(The study of) the causes of disease.
The potential for a reduction in the outcome of disease if a risk factor is removed. If Ie is the number of people exposed to the risk factor of interest who have a disease and Io is the number of people exposed to the risk factor without disease, then the aetiological fraction is (Ie-Io)/Ie. Also known as the attributable fraction.
A mathematical model which take into
consideration the division of the host population into different age classes. Such models can used to consider the consequences of such factors as age-dependent infection, morbidity or mortality rates or of age-specific vaccination schedules.
A distribution of parasites among hosts is said to be aggregated, or overdispersed, if parasites are found to co-occur in particular hosts more often than if the parasites were distributed at random among all hosts.
A more precise test would be if the distribution differed significantly from a Poisson distribution; a good heuristic is whether the variance to mean ratio is bigger than unity (in appropriate units).
Macroparasites are typically aggregated in their host populations, so that the majority of hosts harbour few or no parasites while a few hosts harbour large parasite burdens. Aggregated distributions are often well described empirically by the negative
The period between conception and
birth. Same as prenatal.
A protein produced in the blood of vertebrates following exposure to an antigen. The antibody binds specifically to the antigen and thus stimulates its inactivation by other parts of the immune system.
The major classes of antibody are
immmunoglobulin A, or IgA, found predominantly in bodily secretions like saliva; IgM and IgG which are typically produced sequentially in response to microparasitic infections; and IgE which is often elevated in the response to helminth infections. Only IgG is able to cross the placenta to provide
A protein, typically foreign, that elicits a specific immune response.
A drug, for example praziquantal, used specifically against helminth or worm infections.
A virus which uses Arthropods as
vectors and is transmitted in their saliva to the definitive host. For example, yellow fever.
(From Arthropod borne
The same as aetiological fraction.
A white blood cell which produces
The presence of bacteria in the blood.
Basic Reproductive Rate, Ratio
See Reproductive Ratio.
Birth, Immigration, Death, Emigration: the four demographic processes which might act on a population compartment in a typical compartmental model.
See transmission breakpoint.
An individual who is infected but has no symptoms of disease.
There are two types of carrier state:
silent carriers retain their infectiousness, while latent carriers are not infectious. For example, many of those infected with tuberculosis are silent carriers, while infection with herpes virus may create latent carriers.
The maximum number of individuals a habitat can sustainably support. Typically defined so as not to include losses from predation or disease.
A (rather misleading name for a) type of compartmental model in which the force of infection is treated as a parameter to be estimated.
A study in which the risk factors of people with a disease are compared with those without a disease.
Drug treatment of a diseased individual.
Drug treatment designed to prevent future occurrences of disease. Treatment may be chemotherapy
as far as an individual is concerned but chemopropylactic for the population as a whole.
Our term for the varieties of epidemiology
primarily concerned with the statistical relationships between disease agents, both infectious and non-infectious; for example a study to establish the relative risk of lung Cancer associated with smoking.
We contrast this with ecological epidemiology.
Close contact infection
An infection which requires close contact, other than sexual contact, between susceptible and infectious individuals, for transmission.
Cytomegalovirus: a herpes virus which
causes glandular fever (as does EBV).
Changes in the genotypes of two or more species that are a direct consequence of the species' interaction with one another.
A subsection of a population with a common feature, usually age. For example, all those individuals in the UK born in 1964 form a birth cohort.
A mathematical model which divides hosts into different compartments according to their infectious state. A typical model for microparasites might be an SEIR model. Sometimes referred to as a prevalence model.
The rate at which
susceptibles meet infecteds.
Usually measured as individuals per unit time.
Same as an aggregated distribution.
Continuous time model
A model in which the system changes
continuously over time. Derivatives (e.g. dY/dt) are the mathematical formalism for describing such continuous change. The differential equation which embodies a model provides the values of these derivatives at any particular time point; calculus or a computer can then be used to move the state of the model forwards in time.
Continuous models have the advantage
over discrete time models in that they are more amenable to algebraic manipulation, although they are slightly harder to implement on a computer.
The same as a differential equation model.
Congenital rubella syndrome.
Same as a horizontal study.
Crude birth rate
The number of live births in a year divided by the population size.
