This is some really neat stuff. It’s from a recent episode of This Week in Virology(TWIV), which is generally worth listening to in its entirety, but sometimes their side-topics are so interesting it’s delightful.
[The topic is the kind of viruses that were transported during the triangle trade – it wasn’t just people being kidnapped from Africa to the new world it was also their viral loads.] Full episode: https://www.microbe.tv/twiv/twiv-801/ So, if you examine the bodies of enslaved people who were buried when they died shortly after making the “middle passage” you can extract DNA from inside the cement capsule of their teeth. Each tooth is a little time-capsule that often preserves material that tells about the person’s life.
V = Vincent Racagniello
A = Alan Dove
R = Rich Condit
B = Breanne Barker
@59:46
V: They actually mention the oldest RNA – it’s not very old – that’s been recovered ‘cuz it’s too fragile; I think 1000 years, maybe, that’s the oldest RNA
R: Really wimpy stuff, RNA.
V: But the teeth – getting what’s in the pulp of the teeth is also used to look at plague victims – they pull out the teeth and go “ah there was bubonic plague here, it’s very common.”
A: In this study they point out that a portion of these samples were used for a study on bacterial microbiomes of these people, and that’s been published elsewhere, because these are samples that are not easily available and not replaceable so you want to get as much information as you can out of them.
V: So they selected from this HSJN21 dental samples, which were based on these analyses that suggested an African ancestry and then they also had 5 other additional samples from the La Concepcion chapel 10 kilometers south of the HSJN – which they call the first Spanish settlement in Mexico City after the fall of Tenochitlan. Then they processed the DNA from the pulp and isolated ancient DNA and then they sequence it. They found 17 of these had at least 1 hit to viral DNA, they picked 12 of them for further sampling, and they had reads similar to herpes virus, parvoviruses and pix viruses. They picked 12 samples for further screening, they enriched the DNA, to get more sequences, and made more complete libraries. So they end up having very good coverage for a Hepatitis B genome and 3 parvovirus hits.
R: I was surprised that they didn’t come up with any papillomaviruses but, well, they’re mostly cutaneous, right? So maybe there’s not as much of that in the blood? It could be that the pathogenesis of the papillomaviruses made them less accessible as well. Circoviruses should be there..
V: Yeah…
R: But they’re single-stranded but they must have a double-stranded intermediate …
B: They also talk a little bit about part of the reason they focus on herpesviruses and parvoviruses is that those are the ones where they had the complete genome – they had the genomes of the smaller viruses and could do this work.
(All:) lots of “yeah”s
V: Rich, the parvos, you know, are single-stranded so that’s not a limitation. The Circos should be in there because they’re probably in the blood all the time, so that’s a good question.
A: The other reason that I think they might have been focusing particularly on the hepatitis virus is later in the paper they mention some autopsy reports. Because autopsies were done on these people and they are consistent with hepatitis.
V: The more you look at it, the more you’re going to find these other viruses as well. These are not trivial experiments to do, so they’re not …
A: Like I said, these aren’t samples that you find all over the place…
R: The other thing is maybe hepatitis B and parvo may be more persistent – certainly than pox viruses? So there’s all sorts of considerations.
I pause for a moment to boggle at the way scientists are able to learn about how various viruses spread intercontinentally centuries ago, using the teeth of buried bodies as time-capsules for viral loads.
V: As Rich mentioned earlier, they can evaluate the damage-patterns in the DNA to confirm that they are ancient. C to T changes, mutations near the 5 prime end, symmetrical G to A near the 3 prime ends, which you would expect, so these are ancient genomes and as I said they reconstructed 3 parvovirus B-19 genomes and an ancient hepatitis B genome. The hepatitis B genome sequence is typical of genotype A and genotype A has a broad presence in Africa, it’s been on that continent for a long time – there’s a sub-genotype called A4 which has been found in Africans living in Belgium and never found in the Americas. So that’s great. If you now find it in buried people, it must have come over from somewhere else. The B the parvovirus genomes, there are three of them that have long letter/number names they seem to be close to genotype 3, type 3A is mainly in Africa and 3B has been proposed to spread out of Africa more recently. So, essentially, the phylogenetic analysis of these genomes suggests that they originated in Africa. It doesn’t mean that those people who were buried came over from Africa, but the viruses in them came from Africa.
