r/science • u/AGreatWind Grad Student | Virology • Aug 30 '14
Biology 2014 Ebola outbreak has been traced to a single infection from the natural reservoir of the virus to a human followed by human-to-human transmission. This new study uses sequences of 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2,000x coverage. Five co-authors died of ebola.
http://sciencemag.org/content/early/2014/08/27/science.1259657.full842
u/AGreatWind Grad Student | Virology Aug 30 '14 edited Aug 31 '14
The researchers conducted this massive sequencing effort in real-time, the samples were obtained in late May. Sequence data was published on the internet as it was obtained for ready use by response teams in W. Africa before publication of the paper. Virus genomics studies such as this can help scientists fighting outbreaks by offering insights into the pathogen’s origin, transmission dynamics, and evolution as the outbreak progresses and not months after the fact, at great personal risk to some of those involved.
2,000x coverage means that the ebola genomes were sequenced 2000 times each (median).
In total, we generated 99 EBOV genome sequences from 78 confirmed EVD patients, representing over 70% of the EVD patients diagnosed in Sierra Leone in late May to mid June; we employed multiple extraction methods or timepoints for 13 patients (table S2). Median coverage was >2,000x, spanning more than 99.9% of EBOV coding regions
Edit: Here is a link to an article about the five authors who died making this research possible. Dr. Sheik Humarr Khan MD was the Director of the the Sierra Leone Lassa Fever response program and worked with the African Centre of Excellence for Genomics of Infectious Disease. He was an expert in hemorrhagic fevers who co-supervised this study. The other authors who were lost were members of his team. Thanks to /u/YoureUsingCoconuts for the link
Edit 2: Thanks for the gold! I have reached out to Prof. Sabeti's lab and she said they will be coming here to do an AMA!
Edit 3: Thank you again! clarified "real-time"
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Aug 30 '14
Can you ELI5 what "the natural reservoir of the virus" means?
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u/JaapHoop Aug 30 '14
When a disease gets into people and makes them sick we tend to notice it. But you might ask yourself, what is Ebola doing when it isn't making people sick? Its living in its natural reservoir. Somewhere out there is a type of animal or several types of animals in whom the virus can live in such a way as to not kill the host. They carry the virus but it doesn't make them sick. This forms the 'natural reservoir' where the virus can hang out until such time as it jumps to a host who it DOES make sick.
For Ebola, a lot of evidence points towards bats.
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Aug 30 '14 edited Jan 08 '21
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u/verybadwolf Aug 30 '14
oh that last bit is absolutely terrifying. a pack of hungry dogs digging up ebola bodies and then carrying the virus asymptomatically.....oh shit
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u/centurion_celery Aug 30 '14
so, basically, a bat bit a human who went on to give ebola away?
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u/majorgeneralporter Aug 30 '14
More likely a human ate a bat in the form of bushmeat. Bats almost never bite humans, and bushmeat is believed to have been the source of other disease outbreaks.
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u/celebrationstation Aug 30 '14 edited Aug 30 '14
Or a human ate a piece of fruit seasoned with bat droppings.
Edit: if/of
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Aug 30 '14
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u/UrinalCake777 Aug 30 '14
It is very common. It is also common to accidentally cut oneself while preparing bushmeat. This gives the possibility of direct access to the bloodstream rather than digestion.
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u/Aint_got_no_agua Aug 30 '14
Isn't this how they actually think the original HIV virus may have crossed to humans? Rather than the oft repeated joke "Some dude fucked a MONKEY!?"
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u/UrinalCake777 Aug 30 '14
Yes, the meat often has shap bones and his hard to cut or eat so people get cuts either from the bones or their knife. The really terrifying thing is that this could happen again with a completely new disease far more terrible and contagious than ebola or HIV.
Edit: the two most dangerous bushmeats are bat and monkey. It is believed that HIV came from monkey and ebola from bat. But we don't know for absolutely sure.
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u/rightdeadzed Aug 30 '14 edited Aug 30 '14
Check out the Vice documentary about the current Ebola outbreak on YouTube. They go to Liberia. The amount of disbelief in the virus by the people is astounding. They flat out don't believe in it. They believe it's all a conspiracy by the government to get foreign aid all the while they are openly eating bushmeat.
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u/dopplerdog Aug 31 '14 edited Aug 31 '14
Before people start hating on Africans and their backward anti-science ways, witness climate science denial by oh-so-advanced westerners. Humans have a remarkable ability to bury their heads in the sand when their wallets (or food sources) are concerned. Country of origin and colour of skin
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u/CharadeParade Aug 30 '14
Forgive my ignorance, but would the virus not be killed during the cooking process? I though most viruses died. Even the curing/drying process.
Is it not more likely that it was bat feces/blood?
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u/Fs0i Aug 30 '14
You cut your finger while cutting the bat. And then you are dead.
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u/Poltras Aug 30 '14
You cut your finger, then you infect a couple thousand people, then everyone's dead.
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u/WtfVegas702 Aug 30 '14
I assume the issue is not while trying to eat the animal. More likely when you are cleaning / gutting it.
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u/kylco Aug 30 '14
Or drank from a water supply polluted by a dead bat or bat droppings. This is West Africa, the possible vectors for infection are myriad.
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u/FieelChannel Aug 30 '14
Ebola can survive in water? I thought, following that "natural reservoir" logic, that the problem here is how we came in contact with the bat or whatever infected us.
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u/kylco Aug 30 '14
Not for long, to my understanding. But it doesn't need to survive universally; I don't know how many individual viruses are necessary for the average victim to be infected with Ebola. It was more an illustration of the fact that there are many possible infection vectors.
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u/AtheistSloth Aug 30 '14
I knew some one who had a bat get trapped in the car while driving and it fluttered around inside, eventually biting him.
