Classification of Viruses

Virus Properties    

• Infectious – must be transmissible horizontally

• Intracellular – require living cells

• RNA or DNA genome, not both

• Most all have protein coat

• May of may not have lipid envelope

• May have broad or narrow host range

• Adsorption, entry, uncoating, replication, assembly, release.

• Use host factors for to complete replication cycle

Composition of viruses infecting different hosts

• No “rules” about virus families that may or may not be present in a given kingdom.

• Some types of viruses are found more commonly in some kingdoms than in others.

– Many plant viruses contain ssRNA genomes

– Many fungal viruses contain dsRNA genomes

– Many bacterial viruses contain dsDNA genomes

• Host properties determine the types of viruses that tend to be found in members of a biological “kingdom”

Overview of Virus Properties

• Animal

– RNA – 5-30 kb

– DNA: 5-350 kb

– Many enveloped

– Range of complexity

– Range of morphologies

– Some divided genomes

• Prokaryote

– RNA – 5-8 kb

– DNA – 10-200 kb

– Few enveloped

– Range of complexity

– Range of morphologies

– Few divided genomes

• True Fungi  

– RNA – 2.5-28 kb

– DNA – none

– Enveloped

– Little genome complexity

– Little morphological complexity

– Some divided genomes

• Plant      

– RNA – 0.3-28 kb

– DNA – 3-10 kb

– Few enveloped

– Little genome complexity

– Little morphological complexity

– Many divided genomes

• Lower eukaryote

– RNA – 5-10 kb

– DNA – 180-1200 kb

– Envelope

– Range of complexity

– Range of morphologies

– No divided genomes

Tobacco mosaic virus – a typical small RNA virus

• 18X300 nm

• Single 6400 nt RNA

• 2130 molecules of single 17

kDa coat protein.

• 3 essential genes.

• Simple regulatory elements.

Poxvirus – a typical large dsDNA virus  

• 120X200 nm

• Single 180 kb DNA

• Complex coat made up of numerous proteins

• >100 essential genes

• Complex regulatory elements

Virus at the edge: Mimivirus

• Acantamoeba polyphaga Mimivirus (APMV)

• 400 nm particle, 1.2 megabase genome, dsDNA virus

• Represent the 3rd largest virus identified yet

• Many genes for normal cellular functions

• Mimivirus (mimicking microbe)

• Mistakenly thought to be a gram-positive bacterium.

• Placed at the boundary of living and non-living.

• Has genes for nucleotide and amino acid synthesis.

• Does not exhibit many characteristics, including genes for ribosomal proteins, etc.

Naming viruses

Animal viruses 

1. Diseases that they cause: small pox, foot and mouth disease, hepatitis

2. Places where virus was first identified

Norwalk virus, West Nile virus, Hanta virus

3. Other

1. Organ virus was isolated from: adenoids-Adenovirus

Sin Nombre

Plant viruses and many insect viruses (two components) 

1) Host

2) Disease

Tomato bushy stunt virus

Cricket paralysis virus

Classification of Viruses

Classical: morphology

Physical and chemical composition

Genetic relatedness

Modern: Phylogenetic, based on nucleic acid sequence analysis.

Classical criteria for classification of animal viruses

• Several parameters are used for classification

– Type of genomic nucleic acid

– Size of virion and genome

– Capsid structure

– Host

– Replication mechanism

All these approaches fail to predict fundamental features of the viruses.

Problem in Viral Classification

• Similar disease, but different viruses

o Hepatitis A virus: a Picornavirus

o Hepatitis B virus: a Hepatoavirus

o Hepatitis C virus: a Flavivirus

• Similar viruses, but different diseases

o HSV 1: Cold sores

o HSV 2: Genital Lesions

o VZV: Chicken Pox

o CMV: Organ Failure

o EBV: Mononucleosis, Burkitt’s Lymphoma

So simple classification system did not work well. Virologists had to devise more orderly systems.

Modern Criteria for classification

The Baltimore classification system

Based on genetic contents and replication strategies of viruses.