That’s some sleuthamacatin’. There’s another bit later where they talk about @1:19
V: They do point out that the slave trade carried viruses from West Africa and this provides evidence for that and local circulation. They say “We don’t know exactly when these infections happened.” It’s just an implication of it. But they also say there are other virus infections that may have been brought over including yellow fever and hepatitis C, herpes simplex virus and those are proposed to have been brought from Africa to the Americas as well. Clearly more work needs to be done to look at that. Ancient DNA!
B: This has now made me sad, to think about how you can take a really bad thing and even make it a little worse.
V: It’s very sad. What people do, Breanne, is just terrible. And it continues to this day, unfortunately. It’s not like we outgrew it – we still do the same nonsense.
On a tangent, at the end, Alan Dove has some grim thoughts for us all:
A: You know, at some point, and I think as virologists we all probably understand this but maybe we haven’t admitted it even to ourselves – but, at some point, we’re all going to get this virus. Am I out on a limb, here?
R: No, I’ve been thinking the same thing.
V: We may have already gotten it!
A: My wife’s going to get it, my daughter’s going to get it, my suriving parents are going to get it – which is maybe a little scary – we’re all going to get it, even if we’re fully vaccinated. The vaccine is not 100% and it’s not going to last forever. Eventually, we will get infected with SARS COV-2, probably within the next couple years. So the question here is should we have emphasized masks more and avoiding the virus? I don’t know, because at some point we’re going to have to say we’ve done all we can and you’re going to face the virus with whatever immunity you have and, if you’ve been fully vaccinated, your odds are as good as they’re going to get. We’re not going to get better vaccines – these vaccines are fantastic – I don’t anticipate that improving, the state of medical care is about as good as it’s going to get and this is what we’re faced with. We’re all going to get it and you can get it vaccinated or unvaccinated but you’re gonna get it.
I just scheduled myself for a 6-month booster shot because, why not?
I just recently got my booster shot, and it was the first time I experienced a side effect from a vaccine. The first two doses (pfizer-biontech) didn’t cause and adverse reactions, and I’ve never had reactions to other vaccines, even tetanus and anthrax, which both seemed to bother a lot of people.
My reaction was pretty mild, set in about a day later, and only lasted a day. Got the Johnson&Johnson booster in the afternoon, and the next day I was really tired and a little cold, and just not feeling quite right. I probably could have worked through it if I needed to, but things at work are slow, and I have the sick leave, so I took the day off in advance, and I’m glad I did. I think most of my coworkers had similar reactions, the booster seemed to give most of them more severe side effects than the second dose, but also much shorter, just lasting a day or two.
Hope you experience minimal side effects and recover quickly, and hopefully people in your area aren’t being too contrarian…
It takes a lot of work to transcribe a podcast, so only a total wowser would gripe about the spelling of “hepatitus” (5 times!).
We’re not going to get better vaccines …
Why not? Thousands of experts are already hard at trying to improve the several first-generation vaccines, with very specific goals.
Pierce R. Butler:
Why not?
The effectiveness of the current vaccines is basically as good as vaccines get. We’ll have different vaccines for variants but they won’t be better – just different.
I remember when the pandemic started, Vincent said we’d be collectively thrilled if there was a 60% effective vaccine. We’re collectively spoiled by how good these are – and it’s just more egregious that the republicans decided to make a pandemic go endemic.
Marcus@3:
Let me engage in some “idle speculation” here: What if they could develop a vaccine (and with all the DNA/RNA advances, I would not put it pas them) that constantly reinforced the T-cells (or whatever the anti-bodies are)? The idea is something that would stay in the body for an extended period pumping out a low level of the nasties so the vaccine would not lose its effectiveness as quickly as it does now. (And you would not need continuous boosters.)
Let’s say a very good vaccine reduces infection by 90%.
Let’s also say the omicron variant increases transmission – infectiveness – so that VG vaccine now only protects by 80%.
Now let’s say a new omicron-optimized 2nd-gen vax gets that up to 90% again.
So the new infection-reduction rate is exactly the same – but only by that logic can you claim it’s not “better”.
As for the Republicans, last I heard no one has discovered better-than-placebo preventives, therapeutics, or cures.