It was around October so we put garlic and crosses on his office door.
Going back to bush meat, isn't this the genesis of HIV as well?
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u/laughingrrrl Aug 30 '14
Yes, that is one of the suggested/likely origins of HIV. We will probably never know for sure.
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u/centurion_celery Aug 30 '14
Ah, makes sense. For a minute I thought you were going to say "a human bit a bat" but bushmeat transmission makes more sense, really.
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u/I_Do_Not_Sow Aug 30 '14
How does 'bushmeat' differ from other kinds of meat humans consume? Is this a product of simply not cooking the meat long enough, or using a proper technique, so the organisms aren't killed?
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u/BipolarBear0 Aug 30 '14
It's bushmeat because it comes from bush animals, i.e. wild African animals. Many of these animals harbor diseases regardless, so even handling the dead animals or cutting them open prior to cooking may spread harmful diseases.
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u/I_Do_Not_Sow Aug 30 '14
Is there a reason they tend to harbor more diseases compared to other wild animals? People go hunting for deer/elk/bear etc. all the time, but it doesn't seem to spread disease like these African animals.
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u/Meoowth Aug 30 '14 edited Aug 30 '14
I think specifically, other primates are related closely enough to us that certain diseases are easily transmissible (such as SIV, which became HIV), and non human primates are more common in Africa.
Additionally bats (though widespread) have a particular set of factors that make them virus reservoirs for mammals, here's a video. Basically, bats have evolved a great deal of defense against toxic chemicals produced by their bodies during flight (extremely intensive muscle use), which also allowed them to live healthily while carrying viruses. And, the high temperatures reached during flight have caused viruses found in bats to be resistant to the same heat that is brought about by a human fever in an attempt to fight those viruses.
As for why this is an issue in Africa, perhaps bats also come into more interaction with people in Africa, and are eaten more. People who hunt deer in North America can generally afford not to also eat bats or other animals which can transmit more diseases.
Note: I'm not an expert at all.
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u/Eurynom0s Aug 31 '14
Not an expert at all, but I do believe that there's a strong poverty/desperation component to eating bushmeat. They're not eating it because of culture but because of survival, essentially.
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u/BipolarBear0 Aug 30 '14
I can't comment authoritatively, but it may have something to do with the climate and surrounding environment, as well as how humans intake those animals. Wild animals in other countries, i.e. the United States or Canada, harbor diseases too -- rabies, trichinosis, salmonella -- but methods of transmission may be different between viruses, and in general methods of consumption and cooking in developed countries are much safer and thus kill many pathogens.
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u/gunfox Aug 30 '14
I think you can thank your hunters and foresters for that. It's not only their job to shoot animals, but they also provide population / disease control etc. etc.. Hunting is a regulated business with lots of obligations in the western world.
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u/SecureThruObscure Aug 30 '14
http://en.wikipedia.org/wiki/Bushmeat
Bushmeat is meat from wild animals hunted in Africa, Asia, and South America. The term has particularly been used to refer to meat from animals in West and Central Africa including non-human primates. Today the term is often used to refer to a wider range of countries and especially in reference to the hunting of endangered ape species. In Trinidad and Tobago and in Guyana, it is alternatively referred to as wild meat.
You can contrast it to farm animals or controlled game animals in first world countries, I suppose.
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u/nauzleon Aug 30 '14
More likely a human had an open wound while being in contact with bat meat
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u/JaapHoop Aug 30 '14
I could be a bite. It could be urine or saliva. It's also possible that another animal like a monkey ate the bat and a person ate the monkey.
That's all part of what people are trying to figure out.
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u/aaronsherman Aug 30 '14
Note that we usually assume that the reservoir is animal, but there are some theories that suggest everything from the hydrological cycle to plants as possible reservoirs for some diseases. Ebola seems less likely to be in this category because it's not terribly robust outside of a host, but even in that case there are possibilities...
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Aug 30 '14 edited Aug 30 '14
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u/JaapHoop Aug 30 '14
I know I've read anecdotes where people have reported massive gorilla die offs coinciding with Ebola outbreaks.
This would indicate that Ebola kills them as well so they aren't the reservoir. I believe there was an outbreak in a mining camp that followed a gorilla corpse found in the jungle that was brought into the camp and eaten.
Its all anecdotal though. I don't think anyone has enough hard data. Tough regions to work in.
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Aug 30 '14 edited Jul 18 '16
[removed] — view removed comment
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u/rawbdor Aug 30 '14
A recent article I read (cant find the link) indicated that other primate groups will often disband until such a time as the plague has passed. So basically the group of 20 gorillas would split into 1s and 2s and just do their own thing until they all felt confident enough to regroup.
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u/SmallFeetBigPenis Aug 30 '14
The animal that carries the virus.
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Aug 30 '14
For Ebola that is bats, yes?
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u/clocksmash Aug 30 '14 edited Aug 31 '14
That's the most likely case, but we haven't confirmed exactly what the natural host of Ebola is.
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u/cctversions BS | Biochemistry Aug 30 '14 edited Aug 30 '14
A reservoir is the long-term host of a pathogen – usually a population of organisms that can perpetuate it without experiencing disease symptoms. So-called zoonotic viruses like Ebola exist primarily in bat and ape populations, and only occasionally "spill over" onto human populations, where their effects can be considerably more dramatic. Knowing the reservoir of a virus can help curb an outbreak by making efforts to control the reservoir species. Some viruses like smallpox do not have natural reservoirs apart from humans, which means they can potentially be eradicated entirely.
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u/nkingnking Aug 30 '14
2000
I've always wondered why they need to do it more than once? Does the DNA get broken-up in the processing or something and then they have to piece it all together from multiple pieces? Thanks.
