Ron writes:
Hi Twiv team I am in a discussion with a friend who insists that vaccines are designed to “prevent“ infection, and I remember this issue as vaccines are designed not to prevent infection of a pathogen, but rather to minimize disease after an individual has been infected. In our discussion, my friend used polio vaccine as a example of a vaccine that prevented infection “so who better to ask than all of you and of course, Vincent“. My friend’s point is of course, that the Covid vaccine should not be called a vaccine because it doesn’t prevent an individual from being infected and that’s why people get sick still, even after receiving the vaccine. Hopefully you can help clear this up for both of us.
Ron
Lisa writes:
Hello TWIV gurus,
I have forwarded slides from the most recent CDC One Health Partners webinar. Beginning on Slide 19, the current known non-human species that have been naturally infected with SARS-CoV2 are outlined. I thought you might be interested based on the discussion in Episode 985.
Thank you very much for all you do.
Lisa Last, DVM
Eugene, OR
41oF and sunny this minute, but likely to change very soon. 🤣
Jens writes:
Dear TWiV Team,
I feel like batman being summoned via a light in the sky – so since you called…
In TWiV #973, you replied to a letter by Joe who asked about the differences between species, strains, and variants. You answered that a variant is basically like “You, Kathy, Dickson, me”. That is incorrect, in particular regarding SARS-CoV-2 (but also Ebola virus etc.). Variants are defined genetic lineages of a virus that have certain constellations of (within the lineage) fixed (i.e., selected-for) mutations. SARS-CoV-2 variants Alpha, Beta, … Omicron are such defined lineages and each lineage is represented by thousands/millions of individual viruses that have additional genetic changes that come and go. In short, you and I may be infected “with Omikron”, but that does not mean that you and I have the same virus – once sequenced, the virus that infected us will have the necessary genetic makeup to make it SARS-CoV-2 and to assign it to variant Omikron, but once the genomes are aligned you may find many nucleotide differences nevertheless.
Subvariants therefore are new lineages within a defined lineage that gained additional fixed mutations on top of the variant-defining trait – and once again the sublineage is represented by thousands of viruses that are variable on the individual level but share a common genetic trait. To go back to you guys: all of you are *isolates* of “human” and you may or may not belong to the same genetic lineage.
[vr: disagree, a variant is any isolate with a genome change. You are redefining variant in light of SARS-CoV-2]
In TWiV #979, you began discussing realms and megataxa in viruses and finally called me out in apparent desperation. Given that yours is a podcast all about viruses and given the seismic shift that has happened in recent years regarding our understanding of the virosphere, maybe dedicate some time on an episode on this topic, going through and summarizing some crucial papers, as it this is way too much for a reader’s letter:
https://pubmed.ncbi.nlm.nih.gov/32132243/, “Global Organization and Proposed Megataxonomy of the Virus World” by Eugene Koonin et al. is the most important of them, as it lays the groundwork for what now are the ICTV-accepted realms (four proposed at that time; later an additional two were added, see also https://pubmed.ncbi.nlm.nih.gov/34011550/, “Adnaviria: a New Realm for Archaeal Filamentous Viruses with Linear A-Form Double-Stranded DNA Genomes” by Mart Krupovic et al.; Ribozyviria was the lastest added). Eugene’s paper also discusses the polyphyly of viruses. The meat of the paper, i.e., the framework for the current virus megataxonomy is laid out in Figures 11 and following
https://pubmed.ncbi.nlm.nih.gov/34468181/, “Viruses Defined by the Position of the Virosphere within the Replicator Space” by Eugene Koonin et al. was the development of the now accepted ICTV definition of “virus”, as well indirectly the definitions of “viroid”, “satellite nucleic acid”, and “viriform” (see current version of the taxonomic Code, Rules 3.23-3.26; https://ictv.global/about/code). This paper also defines the terms “virosphere” and its subdivisions into “orthovirosphere” and “perivirosphere”. And if you haven’t yet heard the term “viriform”, I would recommend https://www.mdpi.com/2218-273X/13/2/289, “Viriforms—A New Category of Classifiable Virus-Derived Genetic Elements” by myself (ha!) and Eugene as a primer.
