TWiV reviews RFK Jr’s demand to revoke polio vaccine, Wuhan lab samples do not include close relatives to SARS-CoV-2, using artificial intelligence to discover the RNA virosphere, and biomarkers that discriminate early and late phases of respiratory virus infections from a SARS-CoV-2 human challenge study.
Hosts: Vincent Racaniello, Alan Dove, Rich Condit, Kathy Spindler, and Angela Mingarelli
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Links for this episode
- Support science education at MicrobeTV
- ASV 2025 7:23
- RFK Jr lawyer wants revocation of polio vaccine (CNN) 11:05
- Wuhan lab has no samples close to SARS-CoV-2 (Nature) 13:46
- Using AI to discover RNA virosphere (Cell) 16:33
- SARS-CoV-2 human challenge reveals biomarkers (Nat Comm) 39:51
- Does this challenge study pass the smell test? (TWiV 863) 47:05
- Letters read on TWiV 1179 1:24:55
- Timestamps by Jolene. Thanks!
Weekly Picks 1:32:16
Angela – Science’s 2024 breakthrough of the year, Lenacapavir “the long shot”. NEJM papers with Lenacapavir trials: one and two.
Kathy – Bach Toccatta and Fugue on floor piano
Rich – Never Cry Wolf
Vincent – Common Raven and American Crow
Listener Pick
Jaan – Meute (one, two, three)
Intro music is by Ronald Jenkees
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Content in this podcast should not be construed as medical advice.
The post TWiV 1179: Dark matter and warning signs first appeared on This Week in Virology.
Is it necessary to make a survey of giant viruses in different parts of the world? and also, what approach is better to use: metagenomics – searching for similarity with already known giant viruses, different from others or trying to find new ones in the bottom samples and protists by using microscopy?
If you asked the meeting participants they would say that we need to look all over the world, because you never know what you might miss by looking only in one area. That’s a lot of space but I don’t know how else to make sure we get a good sampling. I suspect that metagenomic analyses would be the method of choice, but not just by looking for similarity to known giant viruses – remember, Pandoravirus is barely similar to anything. You have to exclude what sequences we do know and look at the rest. But perhaps someone from the giant virus meeting will chime in here and give a good answer.
Thank you. That’s so interesting groundbreaking topic. And nobody wants to start studying it in my country. It seems that researchers may not completely comprehend the reasons to study it in the rest of the world. Personally I think the data about how these giant viruses are distributed throughout the world (phylogenetic analyses linked with geografical positions) may be supporting to understand their evolution and coevolution with the hosts. Furthermore, new questions may be elicited from such data. Or the direction of my thoughts is wrong? I try to find some advantages or disadvantages of such kind of survey.
Both approaches are important and I wouldn’t call one “better” than the other. It really depends on the question you’re asking. If you want to find relatives of known genomes, metagenomics will give you tons of useful data. But as Vincent said, this will not help you with the large percentage of unknown sequences that dominate metagenomic surveys. We need to have at least one representative for each major type of virus in culture, so we can link the genome data to a host and other information about the virus (virion structure, infection cycle etc.). And this is not just true for genes that are exclusive to giant viruses and have no recognizable homologs in cells.
Take the DNA repair gene MutS for example. Before the Mimivirus genome was sequenced, any MutS homolog from a Mimiviruses found in metagenomic datasets would have been classified as coming from a bacterium or a marine invertebrate. Now we know that giant DNA viruses have their own distinct version of MutS, which can even be used as a marker gene to identify giant viruses (see Ogata et al, ISME J 5:1143-51, 2011).
Isolation and metagenomics complement each other. Laboratory isolation of new viruses is cumbersome and involves a great deal of luck, but once you have a new virus in culture, you can characterize it in detail and then search for relatives in metagenomic databases.
Metagenomics is high-throughput and will give you millions of gene sequences from a certain environment, but without cultured representatives you won’t be able to interpret the data.
So if viruses have no ‘desire’ to regain functionality they have shed and learned to hijack something else’s, does this mean Mimiviruses are in a transition phase of minimizing their genome? Or are they keeping the functionality they currently have because there’s less selective pressure that way? I’m sorry if I missed this in discussion.
This is indeed one hypothesis about giant virus evolution and there is some experimental evidence that the genome termini of Mimiviruses are prone to rearrangements, including large deletions. See TWiV 139 for the full story. However, it is difficult to generalize, as giant viruses seem to inhabit a diverse range of environments, which influences the kind of selective pressure a given virus population will experience. Hence different genes will be important to reproduce in different environments.