Classification and Patterns of Disease

Lessons

Senior 4 · Biology

Classification and Patterns of Disease

5 lessons

Lesson 3 of 5

Case studies of infectious diseases: malaria, TB, cholera and HIV

25 min

From 4.8 million to 620 000, and back up

In the year from July 2016 to June 2017, Rwanda's health facilities and community health workers treated about 4.8 million cases of malaria, in a country of about 12 million people. By 2023–24 the number had fallen to about 620 000. Then, in 2024, cases rose again by almost half. A disease does not rise and fall by chance: each change has causes in the pathogen, its route of spread, the people at risk and the measures used against it.

This lesson studies four infectious diseases that matter in Rwanda (malaria, tuberculosis, cholera and HIV) in the same way an epidemiologist would, and uses Rwandan data to judge how well control measures work. You met their basic signs and prevention in S2; here the focus is on why they spread, and on the evidence.

Definition

Reservoir: where a pathogen normally lives and multiplies, for example infected people (HIV, TB), water and infected people (cholera).

Vector: an organism, usually an insect, that carries a pathogen from one host to another, for example the female Anopheles mosquito for malaria.

Carrier: an infected person who has no symptoms but can pass the pathogen on.

Incubation period: the time between infection and the first symptoms.

Latent infection: an infection in which the pathogen is present but inactive and causes no symptoms, as in latent tuberculosis.

Opportunistic infection: an infection that causes disease mainly in people whose immunity is weakened, for example TB or oral thrush in a person with untreated HIV.

The chain of infection

Every infectious disease spreads through the same six links. Control works by breaking at least one of them; the best programmes break several at once.

Four diseases compared

	Malaria	Tuberculosis (TB)	Cholera	HIV infection and AIDS
Pathogen	Protoctist Plasmodium (several species; P. falciparum is the most dangerous)	Bacterium Mycobacterium tuberculosis	Bacterium Vibrio cholerae	Human immunodeficiency virus (a retrovirus)
Transmission	Bite of an infected female Anopheles mosquito (vector)	Airborne droplets from coughing by a person with active lung TB	Faecal–oral: water or food contaminated with faeces	Unprotected sex, infected blood or needles, mother to child in pregnancy, birth or breastfeeding
Main signs	Fever, chills, headache; severe malaria can cause anaemia, coma and death	Cough for 2 weeks or more, night sweats, weight loss, fever, sometimes blood in sputum	Sudden, profuse watery diarrhoea and vomiting; rapid dehydration	Years without symptoms, then falling CD4 cells, weight loss and opportunistic infections (AIDS)
Diagnosis	Rapid diagnostic test or blood smear under the microscope	Sputum test (GeneXpert or acid-fast stain), chest X-ray	Stool test; mainly signs during an outbreak	HIV antibody rapid tests, confirmed by a second test
Prevention	Insecticide-treated nets, indoor residual spraying, draining breeding sites, prompt treatment	Find and treat cases early, ventilation, BCG vaccine for infants, preventive therapy for contacts	Safe water, latrines, handwashing, food hygiene, oral cholera vaccine	Condoms, testing, treatment as prevention, prevention of mother-to-child transmission, sterile needles
Treatment	Artemisinin-based combination therapy (ACT)	At least 6 months of combined antibiotics, taken under supervision	Oral rehydration solution; intravenous fluids and antibiotics if severe	Lifelong antiretroviral therapy (ART); no cure

Case study 1: malaria

Rwanda's malaria rose steadily from 2012 to a peak in 2016–17. The national programme then scaled up indoor residual spraying (IRS) of houses in the worst-affected districts, net distribution, and "home-based management": community health workers in every village test anyone with fever using a rapid test and treat positive cases on the spot, so the parasite is cleared before mosquitoes can pick it up from the patient's blood. By 2018–19 community health workers were treating 57 % of all cases. The fall reversed in 2024: a 2025 review links the rise to warmer weather letting Anopheles gambiae breed at higher altitudes, mosquitoes resistant to pyrethroid insecticides, a parasite mutation (K13 R561H) that reduces the effect of artemisinin, and people travelling with infections that cause no symptoms.

