BIOL 0380 Epidemiology Study Guide PDF

#separator:tab #html:true #tags column:3 The study of epidemics using statistics and probability to stuudy disease is known as {{c1::epidemiology}}  The father of epidemiology was {{c1::John snow}} due to contact tracing a water pump during a cholera outbreak. Due to cases being clustere...

#separator:tab #html:true #tags column:3 The study of epidemics using statistics and probability to stuudy disease is known as {{c1::epidemiology}}  The father of epidemiology was {{c1::John snow}} due to contact tracing a water pump during a cholera outbreak. Due to cases being clustered around a street pump {{c1::Epidemic}} is the sudden, short-term outbreak in humans to a specific location or population over a short time.  {{c1::Endemic}} is a longterm, consistent presence at a baseline level wtihin a specific region  "{{c1::Crowd diseases}} spreads rapidly and is sustained in large populations, typically in dense communities. Smallpox, measles" {{c1::Critical community size}} is the minimum population size needed for a disease to sustain itself in a community without dying out.  Endemic diseases, unlike crowd diseases, often have other mechanisms {{c1::(e.g., environmental factors, animal reservoirs)}} to maintain their presence beyond CCS.  3 clinical forms of the plague: {{c1::Bubonic}}: inflammed lymphnodes transmitted by fleas Mortality 30-90%Death occurs within 10 days {{c1::Pneumonic}}: lung infection Human-human via spread of droplets Mortality of 90-100% {{c1::Septicemic}}: flea-human transmission within blood {{c1::Zoonotic}}: animal to human disease  {{c1::Sylvatic cycle}}: the transmission cycle of a pathogen that primarily circulates in wild animal populations without immediate human involvement.  {{c1::Enzootic}}: a longterm consistent presence of a disease within an animal population in a specific region.  {{c1::Epizootic}}: a disease outbreak that briefly affects animal population in a short period of time.  SIR model answers the question: {{c1::will an epidemic occur }}Compartment model via measuring rate of individuals moving across compartments {{c1::ß}}: the transmission rate or rate of an infected person getting someone sick.  {{c1::v}}: clearance rate or rate of recovery/death  SIR model assumptions Population size is {{c1::constant}}, N = S(t) + I(t) + R(t) No births/deaths Well mixed populations: everyone has an equal chnace of coming into contact with one another {{c2::Mass action}}: rate of change of new infections, ß, is proportional to S x I, well mixing Everyone starts susceptible except for one infected Once removed cannot come backRates are uniform  "Susceptible population equation. Susceptible population, S(t) decreases over time as people become infected. \[{{c1::\frac{dS(t)}{dt} = -ß*\frac{I(t)*S(t)}{N}}}\]{{c1::-ß}} transmission rate {{c1::I(t)*S(t)}} --> mass action principle where # new infections proportional with encounters between susceptible and infected people. " Formula for infected population \({{c1::\frac{dI(t)}{dt}=ß *\frac{I(t)*S(t)}{N} *-v*I(t)}}\){{c1::-v*I(t)}} --> rate of infected recovering  Recovered population equation: \({{c1::\frac{dR(t)}{dt}=v*I(t)}}\)Mass action not present due to population being seperate - recovery rate  Basic reproductive number, R0. {{c1::R0 > 1:}} more infected than recovered (epidemic){{c1::R0 <1:}} more recovered than infected  Effective reproductive number, Re accounts for changes in the {{c1::susceptible population over time}} \(Re = R0 *\frac{S(t)}{N}\){{c2::Re > 1}}: each infected person causes more than one new infection, leading to exponential growth in the number of cases and an epidemic spread.{{c2::Re < 1:}} Epidemic decline, where each infected person, on average, transmits the disease to less than one other person Slowing epidemic spread: {{c1::Increasing v:}} reducing duration of infection via antibiotics and vaccine {{c1::Reducing ß}}: public health measures such as masking/quarantine  Breaking SIR model assumptions: N = constant. {{c1::Reasonable assumption }}Everyone starts susceptible except for infected {{c1::Herd immunity}} Rates are uniform between individuals {{c1::superspreaders}} Mass action{{c1::social distancing/quarintine decreases freq}} Once removed cannot get sick {{c1::More compartments}}  Herd immunity threshold: used to calculate fraction of population that needs to be innoculated\({{c1::\frac{R(t)}{N}>1-\frac{1}{R0}}}\) v can act as the inverse of infection time \({{c1::v= \frac{1}{infect.time}}}\) At the beginning of an epidemic (time t=0), the entire population is typically susceptible to the disease because no one has been infected yet. This means that\({{c1::S(0)=N}}\) "Formual to estimate basic reproductive number post-epidemic: \(R0=\frac{ln(\frac{S(∞)}{N}) }{[\frac{S(∞)}{N}-1]}\)\({{c1::\frac{S(∞)}{N}}}\): explains the fraction of the population that remains susceptible at the end of the epidemic." SIR is a good model for the {{c1::initial}} exponential rise in cases  {{c1::Cordon sanitaries}} is the restriction of movement of people into or out of a defined geographic area to control disease spread.  {{c1::non-pharmaceutical intervention (NPI)}} can flatten the curve. Effects of social distancing for 1918 fluSt. louis (approp) vs Philly (inapp) Early covid mortality in china decreased due to availability of resources  {{c1::Stochastic}} models presents data and predicts outcomes that account for certain levels of unpredictability or randomness. {{c1::Backward}} tracing looks for source of infection by identifying who infected the patientPro: useful for identifying superspreaders Con: harder to keep up with transmission chains  {{c1::Forward tracing}} identifies ppl who were in contact with an infected personPro: effective for stopping future transmissions Con: may miss superspreading events  Contact tracing decreases {{c1::transmission rates, ß,}} due to decrasing number of infected people Novel strategies for contact tracing:{{c1::Wastewater}}50% of asymptomatic/symptomatic patients shed virus in feces Correlates will with number of cases and helps identify novel variants. {{c1::Genetic epidemiology}}Everyone with the same strain - hot spot two ppl with different strains - didnt infect eachother Supplement contact tracing