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In an ideal world, we should be sequencing viruses for each single patient, just like we measure blood pressure.
That does imply that the UK and Netherlands have seen the virus introduced from many sources, which suggests much more widespread transmission than eg New Zealand, which appears to have one lineage.
However, there's probably a huge sampling bias present. Hopefully we can keep doing this sort of genetic lineage testing at greater rates - it's incredibly informative on how it spreads.
For instance, there is a chicken virus (SMAM-1) that unconditionally increases adiposity in the infected bird, even when the chicken is fed the same amount as inunfected chickens. SMAM-1 is zoonotic to humans. It also makes them fat. Several human adenoviruses are suspected of doing similar things. But they have not been studied extensively, because the general prejudice is that people become morbidly obese due to their own lifestyle choices, and therefore excessive adiposity is a condition that should be first-treated with lifestyle intervention, rather than applying evidence-based medicine.
There are still a lot of nonscientific prejudices in general medicine. "Let's sequence all viruses in our patients," sounds a whole lot like "let's wash our hands before touching a new patient, so we don't spread diseases between them," which was once rejected by the experts as implausible hogwash.
Edit: to clarify, I'm aware of the criterion of sexual incompatibility, and that genes don't usually work one-by-one, but still—slapping an arbitrary Latin-ish name on each of the millions of, say, fly species seems of dubious use, at least to an outsider.
With sexual reproduction, individuals can differ genetically but still be compatible, so there is some notion of a pool with a clear boundary. For viruses, this is of course a bit trickier because they "reproduce asexually"[0] and quite rapidly, so mutations happen at a high rate. But one useful property to distinguish them is which receptors (and thus which cells) they bind to, generally affecting what symptoms and diseases they cause.
[0]: Viruses are not considered living things, so the concept of reproduction is already quite a stretch.
That's a model that kind of works most of the times, but not always: the most known example are Bisons and Cows which can breed together and the offsprings are fertile : https://en.m.wikipedia.org/wiki/Beefalo
In fact, most of today's bisons have cows' genes in their genome.
The boundary isn't very clear.
https://en.wikipedia.org/wiki/Ring_species
A can breed with B, B can breed with C, C can breed with D, and D can breed with A.
But A cannot breed with C.
Are A and C part of the same species, or not? These "ring species" occur around geographic rings, such as the Arctic Circle, so each population remains genetically compatible with its neighbors... but not "across the ring".
https://upload.wikimedia.org/wikipedia/commons/thumb/8/8d/Ri...
Perhaps you mean to say that strains should be defined in a fuzzy manner? If so, from my very limited knowledge of systematics, they already are.
I guess ‘behavior and appearance’, mentioned in another comment, are the more practical dimensions, but I still wonder how useful the distinctions are.
The evolution of seasonal influenza viruses - Velislava N. Petrova & Colin A. Russell
I like to think of genes as their amino acid or dna sequence only, and internally whenever I need to manage a ton of sequences their names are just hashes of those sequences.
One interesting thing I remember is that virtually every human over a year old or so is "infected" with at least a handful of viruses for life. The scare quotes are because we really don't know what effect these viruses have on us. They could be beneficial for all we know.
To add further complexity consider that bacteria get infected by viruses (called bacteriophages). All those bacteria inside you are in turn "infected" by viruses. Phages are so numerous that a drop of seawater contains about ten million of them. Also they are literally like microscopic genome injection machines. Look up some pictures and electron microscope images.
> virtually every human over a year old or so is "infected" with at least a handful of viruses for life
That sounds like a very interesting concept, and it's one that I haven't heard of before. If you don't want to write yourself, linking me to some reputable sources would be awesome too.
A large proportion of adults have had it as kids. The immune system fights it off but virus particles can still 'hide' from it and lay dormant inside pheripheral nerve tissue.
A proof of this is 'shingles' in adults. i.e. a virus which probably infected the host +50 years ago and went dormant in their nerves finds the host immune system weak enough to come out again and start replicating.
> Approximately 8% of the human genome is made up of endogenous retroviruses (ERVs), which are viral gene sequences that have become a permanent part of the human lineage after they infected our ancient ancestors.
> ..their expression has been implicated in diseases like autoimmune disorders and breast cancer.
> they can also be extremely useful for human survival. For example, they play a very important role as an interface between a pregnant mother and her fetus by regulating placental development and function.
> It has been suggested that viruses are not only necessary for the existence of placental mammals, but also for the existence of life in general.
The above is from a Medium article by a non-specialist: https://medium.com/medical-myths-and-models/the-human-genome...
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It cites a paper presenting a "virus-first" perspective on the evolution of life:
Viruses and the placenta: the essential virus first view - https://onlinelibrary.wiley.com/doi/full/10.1111/apm.12485
> viruses were involved in most all major transitions of host biology in evolution
I'm learning as I read it, but quoting some passages that seem relevant:
> viruses are fully competent agents and editors of all host systems of instruction (DNA, RNA, epigenetic, translational etc.). Thus, they provide the host with new sources of instruction systems (not errors).
> In addition, they promote network formation by providing coherent societies (quasispecies populations) of agents able to edit host code content (and add new identity) in a diffuse, distributed manner, which promotes the creation of and editing of host regulatory networks.
> Thus, a viral role in the origin of the placental regulatory network can be expected. Viruses possess all the advantages of evolution relative to host: extreme genetic adaptability, extreme diversity, extreme numbers, extreme rates of genetic exchange, tolerance for ‘unfit’ variation, and the ability to reassemble from cryptic or ‘dead’ parts. They can transition between the chemical and living world.
> ..most initial genetic and selective events that transform host regulatory complexity are usually ‘pushed’ by virus action in a general direction of increasing complexity.
> Hence, we must always consider how any virus action on host will affect virus–host survival in their respective virosphere or virus habitat (e.g., reproductive tissue).
> A most significant development would be the emergence of a stable persistent relationship between virus and host as this represents a virus–host symbiosis that now protects the host form the same and often other lytic (disease causing) viruses.
[0] https://www.sciencedirect.com/book/9780123737410/viruses-and...
Edit: https://www.amazon.com/Planet-Viruses-Second-Carl-Zimmer/dp/... might be good, haven't read it though
I've read it and (excuse me) it's fucking fanstastic!
Short and sweet, and mind-blowing on every page.
https://en.wikipedia.org/wiki/Virophage
Sure would be convenient if we had a predator for out most recent emerging predator. Big ask when putative prey has only been in existence for about three months in its current form though..
In other words, it becomes a new species when there's a change to the phenotypic traits above.
Sometimes two different viruses infect the same cell and we get a hybrid. Doing that in a lab and looking at the offspring vitality rate would be interesting, and mathematically coherent.