Crude death rate
The number of deaths in a year divided by the population size.
The host in which a parasite reproduces
1) Effects whose intensity changes with increasing population density.
2) Effects whose intensity increases
with increasing population density, for example a mortality which becomes very high near a carrying capacity. Effects which become less pronounced at higher population sizes (perhaps the reduction in fecundity caused by the difficulty of mating) are sometimes called inverse density dependent. Density dependent effects are often a cause of nonlinearity in a model.
A mathematical model in which the
parameters and variables are not subject to random fluctuations, so that the system is at any time entirely defined by the initial conditions chosen. Contrast with a stochastic model.
A device for starting futile arguments over definitions.
The mathematical formulation corresponding to a continuous model; an equation involving
The mathematical formulation corresponding to a discrete time model.
Having separate sexes, opposite of
Direct life cycle
A life cycle in which a parasite
is transmitted directly from one host to the next without an intermediate
host or vector of another species.
Discrete time model
A model in which the system jumps from one state to the next at fixed intervals or timesteps. These difference models are simple to understand but often difficult to analyse; Contrast continuous time models.
The parameters in such a model refer
to the amount of change over the finite timestep; they are sometimes referred
to as finite rates.
In a (rather precise) sense, a differential
equation is what you eventually get from a difference equation when you
let the timestep get smaller and smaller and smaller.
The debilitating effects on a host of infection by a parasite.
The pattern by which parasite numbers
are partitioned among available hosts. If the fraction of the population who have i parasites is p(i) then the distribution is the set of numbers p(0),p(1), p(2), ... . Summary statistics of this distribution include prevalence (1-p(0)) and mean intensity ( p(1)+ 2p(2)+ 3p(3)+...). Useful distributions include the Poisson and negative binomial.
Epstein-Barr virus: a herpes virus which causes glandular fever (as does CMV) and some Cancers.
A branch of epidemiology which views
disease as a result of the ecological interactions between populations
of hosts and parasites; what we do. We contrast this with classical
An index of the potency of a drug or disease treatment.
For an anthelmintic, usually estimated as the proportion of the worm burden in a host killed by a single dose or short-term course of the treatment. For a vaccine, efficacy is the percentage of persons who are protected by the vaccine.
Specifically, if Iv is the incidence in vaccinated individuals and Iu then vaccine efficacy is v=1-Iv/Iu. Note that this may include the effects of protection due to herd immunity, and so is not the same as same as Immunogenicity, even if the presence of an immune reaction always indicated individual protection.
A technique using the antigen binding
properties of antibodies to detect specific antigens or antibodies. Visualisation is typically made possible by enzyme induced colour formation.
From Enzyme Linked ImmunoSorbent Assay.
A term to describe levels of infection which do not exhibit wide fluctuations through time in a defined place.
For microparasites like measles, the
term is used slightly differently to indicate an infection which can persist in a population in the long term without needing to be reintroduced from
Stable endemicity is where the incidence of infection or disease shows no secular trend for increase or decrease.
Parasite extinction occurring because
endemic levels are so low that it is possible for small stochastic fluctuations to remove all parasites. Contrast epidemic fadeout.
A rapid increase in the levels of an infection. Typical of the microparasitic infections (with long lasting immunity and short generation times) an epidemic is usually heralded by an exponential rise in the number of cases in time and a subsequent decline as susceptible numbers are exhausted.
Epidemics may arise from the introduction of a novel Pathogen (or strain) to a previously unexposed (naive) population or as a result of the regrowth of susceptible
numbers some time after a previous epidemic due to the same infectious agent. Contrast endemic, pandemic.
Parasite extinction occurring because
numbers are so low immediately following an epidemic that it is possible for small stochastic fluctuations to remove all parasites. Contrast endemic fadeout.
An epidemic in
an animal host population. (But see Nature, 368, 284, (1994))
An epidemic in a plant host population.
A state in which a system is not changing. A population size might be at a static equilibrium at which nothing is happening (there are no births or deaths) or a dynamic equilibrium at which different processes are balanced (there are the same numbers of births and deaths). More generally, the state to which a system eventually evolves, for example sustained periodic oscillations, might be called an equilibrium.
