hello everyone my name is elena and today i'm going to be the one talking to you about epidemiology so i do want to give you a content warning this lab is going to deal with some of the topics that we're currently seeing come up with covid19 i know a lot of you work in healthcare or you may know someone who is affected by covid19 so i just want you to be aware that yes that will be mentioned in today's lecture so one of the first things i want to do is to kind of get you thinking in terms of pandemics so sicily in 1348 this is a letter written by someone who was living there at that time he says tell o sicily and ye the many islands of the sea the judgments of god confess so genoa what thou hast done since we of genoa and venice are compelled to make god's chastisement manifest alas our ships enter the port but of a thousand sailors hardly ten are spared we reach our homes our kindred and our neighbors come from all parts to visit us woe to us for we cast at them the darts of death whilst we spoke to them whilst they embraced us and kissed us we scattered the poison from our lips going back to their homes they in turn soon infected their whole families who in three days succumbed and were buried in one common grave priests and doctors visiting the sick returned from their duties ill and soon were numbered with the dead o death cruel bitter envious death which thus breaks the bonds of affection and divides father and mother brother and sister son and wife lamenting our misery we feared to fly yet we dared not remain so what this is talking about is a man who lives in sicily and travel on these ships where they were gathering goods for trade ended up spreading this illness and the people who were traveling on these ships they knew they were sick and once they got home when they met with their families and their friends they infected them now right at the end where it says we feared to fly yet we dared not remain these people are afraid to leave because they don't know what may be going on outside the confines of their city but they know what they do have to deal with is terrible so in this case the rich were able to leave while the poor people had to mostly stay so this of course is referring to black death black death was a pandemic that occurred in the 14th century it started out on the silk road so the thought is that this particular instance of plague started out in eastern asia and it followed the silk road until it got to europe it was in europe 1347 to 1351 and in europe alone this killed more than 50 million people it's about a third of the population of medieval europe what we know that they were not aware of at the time is that black death was caused by a bacterium known as yercinia pestis this is a gram-negative bacillus bacteria and this is what causes what we know as bubonic plague so plague is spread through flea bites the flea bites an infected animal so some of the animals that are naturally reservoirs for this illness are rats prairie dogs even my beloved rabbits so when these animals are bitten by a flea the flea takes the blood meal that has that yersinia pestis in it the your sanity yersinia pestis clogs up an organ in the flea known as the proventriculus when the proventriculus is clogged up as the flea hops on to take another blood meal maybe from a human this time it ends up regurgitating the blood with those bacteria in it however at the time they didn't know this so their contemporary knowledge was telling them that this is from bad air from being around bad people dirty places and that is what they thought was giving them this illness there was a huge cultural impact associated with plague we saw some works by famous writers and philosophers come out of this time period vocatio who wrote the de cameron uses the plague kind of as the backbone of that story additionally we see le dance macabre so this is a motif that was used commonly in medieval art where it will depict kings and queens popes rich people merchants and then the lowliest of all the serps all joined in hands dancing because the whole idea was it does not matter your station in life you cannot flee from death and in the end we are all joined in the dance of death additionally scandinavian countries had a concept called the plague hag and the plague was essentially a witch and she carried around a rake if you think about the way a rake looks you've got the tines and then you've got spaces between them so when the plague hag decided to use her rake all the areas that ended up getting hit with those times those are areas that got the plague they explained people who were not susceptible to plague who did not get plagued as just barely slipping through those times so plank itself came in three different flavors if you will there was septicemic which is going to infect the blood this is also the rarest and the most severe form people did not live with this one for long there's also pneumonic pneumonic is going to infect the lungs this is going to also be able to be spread through droplets so when a person is coughing they may be coughing up parts that are bacterial laden and they can thus infect others and then there's also of course bubonic the bubonic here refers to buboes so these are swellings of the lymph nodes normally in the armpits and groin and these buboes are filled with pus common knowledge at the time said that where there is pus you must remove it so they would express the pus from these boobos and in doing so their hands are covered in pus and thus infected so i don't want you to think that people in the middle ages are just getting black plagued because everyone has fleas it's true there were a lot of fleas but they're also spreading this person to person through contact with the dead or dying and their bodily fluids so i want to leave you with this adieu farewell earth's bliss this world uncertain is fond our life's lustful joys death proves them all but toys none from his darts can fly i am sick i must die and this is known