Worked example 1: is the malaria programme working?

Rwanda Biomedical Centre (RBC) reported these figures for two fiscal years (July to June):

Indicator	2016–17	2018–19
Uncomplicated malaria cases	4 833 895	3 969 881
Incidence per 1000 people per year	418	321
Malaria deaths	536	264

(a) Calculate the percentage fall in cases and in incidence. (b) Calculate deaths per 100 000 cases in each year. (c) Why did incidence fall by more than the number of cases?

(a) Cases: $\frac{4\,833\,895 - 3\,969\,881}{4\,833\,895} \times 100\,\% = 17.9\,\%$ . Incidence: $\frac{418 - 321}{418} \times 100\,\% = 23.2\,\%$ .
(b) 2016–17: $\frac{536}{4\,833\,895} \times 100\,000 = 11.1$ . 2018–19: $\frac{264}{3\,969\,881} \times 100\,000 = 6.7$ . Deaths per case fell by about 40 %, so patients were also being treated sooner.
(c) Incidence is a rate: cases divided by the population. The population grew between the two years, so the same number of cases would give a lower rate; with fewer cases and more people, the rate fell faster than the count.

Case study 2: tuberculosis

Mycobacterium tuberculosis has a thick, waxy cell wall rich in mycolic acids. It resists drying, many disinfectants and the Gram stain, so it is identified with the acid-fast (Ziehl–Neelsen) stain, in which it stays red after acid-alcohol has washed the dye out of other cells. Most people who breathe in the bacteria wall them off in the lungs and develop latent TB; they are not ill and not infectious. The infection becomes active TB when immunity falls, which is why TB is the commonest serious infection in people with untreated HIV. Because the bacteria divide slowly (about once every 15 to 20 hours) and hide inside macrophages, treatment needs several drugs for at least six months; stopping early selects for drug-resistant strains.

Worked example 2: reading TB data

RBC's TB report for July 2023 to June 2024 gave a national notification rate of 62.8 cases per 100 000 people, ranging from 19 per 100 000 in Nyamasheke District to 234 per 100 000 in Nyarugenge District (central Kigali). Of 9 351 people with drug-sensitive TB who started treatment in 2022–23, 8 464 were treated successfully; among 1 162 who also had HIV, 921 were treated successfully. (a) Calculate both treatment success rates. (b) Suggest reasons for the difference between the two districts.

(a) All patients: $\frac{8464}{9351} \times 100\,\% = 90.5\,\%$ . Patients with HIV: $\frac{921}{1162} \times 100\,\% = 79.3\,\%$ . TB is harder to cure when HIV has weakened the immune system, and more of these patients die during treatment.
(b) Nyarugenge's rate is about $\frac{234}{19} \approx 12$ times Nyamasheke's. TB spreads through the air, so crowded urban housing and workplaces favour it; a city also draws people at higher risk, and its large hospitals diagnose and register more cases. A notification rate counts cases found, so part of a difference can come from how hard each district looks (case finding), not only from how much TB there is.

Case study 3: cholera

Vibrio cholerae is a curved, comma-shaped bacterium with a single flagellum. After it is swallowed, those bacteria that survive the stomach acid attach to the lining of the small intestine and release cholera toxin. The toxin makes the intestinal cells pump chloride ions into the gut; water follows by osmosis, producing litres of watery diarrhoea a day. Symptoms appear 12 hours to 5 days after infection, and severe cases can die of dehydration within hours. Yet WHO notes that most people infected show no symptoms at all, while still shedding the bacteria in their faeces for 1 to 10 days: a perfect example of carriers.