A decline in which the rate of decay is always proportional to the amount of material remaining; the constant of proportionality is the rate constant.
An increase in which the rate of
growth is always proportional to the amount of material remaining; the
constant of proportionality is the rate constant.
See Odds ratio.
The capacity to produce offspring;
the rate of offspring production.
Force of infection
The per capita rate at which susceptibles
Hepatitis A, B and C virus. These
very different viruses all cause the liver disease hepatitis. Hepatitis
B and C are blood borne, while Hepatitis A is an enterovirus which is faeco-orally
transmitted. Other known hepatitis viruses include Hepatitis D and Hepatitis
Worms, in particular the five groups
of parasitic worms: Monogeneans (flukes), Digeneans (flukes, schistosomes),
Cestodes (tapeworms), Nematodes (roundworms) and Acanthocephalans (spiny-headed
Specifically, the mechanism by which
an infection may be eradicated from a population although some susceptibles
still remain, because the remainder of the population is immune and thus
transmission is reduced.
More generally, the Immunological
status of a population of hosts and its effect on transmission rates.
Haemagglutination inhibition test,
a serological test used to detect antibodies specific to a particular family
of viruses which possess the ability to agglutinate red blood cells e.g.
measles, rubella and influenza.
Haemophilus influenzae B.
Human Immunodeficiency virus: the
cause of Acquired Immune Deficiency Syndrome (AIDS).
Human papillomavirus, causing genital
warts and genital Cancers.
Herpes simplex virus. Types one and
two, HSV-I and HSV-II, are among the causes of cold sores and genital ulcers.
An infection whose prevalence is
fairly uniform throughout a region, country or continent.
Often used in the malaria literature.
A study of a community, perhaps stratified
by age, sex, ethnicity etc., but at one point in time or over a short time
Although a snapshot, horizontal surveys
of prevalence and intensity within different age classes of a community
can nevertheless provide valuable information on the rate at which hosts
acquire infection through time, provided that the host and parasite populations
have remained approximately stable for a period of time (ie stable
endemicity). Same as cross-sectional study, converse of longitudinal
Transmission occurring generally
within a population, but not including vertical transmission.
A term from the malaria literature
used to mean (roughly) an area with little transmission.
1) A state in which a host is not
susceptible to infection or disease, or
2) the mechanisms by which this is
achieved. Immunity is achieved by an individual through one of three routes:
natural or innate immunity Genetically inherited or acquired
Also termed specific immunity, resistance
or specific resistance.
Specific immunity is divided into
cellular immunity acting via the direct involvement of T
cells and humoral immunity involving antibodies
and B cells.
The ability of a vaccine
to stimulate the immune system, as measured by the proportion of individuals
who produce specific antibody or T cells, or the amount of antibody produced,
say. Not the same as efficacy.
Damage to the host caused by its
own immune response against a Pathogen.
A reduction in the capacity of the
immune system. Caused by infection (eg HIV), drug treatment,
pregnancy and malnutrition among others. Immunosuppressed individuals are
commonly referred to as Immunocompromized.
The rate at which new cases of infection
arise in a population. Classically measured as an attack
The time that elapses between infection
and the appearance of symptoms of a disease. Not the same as the latent
A life cycle which requires one or
more intermediate hosts before the definitive
host species is reinfected. Compare direct, nondirect.
Transmission of a parasite through
an indirect life cycle.
The presence of a parasite within
a host where it may or may not cause disease.
n., A host who has an infection.
The time period during which infecteds
are able to transmit an infection to any susceptible
host or vector they contact. Note that the infectious
period may not necessarily be associated with symptoms of the disease.
The amount of parasite to which an
individual host is exposed at transmission.
In a short time interval (e.g a week),
the number of events (e.g. births in the UK) taking place during the interval
is approximately proportional to the length of the interval. The constant
of proportionality is the rate at which these events occur. This
argument becomes more and more exact as the length of the time interval
becomes shorter and shorter. When the time interval has shrunk to an instant,
the rate has become an `instantaneous rate'. A bad term; just call it a
The mean parasite burden within all the infected
members of the host population. Also called mean abundance.
