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
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..
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?