as a litany in time of plague so during plague years we saw a lot of people start to come to terms with their mortality they knew they could not run from death it's just something interesting to think about because for many people this is the first pandemic we really think of however the thing is that plague didn't quite disappear with the black death we still have plague endemic in many areas here in 2015 a boy in larimer county colorado died from plague that he had caught from an infected rodent on his family's farm one of the things that you may be wondering about plague is this idea of a plague doctor so i'm sure you've seen the pictures it is kind of scary looking it is a guy with a wide brimmed hat a mask with a long beak a long leather overcoat and a super long stick and the whole idea of the plague doctor was born in the 17th century london experienced another bout of plague in 1665 through 1666 and this was called the great plague of london just to kind of give you a time frame isaac newton was alive during this so when they started having that plague they were still thinking it was the miasma theory so they thought it was bad air and because they were spending so much time around diseased people they realize that yes being around these ill people can make us ill so plague doctors were born out of basically the knowledge at the time that okay if i'm around them i may get sick so how can i protect myself so that beak they filled with fresh smelling herbs because remember it's bad airs that's thought to be spreading this so if you have nice smelling errors you might be okay that long leather coat was actually waxed so that any of the bodily fluids these doctors came into contact with would slide off and not soak into their clothes and they use that super long stick as a way to point at things without having to get their hands dirty literally touching these patients so today we're going to be dealing with epidemiology epidemiology is the study of the spread the control and the prevention of disease so some of the principles of epidemiology are we are concerned with the rate of disease in a population so epidemiologists want to know how many people in a given population are infected with a disease now remember when we're talking about a rate it's always going to be a percentage we also have a whole bunch of terms that we use in epidemiology including the morbidity rate which are going to be the number of cases divided by the population at risk now here it's important to note that that population at risk could change so it may not necessarily be every human being alive for something like covet 19 it is absolutely the world's population but for something like malaria it's going to be the population that either live in tropical areas or travel to tropical areas the mortality rate is going to be the population that does not that dies from that disease likewise the incidence rate is going to be the number of new cases we have in a specific time period so when you look at say the worldometers site and it says okay the number of new cases in new york city yesterday was eighteen thousand that's eighteen thousand cases per day that's the incidence rate for day normally we express this in terms of weeks or months prevalence is going to be the total number of existing cases and endemic diseases are diseases that are constantly present in a particular area so malaria is constantly present in the tropics we have the common cold which we've always got we have seasonal flu these are endemic an outbreak is going to be a cluster of cases in a brief time that affects a very specific population maybe the school's banned all came down with food poisoning an epidemic is when you have an unusually large number of cases in a population so perhaps 60 of the people who live in a certain town came down with food poisoning and a pandemic is going to be when that epidemic goes worldwide so that means it's going to have people sick in every single continent with antarctica of course being excluded so the thing about pandemics is a lot of people think that covid19 is the first pandemic we've had in about a hundred years and unfortunately that's not the case so sars and mers were both considered pandemics as was 2009 swine flu just to kind of put this in perspective one of the other things that we're concerned about in epidemiology is figuring out the reservoirs of these infectious diseases so the reservoir can affect how far these pathogens can spread how they're distributed and when we're able to figure out what the reservoir is we can better protect the population some of these reservoirs can be human they can be non-human animals so for example west nile virus that's going to be normally found in anything that is not human but it gets spread to humans environmental of course we've got tetanus so epidemiologists are going to investigate disease outbreaks because they want to figure out number one what's causing this illness so the causative agent is going to be the microbe or the toxin that is responsible for the illness they want to figure out the reservoir where is this naturally found and they also want to figure out how is it getting from the reservoir to our population and making us sick so the route of transmission this is going to allow them to figure out how they can minimize spread for example if we know that maybe we are getting sick from mosquitoes mosquitoes are carrying this illness to us and it's going to be mosquito-borne we can use mosquito nets we can use our bug spray uh one of the things that's interesting to note right now with a very um timely movie as it were is in the movie contagion there's a lot of epidemiologists if you've never seen it if you're interested in seeing it is currently on netflix so just you know a little plug there if you really want to scare yourself or watch something that has a lot to do with what we're living with today go check out contagion so we do have ways that we can kind of keep tabs on these