The mean parasite burden within both infected and uninfected hosts.
It is important to indicate which
usage is adopted, since they give different statistics, unless the prevalence
is 100%. Macroparasites, and infections like malaria, are usually measured
in terms of intensity.
The time from infection to when the
individual is infectious to others. In helminths
it is termed the pre-patent period. Not the same as the incubation
Longevity, the average length of
life of individuals in a population.
Given some data (for example maternal
antibody levels), and a model for how a process supposedly generating it
occurs, (for example, exponential decay with rate m ), and for how
variance is likely to occur in observations of the process (for example
sampling error), the likelihood that a particular model (ie a particular
m plus the error in observation can generate the observed data.
Picking the parameter value which is most likely to have generated the
observed data is the method of maximum likelihood.
A process is linear if doubling the
starting conditions doubles the outcome. For example, the number of new
schistosome infections establishing in mice is directly proportional to
the number of cercaria the mice are exposed to, over a certain range. Outside
this range, the response is nonlinear: there is
no longer a direct proportionality.
equations are ones whose solutions are linear. This property allows
us to solve linear differential equations completely: most nonlinear differential
equations can't be solved analytically.
A study taking place over time. If
individuals are followed, this is a longitudinal cohort study. If individuals
are not followed, but classes (usually age classes) are restudied, this
is a longitudinal cross-sectional study.
The converse of a horizontal
Transmission of infection which occurs
at a rate directly proportional to the number or density of both susceptibles
and infecteds present.
Some authors reserve the name mass
action for transmission processes of the form b X Y/N, which we
associate with STD-type transmission, and describe transmission rates of
the form b X Y, as pseudo-mass action; the two are equivalent
if the population size is unchanging.
Typically, the parasitic helminths
and arthropods. In general, parasites which do not multiply within their
definitive hosts but instead produce transmission
stages (eggs and larvae) which pass into the external environment. Immune
responses elicited against macroparasites generally depend on the number
of parasites present in a given host and tends to be of a relatively transient
nature. The key epidemiological measurement is generally the number of
parasites per host.
Such parasites are often found in
a highly aggregated distribution.
Immunity for a neonate provided by
IgG antibody generated by a mother and passed across
the placenta to the unborn offspring. This provides short lived protection
(with a typical half life of 3-6 months) to the neonate. Also known as
A formal framework to convey ideas
about the components of a host-parasite interaction. Construction requires
three major types of information: (a) a clear understanding of the interaction
within the individual host between the infectious agent and the host, (b)
the mode and rate of transmission between individuals, and (c) host population
characteristics such as demography and behaviour.
Mathematical models can aid exploration
of the behaviour of the system under various conditions from which to determine
the dominant factors generating observed patterns and phenomena. They also
aid data collection and interpretation and parameter estimation, and provide
tools for identifying possible approaches to control and for assessing
the potential impact of different intervention measures.
A term from the malaria literature
used to mean (roughly) an area with some transmission.
Typically, viruses, bacteria, fungi
and protozoa. More generally, parasites which multiply within their definitive
hosts. Microparasites are characterized by small size, short generation
times, and a tendency to induce immunity to reinfection in those hosts
that survive. The duration of infection is usually short in relation to
the lifespan of the host, but there are important exceptions, such as the
slow viruses. The key epidemiological variable, by contrast with macroparasites,
is whether or not the individual host is infected.
Chemical substances which kill snails
or other molluscs.
Male and female sexual apparatus
present in the same individual. Same as hermaphrodite; opposite
State of ill-health produced by a
The per capita death rate in a population.
The mortality rate is the reciprocal of the population life expectancy.
An infection in which an individual
is infected by parasites of more than one species.
which is parameterised by a mean m and an aggregation parameter
k which is large when aggregation is
small; in fact as k becomes large, the negative binomial distribution
approximates the Poisson distribution.
Diseases, usually of an infectious
nature, whose occurrence is required by law to be made known to a health
officer or local government authority.
A mode of transmission that differs
in some mysterious way from indirect transmission;
we don't make a distinction in this course.
