Chapter 280 — Infectious Diseases & Epidemiology
2025-01-04
Russell E. Lewis
Associate Professor of Infectious Diseases
Department of Molecular Medicine
University of Padua
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russelledward.lewis@unipd.it
https://github.com/Russlewisbo
Slides and course materials: www.padovaid.com
By the end of this lecture, students will be able to:
WHO World Malaria Report 2024
| Species | Subgenus | Cycle | Hypnozoites |
|---|---|---|---|
| P. falciparum | Laverania | 48 h | No |
| P. vivax | Plasmodium | 48 h | Yes |
| P. ovale curtisi | Plasmodium | 48 h | Yes |
| P. ovale wallikeri | Plasmodium | 48 h | Yes |
| P. malariae | Plasmodium | 72 h | No |
| P. knowlesi | Plasmodium | 24 h | No |
Incubation period: 8–25 days (may be longer with partial immunity or prophylaxis)
Hypnozoites (P. vivax, P. ovale):
Cyclical fever reflects synchronous schizont rupture
Gametocytes — the transmission stage:
The Great Decline (2000–2015)
The plateau and reversal (2015–present)
| Metric | Value |
|---|---|
| Cases | 263 million |
| Deaths | 597,000 |
| % deaths in Africa | 94% |
| % deaths in children <5 | 76% |
| Countries with malaria | 83 |
| Pregnancies exposed | ~36% in WHO African Region |
Semi-immune travelers from endemic countries who visit family often don’t seek pre-travel advice, underestimate their risk, and are thus at higher risk
They may have partial immunity, but their immunity wanes after years in a non-endemic country
Cytoadherence system:
Infected RBCs express PfEMP-1 (var genes, ~60 variants)
PfEMP-1 binds endothelium via CD36, ICAM-1, EPCR, CSA
Results in microvascular obstruction
Rosetting:
iRBCs bind uninfected RBCs → clusters obstruct capillaries
High parasitemia: - Invades all RBC ages → can exceed 10%
(A) P. knowlesi merozoite invading RBC. (B) P. falciparum trophozoite with hemozoin. (C-D) Knobs and membrane deformation by P. falciparum. (E) Cytoadherence. (F) Rosetting.
| Binding molecule | Syndrome |
|---|---|
| EPCR | Cerebral malaria |
| CSA | Placental malaria |
| CD36 | Microvascular sequestration |
| ICAM-1 | Cerebral/systemic |
Left: Brain histology showing sequestration of parasitized erythrocytes (autopsy). Right: Fluorescein angiography showing retinal whitening (whitened vessels = occluded, nonperfused).
How immunity develops
Key features
| Population | Immunity | Risk |
|---|---|---|
| Children <5 y in endemic areas | Minimal | Highest morbidity/mortality |
| Older children/adults in endemic areas | Partial (premunition) | Asymptomatic parasitemia |
| Emigrants from endemic areas (years later) | Waned | At risk again |
| Non-immune travelers | None | Severe disease at any age |
| Pregnant women (primigravida) | Reduced for placental variants | Placental malaria |
Malaria = strongest known evolutionary selection force on the human genome
Protective traits (Heterozygote advantage)
| Trait | Protection | Mechanism |
|---|---|---|
| Sickle cell trait (HbAS) | ~90% vs. severe Pf | HbS polymerization → reduced sequestration; enhanced innate immunity |
| α-thalassemia | ~60% vs. severe Pf | Oxidative stress in parasitized RBCs |
| G6PD deficiency | ~50% vs. Pf | Increased oxidative damage to parasite |
| Hemoglobin C (HbAC) | ~30% vs. severe Pf | Impaired PfEMP-1 display |
| Hemoglobin E (HbAE) | Variable | Common in SE Asia |
| Duffy-negative (Fy a−b−) | ~100% vs. Pv | Blocks P. vivax RBC invasion receptor |
| SAO (ovalocytosis) | Variable | Altered RBC membrane |
Note
Malaria has shaped more human genetic diversity than any other infectious disease. HbAS hits a “sweet spot” — enough abnormal hemoglobin to thwart the parasite, but not enough to cause sickling under normal conditions. This is why natural selection has maintained the HbS allele at high frequency in sub-Saharan Africa despite it being lethal in homozygotes.
WHO-recommended bundle

Critical receptor for P. vivax invasion
“The long persistent parasite”
“The zoonotic danger”
Key Clinical Rule
All non-immune travelers from a malaria-endemic area within the past 3 months who present with fever should be considered to have malaria until proven otherwise — regardless of prophylaxis taken.