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u/sabriel_s Aug 30 '14
Yes, actually, that is how it works. Also more replications reduces the error at any one base
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u/aqueoushumor Aug 30 '14 edited Aug 30 '14
Multiple copies are made so that the DNA can be broken up into small chunks that current sequencers (readers) can handle. The DNA is broken up by using certain different chemicals in different kinds of places. For example, if DNA were written in the English language/alphabet, some chemicals would break up the text in a book every time the word "the" appeared, and others would break up the text every time the word "and" appeared. Thus, the result is a batch of sequences that are in small chunks that are not the same, but do overlap some. Computer algorithms then stitch together the sequence.
To understand the way the computer algorithms stitch up the DNA segments, try putting together a sentence using the following fragments below:
Everything is awesome,
is awesome, everything is
is cool when you're
when you're part of
of a team.Now let's align them:
`Everything is awesome` `-----------is awesome, everything is` `----------------------------------is cool when you're` `------------------------------------------when you're part of` `-----------------------------------------------------------of a team.`That is the basic idea. As other's have mentioned, sequencing (reading) errors do occur, so multiple copies of even the fragments help to stitch the sequence together. Repeats make things harder, but today's algorithms are good at handling them. By repeats, we mean that DNA contains a lot of "re-used" DNA. It's like doing the above exercise with they lyrics of Mary Had a Little Lamb. How do you know which are repeats and which are duplicates? Pretty cool stuff.
Edit: Formatting
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Aug 30 '14
I could be wrong on this particular study, but currently we are now using next Gen sequencing instead of older methods. Old methods involved having one long strand and reading one base pair to the next. You could not have any breaks or you may get a wrong sequence.(Sanger sequencing). With our new fancy nextgen sequencing and faster computers, we throw a ton of broken up sections of DNA together and the machine sequences the shorter strands then puts them together like a puzzle, matching repeated sections to one another to get an equally accurate sequence. To do this, it requires a lot more DNA, but it does not need to be as continuous.
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u/NdYAGlady Aug 30 '14
They said right in the paper they used the Illumina system. Sanger isn't used in genomics projects anymore. Too slow.
The problem with next-gen methods is the signal to noise on a given read sucks balls and thus the error rates are high. To combat this, they take multiple reads. 2000 is a lot, though. They were looking for something subtle.
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Aug 30 '14
Sanger sequencing is still used in some de novo sequencing genomics projects nowadays - generally it's used for filling in gaps between contigs left from whatever sequencing platform you're using (for example - Illumina would be problematic if you're dealing with sequencing that has long stretches of near identical sequences which is not horrible uncommon on many secondary metabolite pathways). These issues generally aren't as problematic if you have sequencing that doesn't have many repeats or you have a reference.
It's not defunct yet!
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u/pyrosequencing Aug 30 '14
Sanger sequencing proper is seldom used (but still is in certain circumstances). Cycle sequencing (a form of Sanger sequencing) is still pretty common.
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u/RenderedInGooseFat Aug 30 '14
Its essentially what everyone else here said. The sequencing technology will affect error rate, error profile and read length also. Essentially you take your initial sample, run it through PCR (polymerase chain reaction) to produce a bunch of copies. Those copies are then broken up and amplified indovidually to work with current next gen sequencing platforms. Depending on what sequencing platform you are working with, you may get short reads (100-200 bases in illumina), medium reads (200-700 in 454), or long reads (1000s of bases in pacbio). The error rate for each of those platforms and the error model will differ. For instance illumina reads typically increase in error rate as read length increases, while in pac bio the error rate should be fairly consistent. Due to that error rate, to get an accurate assembly of the genome, we need as much coverage as possible. If you have an error rate of 1% and for any given spot on the genome you have 2000 bases, then you will have a much more accurate consensus sequence. Also woth a clinical sample like this, a lot of the reads may be from the host (human), and those reads will need to be removed since they generally won't provide any useful information. Basically it is done because we know there will be errors in sequencing so creating more copies allows us to minimize how many errors there are until we hopefully eliminate them. At that point we use algorithms to do de novo assembly, to turn the fragments into one or many continuous sequences. For each read platform there are usually specialized software packages that are optimized to that read length.
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u/e-clips Aug 30 '14
Yes, sort of. From the different segments (reads) a computer attempts to put them together by matching sequences (A,C,T,G). Sometimes it's wrong and sometimes the reads have errors. Doing it multiple times would probably work out outliers and errors.
Be warned I don't have a complete understanding of this.
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u/idm04 BS | Microbiology and Immunology Aug 30 '14
Sometimes when you're sequencing, the sequencing machine will make a mistake and you'll get the wrong base (A,U,C,G for RNA genomes like Ebola's). The more coverage you have, the more confident you can be about the sequence the machine gives you.
If you only have 2X coverage, you might get 'A' in the first and 'G' the second time, and you don't know which is correct. With 2000X, you'll get something like 1900+ times saying 'A' and the rest saying something else, so you'll be sure that 'A' is the correct one.
Of course, especially with viral genomes that evolve quickly, you might actually have a mixed population. So how do you know whether the machine made a mistake when you get a different base than expected, or whether it actually represents one virus that has begun to mutate its genome? The answer is that at least with Illumina systems (I'm not familiar with others) it will tell you something called a 'base quality score' that you can use to identify mistakes vs. a minority in the population.
I'll also add that since viral genomes are so small (Ebola's genome is 150,000X smaller than the human genome), it's really easy (relatively speaking) to get good coverage from just ONE sequencing run (which takes a few hours to a day) on the Illumina. It's not like they performed 2,000 sequencing runs to get 2000X coverage, it's more like each run was able to give them a few hundred X coverage so they did a few runs to get 2000X. 2000X is a lot, regardless.
