9 ms·

DNA confirms cause of 1665 London's Great Plague

94 points by grahamel 10y ago

runarb 10y ago
Can thus bacterias be dangerous somehow? For example be more potent than the plague that sometimes surfaces today. The people in the pictures do not appear to wear much protection.
- loxs 10y ago
  Not very likely. Most pathogens are only able to survive outside host for only a limited amount of time. I can't give you exact numbers for Yersinia pestis, but it's certainly not centuries. One recent example of what you suggest is the recent Anthrax outbreak in Siberia. Though in this situation we are talking 1) about a pathogen that is particularly famous for ability to form spores and survive a long time and 2) frozen state
- hga 10y ago
  It can no doubt be treated with an antibiotic, and they've probably determined some that work that are also comparable with humans. The real trick is to avoid creating and breathing in an aerosol, which has I'm sure killed more than one researcher before he and his doctor realized what was happening, I heard of one such case in the '70s when I was doing work on E. Coli during a summer program involving salmonella. If you get too much lung tissue---lots of surface area---infected too quickly, well, see pneumonic plague, it's anthrax equivalent, which an Air Force flight surgeon's manual said the first clear diagnostic sign from a patient is his sudden death, etc. And echoing loxs, it's very unlikely they're working with viable bacteria, if they're just sequencing DNA or the like they're far, far from something viable, and I don't believe it creates spores.
  - kijin 10y ago
    I wonder whether these 17th-century strains of bacteria, if they survived and infected someone today, would have less resistance to modern antibiotics than modern strains do. That would make them much easier to manage.
    - fdgdasfadsf 10y ago
      They would - until they started exchanging DNA with modern bacteria.
      - hga 10y ago
        "Modern", sort of, since these antibiotics have generally started from compounds molds etc. use for attacks on bacteria in the same ecological niche, many if not most?? of these counters have by and large been there all along in the modern age of antibiotics, it's just that they now spread a lot more since they give bacteria attacking humans a competitive advantage (few if any of these otherwise help the bacteria, especially unless the plasmid or whatever has a regulatory system to turn it off when not needed). And many can be countered with standard mutations, i.e. something that messes with the surface protein that transports them inside. When I was doing a bit of E. Coli microbiology in the summer of 1977 the conventional wisdom was for a generic antibiotic, like the colicin we were working with, 1 in a million bacterial would spontaneously develop a mutation (which I further did the grunt work to prove the ones we had were of the surface protein type, by and large). Streptomycin, though, would take 1 in a billion.
    - hga 10y ago
      Oh, they survived, if you play around with cute rodents in the right parts of the US West you can get yourself a nice case of the plague, look here for an excellent map and more details on cases and deaths per year etc.: https://www.cdc.gov/plague/maps/ https://www.cdc.gov/plague/maps/ Of course, passing through humans for a half century, and then through these rodents, it won't be quite the same, but...
  - BorisVSchmid 10y ago
    The average length of intact Y. pestis DNA that researchers are capable of extracting from medieval teeth is something in the order of 55 basepairs. To put that into perspective - Y. pestis' main chromosome is a little over 4 million basepairs. So it is only broken pieces of code that they can recover, not the whole, intact bacterium. No risk here. http://www.nature.com/nature/journal/v478/n7370/full/nature10549.html#main http://www.nature.com/nature/journal/v478/n7370/full/nature1...
loxs 10y ago
TL;DR - Yersinia pestis -https://en.wikipedia.org/wiki/Yersinia_pestis https://en.wikipedia.org/wiki/Yersinia_pestis
- pjlegato 10y ago
  So the story is that the Great Plague actually was bubonic plague, as had always been believed.
  - hga 10y ago
    Not exactly always, some of the no doubt distorted by the passage of time reported symptoms don't align with what we know of at least more modern strains of the plague, e.g. stuff more like what's seen with modern hemorrhagic viruses. The official third and most recent pandemic started in 1855 in China and reached the US by the turn of the century, so we have much more solid reports of that strain's behavior: https://en.wikipedia.org/wiki/Plague_(disease)#Third_pandemic:_19th_and_20th_centuries https://en.wikipedia.org/wiki/Plague_(disease)#Third_pandemi...
