Virus Genomes

[lpetrich]

Viruses have a lots of variety of genomes, much more than what cellular organisms do.

I'll be talking about the virions, the virus particles that spread outside of their host cells.

Their genomes can be linear or circular, DNA or RNA, single-stranded or double-stranded, with the single-stranded ones having either positive or negative "sense". Some RNA viruses are copied onto DNA as part of their replication, making them "retroviruses".

 Sense (molecular biology) - RNA has positive sense if it can be directly used as messenger RNA to make the target protein, and negative sense if one has to make a copy of it for that. DNA has positive sense if RNA copied from it can be directly used as messenger RNA, and negative sense if either the DNA or the RNA has to be copied for that.


This is related to the question of the origin of viruses. There are three main theories, theories that are not mutually exclusive, and theories that may involve multiple origin events.

• Primordial organism
• Degenerate cellular organism
• Escaped transposable element in the genome (transposon)

 

[lpetrich]

Complete genomes: Viruses

With that and Wikipedia, I found

• DNA ds -- variola major virus (smallpox, 185578 nt), varicella zoster virus (chickenpox 124884 nt, a herpesvirus), human papillomavirus (7746 nt)
• RNA, ss, +ve -- rubella virus (9762 nt), Zika virus (21602 nt), yellow-fever virus (10862 nt), SARS‑CoV‑2 (COVID-19 29903 nt), human immunodeficiency virus (AIDS, 9181 nt, a retrovirus), poliovirus (7440 nt), tobacco mosaic virus (6395 nt)
• RNA, ss, -ve -- morbillivirus (measles 15894 nt), mumps virus (15384 nt), Zaire ebolavirus (18959 nt), rabies lyssavirus (11932 nt)

 Bacteriophage - viruses that attack bacteria, with plenty of variation in genome composition, structure, and size.

Viruses at the Tree of Life web project

• Double-stranded RNA Viruses (monophyly uncertain)
• Single-stranded Negative Sense RNA Viruses (monophyly uncertain)
• Single-stranded Positive Sense RNA Viruses (monophyly uncertain)
• Single-stranded DNA Viruses (non-monophyletic)
• Double-stranded DNA Viruses (non-monophyletic)
• DNA-RNA Reverse Transcribing Viruses (monophyly uncertain)

Monophyly: having a shared ancestor in the group, meaning only one origin event.

 

[Swammerdami]

Viruses at the Tree of Life web project

• Double-stranded RNA Viruses (monophyly uncertain)
• Single-stranded Negative Sense RNA Viruses (monophyly uncertain)
• Single-stranded Positive Sense RNA Viruses (monophyly uncertain)
• Single-stranded DNA Viruses (non-monophyletic)
• Double-stranded DNA Viruses (non-monophyletic)
• DNA-RNA Reverse Transcribing Viruses (monophyly uncertain)

In the Baltimore scheme there are seven Groups of virus instead of six.

• III (rotavirus)
• V (influenza)
• IV (coronavirus)
• II (parvovirus)
• I (herpes)
• VI (HIV)
• VII (hepatitis B)

I've shown these groups each with an example and in the same order as Ipetrich's list, except that Ipetrich's final group — "reverse transcribing viruses" — includes both Group VI (single-strand RNA) and Group VII (Double-strand DNA with an RNA intermediate).

 

[lpetrich]

 Baltimore classification

• Group I: double-stranded DNA viruses
• Group II: single-stranded DNA viruses
• Group III: double-stranded RNA viruses
• Group IV: positive sense single-stranded RNA viruses
• Group V: negative sense single-stranded RNA viruses
• Group VI: single-stranded RNA viruses with a DNA intermediate in their life cycle
• Group VII: double-stranded DNA viruses with an RNA intermediate in their life cycle

• DNA, ds -- hepatitis B (3182 nt, RNA intermediate), Epstein-Barr virus (172764 nt, a herpesvirus)
• DNA, ss -- parvovirus
• RNA, ds -- rotavirus (A 18562 nt)
• RNA, ss, +ve -- hepatitis A, C, E, G
• RNA, ss, -ve -- hepatitis D