Virus Classificaiton and Evolutionary Orgins

Question 1

1. Viruses evolved from RNA molecules at the early stage of the ea

Answer 1

th(Virus-first hypothesis): Scientists perceived viruses as the first cellular organism on earth and are descendent of RNA molecules that existed before cells. RNA evolved to have enzymatic activities (ribozymes) and potentials to replicate themselves.As cells evolved later, they were parasitized by virus which picked up capsid protein genes from RNA

Question 2

2. Descendants of cell components(Escape hypothesis):

Answer 2

Viruses may be descendent of cell components which have evolved ability to replicate themselves independently of host cells and later act as parasites for the cells. Potential virus precursors are DNA and RNA molecules such as plasmid

Question 3

3. Viruses evolved similarly as prokaryotic cells(Reduction hypothesis):

Answer 3

Virus have been speculated to evolved like primitive intracellular bacteria parasites through reduction of eukaryotic cell components such as mitochondria and chloroplast. These organelles later evolved to become parasites of cells and lost the ability to function as normal cellular organelles; but rather as a virus.

Question 4

Hypothesis in virus evolution

Answer 4

• Differences in viral architecture, genome and replication strategies may indicate that viruses have diverse evolutionary origin.
• Scientists speculate that small simple viruses (parvoviruses, picornaviruses) might have originated from molecular precursors
• Large complex viruses (mimiviruses) might have originated from cellular precursors.
• Recent evidences suggest that viruses originated from molecular and cellular precursors

Question 5

Recent Molecular Evidences for Virus Evolution

Answer 5

• Since its difficult to recover fossils of viruses from the external environment, indirect ways have been adopted to analyze their ancestors.
• Viruses possess genes which they strive to replicate similarly as with cellular organisms.
• Genomes of hosts have clues in the form of retro-elements.
• Retroviruses are DNA fragments that has been incorporated into the DNA of hosts by attacking viruses.
• Thus, there is Darwinian evolution in viruses as they are rapidly evolving and changing their DNA composition with that of the host in order to survive and perpetuate themselves.
• New viral genome could be more successful than parents

Question 6

Molecular Discovery of Past Viruses

1.RT-PCR (Reverse Transcriptase-polymerase chain reaction).

Answer 6

1.RT-PCR (Reverse Transcriptase-polymerase chain reaction).

• The technique has enabled the isolation and gene amplification of several virus genes during past pandemic. E.g., the influenza virus pandemic between 1918-1919, tomato mosaic virus and SARS-COV-1 (2002).
• Virus fossils can now be recovered from different host ancestors (bacteria, plants, animal) for which the viral genome has been incorporated during past infection.

Question 7

Examples of Viruses discovered with molecular techniques

Answer 7

•Some examples of viral genome recovered from ancestors:

• Flavivirusesin mosquitoes
• Hepadnavirusesin birds
• Caulimovirusesin plants
• Retroviruses in mammals

Question 8

Molecular Discovery of Past Viruses

2. Construction of Phylogenetic trees of virus ancestors

Answer 8

• This can show relationship between viruses by comparing their genome sequences.
• Virus groups closest to each other are more likely to have evolved from a common ancestor

Question 9

Mechanisms of Virus Evolution

Answer 9

1. Mutation: one or more errors in the protein-coding nucleotide sequences in the genome of a virus.
2. Recombination: A process which involves the combination of two related parent viral genomes in host cells to yield a progeny
3. Re-assortment of genome segments: Is a type of recombination whereby segmented viral genome fragments are packaged in a virion.
4. Acquisition of cell genes: Evidence of host genes (oncogenes) and proteins have been detected in some viruses such as the retroviruses. These host molecules disguise the virus and prevent it from immune attac

Question 10

Factors influencing Viral success

Answer 10

1. Growth potential
2. Abundance
3. Biodiversity
4. Adaptability (Coronaviruses)
5. Impact

Question 11

Early methods of virus classification

Answer 11

•In the early days of virus discovery when little is known about viruses, early classification was based on the following:

1. Host type (bacteria, plant or animal)
2. Type of disease caused by infection -Severe Acute Respiratory Syndrome (SARS) virus.
3. Mode of transmission
4. Place the virus was first reported (Middle East Respiratory Syndrome (MERS virus); Ebola
5. Disease caused: Smallpox, foot and mouth disease virus, measles

•Because of the unique nature of viruses, no definite system of classification have been strictly imbibed as at the tim

Question 12

Recent viral classification depends largely on molecular evidence

Answer 12

1. Shape of capsid symmetry whether helical or icosahedral
2. Presence or absence of envelop
3. If the genome is segmented or not segmented
4. The size of the virion
5. If the nucleic acid is DNA or RNA
6. If the nucleic acid is single stranded or double stranded

Note that a combination of these factors might be applied in the classification of a single virus or placing them into group

Question 13

naming

Parvoviruses

Answer 13

s (Parvusin Latin means small =small viruses) were so named due to their small size with icosahedral-shaped capsid, surrounding a single stranded DNA commonly known to infect humans

Question 14

Naming

nepoviruses

Answer 14

The Nepoviruseswere so named because a Nematode which transmits the Polyhedral or icosahedral-shaped virus to plants.