One or more of the following, with parasitemia, excluding alternative causes:
| Manifestation | Threshold |
|---|---|
| Impaired consciousness | GCS <11 adults; Blantyre <3 children |
| Prostration | Unable to sit/stand/walk without assistance |
| Multiple convulsions | >2 fits in 24 hours |
| Metabolic acidosis | Base deficit >8 mEq/L, or bicarb <15, or lactate ≥5 mmol/L |
| Hypoglycemia | Glucose <2.2 mmol/L (<40 mg/dL) |
| Severe malarial anemia | Hgb ≤5 g/dL (children) / <7 g/dL (adults) + parasitemia |
| Manifestation | Threshold |
|---|---|
| Renal impairment | Creatinine >265 μmol/L (3 mg/dL) or urea >20 mmol/L |
| Jaundice | Bilirubin >50 μmol/L with high parasite count |
| Pulmonary edema | Radiographic confirmation, or SpO₂ <92% with RR >30 |
| Significant bleeding | Hematemesis, melena, prolonged bleeding |
| Shock | Decompensated: SBP <80 mmHg adults, <70 mmHg children |
| Hyperparasitemia | P. falciparum >10%; P. knowlesi >100,000/μL |
Warning
In severe malaria: START TREATMENT FIRST. Diagnostic confirmation is important but should not delay therapy.
| Feature | P. falciparum | P. vivax | P. ovale | P. malariae | P. knowlesi |
|---|---|---|---|---|---|
| RBC size | Normal | Enlarged | Enlarged | Normal | Normal |
| Schüffner’s dots | ❌ | ✅ | ✅ | ❌ | ❌ |
| Max parasitemia | >10%* | <2% | <1% | <1% | Variable |
| Gametocyte shape | Banana | Round | Round | Round | Round |
| Distinctive feature | Multiple rings, no mature stages in periphery | Ameboid trophozoites | Fimbriated RBCs | Band trophozoites | Resembles P. malariae |
| Cycle | 48 h | 48 h | 48 h | *2 h | 24 h |
Warning
P. knowlesi resembles P. malariae on light microscopy — molecular testing (PCR) is required for definitive speciation of P. malariae-like morphology in travelers from SE Asia.
Gold Standard
Sensitivity: ~50–500 parasites/μL
Frontline Tool
Do NOT use to monitor response
Reference Standard
Best for: speciation confirmation, low-density infections, mixed infections
| Feature | Expert Microscopy | Conventional RDT (HRP2/pLDH) | Ultrasensitive RDT | PCR / LAMP | qRT-PCR |
|---|---|---|---|---|---|
| Detection limit | 50–500 parasites/μL (thick); 200–500 (thin) | 100–200 parasites/μL (HRP2); 200–500 (pLDH) | 1–10 parasites/μL | 0.5–5 parasites/μL | 0.02–1 parasite/μL |
| Turnaround time | 30–60 min (trained reader) | 15–20 min | 15–20 min | 1–3 hours (PCR); 30–60 min (LAMP) | 2–4 hours |
| Species ID | Yes (thin smear) | Pf only (HRP2); Pf + pan (combo) | Pf only or Pf + pan | Yes (all species) | Yes (all species) |
| Quantification | Yes (parasites/μL) | No (qualitative) | No (qualitative) | Semi-quantitative | Yes (copies/μL) |
| Equipment | Microscope, stains, trained reader | None (lateral-flow strip) | None | Thermal cycler (PCR) or heat block (LAMP) | RT-PCR instrument |
| Drug resistance | No | No | No | Possible (K13, pfcrt, pfmdr1) | Possible |
| Post-treatment monitoring | Yes | No — HRP2 persists 28+ days | No | Yes | Yes |
| Key limitation | Expertise-dependent; false negatives in early Pf (sequestration) | HRP2 deletions → false neg; no quantification | Limited availability | Not point-of-care; cost | Not point-of-care; cost |
A Critical Diagnostic Pitfall
PfHRP2 deletions in P. falciparum cause false-negative RDTs based on HRP-2 detection alone.
Clinical implication: A negative RDT does NOT rule out severe P. falciparum malaria. Treat on clinical suspicion if the test is negative but malaria is likely.
Malaria mimics many diseases — and many diseases mimic malaria
| Category | Diagnoses to Consider | Distinguishing Clues |
|---|---|---|
| Viral | Influenza, dengue, chikungunya, Zika, yellow fever, COVID-19, VHF, viral meningitis | Dengue: more severe myalgia/arthralgia, rash, shorter incubation (4–7 d); Yellow fever: biphasic, relative bradycardia; COVID: anosmia, respiratory Sx |
| Bacterial | Enteric fever (typhoid), nontyphoidal bacteremia, leptospirosis, rickettsiosis, bacterial meningitis | Typhoid: rose spots, relative bradycardia, diarrhea/constipation; Lepto: conjunctival suffusion, biphasic illness; Rickettsia: eschar, rash |
| Parasitic | Acute schistosomiasis (Katayama), African trypanosomiasis, visceral leishmaniasis | Schisto: freshwater exposure, eosinophilia, urticaria; Tryps: chancre, posterior cervical LN; VL: massive splenomegaly, pancytopenia |
Important
Key Principle: In any febrile returned traveler, consider co-infections — malaria + typhoid, malaria + bacteremia, or malaria + dengue are common combinations, especially in sub-Saharan Africa.
