

Question 6

Class III

Answer 6

dsRNA viruses

Example: Reovirus (Rotavirus)

• All happens in the cytoplasm
• Carry RdRp in viral particle : make viral mRNAs (transcription) and to make copies of the RNA genome (replication)

Question 7

Class IV

Answer 7

(+) ssRNA viruses

Example: HCV, Poliovirus, SARS-CoV-2

• All happens in the cytoplasm
• Transcription: The positive-sense viral RNA genomes can be used directly to
translate to viral proteins by host ribosomes
Biosynthesis of RNA viruses
- encode RdRp gene in genome

• Replication: synthesis of complementary (-) strand by viral RdRp. The (-) strands then serves as a template for (+) strand synthesis

Question 8

Class V

Answer 8

(-) ssRNA

Example: Influenza virus

• All happens in the cytoplasm

• (-) ssRNA genome cannot be used by host ribosomes, it complement to mRNA

• Transcription: physically carry their RdRp in the viral particle

• Replication: (+) ssRNA is then used as a template for replication of additional copies of (-) ssRNA

Question 9

Class VI

Answer 9

Retroviruses or ssRNA reverse-transcribing (RT) viruses

Example: HIV

• Carry reverse transcriptase (RT) to convert (+) ssRNA to dsDNA in cytoplasm

• Using viral enzyme integrase (carries) to insert viral dsDNA to host genome in the nucleus → Provirus
-Provirus: host genome integrate with virus genome

• Transcription: integrated “provirus” used as a template to make mRNAs by the host cell transcription machinery

• Replication: provirus used as a template to make (+) ssRNA by host machinery

Question 10

Class VII

Answer 10

Pararetroviruses or DNA reverse-transcribing viruses

Example: Hepatitis B virus
• Partially dsDNA (gapped DNA)
• Partially DNA is converted to fully dsDNA by cellular DNA repair mechanisms or forms a covalently closed circular DNA (cccDNA)

• Transcription: dsDNA is then transcribed into mRNA in nucleus

• Replication: uses ssRNA intermediate as a template for viral reverse transcriptase to produce more DNA copies in cytoplasm

Encode for reverse transcriptase