According to the Baltimore classification, viruses are divided into the following seven classes:

1. dsDNA viruses

2. ssDNA viruses

3. dsRNA viruses

4. (+) sense ssRNA viruses (codes directly for protein)

5. (-) sense ssRNA viruses

6. RNA reverse transcribing viruses

7. DNA reverse transcribing viruses where "ds" represents "double strand" and "ss" denotes "single strand".

Comparisons of Vertebrate and Plant Viruses

 Vertebrate Infecting Viruses               Plant Infecting Viruses

Classification and Nomenclature

ICTV-International Committee on Taxonomy of Viruses (meets every 3 years).

Considerations:

– Host range (eukaryote or prokaryote, animal, plant etc.)

– Morphological features (enveloped, shape of capsid)

– Nature of genome

Taxonomy scheme

Total

Family: 87

Subfamily: 19

Genus: 348

Species: 2290

Characteristics of the ICTV system    

• “Non-systematic”

• Polythetic

• Employ hierarchical level to species as lowest level

• Universal

• Limited (very conservative)

• Latinized, but no binomials

• Preserves common or trivial names at species level

Family            

• A group of genera with common characteristics.

• Capitalized, Italicized, and end in -viridae.

Examples:

– Picornaviridae (picornavirus family is also acceptable).

– Herpesviridae (herpesvirus family).

– Flaviviridae (flavivirus family)

Origins of family names 

1) Symptoms or disease caused by viruses

Herpes: produce scaly (snake skin) lesions

Pox: infections produce pox lesions

Papilloma: infections result in papilla (bumps on skin), e.g. warts

Flavi: Latin for yellow

2) Sites of infection

Adeno: infections of respiratory tract

3) Physical characteristics of the viruses

Picorna: Pico (small) + RNA

Corona: wearing a crown

Filo: Look fibrous

4) Combination

Hepadna: hepatitis + DNA

Subfamilies

• Groups within some large families. To solve a complex hierarchical problem.

• Capitalized, Italicized, end in -virinae.

• Examples

– Alphaherpesvirinae

– Betaherpesvirinae

– Gammaherpesvirinae.

Genus           

• A group of virus species sharing common characteristics.

• Capitalized, Italicized, ends in -virus.

Type member: a single virus designated by the ICTV that serves as a reference for the genus

Example from Flaviviridae:

• Flavivirus-yellow fever virus

• Pestivirus- Bovine Diarrhea virus 1

• Hepacivirus-Hepatitis virus C (HCV)

Species      

• A cluster of strains from a variety of sources or a population of strains from one particular source, all of which have in common a set pattern of stable properties that separates the cluster from other clusters or strains.

• Not capitalized.

• Not italicized.

Examples:

– Poliovirus

– Human immunodeficiency virus

– West Nile virus

Taxonomy: two examples

Example 1: herpes simplex virus 1   

_ Family: Herpesviridae or herpesvirus family

_ Subfamily: Alphaherpesvirinae;

_Genus: Simplexvirus;

» Species: herpes simplex virus 1.

Example 2: Poliovirus      

_ Family: Picornaviridae or picornavirus family;

_ Subfamily: None;

_Genus: Enterovirus;

» Species: poliovirus

Further breakdowns not recognized by the

ICTV

• Strain- different lines of isolates of the same virus.

– Example: Isolated from different geographical locations.

• Type- different serotype (different antigenic specificity) of the same virus.

– Example: Influenza type A or B. There may also be “subtypes” within a particular type.

• Group- sub-category of species, division often based on genomic sequence similarities or origin.

– Example: HIV group M (Main), N (Neither M or O), or O (Outlier).

– There may also be “subgroups” (sometimes called clades) within a particular group (subgroups A-J of group M HIV).

• Variant-Virus whose phenotype differs from original wild type strain but where the genetic basis for the difference is not known.

Satellite virus

Common features:

1) Do not encodes enzymes required for replication.

2) Therefore require co-infection with a conventional (helper) virus

3) Satellite genome is significantly different from the helper virus

4) May affect replication of the helper virus.

