This document discusses the origin and evolution of viruses. It begins by defining key terms like isolate, variant, and strain. It then presents three main hypotheses for the origin of viruses: 1) the virus first hypothesis which proposes viruses evolved independently from self-replicating RNA, 2) the reduction hypothesis which suggests viruses originated from reduced cellular organisms, and 3) the escape hypothesis where genetic material escaped cellular control and became parasitic. The document also discusses types of virus variation like mutation, hybridization, and pseudorecombination, as well as microevolution and macroevolution. It provides an example of how plant viruses can overcome Muller's Ratchet, which is the loss of critical functions in a population.

1. Origin of viruses and
virus strains
N. H. SHANKAR REDDY
Ph.D., Plant Pathology
Annamalai University

2. • Isolate
When a virus is derived from a field or experimentally from infected
host by a single isolation is known as isolate
• Variant
Isolate of the same virus that is differ in some property
(host range, transmission, serology or nucleotide sequence)
• Strain
A variant of virus within a species that can be recognized by some
phenotypic characteristic is known a “strain”

3. There are three hypothesis
1. The virus first hypothesis (Independent entities theory)
2. The reduction hypothesis (The second virus theory/ Degenerate hypothesis/
Regressive evolution theory)
3. The escape hypothesis (The third virus hypothesis)

4. 1. The virus first hypothesis (Independent
entities theory)
 Viruses have evolved from a self-replicating material that existed in the prebiotic
mRNA world.
 They are the remnants of the pre-cellular life forms. RNA and its origin,
perceived as the first molecules of life, was able to act as a nucleic acid carrying
information and capable of self-replication hence an entity of independent
existence.
 In this theory, RNA viruses are thought to have been descendants of the RNA
world and the DNA viruses evolved later from RNA.

5. 2. The reduction hypothesis (The second virus
theory/ Degenerate hypothesis/ Regressive
evolution theory)
 This states that viruses originated as a result of reduction of unicellular organisms
via parasitic-driven evolution.
 This means that cells of unicellular organisms lost their membranes, cell walls
and other structures as well as their cytoplasm, hence retaining only the nucleic
acid and some vital proteins in order to live in other cells as parasites.

6. 3. The escape hypothesis (The third virus
hypothesis)
 Viruses are thought to have originated from fragments of genetic material that
escaped from the control of the cell and became parasitic.
 Plasmids and mobile genetic elements are extracellular genetic materials capable
of exit and entry into the genomes of other cells. This phenomenon provides a
glimpse of the possibilities of escape by the genetic elements provided by this
theory.

7. Variations in viruses
1. Mutation - A single nucleotide change either insertion or deletion either in the
non coding region; The change in coding region - resulting in change in amino
acid.
(It may occur during replication; purine or pyrimidin is replaced by purine or
pyramidin respectively it is called transversion).
2. Hybridization/ Recombination - exchange of segments of genome - both in
RNA and DNA viruses.
3. Pseudorecombination/ reassortment - In viruses with divided genome
shuffling of genomic segments – gemini viruses.

8. Types of evolution:
• Microevolution – mutations or small insertion or deletion changing some regions of
the virus but not affecting the major functions.
• Macroevolution – by recombination, acquiring new genes lead to generation of new
species/ genera/ family

9. Muller’s Ratchet
• Mutations that lead to loss of critical functions would not be propagated in a
population unless they were complemented by other members of population.
• If mutation only cause slight decline in fitness they will survive.
• Plant viruses can overcome constraint of Mullers Rachet for eg. Nematode
transmission of Tobacco rattle virus (TRV).
• Defective RNA of RNA2 has modified coat protein, which will interfere with
replication. Instead of removal of this variant virus has overcome this problem by
encapsidation of both defective RNA and RNA2 together. Which are
nonfunctional and functional in transmission.

10. Video available at you tube
Channel – Geeky Researcher