h2g2 The Hitchhiker's Guide to the Galaxy: Earth Edition

How does one determine whether two viruses are separate species, or subspecies, or the same species with a different genotype?

DNA-testing?

Remember that it's people who divide things into categories, Nature doesn't. You don't have set distinctions between species, between alive/dead, between plant/animal.

I was reading about Dengue virus where it is said that four serotypes of the virus cause dengue fever. A serotype is said to be a distinct variation within a species of bacteria or viruses. Hence the question on viruses. I suppose we need someone with expertise in microbiology and disease. I think we have a few medics and microbiologists on H2G2, but it seems that h2g2 is nowadays a fairly quiet place - although to be fair I wouldn't expect an immediate answer.

It is believed that the dengue virus evolved in the 19th century and one of the deadly strains is supposed to have evolved during about 1907 to1949 ish

Generally with larger critters, we can fairly easily say one is one species, and another is another species, this works fairly well for most multicellular organisms, both being able to look t at them genetically, but also morphology, their ability (or not) to sexual reproduce etc....

With viruses, and bacteria, things get trickier, mainly because they don't do sex the right way... (queue joke).

True some of them can reproduce sexually, or at least by a 'coming together' of two very slosely related (genetically), organisms, but a lot seem to prefer doing it alone, asexually.... then, of course, there is bits of sideways movement of DNA: eg, bacteriophages putting extra bits of DNA into bacteria, viruses stealing bits of the host DNA, or bits of other microorgasims DNA, who happen to be living near by and deviding/reproducing at the same time...

Most viruses of course tend to prefer the asexual route to reproduction, getting their host cells to pump out copies of themselves... then of course there is the matter of random errors in DNA/RNA (depending on what the virus has) replication in the host cells replication machinary... (which may useually involve some elements of DNA/genetic matterial from the virus, causing host cells to produce viral specific proteins involved in their own replication...

Anyhow, this not doing sex properly thing makes it hard to stick with the species and genus etc., way of classifying viruses, so for a lot it comes down to subtypes, serotypes etc...

Of course, if by one or another method, random mutation, taking on of extra genetic matterial etc., one gives rise to a virus which is better suited to its environment than the origional version, its likely to do rather well, and may superseed the origional version/serotypes of the virus.

,From memory, the useual way to determine serotype of the virus doesn't necessarily involve looking at their DNA/RNA (that oughta work well enough though, assuming its been sequenced), instead enzyme linked immunoasorbant-assay techniques (ELISA tend to be used...


The viral envelope (bit like our eukarryoatic cell membrane)) ande the viral membrane proper, contain various proteins, and useually the presence or abscence of certain proteins in these areas, is a good determinant of 'species', or as in this case, serotypes...

Basically you raise in a lab, an antibody to proteins specific to the strain/serotype your looking at, then get all your test tubes and stuff out, and mix these antibodies with your samples of the critter, and using various techniques, measure if there is binding of these antibiodies with the proteins; if there is, then the proteins are present, and if the proteins are present, you've found the serotype to which the antibiodies were raised to attach too... Of course, for a lot of stuff, you can just go buy the monoclonal antibodies, already made, often in hand little strip form, so the test is quite automated ; and it may have the antibodies for several differnt strains/serotypes of the virus, so you can not just look for the one, but identify which serotype it is, rather than just saying yes/no to the one serotype....

I might be a bit out of date nowdays though... maybe its morelikely to be done looking at the den virus RNA, rather than membrane and other proteins, but sometimes I think looking at the DNA/RNA can be too specific; even within serotypes there will be genetic differnces, and this might interfer with correctly identifying the serotype.... Sometimes, also, but I think mainly with bacteria rather than viruses, you can just look for the 'thing' which makes a particular strain/serotype, really nasty (or more nasty than the normal/other serotypes), E.G., one population of the bacteira/virus, learns a new trick to, E.G., produce a really nasty toxin, and this toxin production sets it apart from other serotypes, then you can just look for the presence or abscence of this toxin/protein....

Thanks, I think I understood most of that although there are some bits I would be a little hazy on

Viruses are curious organisms.

From Wiki:
A dengue virus has about 11000 bases.
The rate of nucleotide substitution for this virus has been estimated to be 6.5×10−4 per nucleotide per year.
So that makes about 7 nucleotide substitutions per dengue virus per year (I think). With countless dengue viruses that seems to be a lot of exploration of RNA coding possibilities. No wonder evolution is rapid in the virus world.


I wonder whether viruses actually serve some form of "service" in generating new genes that might be spliced and retained by eukaryotes (etc) - rather than just providing a destructive service.

Oh, Viruses have certainly given us a certain amount of DNA over the evolution of our own genes... Weather its always useful or not I'm not really sure.... Don't forget most of the DNA in our cells is the long bits of so-called junk DNA between the actual genes which encode proteins and thereby perform useful functions... Although its called 'junk DNA', a lot of it seems quite useful, in that its structural and helps in the shape and structure of the DNA... ; when DNA folds inside the cells, this enables, often, the actual coding bits, (I.E., the genes), to face outwards, and so be 'visible' to the various enzymes involved in transcription and replication of the genes, and also in the expression of the genes (so they can be converted from the nucleotide sequence into an amino acid sequence in a protein)...

Don't forget, though, with that rapid rate of mutation in the virus genome, some of the mutations, may result in, a change, which, for example, might change a protein on the virus, which is essential to allow it to bind to the exterior of the host cells its trying to affect, or, affect a protein involved in replication of its DNA/RNA, etc., and so mean that the resultant mutated version of the virus, might actuall be unable to be replicated as it can't enter or find the host cells... Of course, some of the mutations throw up very nasty bits of things, which makes that particular mutation able to kill its host quicker, or cause more disease, easier infection, quicker spreading etc., etc.,....

Also, of course, its these sort of random mutations in some viruses, that can make an animal specific virus, one day randomly get a protein, which could/would allow it to infect human hosts

Not sure if I'm acting as a vector for viruses at the moment... though the antibiotics I'm on are doing a fairly decent job at zapping the bacteria trying to set up home inside me