5) May increase or decrease severity of disease

Satellites viruses

Encodes structural proteins, which form the viral capsid

They rely on the helper virus replicative machinery to replicate their genomes.

Examples: adeno associated virus (helper: adenovirus)

DI Particles

Defective interfering particle: A virus that lacks part of its genome and interferes with the replication of a standard virus.

1. Require helper virus

2. Derived from helper virus: They tend to be deletion mutants that have lost their ability to encode proteins, but retain their ability to be replicated by the helper virus replicative machinery. (defective)

3. Interfere with helper virus replication by their ability to out compete for helper virus resources.

Viroids: Novel agent of disease in plants

• Single circular ssRNA molecule with no protein component

• High complementary (70% base-paired)

• Extremely small in size ranges from 246-267 nucleotides

• Disease from RNA interfering with essential host cell mechanisms

• Viroids RNA does not code for any protein.

• Long been a confusion over how viroids are able to produce symptoms without encoding any protein.

• They are cleaved by dicer enzymes into small interfering

RNAs (siRNAs).

• siRNA sequences are capable of complementary base pairing with plant’s own mRNA.

• Induction of degradation or inhibition of translation is what causes the symptoms of classic viroid infection.

Prions

- Shortened form of proteinaceous infectious particles.

- Prions are single molecules containing about 250 amino acids.

- They are abnormal variants of proteins which normally occur in cells.

- Prions have the ability to convert the normal forms that they come into contact with into abnormal forms

Prion Hypothesis  

• PrP is a normal cellular protein referred to as PrPc

• Diseased brain contains aberrant PrP which is referred to as

PrPSc . PrPSc has the ability to convert PrPc to itself.

• A chain reaction follows, resulting in a cluster of tangled, nonfunctional proteins called plaques, which are aggregates of PrPSc in the brain.

• The body defences remove these PrPSc aggregates leaving behind holes.

• This causes degeneration of the brain cells leading to mental changes and ultimately, death.

Transmission    

• Prion in cattle is mainly are from the carcasses of scrapie-infected sheep.

• After these infected sheep having died their brains and other sheep byproducts infected with scrapie is used to feed cattle with the meat and bone meal (MBM).

• Feeding cattle animal bi-products such as meat-n-bone meal that has an infected prion causes the infection in the cattle.

• The prions are concentrated in the brain, and spinal cord of these animals.

• There is no evidence that it is concentrated in the muscle mass of cattle, and they are considered safe as long as they are not in contact with the brain and spinal cord during the slaughter process.

• Sheep with Scrapie used in Meat and Bone Meal

(MBM) – known as “Offal”

• MBM fed to cattle.

• Infected Beef eaten by humans

– When cattle brains and other cattle byproducts infected with BSE are ingested by humans, there is a risk of the Creutzfeldt Jakob Disease.

– Not affected by cooking.

– One person per million worldwide each year.

– New Guinea cases in 1900, due cannibalism.

Transmissible Spongiform Encephalopathies

_ The Mad Cow Disease in Cows, Scrapie in Sheep, the Creutzfeldt-Jakob Disease in human beings belong to a class of disease called Transmissible Spongiform

Encephalopathy (TSEs)

_ Initially thought to be due to “slow viruses”, due to the long incubation period between time of infection and appearance of disease, these are now known to be caused by agents called prions.

_ Transmissible Spongiform Encephalopathy (TSEs) are rare forms of progressive neurodegenerative disorders that affect both humans & animals

Transmissible Spongiform Encephalopathies

 _ It is found on any type of cloven hoofed animals such as: pigs, sheep, and cattle

_ Scientific Name: 

_In cows: Bovine Spongiform Encepalopathy (BSE)

_In Sheep: Scrapie Spongiform Encepalopathy (SSE)

_In human: Creutzfeldt-Jakobs Disease (CJD)

Transmissible Spongiform Encephalopathies

• Transmissible Spongiform Encephalopathy (BSE) is so named because of the spongy appearance of the brain tissue of infected cattle (and also in the human beings) when sections are examined under a microscope