PhiBabs935
commented
3 years ago Current definition for antigenic drift:
antigenic drift =def Antigenic variation involving the gradual accumulation of small alterations in the antigenic determinants of a virus, due to the gradual accumulation of minor mutations in the virus genome, which leads to decreased recognition of the virus by the immune system.
I should note that another route to go in for 'antigenic shift' is this:
Perhaps rather than saying it is i) a type of virus reassortment; or ii) a separate process that is caused by virus reassortment, we could say that iii) it is a process involving virus reassortment as a process part. (We could say something similar for 'antigenic drift' and the process of accumulating viral genome mutations)
Honestly, when I read through the literature, it is not clear to me whether ii) or iii) is definitively reflected by the literature.
Antigenic shift depends on virus reassortment, a term we should add to VIDO. I am currently thinking something like this:
virus reassortment =def Genetic recombination involving the exchange of entire viral genome segments that are released into a host cell when it is co-infected by two or more segmented RNA virus strains, resulting in the formation of novel viral progeny inheriting genome segments from multiple parental strains.
*Note on the use of 'genetic recombination'. This is a broad term used by scientists for any exchange of genetic materials between two parents resulting in offspring with novel straits. Unfortunately, there is no existing ontology term for this broad class. The closest thing is GO's 'DNA recombination', [http://purl.obolibrary.org/obo/GO_0006310] which is reused by many ontologies. This term raises a serious issue of its own though:
DNA recombination =def Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
The problem is the first line of this definition is so broad that it seems to includes viral RNA reassortment, which itself is a process of gene reassortment resulting in viral progeny with a new genotype. Thus resulting in the misclassification of RNA reassortment as a type of DNA recombination. It seems to me that this definition for DNA recombination would be more appropriate for the more general term 'genetic recombination'.
Related, we will need to distinguish 'virus reassortment' from 'RNA virus recombination'. The latter is a term used by scientists to describe a process that is mechanistically different from virus reassortment; it is a genetic recombination process, occurring during host cell co-infection, involving two or more non-segmented viruses, viruses with a single genome segment. In this case, exchange of genetic material occurs within a single genomic segment. Thus, while reassortment is a type of genetic recombination, it is NOT a subclass of what virologists call ‘RNA virus recombination’. Reassortment is exclusive to RNA viruses with segmented genomes. [See "Why do RNA viruses recombine"; PMC3324781] -That said, I haven't been able to fully wrap my head around the mechanisms involved in 'RNA virus recombination', so I have yet to work on a definition.
Given the above definition of 'virus reassortment', here is my current thinking on defining antigenic shift:
antigenic shift =def Antigenic variation involving a sudden and dramatic change in the antigenic determinants of a virus, owing to reassortment of viral genome segments from segmented RNA virus strains of differing antigenic types, which results in failure of the immune system to recognize the new antigenic type. [based on p. 199 of Cann's Principles of Molecular Virology]
Notice I am asserting antigenic shift as a subclass of 'antigenic variation', which is found in GO [http://purl.obolibrary.org/obo/GO_0020033]. When I first started thinking about antigenic shift on Slack over the summer, I was inclined to say it was a subclass of 'virus reassortment'. When I recently perused the literature on these processes, some discussions do seem to suggest that antigenic shift is a specific case of reassortment, in which case it would be a child of reassortment. But other discussions seem to imply that antigenic shift is an effect of reassortment.
I am currently leaning towards the second view, where reassortment would be the exchange of genome segments, and antigenic shift would be the sudden change in the antigenic phenotypes that, in some cases, is caused by this. But I am not totally sure this. I am conferring with Lindsay. Any thoughts?
Antigenic shift is usually described as a type of antigenic variation (along with antigenic shift), which is why I am inclined to assert it as a subclass of the GO term for antigenic variation. Thus, classifying antigenic shift as a type of reassortment would lead to multiple inheritance, given that reassortment is not a subclass of antigenic variation. [From my understanding of the literature, not all viral genomic reassortment necessarily leads to antigenic shift in phenotypes, but I am not entirely clear on this.]
Related terms
GO has a variety of obsoleted terms that are pertinent to these processes, which I think we should adapt into new VIDO terms (providing cross reference annotations to the deprecated GO terms). This includes obsolete terms for viral genome, segmented viral genome, non-segmented viral genome, DNA viral genome, RNA viral genome, etc. See the deprecated terms here, when you scroll to the very bottom of the search results: http://www.ontobee.org/search?ontology=&keywords=viral+genome&submit=Search+terms
Other relevant literature I have been working from: "Reassortment in segmented RNA viruses: mechanisms and outcomes"; https://doi-org.gate.lib.buffalo.edu/10.1038/nrmicro.2016.46 "RNA Virus Reassortment: An Evolutionary Mechanism for Host Jumps and Immune Evasion"; https://doi.org/10.1371/journal.ppat.1004902