yitchelle 10y ago
"To reassure anyone worried whether plague bacterium was released from the excavation work or scientific analysis, it doesn't survive in the ground."
jlebrech 10y ago
now we just need to bring it back to save the planet
- tekacs 10y ago
  https://www.goodreads.com/quotes/251836-we-re-so-self-important-everybody-s-going-to-save-something-now-save https://www.goodreads.com/quotes/251836-we-re-so-self-import... (no affiliation or particular interest in George Carlin, just remembered the quote (via Stargate episode 'Brain Storm'))
  - booleandilemma 10y ago
    He's spot on about plastic. They recently discovered bacteria that can degrade it: http://arstechnica.com/science/2016/03/does-newly-discovered-bacteria-recycle-plastic/ http://arstechnica.com/science/2016/03/does-newly-discovered...
    - tekacs 10y ago
      They money quote for me, especially relevant to the parent, is: 'The planet isn’t going anywhere. WE are!' (but yes, more generally short term thinking has to go both ways - we do things that damage the biosphere because we don't think ahead, but we also think far enough ahead to see the ways the planet (or even just our economy/ecosystem) will react - see plastic degrading bacteria, peak oil)
  - dredmorbius 10y ago
    Lifeforms have profoundly changed the Earth before, and will quite likely do so again. Meantime, what humans are doing -- not generally maliciously -- to the planet and biosphere has quite profound effects on what sort of life future humans might be able to live. Looking simply at terrestrial vertebrate biomass gives some indication of this (there are many, many other measures): https://m.facebook.com/notes/paul-chefurka/more-thoughts-on-carrrying-capacity-and-sustainability/10153280720982589 https://m.facebook.com/notes/paul-chefurka/more-thoughts-on-... And it's quite likely that some form of disease will play a large role in reversing this situation.
pjlegato 10y ago
Defoe's account of people being buried in heaps is not necessarily at odds with this excavation of neat coffin burials. The plague didn't instantly reach full intensity on day one. During the early phases of the epidemic, deaths were not yet widespread enough to require mass graves, and burials proceeded semi-normally. During the later, more intense phases, things were much worse. There were both more bodies needing to be buried and fewer available funerary service providers such as coffinmakers and undertakers around to deal with them, since many had themselves either died of the plague or fled the city. Faced with growing heaps of rotting infectious corpses in the streets, hastily dug mass graves were often resorted to by the survivors.
- oh_sigh 10y ago
  I'm sure there were socio-economic factors in burial as well. I suspect the lower class were much more likely to be thrown into mass graves than more well to do merchants
  - pjlegato 10y ago
    Well to do people could also much more readily flee the city to their country houses and escape infection, while poorer people had nowhere else to go.
    - hga 10y ago
      Are you really sure about that? Back then, most would have roots in some farm. Heck, that's true for many many people today, my parents, for example, my mother's home is still a working farm.... Now, if you had to become a serf again to go back to the farm....
      - pjlegato 10y ago
        Of course, not all poor people were confined to the city. As you say, some came from a village where they still had relatives... who were not going to be very happy when a walking disease vector showed up from London and recent exposure to the Great Plague, even if he had a few pennies to contribute to his upkeep. Many were, however, unable to leave because they had nowhere to go. Many came from families that had been in the city for generations and now had no contact with their ancestral villages. There was no Facebook or telephones, and poor people could usually neither write nor afford postage even if they could write. Moreover, families were frequently fractured. Unwanted children were simply turned out into the street, or they might wind up there when their parents died. They then had no clue who their relatives were or what village they'd come from. Classical medieval serfdom had largely died out by the 17th century in England, but the villages were still often grindingly poor. There wasn't enough food to feed the (poor) people who lived there normally. Even during normal times, some penniless distant cousin showing up from London would often be despised as yet another mouth to feed (which is why they'd moved to the city in the first place.) Many others just couldn't afford the trip. The sheer level of extreme poverty in which