infectious diseases we have the national disease surveillance network and that one's going to depend really heavily on our local agencies and state agencies so these are going to monitor disease development so if you go to the doctor and you're diagnosed with flu the doctor has to notify the health department and through these notifications the united states is able to get an idea of okay flu is hitting our citizens very hard this year we have an instance rate of this so these agencies can be your public health departments at the state level at the county level we also have the centers for disease control and prevention in atlanta we have the national institutes for health and we have who the world health organization and these are basically all there to make sure that we can keep an eye on infectious disease and when infectious disease does rear its ugly head that we have some sort of way that we can come together and try to figure it out so some of the things that we're seeing with these diseases is that we genuinely are reducing the number of infectious disease deaths we have in fact we're aiming to eradicate a lot of disease and we've been pretty successful at that some of the ways that we've found success is by improving our sanitation so making sure that human waste never comes in contact with the drinking water it seems obvious now but it has not always been so we can also control the reservoirs we can control the vectors we can vaccinate against some of these illnesses and additionally because we have antibiotics a lot of our bacterial illnesses we can just outright treat and people will not have to die it's important to note that smallpox is the only disease that we have actually globally eradicated and that's the disease that is afflicting that boy on the right hand side of the screen so he has smallpox we have luckily been able to get rid of all smallpox cases in the world another disease that we've been trying to get rid of is one that is not caused by bacteria it's not caused by viruses it's parasitic so guinea worms it's dracunculus mendinensis and these are animals so animals can spread parasitic illness and we can also be infected by animals so this nematode is basically spread through drinking contaminated water there's no medication for this and there's not a vaccine for it and think about how difficult that would be to begin with this is eukaryotic like you and i are so treatment for that is going to have to be very specific if we don't want to get sick also so the guinea worm life cycle is very interesting i know all of you have taken bio 110 i'm going to tell you a secret and give you a reason to hate copepods and if you tell dr fisher don't mention my name so what happens is a copepod that is infected with the larvae gets drank by a human so a human is drinking from some stagnant water somewhere there happens to be a copepod in it they ingest the copepod the copepod dies in the stomach acid but the parasite larvae are just fine and they end up going through the stomach into the intestine where they hang out they grow up they go to prom they get married and uh they start having babies so it's interesting that dracunculus mendinensis is dioecious and sexually dimorphic so males and females are separate creatures and they look different in this case the males are itty bitty worms and the females are very long worms so while these worms are hanging out in the intestine they reproduce once the female is fertile so she's got larvae in her body she is going to swim down from your intestine to a lower extremity normally and this actually takes about a year from when you first drank that copepod but once the female worm with all her larvae gets down to your foot or your leg it forms a little ulcer or a blister and it hurts like crazy and the best way to get relief is by putting your foot in some cold water once you put your foot in the water the worm starts squirting out her larvae so those larvae swim through the water they get eaten by the copepods within the copepods they mature a little bit more and eventually someone drinks a copepod that has the larvae in it thus perpetuating the worms life cycle so there is a reason copepods are bad we have been trying to eradicate this disease however so in 1986 the carter center starts trying to eradicate getting worm and they're really focusing on doing this through filtering water and through treating the water with different chemicals they also tell the people who live in these regions how they can best get rid of the parasite so what we see over on the right hand side is a woman who is using a life straw this is a straw that has a filter built into it so that even if you see the nastiest water it is supposed to filter out the majority of parasites bacteria protozoans and viruses so this is how we are able to try to treat this earlier attempts included telling people that if they wanted to drink the water to make sure that they had a drinking straw and that they could put a piece of nylon pantyhose over it because those pantyhose had pores big enough for the water to come through but the copepods could not come through and we have been wildly successful with trying to eradicate getting worm it still exists however we have decreased infections by 99 percent there were only 28 total cases worldwide in 2018 so look at that we went from three and a half million cases in 1986 down to 28 total cases in 2018 so it's definitely been very successful there's still work to do though another thing that's kind of helped us in treating infectious disease has been the recent developments we've really had in the science and medical industries so if you look at this graph on the x-axis that's actually supposed to start at 1900 but 1900 states are starting to develop health departments those health departments are going to monitor the diseases and they're going to say okay it looks like maybe the people in this area have been exposed what can we do to treat it on top of that you'll