Ne-po-virus (Nematode-Polyhedral-virus)

Question 15

Virus nomenclature

Answer 15

•The naming of viruses isn’t based on a single taxonomic criterion but a combination of earlier and recent taxonomic factors of the particular virus.

Question 16

Bacteria viruses (phages)

Nomenclature

Answer 16

are assigned numbers (Phage T1, T2, T4, T6).

Question 17

•Plant viruses nomenclature

Answer 17

are mostly named based on hostand type of disease.

Question 18

•Vertebrates virus nomenclature

Answer 18

named based on:

1. Diseases caused: smallpox virus, measles virus, foot and mouth disease virus
2. Place the virus was first discovered: Norwalk virus, Newcastle disease virus, Ebola virus, Lassa fever virus

Question 19

CLassification based on Shape/ Symmetry

Answer 19

•Three major forms can be distinguished

1. Helical capsid symmetry (E.g. Tobacco mosaic virus, measles, rabbies
2. Icosahedral shaped virus (E.g. Herpes virus, Polio virus, Parvovirus
3. Complex shaped virus (smallpox, bacteriophages)

Question 20

Taxomonic classificaiton of viruses

Answer 20

• Recent methods for classification:
• In 1966, a regulatory body known as the International Committee on Taxonomy of Viruses (ICTV) was set up to coordinate the naming of viruses.
• The ICTV lays down the rules for the nomenclature and classification of viruses, and it considers proposals for new taxonomic groups and virus names.
• Accepted proposals published in a boo

Question 21

Modern virus classification and nomenclature

Answer 21

• This method attempts to group and name viruses into taxonomic groups using the hierarchical method of cellular classification
• Note that the kingdom and Phylum hierarchy of classification is excluded in viruses.
• It is the most accepted basis of viral classification because it group viruses mainly based on genetic similarity.
• Note that some virus classification is still based on a combination of criteria.
• Defined viral characteristics are required prior to placing them in specific orders, family, subfamily and genus while species grouping is based on a number of similar characteristics.
• Thus, member of a virus species may vary in:
• Strain
• Serotypes: differences in virus antigen reaction to antibodies
• Genotype: differences in a virus gene sequen

Question 22

Virus classification based on taxonomy hierarchy

Answer 22

The hierarchy of virus begins with:

• Order (ending in virales)
• Family (ending in viridae)
• Subfamily (ending in virinae)
• Genus (ending in virus)
• Species (ending in virus)
• Subspecies (may end in a number)
• strain

Question 23

Modern virus taxonomy and nomenclatur

Answer 23

Naming of some virus taxonomic groups incorporated the old name together with the taxonomic suffix. E.g. the generic and family name for picornaviruses(small viruses) were derived by placing the suffix (virales) and (viridae) respectively, in place of the word virus

Question 24

Taxonomic classification of Coronavirus

Answer 24

•Coronaviruses (Derived from Corona meaning crown-like)
•Order: Nidovirales
•Family: Coronaviridae
•Superfamily: Coronavirinae
•Genus (4 Genera): 
1. Alpha coronaviruses
2. Beta coronaviruses
3. Gamma coronaviruses
4. Delta coronaviruse

Question 25

Genetic classification of viruses

Answer 25

• A virus is made up of genetic material which is either DNA or RNA.
• This differentiates viruses from cellular organisms whose genetic unit is a DNA.

•Viruses can be divided into four groups of based on the number of strand in its genome

1. double-stranded DNA (dsDNA)
2. single-stranded DNA (ssDNA)
3. single-stranded RNA (ssRNA)
4. double-stranded RNA (dsRNA)

•This approach to virus classification was first suggested by David Baltimore.

1. DNA virus
2. RNA virus
3. Reverse-Transcribing Viruses

•seven classes of viruses exist based on:

1. type of genome
2. the way in which the genome is transcribed and replicated

Question 26

class 2

Answer 26

see pictures

Question 27

Naming plant virus families, superfamiliesand genera

Answer 27

•Most plant viruses are named according to host and signs of diseases. •These factors have been incorporated into naming of virus families, superfamiliesand genera.

Question 28

Viral genome replicatio and viral classification

Answer 28

• Due to the unique mode of virus transcription among dsDNAand ssRNAgene groups, the four groups of viruses can be subdivided into seven.
• This discovery was made by David Baltimore and now named after him.
• He developed the system for classifying viruses based on genome type and was named Baltimore method for virus classification.
• This classification places virus into classes I -