most Londoners lived at the time is hard to imagine for westerners today. Travel itself was expensive and dangerous during normal times, even for those who had some place to go. The plague made it more expensive and more dangerous. For bottom-rung workers ekeing out a marginal sub-subsistence existence, for people who went hungry several days each week anyway during the best times, hiring a horse was out of the question. Their only option was to walk, perhaps for weeks, with whatever food and money they could carry. Poor people (read: almost everyone) had no access to banking services, so if they lost that money, they were screwed. (This wasn't a problem for most, as they didn't have any money to begin with.) They not only faced highway robbery at every turn, but hostile peasants. No rural village was opening its arms to take in people who had just come directly from plague-ridden London. Such people were seen as dangerous threats, walking disease vectors likely to infect the whole town and kill everyone if they were not immediately driven off. Wealthy people, by contrast, had horses, carriages, servants, guards, private food stores, and gated country estates.
CraigLam 10y ago
It seems to me, the people (inn-keepers, etc) were way too accepting of the refugees. They should have been barricading the town gates. Many of them paid with their lives, and their family's lives. I'm still reading A Journal of the Plague Year, it's fascinating and surprisingly modern in tone, despite the archaic language. It's like one of those zombie apocalypse films, except this guy was living it for real. Recommended :)
- maxerickson 10y ago
  Yeah, the germ theory of disease and quarantine are incredibly valuable tools. It's only in the last 150 years that it gained scientific acceptance.
  - kijin 10y ago
    And when it did, it was such a powerful revelation that it temporarily made scientists blind to any other cause of disease. It took a while for the scientific community to accept that some diseases are caused by a lack of vitamins, for example.
    - hga 10y ago
      Another example might be the over-diagnosis of tertiary neurosyphilis as the cause of mental illness and death, e.g. in some of my recent reading great and legitimate doubt was placed on that being a cause of the death of Winston Churchill's father. We now know there's a host of causes, many of which aren't (yet known to be) infectious. Although we must be careful, in one of my more interesting jobs, building a full text database for Year Book Medical Publishers (a part of Time ... -Life? Time as in the LA Times back then), the leading article for the general book for that year was on the proof of gastrointestinal ulcer being caused by a bacteria. The editor of that entry figuratively smiled about "taking away another disease from" ... whichever specialists assigned it all to stress (which of course can predispose someone to getting an infection).
    - saynsedit 10y ago
      Also some bacteria are actually extremely good for you when you eat them, like Lactobacillus, I.e. What you'd find in kimchi, sauerkraut, pickles. Or that the majority of the human body by cell count is actually composed of bacteria...
Alain-Berset 10y ago
Defoe spells out that many of those who fled took the plague with them into the shires. There were also attempts in each parish to deny that plague was killing people - it was put down to other ailments as far as possible. Seems illogical to us, but if you are inclined to believe plagues are divine punishment, you might hope to get on top of it by prayer and right-living: "trying to cleanse the city in both moral and practical terms".
BorisVSchmid 10y ago
I am happy with every new ancient DNA sequence of plague that becomes available. Combined, they can be used to figure out the way the disease spread across Eurasia and persisted in Europe. That said, I would like these news articles to actually link to the scientific paper, or if the paper is not published yet/still under review, at least mention that.
- hga 10y ago
  Eh, isn't that's kinda hard and dangerous, for the simplest way is to infect animals with these strains, and I kinda doubt any humans are volunteering to play their part.... Just having a DNA sequence is quite some distance from the proteins it produces, the regulatory system that governs what, when and how much, and the effect of them on us poor animals. But this has got to be a hot area of research....
aikah 10y ago
> To reassure anyone worried whether plague bacterium was released from the excavation work or scientific analysis, it doesn't survive in the ground. Thank god, what a relief ! To be frank, looking at the pictures of students working on site,that very question crossed my mind.