notice that the trend keeps going down so less and less people are dying from infectious disease once we hit around 1910 or so we have municipal water adding chlorine to kill more of those pathogens however right before 1920 1918 we have an influenza pandemic now a lot of people know this as the spanish flu however it's important to note that this flu did not originate in spain so this is in the world war one era and spain was not participating spain did not have a horse in the race so they were just kind of standing back watching things happen as a result their news was not really reporting war stories so much as they were reporting hey it looks like a lot of people are starting to die from this flu so the rest of the world started deciding okay if spain's reporting on it it must be spanish and origin that is not the case the first described and known case of the so-called spanish flu was actually in fort riley kansas in march of 1918. so it looks like it started a little closer to home yet history reminds the remembers this as the spanish flu however once we get past that influenza pandemic we see a huge drop in the number of deaths from infectious disease in fact right around 1923 or so we have our last human to human transmission of plague so remember plague can be transmitted from human to human people absolutely do still get plague but now it's treated by antibiotics as we continue along this graph we've got antibiotics showing up and that's going to allow even less people to actually have a chance to die from infectious disease then we have the sulk vaccine for polio introduced then we introduce the vaccination assistance act and notice how low this actually drops yet as we get closer to 2000 we start to see a little bit of an uptick kind of think about what some of the reasons for those are now in the world today we have almost 70 percent of the continent of africa vaccinated however los angeles county california it's as low as 20 percent in some areas so people have stopped vaccinating and that's kind of leading to some of these trends we see in diseases so we do have diseases that are brand new and they are just springing up and are super recent within the last 50 years we've got hiv of course we've also got our sars our mers and our coveted 19s that have started to emerge but we also see re-emerging diseases so these are diseases that we had a holdover we were handling them just fine yet they're starting to make a comeback these are things like whooping cough measles and mumps and one of the things that we really want you to know about this is that these re-emerging diseases we had under control because of vaccines so with people not becoming vaccinated that's why we start seeing these diseases re-emerge so for this week's lab you're going to read over the notes and you're going to listen to me talk for a bit then you have a cdc epidemiology mission game you'll take a screenshot of your completed game and answer the questions i will make a second video kind of showing you how that website works just in case you're confused but it's not required to watch additionally we have the typhoid mary video and we also have some questions written about that now typhoid mary is a super interesting case because she was one of the first known asymptomatic carriers of typhoid fever now when you think about asymptomatic carriers that's something we've seen in the news a lot recently and we have been told wear your masks when you go out but there's a lot of misinformation going on a lot of people seem to think that wearing their masks when they're out is going to protect them from picking up the disease and to be fair it's not really meant to do that so an asymptomatic carrier of covet 19 could absolutely be spreading this to people who do become symptomatic and may even die however if an asymptomatic carrier is wearing a mask when they run over to king soups to get whatever they need they're going to likely prevent the large spread of the virus particles so it's kind of interesting to think in terms of asymptomatic carriers typhoid mary was in the 1900s here we are in 2020 and asymptomatic carriers are still an issue so it's something interesting to kind of consider when you're watching that video and answering those questions besides that you are also going to have your lab final next week so the lab finals going to be given on canvas it's going to start at the beginning of your lab period and it will be open for 24 hours so for example for my section that starts at 4 pm on wednesday the lab final will be open from 4 pm wednesday until 4 pm on thursday we really want this to be a closed note closed resource and no collaboration between students so we really want to see how well we have done it teaching you this material it's important to us to know if we were still able to be effective especially as we move to online instruction so please just take it on your own we'll do our best to make sure that you feel good about this okay so if you have questions about any of the material please let us know you do you'll be given three hours to complete the exam if you have a drc accommodation remember to submit that and the questions that will be on there they're going to be over material that we've done since the midterm so all of this online material plus some of the things from before that so you'll want to look at the study guide on the next slide to really get a better idea of what we'll be asking but there's going to be mostly material from after the midterm you can expect questions very similar to what you've seen on some of our previous quizzes and our midterms additionally we may give you some practical questions where we put a picture of inoculated media up and we have you try to identify the readout so with that having been said um we all wish you the best of luck on this and if you have questions please let any of us know we are happy to help out take care cover your cough wash your hands and wear your masks when you go out