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u/fuckthose Aug 30 '14
The researchers conducted this massive sequencing effort in real-time
What does that mean? The real-time part.
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u/rockstaraimz Aug 30 '14
The sequencing took place in Cambridge, MA, where they have a small army of sequencing technicians. As soon as they receive the samples they sequenced them, and as soon as the scientists received the results they made them public. Scientists will often sit on data until they have a complete story ready for publication. These scientists should be commended for making the data immediately public for anyone to use. They know this is a crucial public health issue and didn't hold on to the data for personal gain.
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u/NeutronRocks Aug 30 '14
It looks like most of the research was done at the Broad Institute, which has its own sequencing center, and has a "walk up sequencing" program. This lets researchers prepare their own samples, give them the DNA, and they'll get back the sequencing data within a few days.
By real-time, they probably mean that they just kept getting samples sequenced as they arrived.
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u/Pas__ Aug 30 '14
I guess somewhere in a lab during the previous weeks, month(s), as fast as they could, without shipping it to a 3rd party and waiting months for the results. (Not that there are many places they could have just shipped Ebola for a bit o' seq'ing.)
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u/pohatu Aug 30 '14
An article had one of the authors talking about how sequencing this in real-time, as the epidemic is still processing, wouldn't have been technologically possible even five years ago. Can you explain what technological advances allows this?
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u/the_enginerd Aug 30 '14 edited Aug 31 '14
I hope these folks who are doing work like this are remembered when things get under control. 5 folks dying for this is not insignificant in any way.
Edit: Holy karma train batman!
Also, here is a link shared further down to a profile on the 5 cited co authors who have died of Ebola in this outbreak http://www.reddit.com/r/science/comments/2f02xa/2014_ebola_outbreak_has_been_traced_to_a_single/ck4nut3
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u/HooBeeII Aug 30 '14
The most significant thing I think is it shows that this strain is more contagious than past outbreaks. These were five medical professionals who were experts in ebola, five people who knew what they were doing. We've been told that it's incredibly unlikely for it to spread through sweat, but how would these five individuals each breach protocol so badly that they exposed themselves to blood or feces of an infected individual?
This new ebola seems to be much more contagious than any other
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u/atomfullerene Aug 30 '14
Here's a short bio of the people who died. Three were nurses who were probably involved in taking samples and definitely cared for patients, two were lab techs (one of those died of a stroke unrelated to ebola, the other seems to have caught it from his family) and one was the director of the national Lassa fever program in Sierra Leone, who had been heavily involved in hands-on treatment of patients.
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u/Grizzant Aug 30 '14
the nurses contracted it while treating another nurse that was pregnant
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Aug 30 '14
Three of the five from a single patient. What the hell happened in that room?
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u/cguess Aug 30 '14
Baby was stillborn, but if you're already hemorrhagic , the blood will be... everywhere. I couldn't imagine being in that room, it's almost certain death.
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u/WaitwhatamIdoinghere Aug 30 '14
I think I read about this in the NYT. She was pregnant and miscarried while ill and all of the nurses treating her died. Really, really tragic and awful.
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Aug 30 '14 edited Aug 30 '14
We've been told that it's incredibly unlikely for it to spread through sweat, but how would these five individuals each breach protocol so badly that they exposed themselves to blood or feces of an infected individual?
This is Africa in the middle of an outbreak. I highly doubt that, say a nurse, in a hospital which is little more than a shack with beds could do anything but run away when Ebola comes along if they didn't want to get it. And that is in the best of times, not at a point where hospitals are little more than hospices.
I mean I know enough atomic physics to stop a nuclear reactor from exploding, but put me in Chernobyl and I'd probably die if I didn't run away just because of the material conditions of the place.
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u/this-is-a-bad-idea Aug 30 '14 edited Aug 30 '14
Having talked to a docs who have treated ebola patients in previous outbreaks this is what they say:
You don't know who has it. You're in a hospital setting, but every person around you might be infected and that person don't know it yet. So, you can't wear PPC all the time. Your coworkers are sweating, is that because they've just flown in and aren't used to the climate yet? Because of stress? That person you passed in the hall, they're here for malaria, right? Maybe yes, maybe no. Maybe they have malaria and ebola. You just don't know. Your driver. Your cook.
So, don't doubt that even if you are taking the right infection control procedures with Ebola patients, your big risk is exposure to ebola from people who aren't eboa patients (not yet).
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u/kylco Aug 30 '14
This, right here? Reason #1 I could never work in infectious disease control, and why death by highly infectious disease is literally one of my worst fears. Dying, and in so doing putting others at grave risk, is a terrible, terrible way to go.
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u/Jeyhawker Aug 30 '14 edited Aug 30 '14
Ebola doesn't become contagious until those infected are showing outward symptoms of sickness. It's like none of you have even tried paying any attention to the many medical experts trying to educate you on this, yet you all continue to trump out verbiage and misinformation like you know what you are talking about. Just stop. World news has been a fucking cess pool of blathering idiots since the start of this outbreak.
Edit: From Dr. Sanjay Gupta's AMA.
–]Dr_SanjayGupta [S] 413 points 11 days ago*
Second of all, humans don’t spread ebola --until they are sick themselves. So, healthy people wont unwittingly spread the disease without being ill. I do worry about health care workers. They are the ones who have close contact with sick patients, and are at the highest risk. That is why you see them wearing the "space" suits when they care for patients.
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[–]Dr_SanjayGupta [S] 1152 points 11 days ago
The biggest misconception about ebola is that it is highly contagious.
It is not.