94 points by grahamel 10y ago

Can thus bacterias be dangerous somehow? For example be more potent than the plague that sometimes surfaces today. The people in the pictures do not appear to wear much protection.

loxs 10y ago
Not very likely. Most pathogens are only able to survive outside host for only a limited amount of time. I can't give you exact numbers for Yersinia pestis, but it's certainly not centuries. One recent example of what you suggest is the recent Anthrax outbreak in Siberia. Though in this situation we are talking 1) about a pathogen that is particularly famous for ability to form spores and survive a long time and 2) frozen state
hga 10y ago
It can no doubt be treated with an antibiotic, and they've probably determined some that work that are also comparable with humans. The real trick is to avoid creating and breathing in an aerosol, which has I'm sure killed more than one researcher before he and his doctor realized what was happening, I heard of one such case in the '70s when I was doing work on E. Coli during a summer program involving salmonella. If you get too much lung tissue---lots of surface area---infected too quickly, well, see pneumonic plague, it's anthrax equivalent, which an Air Force flight surgeon's manual said the first clear diagnostic sign from a patient is his sudden death, etc. And echoing loxs, it's very unlikely they're working with viable bacteria, if they're just sequencing DNA or the like they're far, far from something viable, and I don't believe it creates spores.
- kijin 10y ago
  I wonder whether these 17th-century strains of bacteria, if they survived and infected someone today, would have less resistance to modern antibiotics than modern strains do. That would make them much easier to manage.
  - fdgdasfadsf 10y ago
    They would - until they started exchanging DNA with modern bacteria.
    - hga 10y ago
      "Modern", sort of, since these antibiotics have generally started from compounds molds etc. use for attacks on bacteria in the same ecological niche, many if not most?? of these counters have by and large been there all along in the modern age of antibiotics, it's just that they now spread a lot more since they give bacteria attacking humans a competitive advantage (few if any of these otherwise help the bacteria, especially unless the plasmid or whatever has a regulatory system to turn it off when not needed). And many can be countered with standard mutations, i.e. something that messes with the surface protein that transports them inside. When I was doing a bit of E. Coli microbiology in the summer of 1977 the conventional wisdom was for a generic antibiotic, like the colicin we were working with, 1 in a million bacterial would spontaneously develop a mutation (which I further did the grunt work to prove the ones we had were of the surface protein type, by and large). Streptomycin, though, would take 1 in a billion.
  - hga 10y ago
    Oh, they survived, if you play around with cute rodents in the right parts of the US West you can get yourself a nice case of the plague, look here for an excellent map and more details on cases and deaths per year etc.: https://www.cdc.gov/plague/maps/ https://www.cdc.gov/plague/maps/ Of course, passing through humans for a half century, and then through these rodents, it won't be quite the same, but...
- BorisVSchmid 10y ago
  The average length of intact Y. pestis DNA that researchers are capable of extracting from medieval teeth is something in the order of 55 basepairs. To put that into perspective - Y. pestis' main chromosome is a little over 4 million basepairs. So it is only broken pieces of code that they can recover, not the whole, intact bacterium. No risk here. http://www.nature.com/nature/journal/v478/n7370/full/nature10549.html#main http://www.nature.com/nature/journal/v478/n7370/full/nature1...

loxs 10y ago

TL;DR - Yersinia pestis -https://en.wikipedia.org/wiki/Yersinia_pestis https://en.wikipedia.org/wiki/Yersinia_pestis

pjlegato 10y ago
So the story is that the Great Plague actually was bubonic plague, as had always been believed.
- hga 10y ago
  Not exactly always, some of the no doubt distorted by the passage of time reported symptoms don't align with what we know of at least more modern strains of the plague, e.g. stuff more like what's seen with modern hemorrhagic viruses. The official third and most recent pandemic started in 1855 in China and reached the US by the turn of the century, so we have much more solid reports of that strain's behavior: https://en.wikipedia.org/wiki/Plague_(disease)#Third_pandemic:_19th_and_20th_centuries https://en.wikipedia.org/wiki/Plague_(disease)#Third_pandemi...