As candy for dessert, I would recommend going over https://pubmed.ncbi.nlm.nih.gov/36097140/, “The global virome: How much diversity and how many independent origins?”, again by Eugene et al., which discusses the questions how many realms there really may be.
The term “realm” was chosen instead of “domain” because the genetic variability even within one virus clade that now is a realm is much higher than in the entire organismal tree of life and people thought that “domain” then would be misleading. And, correct, viruses do not fit *into* the tree of life – remember TWiV episode #357 with me, which was called “Mistletoe *on* the Tree of Life”? Also see https://pubmed.ncbi.nlm.nih.gov/35218347/, “Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere” by Anja Spang et al.
You also have overlooked the massive expansion of prokaryotic RNA viruses starting with https://pubmed.ncbi.nlm.nih.gov/32083183/, “Expansion of known ssRNA phage genomes: From tens to over a thousand” by Julie Callanan et al. (leading to this https://pubmed.ncbi.nlm.nih.gov/34747690/, “Leviviricetes: expanding and restructuring the taxonomy of bacteria-infecting single-stranded RNA viruses”, also by Julie et al.) and most recently the fantastic predecessor paper of the one you discussed in the episode , i.e., https://pubmed.ncbi.nlm.nih.gov/36174579/, “Expansion of the global RNA virome reveals diverse clades of bacteriophages” by Uri Neri et al., which increased that clade to tens of thousands. If interested in general RNA virus diversity, https://pubmed.ncbi.nlm.nih.gov/36511833/, “The RNA virosphere: How big and diverse is it?” by Guillermo Dominguez-Huerta et al. might be great fun on top of that.
Several of the papers above also address all kinds of cute things, such retroviroids, satellites, virophages, all kinds of “-posons” etc. to assimilate all the vast new knowledge that has been accumulated recently by the various major players in this field (Eddie Holmes, Matt Sullivan, Simon Roux, Curtis Suttle etc. etc. etc.) and their many colleagues. Together, this should be sufficient for a short discussion to frame what virology has become 😊
And if you guys need a quick re-review on how the ICTV works again and on all the ranks and the new binomial species nomenclature etc., there is a great summary article about to be published (February 13) in PLoS Biology, written by the ICTV Executive Committee and additional colleagues.
Cheers,
Jens
PS:
I always say “aubergines”. But “eggplant” is a wonderful example why viruses don’t have to be renamed just because the name label might be “misleading” or “incorrect”. No eggs in eggplant and yet Americans seem to do just fine with the term…
John writes:
Dear TWIVer’s,
After hearing your musings on the root cause of the world’s problems in epitope 1013, I came across this interesting article that cites Blaise Pascal who once wrote, “All of humanity’s problems stem from man’s inability to sit quietly in a room alone.” A 2014 study lends support to this idea:
The money quote from the article with a link to the study in Science:
“A recent study in the journal Science found that many people choose to self-administer an electrical shock rather than sit quietly in a room alone with their thoughts.”
—
John Shea, SJ, Ph.D.
Jesuit Community Creighton University
Alan writes:
Hello TWiV Team!
Here’s a very on-topic and excellent video from last year that not only provides a great introduction to viruses for non-scientists, but also covers the geobiochemical effects of viruses in the ocean, which was featured in TWiV 1011.
It’s a SciShow epitope: https://www.youtube.com/watch?v=cUP8bGWln6M
As always with SciShow videos, all of the material—research papers and articles—are linked in the show notes.
Looking forward to TWiV 1012!
All the best,
Alan
P.S. Count me among the 50+% non-scientists who listen to TWiV on the regular. My TWiV Saves Lives “research paper” that you enjoyed was a way of saying thank you for all your education efforts.