Conquest, slavery and emerging infections in South America

As the world grapples - still - with Covid-19, we’re reminded on a daily basis how diseases spread. Central to this is the saying that, wherever they go, people take their germs with them. And that was equally true 500 years ago, when Europeans first landed in South America, taking with them not just their pathogens, but forced labour - slaves - and their germs too. These arrivals introduced novel viruses among the native inhabitants, causing outbreaks of hepatitis B and parvovirus infections among others. How do we know? Because, alongside historical reports that  document disease outbreaks around this time, it’s now been possible to recover DNA from the remains of victims and inhabitants from that era, and not just human DNA - viral DNA too, as Axel Solis and - first up - Daniel Blanco-Melo, explain to Chris Smith…

Daniel - I've been interested in viruses for the longest time looking at ancient viruses and how those infections impacted the emergence of our human defenses. However, teaming with my dear friend, Maria Avila, we kind of teamed up to see what viruses were in circulation during this very particular interesting point in history, which is when the Europeans came and colonized America. So during that time, they not only brought themselves in of course, religion and language, but they also brought different animal species. But of course also pathogens.

Chris - Indeed. Where people go, their infections go, too - don't they? What time periods then does this coincide with - the era you're looking at?

Daniel - When Cortez conquered Tenochtitlan, now Mexico City, it was 1521 and the colony really extended all the way to 1810. 

Chris - And the people who were doing that, where were they chiefly coming from?

Daniel - Well, it's famously known that the Europeans came to colonize America. However, it also coincide with this tragic period in time where the Europeans were also bringing slaves into the Americas. And those were coming from Africa. And that is what is known as the transatlantic slave trade.

Chris - Hence, your starting hypothesis is these people come, they could not just come alone, they bring with them their infections. And if they've brought people who they've enslaved with them infections that might be in those slaves may also have come.

Daniel - Yeah, exactly. Influx of people, influx of animals and influx of pathogens.

Chris - Your co-conspirator in this is Axel! So, Axel, how did you get involved in this study?

Axel - So I wanted to work with viruses. So I approached Maria and Maria told me about this project that she had with Daniel. So I decided to participate with her.

Chris - And what did she give you to do?

Axel - They obtained bones from these skeletal collections. And basically we were extracting ancient DNA and then screen for like these viruses.

Chris - The bones that Maria provided, where did she get them from?

Axel - So we got two skeletal collections. One was from an indigenous hospital in Mexico City. The other was from the south of Mexico City from, Coyoacán, a chapel. Coyoacán was one of the few Spanish settlements in Mexico City. And this hospital was treating people that died from epidemics.

Chris - Critically, these are archeological sites and therefore you must get presumably some sort of dating information that goes with the skeletons. Do you know where in the timeline they come from?

Axel - Yeah, we performed some carbon dating analysis and it suggests that these individuals survived during the first decades of the slave trade period.

Chris - And that would be what - the 1500s?

Axel - Yes. The first decades of contact.

Chris - So this is mapping onto that time that Daniel's told us is when we know that there were influxes of people from Europe and potentially bringing in other peoples from other parts of the world with them, potentially as slave labor. Do you know the individuals that you looked at the bones? Do you know whether they were Europeans or were they Africans? Asians? Can you tell us anything about that?

Axel - Yeah, so we performed the genetic ancestry of these individuals and they were, in fact, Africans. In the case of the individual from Coyacán, we found that it has a genetic composition similar to an indigenous individual.

Chris - So, Daniel, this fits the point you're making that people came from Europe, but they brought other civilization members, other populations with them. When you went through and asked, apart from human DNA, what other pathogens or viral or bacterial genetic information was in there, what did you find?

Daniel - We were able to enrich and completely reconstruct the entire genetic structure of three human parvoviruses, as well as hepatitis B virus.

Chris - Do you know if people caught these infections from the locals or did they bring them with them? Because that's the critical question, isn't it? Where they harboring these viruses when they came to the Americas?

Daniel - That is exactly the critical question and the way that we tried to answer it, when we compared the sequences of these ancient viruses to sequences that are from modern-day epidemiological analysis, what we were able to find is that the viruses belong to viruses that came from Africa. So they have an African origin, these types of viruses.

Chris - This sounds tantalizingly, Axel, then like your hypothesis, that when people come, they bring new infections with them, it sounds like that this could be the smoking gun.

Axel - Yeah, it's not the first time that somebody reported that viruses were introduced to the Americas from Africa. But this is the first time that we use ancient DNA to try to solve these questions. This is important when we consider also the context of these archeological sites. In the case of the hospital, this hospital was very important because there's an epidemic that killed millions of people in the Americas, the individuals have their body yellow and also their eyes. And they have an enlarged liver, very similar to the symptoms from hepatitis B virus. So it opens the question about the role of hepatitis B virus during, like, this epidemic.

Chris - There's also been speculation in the past that the immune systems of people who were on remote continents away from where, you know, humans first evolved, Africa, as we went further from the garden of Eden, as it were people's immune systems became less competent at dealing with the sorts of germs that were circulating in mass population centers like Europe. Does your finding add credence to that - the fact that there do appear to be these enormous epidemics or at least that there were big outbreaks potentially among the locals, which were spawned by people bringing these sorts of diseases with them.

Daniel - Yeah, absolutely. That is exactly where we want it to take now, these types of studies to really understand how the native population reacts to this influx of pathogens. However, having said that it's not like their immune system is different. It just has not been in contact with them. And therefore there is no immunity to these pathogens. So they're a bit more susceptible because their bodies are starting to learn about this new pathogen. So at the beginning of those introductions there, you see the massive decay in the native population in the Americas. And it's been documented that they are coming from these great epidemics, which are of unknown origin right now. But now that we are able to isolate viral sequences from ancient remains, now it opens a new possibility to really pinpoint which viruses were responsible.