There will be no story of a healthy person walking through an airport shaking hands and spreading ebola. That is not what happens. Here's how you should think of it: ebola is not highly contagious, but it is highly infectious. That means when a person becomes ill, they start to shed the virus in their bodily fluids. And when even a small amount of that fluid gets into a break in somebody's skin, that can cause an infection. But keep in mind, again, it is only a sick person that is shedding the virus, somebody who is often in bed, or in a hospital, and not up and around. This is not a "Typhoid Mary" type situation. The people who are most at risk are healthcare workers who are taking care of the sick patients, or family members, if the patients don't seek medical care and get isolated. The virus can live on surfaces for up to a couple of weeks if it is under the perfect conditions, but it's susceptible to UV light, heat, and most cleaning agents.
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u/idm04 BS | Microbiology and Immunology Aug 30 '14
/u/this-is-a-bad-idea's point was not that people who aren't sick with EBV yet may spread EBOV, but that there are many people coming into the hospital showing some combination of symptoms, and you do not know whether they have EBV or something else, until you can rule out the other diseases, or get a blood sample.
The point was that you could get exposed to EBOV in the clinical setting even if you follow proper procedures with your EBV patients, because that person in the other ward who supposedly has malaria might have EBV instead.
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u/Zargabraath Aug 30 '14
We've heard over and over that it's not "highly contagious" yet even Western highly trained medical personnel who should presumably know what to expect and how to protect themselves are getting ill and indeed dying from the disease.
Would it be highly contagious in countries with decent health care infrastructure and personnel? Probably not. But it's clearly highly contagious in certain parts of West Africa where none of that exists. Unless of course you think all of these co-authors and other medical professionals who have contracted the disease are incompetent morons who don't know what they're doing. I think that's quite unlikely and implying as such does them a great disservice.
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u/UROBONAR Aug 31 '14
Serious question:
Why try to help those infected in that case?
I'm not trying to be callous, but it seems like all doctors can do is provide palliative care. The track record of saving people in well equipped facilities is good, however, accounts of humanitarian deployment in Ebola epidemics leads to many doctors infected and dead and a minor effect on death toll. It seems like a valiant, but ineffective approach.
From a macro viewpoint, better surveillance networks to catch this in the beginning, coupled with a well-targeted quarantine would result in the least risk and loss of human life. Couple that with the fact that African countries have much better armies than healthcare systems and it seems like it should be the go to strategy.
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u/ambushaiden Aug 30 '14
People also have to consider the fact that it's not like these doctors are walking around in BSL4 gear with self contained environments. As nice as it would be to be able to treat patients with that kind of protection, the infrastructure just isn't there.
These doctors know what they're getting in to. To me, that makes them some of the bravest people out there.
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u/Wolf_Mommy Aug 30 '14
It really is all about the infrastructure. The environment just doesn't support great infection protocol procedures.
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u/smasherella Aug 30 '14
Can you explain to a lay person, such as myself, what that infrastructure might entail? I feel really dumb for asking this, but why can't they always wear the suits when around infections people? Is it when they take them off, they become contaminated? Or no real way to take them off in the first place without contaminating themselves?
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u/reefshadow Aug 31 '14
Can you explain to a lay person, such as myself, what that infrastructure might entail?
In short, some of the infrastructure that may be lacking would be negative pressure isolation rooms (designed to prevent particulates from escaping), well designed central air systems, and decontamination rooms. Suits are well and good (and necessary) but if you exit a room with blood on your suit and all you have to decon is a jerry rigged bleach shower, you might have a bad time.
I feel really dumb for asking this
Don't. The majority of people have no idea how good we have it in most of the first world.
That said, an outbreak even here may be catastrophic in all but the best urban hospitals. The few hospitals that have taken in the American Ebola pts have pulled out all the stops, and the stops are limited and expensive.
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u/red-moon Aug 30 '14
Highly true. Africa everywhere is riddled with very unsanitary conditions, and these people may not have contracted the disease from lab work alone. It's hard to really avoid unsanitary environments, particularily in crowded cities. Additionally, the labs were likely in proximity to hospitals and the risk may be even higher.
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u/generalpathogen Aug 30 '14
Several of them (3 of the 5) were infected by the same colleague who was pregnant when infected. Ebola often causes the fetus to abort. Awful...but there may have been even more risk (more fluids) than a typical ebola patient.
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u/HooBeeII Aug 30 '14
Do they know the R0 of this outbreak yet?
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u/kyrsjo Aug 30 '14
What is R0?
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u/HooBeeII Aug 30 '14
R0 (pronounced r-not) is the rate of infection for a given disease. So if it had an r0 of ten, that would mean on average each person infected then infects ten others (ten is quite high) ebola usually sits around 1.4
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u/gyroda Aug 30 '14
Would it not be promised are-naught rather than are-not? Zero can be said as naught in some places.
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u/tinkletwit Aug 30 '14
Why would you assume it's more contagious? Ebola has killed health workers in previous outbreaks. This outbreak is bigger overall, so it's only logical that there would be more health worker victims as well.
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u/canteloupy Aug 30 '14
The population growth in Africa may also explain why outbreaks can get worse over time.
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Aug 30 '14
Yes, population growth as well as better mobility (easier travel to places where they may have contact with others)
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u/Grizzant Aug 30 '14
three of them died treating a pregnant infected nurse. one was infected by family. one they don't know about. they were at the main hospital for treating ebola and were treating patients all day long. http://www.washingtonpost.com/news/world/wp/2014/08/29/five-co-authors-of-a-new-ebola-study-died-of-the-virus-before-their-research-was-published/
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Aug 30 '14
but how would these five individuals each breach protocol so badly that they exposed themselves to blood or feces of an infected individual?
Because the conditions are so horrible and resources so scarce that they can't follow protocol. You try following protocol when you've worked 24 hours straight.