Marcus Ranum @ 3
There could be better vaccines for Covid, the nasal spray vaccines that are being researched on and tested might be able to create antibodies in the nasal mucous membranes, thus being more effective in stopping people from being infected.
https://www.nih.gov/news-events/nih-research-matters/intranasal-covid-19-vaccine-effective-animal-studies
https://med.stanford.edu/news/all-news/2021/11/effort-to-develop-covid-vaccine-nasal-spray.html
(I must say that gold nanoparticles in the nose feels like an icky and expensive thing.)
https://www.helsinki.fi/en/news/healthier-world/finnish-coronavirus-vaccine-developer-rokote-laboratories-finland-secures-significant-funding
from quoted text in OP;
Hell, I thought that was obvious from the beginning. I’m just thankful that the 20 years spent developing mRNA vaccines had reached the stage where such a highly effective vaccine could be introduced so rapidly.
I thank everyone who worked on that task over the last 20 years. They certainly have my gratitude.
ahcuah@4:
That’s probably a very good way to develop tolerance.
Developing long-term, low-level “vaccine boosting” isn’t something that’s been seriously investigated by the scientific community (to the best of my knowledge). It doesn’t really solve any problems that we have with current vaccines, since it isn’t much trouble for most people to get booster shots every so many years.
Rumors of COVID vaccines losing effectiveness have been greatly exaggerated [CDC]. The emergence of Delta has probably reduced their effectiveness at preventing infection, but they remain just as effective against hospitalization and death.
I agree with Alan Dove, I don’t think we’re going to see anything beyond marginal improvements from the current vaccines. 90% efficacy is already impressively high.
I disagree on a couple of point with the last quoted paragraph.
1) Vaccines – As others have mentioned, vaccine coverage may wane as the virus mutates, or recover when new vaccines are brought to cover new variants (classic arms race), and I have seen the articles about nasal vaccines being better at stopping spread.
In addition, protein-based vaccines, as opposed to RNA-based vaccines, may be “better” in terms of being less expensive to manufacture, and easier to distribute due to not needing strong refrigeration.
Furthermore, recent work has been published on the rare blood clots caused by adenovirus-based vaccine (Astra Zeneca, Johnson & Johnson). Scientists identify reaction that may cause rare blood clots after AstraZeneca Covid vaccine
This could potentially lead to the ability to predict who would have a bad reaction, to mitigate the reaction, or to possibly create adenovirus-based vaccines that do not cause the reaction.
2) Treatments – new treatments have been recently introduced; some have been approved and some not. This includes fluvoxamine and the antivirals molnupiravir* (nucleoside analog) and Paxlovid (protease inhibitor).
Also consider that the monoclonal antibody treatments (e.g. Regeneron) could suffer reduced efficacy through the same mechanism as the vaccines do as the virus mutates.
* A recent report says the efficacy of molnupiravir is not as high as originally reported. Still, it is somewhat helpful.
Reginald Selkirk @ #9: The protease inhibitors are the truly good news. They have broad effectiveness (not easy for viruses to mutate to avoid them), can be taken by mouth in pill form, unlike antibodies, and they are safer and have fewer side effects than nucleoside analogs.
1) Vaccines – As others have mentioned, vaccine coverage may wane as the virus mutates, or recover when new vaccines are brought to cover new variants
I know. But it’s not likely that new vaccines will be more effective than the amazingly effective 97% or thereabout of the first generation vaccines.
I’m not saying there won’t be new techniques and vaccines, and that they won’t be great – it’s just that where we already are is kind of at the higher limit of greatness. Given that the republicans have managed to fuck that up, it’s not going to get any better than it is, although getting rid of republicans would probably be the next most optimal thing we could do to improve our response to COVID-19.
Ice Swimmer@#6:
There could be better vaccines for Covid, the nasal spray vaccines that are being researched on and tested might be able to create antibodies in the nasal mucous membranes, thus being more effective in stopping people from being infected.
There could be better, but even a jump to a completely perfect 100% effective vaccine wouldn’t be much better than what we currently have because there are jackassess who would resist even a perfect vaccine. What we’ve got is close enough to perfect for all intents and purposes.
Now, if someone could make a cocaine-flavored nasal spray vaccine, then maybe the republicans would be all over it.
ahcuah@#4:
What if they could develop a vaccine (and with all the DNA/RNA advances, I would not put it pas them) that constantly reinforced the T-cells (or whatever the anti-bodies are)? The idea is something that would stay in the body for an extended period pumping out a low level of the nasties so the vaccine would not lose its effectiveness as quickly as it does now.
Then you’d have cured herpes and they’d build a statue in your honor. Except for the republicans, who’d burn you in effigy for making people’s sex lives better or something.
