The ICTV states on their homepage that taxonomy lies at the "uneasy interface between biology and logic". The latter is dependent on the former, not just in taxonomic classification, but in interpretation of biology (ie: research papers). Linking specific structures as viral tropistic adaptations to host factors requires a certain leap of faith, one the researcher may be willing to take, because finding them is hard enough as is filling the gaps in a paper's relevancy or coherence.
To make a broader statement comparing genetic makeup conferring tropisms from one virus to another I imagine would cause great unease. The practice of viral taxonomy not only utilizes incomplete information to draw conclusions, it subverts importance in information that is missing (there is a lot). Perhaps there is more conjecture than logic. These are ideas I had while doing it review for the capripoxy genus, within an hour finding evidence questioning their grouping of species. My takeaways from just two of many-
In 'The Molecular and Cellular Aspects of the Serpinopathies and Disorders in Serpin Activity', Gary A. Silverman and David Lomas group the triplet codes of a single amino acid sequence in P1 residues at serpin reactive center loops with genera in the poxviridae family. They then then analyze the similarities/differences within these groups. The orthopoxvirus P1 Asp serpins formed orthologus gene clusters, whereas species within the capripoxy genus were strikingly heterogenous. Because serpins are derived from hosts, species within orthopoxvirus likely share common ancestry. The capripoxy likely do not.
Another article compared the viruses within the capripoxy family and found a disruption in 9 genes virulence and host range functions in the sheep and goatpox virus that were intact in the neethling virus. This may indicate a common ancestor between them and a virus very similar to, or perhaps identical to the neethling virus. Also, the neethling virus shares many similarities with the Leporipoxvirus in genes that likely confer tissue tropsim, suggesting further a different lineage history.
I'm just curious if inconsistencies like this are found within other families. If so, should viral taxonomy be taken with a grain of salt?
1. https://books.google.com/books?id=WxNhDQAAQBAJ&pg=PA164&lpg=PA164&dq=small+pox+cow+pox+variola+ancestor+lumpy+skin+disease&source=bl&ots=1a234Vsswf&sig=B82v9C3fmfLXY9MPFncZrbJy3cQ&hl=en&sa=X&ved=0ahUKEwjL_IGpurbQAhUFTCYKHVzbABgQ6AEISDAG#v=onepage&q&f=false
2.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC251106/
3.asmorg/content/76/12/6054)
https://www.researchgate.net/deref/https%3A%2F%2Fbooks.google.com%2Fbooks%3Fid%3DWxNhDQAAQBAJ%26pg%3DPA164%26lpg%3DPA164%26dq%3Dsmall%2Bpox%2Bcow%2Bpox%2Bvariola%2Bancestor%2Blumpy%2Bskin%2Bdisease%26source%3Dbl%26ots%3D1a234Vsswf%26sig%3DB82v9C3fmfLXY9MPFncZrbJy3cQ%26hl%3Den%26sa%3DX%26ved%3D0ahUKEwjL_IGpurbQAhUFTCYKHVzbABgQ6AEISDAG%23v%3Donepage%26q%26f%3Dfalse
Robert - be wary of trying to decide the classification of any virus based on only a handful of its genes, as recombination can shuffle genes laterally. Large DNA viruses like the poxviridae keep a core set of essential genes for virus replication that analysed as a group will give a robust phylogeny, but the virulence-related genes come and go over evolutionary time.
DIsclaimer - I'm no expert on poxviruses, but to give you another example of an "inconsistency" - the tick-borne orthomyxoviruses Thogoto and Dhori are clearly "flu-like" viruses based on the majority of their genes as well as the molecular biology of how they replicate, but somewhere along the line they dispensed with the haemagglutinin gene and replaced it with a glycoprotein pinched from a baculovirus.
Paul
Thank you, Paul. As a second year medical student at the early lit review stages, comments like these help adjust my thinking to better see the forrest from the trees. Tracing the chronology of viral divergence seems fascinating and the process itself seems worthy of examination.
- Badges
- Science topic
- Similar topics
- Biological Science
- Microbiology
- Virology