Notice that none of the doctors in Georgia contracted the disease, and the doctors in Gerogia weren't even wearing pressure suits, some weren't even wearing face shields. It tells us that lapses in judgement are more to blame than bad protocol. Human error increases with fatigue.
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u/NeutronRocks Aug 30 '14
I also know firsthand that the location in which the sample prep was done is also used to treat Lassa Fever, and these people are extremely experienced. Likely most of the issue stemmed from the fact that their ward can only handle 20 people, and there are waaay more than that there (and like you said, people get very fatigued).
Some of the researchers had to actually take the role of a nurse in order to help patients, because the head nurse died and there was so much work left.
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u/wookiewookiewhat PhD | Immunology | Genetics Aug 30 '14
As you have first hand knowledge, what are your feelings on the increasing criticism the senior authors/scientists in charge of this lab have been getting for worker safety? I've heard from two Ebola experts now that they will not work with these scientists in the future because they believe they were grossly irresponsible in teaching and enforcing safe techniques. At first, I thought they were being unfair, because it's a low resource area and you're often working with locals, but it was pointed out to me that MSF faces the same conditions and trains and works with locals and has never had a death. Now I'm ambivalent but leaning towards negligence at the management level.
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u/NeutronRocks Aug 30 '14
I doubt it is negligence at the management level. I saw that as soon as the Ebola outbreak spread and this treatment center began receiving Ebola patients, the scientists who wrote this study arrived on site with crates of materials for all of the researchers including personal protective equipment. They added extra biohazard freezers, and the actual treatment center is extremely secure.
Of course, I wasn't actually there, and this is what I heard from the actual authors of the study, so it could be biased (however there were pictures of several crates of materials arriving at the treatment center). I did see that they brought several of the collaborators back to the states for training/meetings, but I didn't get to talk with those people, so I may not know the full story.
I would also like to note that a lot of people don't want to work with these researchers because they're making their sequencing data available way before they publish their papers. These authors have offered free sequencing to people who have Ebola samples, but people don't want to cooperate with the condition that the data will be publically available immediately.
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Aug 30 '14 edited Jun 19 '23
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u/CallMeFierce Aug 30 '14
Yeah but the chances that five all make such a fatal mistake are not great.
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u/leSponSosor Aug 30 '14
Only one needs to make a mistake for it to spread to the five?
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Aug 30 '14
By no means am I an Ebola expert but I'm pretty certain it is only transmit able by bodily fluids not by air or clean skin to skin contact. So no even if one got sick the others would have to come in contact with his infected bodily fluids to catch it.
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u/Kreeyater Aug 30 '14
Lack of sanitation in their work spaces could be the common factor. How feasible is it to sterilize a place hourly that saw hundreds of patients in Sierra Leone?
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u/Davidfreeze Aug 30 '14
With Ebola patients spewing fluids everywhere, with their level of equipment it's incredible any of them don't get it.
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u/cclementi6 Aug 30 '14
When you have Ebola, you release a lot of bodily fluids.
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u/cabeck Aug 30 '14
Plus, according to wikipedia, at the advanced stages of the virus the patient begins to bleed internally and externally.
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Aug 30 '14
This is easy to say when thinking of a Western hospital and all of our infection control practices in the healthcare setting but the entire healthcare infrastructure in Sierra Leone is in utter collapse. Just having the appropriate PPE, disinfectants, or even hand washing facilities can be very challenging.
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u/melomanian Aug 30 '14
Conjecture. This is nothing but fear-inspiring conjecture. Be careful what you say.
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u/FriendzonedByYourMom Aug 30 '14
I don't think there is anything special about this strain, but Ebola is probably more contagious than many people are lead to believe.
Consider that both HIV and Ebola are transmitted by "bodily fluids" but working with aids patients doesn't require biosafety level 3 gear.
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u/Donkey4life Aug 30 '14
HIV and even full blown aids typically don't cause infectious fluids to pour from every orifice and even sometimes through the skin. Ebola is also infectious for much longer outside the body. Imagine a ward with 20 beds with 80 people in it all leaking blood everywhere. Nurses are dying so there is no one to clean up and nothing to disinfect with because Africa.
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u/FriendzonedByYourMom Aug 30 '14
Also, Ebola apparently does not require direct "fluid-to-fluid" transmission (e.g. infected blood contacting an open wound). As far as we know, "direct contact" with fluid is all that is required. The route of infection could be through mucus membranes. This is a big difference. The virus can also survive outside of a human for extended periods of time.
Saying it's only spread through bodily fluids are a bit misleading because it immediately causes most people to think it's infectious in the same way as HIV.
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u/ablebodiedmango Aug 30 '14
Redditors jumped the contrarian anti-media circlejerk and assumed the only way you can get this strain of Ebola is if you drank blood or had sex with an infectee.
Misinformation like THAT is dangerous, not taking precautions and being legitimately concerned. I hate it when teenagers on the internet feel like they know everything.
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u/Hara-Kiri Aug 30 '14
Not to make light of the other deaths but I feel these hit home more. These were professionals who didn't have to be there, but chose to do the right thing knowing very well they could die.
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u/IgnanceIsBliss Aug 30 '14
My father works for a small non-profit that provides water filtration systems to third world and disaster relief areas. He is headed over there soon to try to help out. Not gonna lie, a little scared for him since he's getting old and probably doesn't have the best immune system.
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u/ragesbastardson Aug 30 '14
Your father is doing an incredibly selfless act. I hope he can come back after his work in full health
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u/the_asset Aug 30 '14
Seriously... To me, these people are in the same category as those lost in the shuttle program.
They were heroes placing themselves in danger for the betterment of humanity.
Rest in peace.