Pierce R. Butler@#2:
It takes a lot of work to transcribe a podcast, so only a total wowser would gripe about the spelling of “hepatitus” (5 times!).
I thought they were referring to the Roman version, Hepatitus Maximus.
Fixed.
No, seriously, I was just brain-farting like mad because I hadn’t had my covfefe yet.
But that 97% effectiveness is against the original form of the virus and is not transferrable to variants. The original vaccines which are now available are excellent against the original virus, somewhat less effective against delta, their effectiveness against omicron is an open question. The same qualification goes for any “natural immunity” a person acquires through becoming infected, and quite probably to the effectiveness of the monoclonal antibody treatments.
So the original question of “we’re going to get the virus, so why not now?” seems to be based on a faulty premise. You could get the virus now, and later, and perhaps again. Compare to influenza for a working example.
But that 97% effectiveness is against the original form of the virus and is not transferrable to variants.
That’s not the point. There isn’t going to be a vaccine that is dramatically more effective than the already dramatically effective vaccine – against anything you can’t go above 100% effective. Nor can you go into negative numbers.
Yes there are going to be effective new vaccines against new stuff but being more or less completely effective is the upper limit on effectiveness. And the republicans are showing us that even a more or less completely effective vaccine can be screwed up by the concerted efforts of armies of propagandized idiots.
@16: “The point” was: given that we will all catch some version of this virus eventually, when is the best time to do it?” Or has the point changed?
Reginald Selkirk @ 17>
because this is no longer about catching “the” virus, but about catching “a” virus, and the number of “a” virus to catch is currently growing.
Wild speculation here, but I’m guessing the best time to catch “a” virus is somewhere in the “late-to-never” category.
You be you, however, and don’t let me stop you from trying to catch every damned variant that pops up. Meanwhile, I’ll be over here being my typical anti-social, hand-washing, fully vaccinated, never-even-had-the-flu, self. And staying the fuck away from people like you…
@18: That question was asked in the quoted portion of the OP, not by me, so your personalization of your attack is entirely misguided.
Reginald Selkirk@#17:
“The point” was: given that we will all catch some version of this virus eventually, when is the best time to do it?” Or has the point changed?
I don’t see anything about ‘when it the best time to do it’ in Dove’s comment.
You can certainly infer that it’s best to be prepared and have your immunity tuned, etc., which just makes sense. What I took from that is that humans should continue to develop effective post-infection responses, e.g.: antivirals, monoclonal antibodies, etc., because the COVID is here to stay and everyone is going to get it, some way or another, eventually. In that sense, the republicans’ dismissal of the pandemic as “just another flu” comes true because it is; it’s just a worse flu but it’s going to be endemic and everyone will get it eventually, maybe multiple times.
lochaber@#18:
never-even-had-the-flu, self
Wow! I’ve had various flus maybe a half dozen times. They get less pleasant as you get older. The last one leveled me for a couple days but my immunity is much better and the last decade or so I’ve been getting the vaccines.
One topic that comes up a lot on TWIV is what does “getting a ${flu}” even mean? From the standpoint of our immune system, we may be exposed to a virus and it starts replicating in us but is crushed quickly by our immune system. We may never know we just “got” the flu. So does “getting a flu”: mean having all the symptoms and downtime, or that we had an immune response that effectively stopped the infection? And, how do we know? I have a friend who’s fully vaccinated [I have no unvaccinated friends, so that’s simple] who turned out to test positive for COVID but never experienced any symptoms except for “COVID toe” (which seems sort of like a shingles reaction) so, it’s not something that the everyday terms we use captures very well.
yeah, granted, I don’t know how many times I may have had the flu asymptomatically, but I’ve never really had flu symptoms. I typically get a minor cold once a year or so, but that’s mostly just a minor annoyance with a runny nose, and maybe a cough. I’ve been pretty lucky that I’m not generally prone to illness or injury, doubly so because I’ve lived most of my adult life without medical coverage. :/
As far as covid, for a while I had to get weekly screenings for my employment, and I’ve also participated in a few research studies, one of which involved submitting blood spots for antibody testing (for research only, and all that…), the last sample collection for that study was immediately before my first dose of the vaccine, and all the (for research only, not official medical advice, etc.) results came back negative.
Pfizer says COVID-19 pill near 90% effective in final analysis
That’s good to hear after the Merck letdown.