yitchelle 10y ago

"To reassure anyone worried whether plague bacterium was released from the excavation work or scientific analysis, it doesn't survive in the ground."

jlebrech 10y ago

now we just need to bring it back to save the planet

tekacs 10y ago
https://www.goodreads.com/quotes/251836-we-re-so-self-important-everybody-s-going-to-save-something-now-save https://www.goodreads.com/quotes/251836-we-re-so-self-import... (no affiliation or particular interest in George Carlin, just remembered the quote (via Stargate episode 'Brain Storm'))
- booleandilemma 10y ago
  He's spot on about plastic. They recently discovered bacteria that can degrade it: http://arstechnica.com/science/2016/03/does-newly-discovered-bacteria-recycle-plastic/ http://arstechnica.com/science/2016/03/does-newly-discovered...
  - tekacs 10y ago
    They money quote for me, especially relevant to the parent, is: 'The planet isn’t going anywhere. WE are!' (but yes, more generally short term thinking has to go both ways - we do things that damage the biosphere because we don't think ahead, but we also think far enough ahead to see the ways the planet (or even just our economy/ecosystem) will react - see plastic degrading bacteria, peak oil)
- dredmorbius 10y ago
  Lifeforms have profoundly changed the Earth before, and will quite likely do so again. Meantime, what humans are doing -- not generally maliciously -- to the planet and biosphere has quite profound effects on what sort of life future humans might be able to live. Looking simply at terrestrial vertebrate biomass gives some indication of this (there are many, many other measures): https://m.facebook.com/notes/paul-chefurka/more-thoughts-on-carrrying-capacity-and-sustainability/10153280720982589 https://m.facebook.com/notes/paul-chefurka/more-thoughts-on-... And it's quite likely that some form of disease will play a large role in reversing this situation.

pjlegato 10y ago

Defoe's account of people being buried in heaps is not necessarily at odds with this excavation of neat coffin burials. The plague didn't instantly reach full intensity on day one. During the early phases of the epidemic, deaths were not yet widespread enough to require mass graves, and burials proceeded semi-normally. During the later, more intense phases, things were much worse. There were both more bodies needing to be buried and fewer available funerary service providers such as coffinmakers and undertakers around to deal with them, since many had themselves either died of the plague or fled the city. Faced with growing heaps of rotting infectious corpses in the streets, hastily dug mass graves were often resorted to by the survivors.

oh_sigh 10y ago
I'm sure there were socio-economic factors in burial as well. I suspect the lower class were much more likely to be thrown into mass graves than more well to do merchants
- pjlegato 10y ago
  Well to do people could also much more readily flee the city to their country houses and escape infection, while poorer people had nowhere else to go.
  - hga 10y ago
    Are you really sure about that? Back then, most would have roots in some farm. Heck, that's true for many many people today, my parents, for example, my mother's home is still a working farm.... Now, if you had to become a serf again to go back to the farm....
    - pjlegato 10y ago
      Of course, not all poor people were confined to the city. As you say, some came from a village where they still had relatives... who were not going to be very happy when a walking disease vector showed up from London and recent exposure to the Great Plague, even if he had a few pennies to contribute to his upkeep. Many were, however, unable to leave because they had nowhere to go. Many came from families that had been in the city for generations and now had no contact with their ancestral villages. There was no Facebook or telephones, and poor people could usually neither write nor afford postage even if they could write. Moreover, families were frequently fractured. Unwanted children were simply turned out into the street, or they might wind up there when their parents died. They then had no clue who their relatives were or what village they'd come from. Classical medieval serfdom had largely died out by the 17th century in England, but the villages were still often grindingly poor. There wasn't enough food to feed the (poor) people who lived there normally. Even during normal times, some penniless distant cousin showing up from London would often be despised as yet another mouth to feed (which is why they'd moved to the city in the first place.) Many others just couldn't afford the trip. The sheer level of extreme poverty in which most Londoners lived at the time is hard to imagine for westerners today. Travel itself was expensive and dangerous during normal times, even for those who had some place to go. The plague made it more expensive and more dangerous. For bottom-rung workers ekeing out a marginal sub-subsistence existence, for people who went hungry several days each week anyway during the best times, hiring a horse was out of the question. Their only option was to walk, perhaps for weeks, with whatever food and money they could carry. Poor people (read: almost everyone) had no access to banking services, so if they lost that money, they were screwed. (This wasn't a problem for most, as they didn't have any money to begin with.) They not only faced highway robbery at every turn, but hostile peasants. No rural village was opening its arms to take in people who had just come directly from plague-ridden London. Such people were seen as dangerous threats, walking disease vectors likely to infect the whole town and kill everyone if they were not immediately driven off. Wealthy people, by contrast, had horses, carriages, servants, guards, private food stores, and gated country estates.