Because the danger is the loss of water and salts, the life-saving treatment is oral rehydration solution (ORS): clean water with glucose and salts. Glucose and sodium ions are absorbed together by co-transport proteins in the gut lining, a route the toxin does not block, and water follows them back into the body. WHO estimates 1.3 to 4.0 million cholera cases and 21 000 to 143 000 deaths worldwide each year, almost all where safe water and sanitation are lacking.

Case study 4: HIV

HIV infects helper T cells (CD4 cells), which co-ordinate the immune response. Untreated, the virus slowly destroys them over years; when the CD4 count falls very low, opportunistic infections such as TB, pneumonia and some cancers appear, and the person has AIDS. Antiretroviral therapy (ART) stops the virus multiplying. A person on ART whose viral load is suppressed stays healthy and does not pass HIV to sexual partners.

Rwanda's national survey, the Rwanda Population-based HIV Impact Assessment (RPHIA, October 2018 to March 2019), found that 3.0 % of adults aged 15 to 64 were living with HIV (3.7 % of women and 2.2 % of men), about 210 200 adults, and that the incidence was 0.08 % per year, about 5 400 new infections a year. Among all adults with HIV, 76.0 % had a suppressed viral load.

Worked example 3: why is HIV prevalence so much higher than its incidence?

Use the RPHIA figures and $P \approx I \times D$ (Lesson 2) to estimate the average time a person lives with HIV in Rwanda, and comment on your answer.

Rearrange: $D \approx \frac{P}{I} = \frac{3.0\,\%}{0.08\,\%\ \text{per year}} = 37.5 \text{ years}$
This long duration is the effect of ART: people infected decades ago are still alive and are still counted in the prevalence. Without treatment, most people with HIV died within about ten years, and prevalence would be far lower for the same incidence.
The estimate is rough: $P \approx I \times D$ assumes incidence and duration have been steady for a long time, which is not true for HIV in Rwanda (incidence was higher in the past). So high prevalence here is mainly a sign of survival, not of a large number of new infections.

Global Health Media Project: "The Story of Cholera", an animated health-education film. Watch for how the bacteria travel from one person's faeces into another person's water or food, and why oral rehydration saves lives.

Warning

Common mistakes

Saying the mosquito causes malaria. The cause is Plasmodium; the mosquito is the vector.
Calling latent TB infectious. Only active TB in the lungs or airways is passed on by coughing.
Saying antibiotics are the main treatment for cholera. Rehydration saves lives; antibiotics are added only for severe cases.
Writing that HIV and AIDS are the same thing. HIV is the virus; AIDS is the late stage of untreated infection, when immunity has collapsed.
Reading a high notification rate as proof of more disease. It also depends on how actively cases are looked for.

Tip

Memory hook. For any disease, ask "Who, How, Where, What, Which": who causes it (pathogen), how it travels (transmission), where it lives (reservoir), what it does (signs), and which link of the chain we can break. Five questions answer any case-study exam question.

✦

Practice: case studies of infectious diseases

For cholera, name the pathogen, its reservoir, its portal of exit and its portal of entry.
Explain why home-based testing and treatment of malaria by community health workers can reduce transmission, not only deaths.
Explain why TB treatment lasts at least six months and why missing doses is dangerous for the whole community.
Explain how oral rehydration solution works, using the words co-transport and osmosis.
In one district, malaria incidence fell from 250 to 90 per 1000 per year after indoor spraying began. Calculate the percentage fall.
A town of 40 000 people notified 30 TB cases in a year. Calculate the notification rate per 100 000 and compare it with the national rate of 62.8 per 100 000.
Use the chain of infection to compare how malaria and HIV are prevented.
Evaluate: "Rwanda has beaten malaria, so the control programme can now be scaled down."