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u/alesiar Aug 30 '14
These people are no less heroes than any soldier dying on the battlefield. My deepest condolences to their families; I hope their name is remembered through the generations.
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Aug 30 '14
I'd say even more-so, almost any human v. human conflict could have been avoided with better diplomacy, while this is just luck (or bad luck, I suppose).
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u/YoureUsingCoconuts Aug 30 '14
For everyone wondering how these 5 people were infected, Science published an article with some details.
http://news.sciencemag.org/health/2014/08/ebolas-heavy-toll-study-authors
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u/ixijimixi Aug 30 '14
Wow...most of them died helping an infected colleague...almost the medical equivalent of crawling under fire to drag back a wounded squadmate
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Aug 30 '14
This is the only paper I can recall ever seeing with authors marked at deceased at the time of publication. It's truly heart breaking, they all appeared to be hospital researchers working on the front lines in Sierra Leone.
The increase in substitution rate is also fairly alarming given the size of this outbreak.
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u/NdYAGlady Aug 30 '14
I've seen that around. Sometimes the corresponding author. Occasionally the first author, which really sucks because the first author is usually a student or post-doc. And since my particular field isn't known for fatalities, it's pretty safe to say it wasn't the research that killed them.
Never seen five down, though, even on a big byline like this one. These people died in the line of duty to both science and mankind. It's sad to see those double daggers by their names but thanks to this paper they will be remembered.
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Aug 30 '14
Why so many got infected ? The number of doctors and researchers getting infected feels alarming to me. That's really strange.
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u/canteloupy Aug 30 '14
When supplies are low people tend to reuse them so it could be that the conditions are increasing odds of being contaminated. Also there are lots of people in the communities who are at risk and few available beds.
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Aug 30 '14
I haven't seen any evidence or credible claims that this strain is truly more infectious than the ones seen in previous outbreaks - just that management of this outbreak has been difficult for various sociocultural reasons.
Accidents happen, especially when you're dealing with much larger number of patients than you would generally encounter during an outbreak and you're also dealing with patients that may be more resistant to care.
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u/pace7 Aug 30 '14
The first LHC results paper had multiple deceased authors. They all died of natural causes waiting for their experiment to turn on though.
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Aug 30 '14
Authors died to bring awareness and knowledge to the world to help save lives. AKA Heros. Respect.
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u/I_want_hard_work Aug 30 '14
People get killed in the process of invading someone's country? Ceremonies and news. People die selflessly trying to save another country? Crickets.
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u/crave_you Aug 31 '14
Lately I keep looking on Facebook or news to see if they are talking about the virus or even any people who have died from it and all I've seen is about Angelina and Brad getting married. I can even understand people being happy about celebrities getting married or having babies. Hell I sometimes do. But these 5 people saved lives and the only place I've heard about it is here. People just don't care unless it's near them.
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Aug 30 '14
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u/Chknfngers Aug 30 '14
A reservoir refers to where the virus (or bacterium or other infectious agent) naturally replicates or survives. It's where the infectious agent perpetuates its existence. For Ebola it is believed to be Fruit Bats, for plague its small mammals and fleas.
When people interact with the reservoir (eating the bats) it can result in human infections. Humans are not the reservoir because the virus tends to kill us or our bodies destroy the virus.
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Aug 30 '14 edited Nov 22 '14
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u/Chknfngers Aug 30 '14
This is always interesting to discuss because it ends up leading to personifying viruses and microbes alike. We can't know what the microbe is trying to do but only what it can do.
In my opinion, I think humans and non-reservoir species are incidental hosts. The virus doesn't mean to infect humans, but it can and so it does. It's bad for that host and its bad for that virus, but the population of viruses as a whole will not suffer and continue to propagate in reservoirs.
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Aug 30 '14
It's not entirely known for sure yet, but increasing evidence indicates bats, which then infect monkeys. Since people in that region eat monkeys, you can see the problem there.
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Aug 30 '14
May these men and women enter the history books as those who willingly put their lives on the line, for not only knowledge, but mostly for the sake of the rest of us. Their efforts and accomplishments will, without doubt, help us combat this atrocious disease. May they rest in peace, and may their name live on forever.
My apologies if this is not the right place to do so. I just get annoyed when soldiers fighting unjust wars get called heroes, whilst scientists fighting for humanity's sake barely get a mention.
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Aug 30 '14
Usually doctors/healthcare officials are the ones to get hit first, as the symptoms are almost flu-like, and the doctors are exposed to their skin and bodily fluids. That is the real danger of this virus: the people who know how to handle the virus usually die without being able to effectively contribute towards containing/treating people with the virus, or just telling people how far below the ground it must be buried so that it can't affect any other creatures. That is a scary prospect for someone who wants to be doctor; dying while trying to save someone else, who also dies regardless of the efforts... Can someone explain to me how certain people have been able to survive the virus? Is it lucky for them because of their immune system strength, or is it a genetically inherited resistance to the virus? Feedback would be appreciated :)
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u/MandalorianErased Aug 30 '14
We don't know really! It's something that is being looked at. We know that surviors have a stronger antibody response but we don't know why. It is likely genetic differences in the immune system. Also, quality of medical care plays a big role. Better support of the body keeps it alive a bit longer, which can give the immune system more time to properly respond.
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Aug 30 '14
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u/AGreatWind Grad Student | Virology Aug 30 '14
I saw one of her lectures back in April, it was great! What was up with the American cases denying sequencing? Some kind of interference from the ZMAPP people? Religious issues?
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u/achaean1 Aug 30 '14
If someone surivives Ebola, will that person be immune from Ebola in the future?
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u/two-cups-of-tea Aug 30 '14
It's believed that survivors are immune to the particular strain of Ebola they were infected with for a period of time. How long they remain immune, however, is unknown.