A comparison of the presence of a
risk factor for disease in a sample of diseased subjects and non diseased
controls. The number of people with disease who were exposed to a risk
factor (Ie) over those with disease who were not exposed (Io)
divided by those without disease who were exposed (Ne) over those
without who were not exposed (No). Thus OR=(Ie/Io)/(Ne/No)= Ie
No / Io Ne. This measure should be used for case control studies where
we retrospectively look at risks in those with and without disease. Also
known as exposure odds ratio.
widely distributed in space.
A widely distributed epizootic,
often one affecting more than one host species.
Immunity which has been acquired
through the transfer of maternal or other antibodies.
Passive immunization does not induce Immunological memory.
1) Any disease causing organizm.
2) An organizm exhibiting an obligatory dependence on another organizm,
its host, which is detrimental to the host.
Same as a parasite.
The degree to which a Pathogen debilitates
Between the 28th week of pregnancy
and the end of the first week of life.
A rate which is proportional to the
number of individuals in a population.
The distribution which arises when
parasites are distributed at random among hosts.
Subsequent to (and within 1 year
The time from infection until when
a female starts to produce eggs in helminth infections, equivalent to latent
period in micro-parasitic infections.
An animal that kills its prey and
then feeds on it to subsist until the next kill.
The proportion of the host population
infected (or with some marker of past or present infection) at a particular
Prevalence models are compartmental
models dividing the host population into, for example, susceptible, latent,
infectious and immune individuals.
A study in which people are initially
enrolled and then followed up at subsequent times.
A unicellular eukaryote.
A period during which an infection
is present but not active within a host: for example the period between
an acute attack of chickenpox (varicella) and a subsequent
recrudescence of shingles (zoster); not the same as latency.
The number of events happening divided
by the length of time over which they happen. A rate of change is the amount
of change happening in a interval divided by the length of the interval;
for small intervals the rate of change might be given by a simple rule
(a differential equation).
Reappearance of disease in a host
whose infection has been quiescent.
reproductive ratio, Ro, a dimensionless parameter
which encapsulates the biological details of different transmission mechanisms.
For microparasites, Ro, is defined as the average number of secondary
cases of infection to which one primary case gives rise throughout its
infectious period if introduced into a defined
population consisting solely of susceptible
For macroparasites, Ro, is the average number of female
offspring (or just offspring in the case of hermaphroditic species) produced
throughout the lifetime of a mature female parasite, which themselves achieve
reproductive maturity in the absence of density-dependent constraints on
the parasite establishment, survival or reproduction.
Also known as the basic
reproduction rate, number.
reproductive ratio, R, The number of secondary cases
(microparasites) or female offspring (macroparasites) produced in a host
population not consisting entirely of susceptible individuals (microparasites)
or within which density dependent constraints limit parasite population
growth (macroparasites). Under conditions of stable endemic infection,
The proportion of diseased people
amongst those exposed to the relevant risk factor divided by the proportion
of diseased people among those not exposed to the risk factor. This should
be used in those cohort studies where those with and without disease are
followed to observe which individuals become diseased.
1) The reduction, due to Genetic
selection, of susceptibility of a parasite or its vector to chemotherapy.
2) The ability of a host to resist
a Pathogen. Compare immunity.
A study in which people are enrolled
and then have their history of risks, infections or disease measured.
A class of compartmental prevalence
models, with compartments Susceptible, Latent (Exposed), Infectious
and Recovered. Takes its name from a common notation. In the notation used
in the course, this would be
an XHYZ model. Many permutations possible.
The ability of a test to work on
people you know have the infection. More precisely TP/(TP+FN), where TP
is the number of true positives and FN is the number of false negatives
The study of antigen-antibody reactions.
More generally, the use of serotype data to infer
an individual's history of infection.
n., an individual whose serotype
suggests that they have experienced infection in the past.
The proportion of a population who
The range of antibodies
which an individual possesses, usually based on sampling from blood serum
Different strains of a Pathogen can
sometimes be distinguished by the different antibodies they induce in a host, or with which they can be made to react in vitro; thus the word serotype has also come to be applied to a particular strain (`the virulent serotype'). This is the more common clinical usage.
The range of antibodies used to define
a serotype obviously depends on those available to the researcher. Sometimes, as for measles, the presence of a known antibody within the Serum of an individual correlates extremely well with the clinical observation that that individual is protected against any further infections.