Show answersHide answers

Pathogen: Vibrio cholerae. Reservoir: infected people (including carriers) and contaminated water. Exit: faeces (and vomit). Entry: the mouth, in contaminated water or food.
Prompt treatment clears Plasmodium from the patient's blood within days, so mosquitoes that bite them later do not pick up the parasite. Fewer infected people means fewer infected mosquitoes and fewer new cases.
M. tuberculosis divides slowly and hides inside macrophages, so the drugs must act for months to kill every bacterium. Stopping early leaves survivors that are the most drug-tolerant; they multiply, the patient relapses, and resistant strains can spread to others, which are much harder and costlier to treat.
Cholera toxin makes gut cells secrete chloride ions and water follows by osmosis. ORS supplies glucose and sodium ions together; carrier proteins in the gut lining absorb them by co-transport, a route the toxin does not block. This lowers the water potential of the cells, so water follows by osmosis back into the body, replacing what is lost.
$\frac{250 - 90}{250} \times 100\,\% = 64\,\%$ .
$\frac{30}{40\,000} \times 100\,000 = 75$ per 100 000. This is higher than the national 62.8 per 100 000, about 1.2 times; it may mean more TB in the town or more active case finding there.
Malaria: break transmission by the vector (nets, spraying, draining breeding sites) and clear the reservoir (prompt treatment). HIV: block transmission (condoms, sterile needles, prevention of mother-to-child transmission) and make infected people non-infectious through ART (treatment as prevention). There is no vaccine for HIV, while malaria vaccines are being introduced in parts of Africa.
Disagree. Cases fell from about 4.8 million (2016–17) to about 620 000 (2023–24), but rose again by almost half in 2024, linked to climate, insecticide and drug resistance and human movement. Anopheles and Plasmodium are still present, so scaling down would let malaria return quickly; control must continue and adapt (new insecticides, resistance monitoring) until transmission stops.

Quick check

Match each disease to how it is transmitted.

Tap one on the left, then its partner on the right.

Key points

Every infection passes along a chain: pathogen, reservoir, exit, transmission, entry, susceptible host. Control breaks one or more links.
Malaria (Plasmodium, mosquito vector): in Rwanda cases fell from about 4.8 million (2016–17) to about 620 000 (2023–24) with spraying, nets and community treatment, then rose again in 2024.
TB (M. tuberculosis, airborne): latent or active; long multi-drug treatment; 90.5 % treatment success in Rwanda's 2022–23 cohort, lower with HIV.
Cholera (V. cholerae, faecal–oral): toxin causes water loss; ORS works by sodium–glucose co-transport; most infected people are carriers.
HIV (retrovirus, sex and blood): 3.0 % of Rwandan adults in 2018–19; ART keeps people alive and non-infectious, so prevalence stays high while incidence is low.

Sources and credits

16.3: How Diseases Spread, from Microbiology by OpenStax (Nina Parker, Mark Schneegurt, Anh-Hue Thi Tu, Philip Lister, Brian M. Forster), via LibreTexts Biology, licensed under CC BY 4.0. Used for reservoirs, carriers, vectors and modes of transmission. Adapted by Ganzaa.
Data: Rwanda Biomedical Centre, Rwanda Malaria and Neglected Tropical Diseases Annual Report 2018–2019, Table 15; N. Julius and others, "Investigating the resurgence of malaria in Rwanda" (2025, CC BY 4.0); Rwanda Biomedical Centre, TB and Other Respiratory Diseases Division Annual Report 2023–2024; Rwanda Biomedical Centre, "Rwanda Population-based HIV Impact Assessment (RPHIA): Key findings", Rwanda Public Health Bulletin; World Health Organization, Cholera fact sheet (29 September 2026).
Figure 1, the tables, worked examples, practice and quick check: written by Ganzaa.
Photos: CDC/Dr. George P. Kubica, public domain; CDC/Dr. Edwin P. Ewing, Jr., public domain; both via Wikimedia Commons.
Video: "The Story of Cholera", Global Health Media Project, embedded from YouTube.

1From 4.8 million to 620 000, and back up

2The chain of infection

3Four diseases compared

4Case study 1: malaria

5Case study 2: tuberculosis

6Case study 3: cholera

7Case study 4: HIV