Lesson 2: How do we classify viruses?

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May 25, 2022

Viruses are classified based on a combination of several criteria that take into account their morphology, nucleic acid type, mode of replication,host organisms,  evolutionary relationships and the type of disease they cause. The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing a standardized classification system.

The International Committee on Taxonomy of  Viruses (ICTV)

The ICTV began to devise and implement rules for the naming and classification of viruses early in the 1970s, an effort that continues to the present.

The ICTV is the only body charged by the International Union of Microbiological Societies with the task of developing, refining, and maintaining a universal virus taxonomy.

Viral taxonomy is the scientific process of classifying and naming viruses, organizing them into a hierarchical system based on their characteristics. This system helps researchers identify, study, and understand viruses by grouping them into related categories. The classification is essential for the scientific study of viral diversity, the development of antiviral treatments, and tracking viral evolution.

The ICTV viral classification starts at the level of the realm and continues as follows, with the taxonomic suffixes in parentheses

  • Realm (-viria)
  • Subrealm (-vira)
  • Kingdom (-viriae)
  • Subkingdom (-virites)
  • Phylum (-viricota)
  • Subphylum (-viricotina)
  • Class (-viricetes)
  • Subclass (-viricetidae)
  • Order (-virales)
  • Suborder (-virineae)
  • Family (-viridae)
  • Subfamily (-virinae)
  • Genus (-virus)
  • Subgenus (-virus)
  • Species

As of 2020, all levels of taxa except sub realm, subkingdom, and subclass are used.

Up to March 2020 based on ICTV classification, there were;

6 realms,

10 kingdoms,

17 phyla,

2 subphyla,

39 classes,

59 orders,

8 suborders,

189 families,

136 subfamilies,

2,224 genera,

70 subgenera,

9,110 species

 

Criteria for viral classification

Viral classification is based on:

i. Type of the nucleic acid including the size of the genome, strandedness (single or double), linear or circular, positive or negative (sense), segments (number and size)

ii. Based on the outer covering (presence or absence of envelope)

iii. Capsid shape and Symmetry

iv. Strategy of viral replication- nuclear/cytoplasm

v. Based on the host they affect (Host range)

vi. Based on the site of pathogenicity (Tropism)

 

1. Genome Type (Nucleic Acid Type)

This is one of the most fundamental ways viruses are classified:

  • DNA viruses: Contain deoxyribonucleic acid (DNA) as their genetic material.
    • Single-stranded DNA (ssDNA)
    • Double-stranded DNA (dsDNA)
  • RNA viruses: Contain ribonucleic acid (RNA) as their genetic material.
    • Single-stranded RNA (ssRNA)
      • Positive-sense RNA (+ssRNA) (e.g., SARS-CoV-2)
      • Negative-sense RNA (-ssRNA) (e.g., influenza virus)
    • Double-stranded RNA (dsRNA)
  • Retroviruses: These are RNA viruses that reverse transcribe their RNA into DNA (e.g., HIV).

2. Capsid Shape and Symmetry

The protein shell (capsid) that encases the viral genome can have different shapes, including:

  • Helical: Capsid is rod-shaped and wraps around the nucleic acid.
  • Icosahedral: The capsid has a symmetrical, polyhedral shape with 20 triangular faces.
  • Complex: Some viruses, like bacteriophages, have a combination of icosahedral and helical features or more intricate structures.

3. Presence or Absence of an Envelope

  • Enveloped viruses: Have a lipid membrane surrounding the capsid, usually derived from the host cell’s membrane (e.g., HIV, herpesvirus).
  • Non-enveloped (naked) viruses: Lack this outer lipid envelope (e.g., adenoviruses, noroviruses).

4. Replication Strategy

Viruses are classified based on how they replicate inside host cells. This can involve:

  • Location of replication: Some viruses replicate in the nucleus (nucleic viruses  e.g., herpesviruses), while others replicate in the cytoplasm (cytoplasmic e.g., poxviruses).
  • Use of reverse transcription: Retroviruses use reverse transcription to integrate into the host genome.
  • Baltimore classification: Is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis. By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a distinct group. Seven Baltimore groups are described that take into consideration whether the viral genome is made of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), whether the genome is single- or double-stranded, and whether the sense of a single-stranded RNA genome is positive or negative.
    1. Group I: double-stranded DNA viruses (e.g., herpesvirus)
    2. Group II: single-stranded DNA viruses  (e.g., parvovirus)
    3. Group III: double-stranded RNA viruses (e.g., rotavirus)
    4. Group IV: positive-sense single-stranded RNA viruses (e.g., SARS-CoV-2)
    5. Group V: negative-sense single-stranded RNA viruses (e.g., influenza virus)
    6. Group VI: single-stranded RNA viruses with a DNA intermediate in their life cycle (e.g., retroviruses like HIV)
    7. Group VII: double-stranded DNA viruses with an RNA intermediate in their life cycle (e.g., Hepatitis B)

5. Host Range

Viruses can also be classified based on the types of organisms they infect:

  • Phagina: -Viruses infecting bacteria e.g. bacteriophages
  • Zoophagina: -Viruses infecting animals and human e.g. Pox virus, Herpes Simplex virus, coronaviruses, influenza.
  • Phytophagina: -Viruses infecting plants e.g. Tobacco Mosaic virus (TMV), Tobacco necrosis virus (TNV).
  • Archaeal viruses: Infect archaea.

 

6. Based on site of pathogenicity (Cell or Tissue Specificity)

a) Neurotropic viruses: -Viruses infecting the nervous system e.g. Polio and Rabies

b) Dermatotropic viruses: -Viruses producing skin lesions e.g. Small pox, Chicken pox and Measles

c) Pheumatotropic viruses: -Viruses affecting the respiratory tract e. g. Rhino virus

d) Hepatotropic viruses: -Infect the liver (e.g., hepatitis viruses).

7. Serology and Antigenicity

Differences in surface proteins (antigens) can also classify viruses. This is often used in medical diagnostics to differentiate between strains or types of the same virus (e.g., different serotypes of dengue virus or influenza subtypes like H1N1).

8. Phylogenetics and Evolution

Advances in genomic sequencing allow researchers to classify viruses based on their evolutionary relationships. Comparing viral genomes helps group viruses into families, genera, species, and strains.

ICTV Hierarchical Classification:

The ICTV organizes viruses into the following hierarchical ranks:

  • Order: The highest rank, ending in “-virales.”
  • Family: Ending in “-viridae” (e.g., Coronaviridae).
  • Subfamily: Ending in “-virinae” (e.g., Orthocoronavirinae).
  • Genus: Ending in “-virus” (e.g., Betacoronavirus).
  • Species: Represents specific viruses (e.g., SARS-CoV-2).

 

Figure 1: Classification based on viral nucleic acid, capsid symmetry, outer covering, strandedness and sense/polarity

Figure 1a: Classification of RNA viruses

 

Figure 1b: Classification of DNA Viruses

 

Figure 2: Baltimore Classification

 

Figure 3: Classification based on genome and host

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