But sometimes, as for malaria, there is as yet no definite relationship between a given
serotype and the presence of a functional immunity, which may make the use of the word serotype unhelpful when trying to distinguish between different parasites for the purposes of understanding transmission.
The ability of a test to fail on people you know don't have the infection. More precisely TN/(TN+FP), where TN is the number of true negatives and FP is the number of false positives
A mathematical model which takes
into consideration the presence of some randomness in one or more of its parameters or variables. The predictions of the model therefore do not give a single point estimate but a probability distribution of possible estimates. Contrast with deterministic.
We might distinguish demographic stochasticity which arises from the discreteness of individuals
and individual events such as birth, and environmental stochasticity
arising from more-or-less unpredictable interactions with the outside world.
An infection in which symptoms are
sufficiently mild or inapparent to escape diagnosis other than by positive confirmation of the ability to transmit the infection or serologically.
Sexually transmitted disease.
An individual accessible to or liable
to infection by a Pathogen.
A condition of the body reported
by an individual when suffering from a disease; here used more loosely
to include signs: any evidence used in diagnosis or identification
of infected individuals.
A white blood cell responsible for
Cell-Mediated immunity in particular and Immunoregulation in general.
Total fertility rate (TFR)
The number of children an average
women would have assuming that she lives her full reproductive lifetime.
The process by which a Pathogen passes
from a source of infection to a new host. There are two major types: horizontal and vertical transmission. The majority of transmission processes operate horizontally.
A critical average worm burden below
which the mating frequency is too low to maintain a dioecious
Occurs for a parasite when the basic
reproductive rate Ro is equal to 1. Below this threshold level the disease is unable to maintain itself within the host population. Typically, for directly transmitted parasites there is a transmission threshold for the host population size.
Type I mortality
A mortality schedule in which all hosts are assumed to live for a fixed number of years equal to the life expectancy.
Type II mortality
A mortality schedule in which all hosts are assumed to die at a constant rate. This constant rate is equal to the inverse of the life expectancy.
A drug intended to induce active
artificial immunity against a Pathogen. Vaccines may be live
or dead. Live vaccines are usually
attenuated versions of the wildtype Pathogen, such as the MMR vaccines,
which are strains of measles mumps and rubella viruses repeatedly passaged
through cell lines until non-Pathogenic. Typically, live vaccines need
only be given as a single dose to induce a full
Immunological response, inducing specific memory.
Dead vaccines are either killed whole parasite, as with the Salk polio strain and pertussis vaccine, or some highly Immunogenic fraction of the parasite, as in toxoid vaccines. Killed
vaccines and toxoids which do not multiply in the host must usually be administered in multiple doses to induce a full Immunological response.
Vaccination should be distinguished
from passive immunization in which concentrated specific antibodies which can be used therapeutically to abrogate an ongoing infection or to provide short term protection (of the order of months), for example against hepatitis A. Passive immunization does not induce Immunological memory.
1) The intermediate hosts of parasites
with indirect life cycles.
2) Anything which transmits parasites.
infections such as malaria, the vectorial capacity is a concept analogous
to the contact rate in directly-transmitted
diseases. It is, thus, a function of (a) the vector's density in relation
to its vertebrate host, (b) the frequency with which it takes blood meals
on the host species, (c) the duration of the latent period
in the vector, and (d) the vector's life expectancy.
Vertical transmission occurs when
a parent conveys an infection to its unborn offspring, as occurs in syphilis
in man or in many arboviruses of arthropods. Perinatal
infection is a special form of vertical transmission.
The presence of virus in the blood.
A mature and infectious virus particle.
(1) The case mortality rate of an
infection. (2) The extent to which a Pathogen harms its host. These are
different usages: what they have in common is that they refer to the effect
on an already infected host, not to the degree of transmissibility to a
Varicella-zoster virus: a herpes
virus which causes chickenpox (varicella) and shingles (herpes-zoster).
The number of worms an individual
host carries. Sometimes directly measurable (Ascaris), sometimes
only indirectly (schistosomiasis).
A parasite naturally transmitted
between man and other vertebrate species