CraigLam 10y ago

It seems to me, the people (inn-keepers, etc) were way too accepting of the refugees. They should have been barricading the town gates. Many of them paid with their lives, and their family's lives. I'm still reading A Journal of the Plague Year, it's fascinating and surprisingly modern in tone, despite the archaic language. It's like one of those zombie apocalypse films, except this guy was living it for real. Recommended :)

maxerickson 10y ago
Yeah, the germ theory of disease and quarantine are incredibly valuable tools. It's only in the last 150 years that it gained scientific acceptance.
- kijin 10y ago
  And when it did, it was such a powerful revelation that it temporarily made scientists blind to any other cause of disease. It took a while for the scientific community to accept that some diseases are caused by a lack of vitamins, for example.
  - hga 10y ago
    Another example might be the over-diagnosis of tertiary neurosyphilis as the cause of mental illness and death, e.g. in some of my recent reading great and legitimate doubt was placed on that being a cause of the death of Winston Churchill's father. We now know there's a host of causes, many of which aren't (yet known to be) infectious. Although we must be careful, in one of my more interesting jobs, building a full text database for Year Book Medical Publishers (a part of Time ... -Life? Time as in the LA Times back then), the leading article for the general book for that year was on the proof of gastrointestinal ulcer being caused by a bacteria. The editor of that entry figuratively smiled about "taking away another disease from" ... whichever specialists assigned it all to stress (which of course can predispose someone to getting an infection).
  - saynsedit 10y ago
    Also some bacteria are actually extremely good for you when you eat them, like Lactobacillus, I.e. What you'd find in kimchi, sauerkraut, pickles. Or that the majority of the human body by cell count is actually composed of bacteria...

Alain-Berset 10y ago

Defoe spells out that many of those who fled took the plague with them into the shires. There were also attempts in each parish to deny that plague was killing people - it was put down to other ailments as far as possible. Seems illogical to us, but if you are inclined to believe plagues are divine punishment, you might hope to get on top of it by prayer and right-living: "trying to cleanse the city in both moral and practical terms".

BorisVSchmid 10y ago

I am happy with every new ancient DNA sequence of plague that becomes available. Combined, they can be used to figure out the way the disease spread across Eurasia and persisted in Europe. That said, I would like these news articles to actually link to the scientific paper, or if the paper is not published yet/still under review, at least mention that.

hga 10y ago
Eh, isn't that's kinda hard and dangerous, for the simplest way is to infect animals with these strains, and I kinda doubt any humans are volunteering to play their part.... Just having a DNA sequence is quite some distance from the proteins it produces, the regulatory system that governs what, when and how much, and the effect of them on us poor animals. But this has got to be a hot area of research....

aikah 10y ago

> To reassure anyone worried whether plague bacterium was released from the excavation work or scientific analysis, it doesn't survive in the ground. Thank god, what a relief ! To be frank, looking at the pictures of students working on site,that very question crossed my mind.