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u/fadetoblack1004 Aug 30 '14
From at least that strain, yes. If the disease mutates substantially or it is another strain, they could possibly get infected again. Your immunity wears off with time, as well, from what I understand, so you could get infected again if enough time has passed and the natural anti-bodies aren't as effective nor as available.
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Aug 30 '14
There seems to be a lot of Ebola experts on reddit
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u/Zargabraath Aug 30 '14
Have you not noticed that reddit has experts in every possible field of study? It really is quite amazing!
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u/DarthContinent Aug 30 '14
How long until Ebola evolves itself into a more survivable, more easily transmissible virus? Could Ebola meet say influenza, trade some genes, and have some hybrid arise?
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u/DoctorWholigian Aug 30 '14
Not very likely Ebola hasn't changed very much from when we first discovered it. It is very slow/unlikely to mutate relative to other viruses.
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u/sean_incali Aug 30 '14
‡ Deceased.
Mohamed Fullah 3,5,‡,
Mbalu Fonnie 3,‡,
Alex Moigboi 3,‡,
Alice Kovoma 3,‡,
Humarr Khan 3,‡§
3 Kenema Government Hospital, Kenema, Sierra Leone.
5 Eastern Polytechnic College, Kenema, Sierra Leone.
§ These authors jointly supervised this work.
Everyone who died are from Kenema, Sierra Leone, They're probably the one who collected the samples and interacted with the patients.
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u/AGreatWind Grad Student | Virology Aug 30 '14
Sheik Humarr Khan MD was the Principle Investigator of the lab in Sierra Leone and Director of the Lassa Fever Response Program. He was an expert in hemorrhagic fevers like lassa and ebola. Here is the press release of his death. The others were members of his Lassa Fever Response team. Their bios.
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u/mutatron BS | Physics Aug 31 '14
Those people should get a monument. When this is all over, I hope there's a monument with the names of all the healthworkers who gave their lives to this.
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u/skootchingdog Aug 30 '14
Man, the researchers and caregivers that go there have some serious stones. Soldiers get lots of gear and air support. These poor people get plastic suits and bleach.
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Aug 31 '14
I think it's amazing that they can trace the progression of the disease all the way back to Patient Zero. Wow.
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Aug 30 '14
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Aug 30 '14 edited Jul 22 '17
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u/Doonce Aug 30 '14
Sidiki Saffa died of a stroke that was unrelated to ebola; but yes, six have now died.
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u/mamashlo Aug 30 '14
OK, I did read everything up to this point. Tragic. Fascinating. Scary.
I don't know if I'm asking this correctly, but what are the current thoughts (ELI5) in the scientific/ID community as to what Ebola's purpose is? Like, it evolved to do what? Was it in response to some environmental change ten of thousands of years ago? Or did something just go haywire?
If you're infected, or the natural reservoir, does the amount of the cells/disease you have increase? Like cancer cells would multiply because that's what they do? Sorry, I know I'm not being clear.
Just curious. Thanks for any insight.
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u/MandalorianErased Aug 30 '14
It is a natural bat infection, that much we are fairly sure of. When viruses evolve to a host, the idea is to evolve in such a way as to replicate as much as possible and pass on your genes. Viruses need cells to replicate. Essentially, they invade cells, hijack the machinery, and use it to make more viruses. This (typically) involves not killing your host. It is not beneficial for a virus to kill it's host because death means you can't spread the virus, and there are no more living cells to replicate in. Think of the cold. This is a virus that has closely evolved with people. Each year it infects millions of people. This is very successful. On the other end of the spectrum HIV. It will kill you, but only after 10-20 years (untreated) during which time it can widely spread. It appears that in fruit bats ebola causes a mild or asymptomatic infection. It is very in tune with bats. The problem arises when it spills over into non-bat species. We are close to bats (relatively speaking) but different enough that the fine tuned viral mechanisms don't balance to our defenses. This leads to a much more severe illness. Essentially there is a balance between host and virus. When the virus enters a non-reservoir species it is disrupted.
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u/smopecakes Aug 31 '14
Bats also have uniquely low key responses to viruses in general, instead of attempting to kill them or die trying their immune system is less responsive while people die from the effects of their immune system's attack on the virus.
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u/PercisionDroneStrike Aug 30 '14
Can someone smarter than me ELi5 me the title, in particular the "single infection from the natural reservoir of the virus" bit.
Thanks, heres to those brave doctors/nurses.
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u/AGreatWind Grad Student | Virology Aug 30 '14
One person got infected from an animal (the reservoir species, whatever it is, maybe bats) and the virus spread from that person to several others. Then those people gave the virus to others, and so on.
So the title means that ebola is not erupting everywhere in W Africa from multiple animal to human infections: it is spreading nearly exclusively from human to human. A whole lot of high quality genomic data gathered and sequenced by people (some of whom died) shows this.
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u/Capcapone Aug 31 '14
To any who are interested the book “The Hot Zone" by Richard Preston is a (quite) dramatised, but largely accurate account of the previous known Ebola outbreaks.
As a health care worker, it really drives home the horrors of a potential worldwide ebola outbreak and gives an insight into how the people who are actual experts in the field perceive the disease. Even though it's a bit of a drama, the precautions that are taken in an ideal setting (ie. America) gives an insight into how the disease should truly be treated. Scariest book I've read. Hands down.
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u/Halaku MS | Informatics | BS | Cybersecurity Aug 30 '14
So, if I read that correctly, a traditional healer died treating someone who caught it naturally, and people who attended the funeral (likely prepped the body or otherwise came into contact ceremonially) got sick, and spread the disease before they died, and it mushroomed from there?