1. VIRAL GENOME
Dr. YALAVARTHI NAGARAJU

3. Terminology
• Virus- infectious particles with nucleic acids and proteins
• Cant reproduce out side the host -Intracellular obligate parasites
• Small in size varies from 20-300 nm
• First virus discovered was – TMV (Tobacco Mosaic Virus)
• At the boundary of life
• Viruses can be found every where
• Viruses got their name from the Latin word for poison
• Virion – complete virus particle i.e. Nucleic acids and protein coat
• Virusoids –
• Satellite viruses - Satellite viruses are satellites that code for their own capsid protein(s). Satellites are subviral
agents (DNA or RNA based) that replicate only in the context of coinfection with a “helper” virus coding for
indispensable functions in trans. Satellites are to be distinguished by viroids, which are the smallest described
pathogens.
• Prions – infectious proteinaceous particles
• Bacteriophages – viruses that infect the susceptible bacterial cells
• Virome – collection of bacterial and eukaryotic viruses
• Virology – the branch of science that deals with the study of viruses

4. Common points
• To see viruses - Electron microscope
• To grow the virus - living tissues/ cells
• Viricides - inhibit the multiplications
• Mutation - High rate
• Multiplication - Intracellular

6. Viroids
• Infectious agent composed of short single stranded RNA (ssRNA),
• Often exist in pairs
• First discovered and Named by Theoder O Deiner in 1971 i.e potato spindle
tuber viroid (PsTVd)
• Don’t contain protein capsid
• They are easily destroyed by ribonucleases
• Requires host cell for multiplication

7. Virusoids
• Virusoids – infectious circular single stranded RNA which requires the helper
virus for infection
• Subviral particles with non self replicating
• They are encapsulated within the helper bacteria

8. Prions
• Prions are misfolded rouge form of a normal protein found in the cell
• No nucleic acids
• Highly heat resistant
• The rogue protein may be caused by a genetic mutation or occur spontaneously
• Discovered by Stanely Prusiner in 1982 while working with Scrapie disease in sheep

9. Prokaryote vs Eukaryote

10. Prokaryote vs Eukaryote vs viruses

11. Sizes

12. Viruses as box of paradox
• They are considered nonliving agents; however, being “dead” does not prevent
them from causing disease or executing various life styles.
• Another paradox is the huge disproportion between the virus size and the
magnitude of complexity they govern. Physically, viruses measure on the
nanometer scale. The flu virus measures 80–120 nm in diameter, therefore if
we line up flu particles along a cross section of a human hair, we will fit about
1000 of them
• On the molecular level, viruses could be considered as “kings and queens” of
exceptions, “utilizing” unique strategies for genome replication and synthesis
of viral components. That makes them an unparalleled resource for molecular
tools that can be applied toward new technology development.

13. Configuration of viral genome
The genome may be either DNA or RNA, which may be single stranded or double stranded
Genome may be either positive sense or negative sense
(+) sense: positive sense RNA is equal to mRNA, thus it can be immediately converted into
protein
(-) sense: negative sense RNA is complementary to mRNA and thus must be converted to
positive sense RNA by RNA polymerase before translation
Exception:
1. Retroviruses
They make DNA from RNA using RNA dependent DNA polymerase or Reverse transcriptase
(RT) Eg: HIV, AMV (Avian Myloblastosis virus)
2. Hepadnaviruses or pararetroviruses
They are DNA viruses carries RT, DNA genome is transcribed into RNA which acts as template
to make new viral DNA strands

14. • Reverse transcriptase contains three enzymatic activities:
• (1) RNA-dependent DNA polymerase- RNA-dependent DNA polymerase
synthesizes a DNA strand complementary to the RNA template
• (2) RNase H, - removes the RNA strand from the RNA–DNA hybrid double
helix and
• (3) DNA-dependent DNA polymerase- completes double-stranded DNA
synthesis
Unlike other DNA polymerases, reverse transcriptase lacks a proofreading
capability and therefore has high error rates during DNA synthesis, up to one
error in 2000 base incorporations. The high error rates of viral reverse
transcriptases provide selective advantage for their survival in the host system.

16. Virus overview

17. Viral structure
• The size, shape and symmetry may vary
• There are three types of capsid symmetry
1. Cubic (icosahydral)
Has 20 faces, each an equilateral triangle Eg:
adenovirus
2. Helical
protein binds around DNA/RNA in a helical fashion
Eg: TMV
3. Complex
is neither cubic nor helical Eg: T-even
bacteriophages

18. Genomes
• Viral genomes contain either DNA or RNA, never both
• RNA and DNA molecules may be double stranded or single stranded
• Linear or circular
• Segmented (composed of multiple pieces of nucleic acids) or non segmented
• Genome segment is unique piece of nucleic acids among the multiple pieces of genome
• Eg: 1. Influenza A virus has segmented genome comprised of eight ssRNA segments
2. Herpesvirus have no segmented genomes comprised of one linear dsDNA molecule and have the so
called UL (Unique long) and US (unique short) segments
3. HIV genome carries two copies of same ssRNA molecules, hence the genome is considered non
segmented and they are called copies not segments

19. • In many viruses the genome ends contain repeated sequences, chemical modifications, or secondary structures,
which often have regulatory functions.
• Genomes are tightly packed inside the capsids and frequently the genome and the capsid are collectively
called nucleocapsid.
• Amazingly, viruses are able to execute productive infection and of course make us sick with very limited
genetic information.
• The flu virus genome, for example, contains only 15,000 nucleotides. For comparison the human genome is
3,200,000,000 nucleotides or approximately 200,000 times longer.
• Needless to say, viruses have to be superefficient, in their quest to invade the host cell and to propagate.
• Bacteriophage Qβ is among the smallest RNA viruses with a genome built from 4217 nucleotides and only 4
genes.
• Among the smallest known animal DNA viruses is TT virus whose genome is comprised of less than 4000
nucleotides and 4 predicted genes.
• On the opposite side of the scale is the giant Megavirus chilensis with genome as large as 1.3 MB (1182 Kb)
coding for 1000 genes (979 proteins).
• What functions viral genomes code for is a tantalizing question. Analysis of viral genome sequences revealed
that approximately 80% of the viral genomes code for virus-specific genes, many of which have no known
homologues or known function.

21. Baltimore system of classification of viruses