| Regimen | Schedule |
|---|---|
| Artemether-lumefantrine (AL, Coartem) | 3 days × 2 daily (weight-based) |
| Artesunate-amodiaquine | 3 days × 1 daily |
| DHA-piperaquine | 3 days × 1 daily |
| Artesunate-mefloquine | 3 days × 1 daily |
| Artesunate-SP | 3 days AS + single SP |
| Artesunate-pyronaridine | 3 days × 1 daily |
| Body Weight | Artemether/Lumefantrine per dose | Tablets per dose (20/120 mg) | Schedule |
|---|---|---|---|
| 5–<15 kg | 20/120 mg | 1 tab | 0, 8, 24, 36, 48, 60 h |
| 15–<25 kg | 40/240 mg | 2 tabs | 0, 8, 24, 36, 48, 60 h |
| 25–<35 kg | 60/360 mg | 3 tabs | 0, 8, 24, 36, 48, 60 h |
| ≥35 kg (adult) | 80/480 mg | 4 tabs | 0, 8, 24, 36, 48, 60 h |
⚠️ Must be given with fatty food/milk (lumefantrine requires fat for absorption — bioavailability ↑16-fold)
| Regimen | Adult dose | Key points |
|---|---|---|
| Artesunate-amodiaquine | AS 4 mg/kg/day + AQ 10 mg base/kg/day × 3 days | Fixed-dose combo available (ASAQ) |
| DHA-piperaquine | DHA 4 mg/kg/day + PPQ 18 mg/kg/day × 3 days | Once daily; no food requirement; QTc prolongation risk |
| Artesunate-mefloquine | AS 4 mg/kg/day × 3 days + MQ 8.3 mg base/kg/day × 3 days | MQ given on days 2–3 to reduce vomiting |
| Artesunate-SP | AS 4 mg/kg/day × 3 days + single SP (25/1.25 mg/kg) day 1 | Contraindicated in sulfonamide allergy |
| Artesunate-pyronaridine | AS 4 mg/kg/day + PYR 6 mg/kg/day × 3 days | Repeat courses: check ALT |
| Regimen | Dosing | Indication |
|---|---|---|
| Atovaquone-proguanil (Malarone) | Adult: 4 tabs (1000/400 mg) daily × 3 days | Uncomplicated Pf; common in US/Europe |
| Quinine + doxycycline | Quinine 650 mg (10 mg/kg) q8h × 3–7 days + doxy 100 mg BID × 7 days | Alternative; not in pregnancy/children <8 y |
| Quinine + clindamycin | Quinine 650 mg q8h × 3–7 days + clinda 20 mg/kg/day ÷ 3 doses × 7 days | Pregnancy-safe alternative to quinine-doxy |
| Chloroquine | 600 mg base, then 300 mg at 6, 24, 48 h (total 25 mg base/kg) | P. vivax/ovale/malariae & CQ-sensitive Pf areas only |
Mandatory for P. vivax and P. ovale
ALL cases must receive an 8-aminoquinoline class agent to eliminate hypnozoites. ACTs/chloroquine treat only the blood stage — they do NOT prevent relapse.
G6PD Testing is MANDATORY Before Prescribing Either Drug
Qualitative testing sufficient for primaquine if no severe deficiency; quantitative/semiquantitative required before tafenoquine.
Standard dose: - 2.4 mg/kg IV at 0, 12, 24 h (3 doses) - Then 2.4 mg/kg IV once daily
Children <20 kg (WHO recommendation): - 3 mg/kg per dose
Post-treatment hemolysis: Monitor for delayed hemolytic anemia (especially non-immune travelers with hyperparasitemia)
(SE Asia, parts of East Africa)
Use IV artesunate PLUS IV quinine simultaneously: - Quinine loading: 20 mg salt/kg over 4 h - Then 10 mg salt/kg q8h
Once parasite density ≤1% and tolerating oral: - Artemether-lumefantrine (preferred) - Or another ACT
Clinical pearl
Parasitemia may transiently increase in the first 12–24 hours of treatment with artemisinins — this is due to splenic release of sequestered parasites and does NOT indicate treatment failure.
| Trimester | Preferred Treatment | Notes |
|---|---|---|
| 1st trimester | Artemether-lumefantrine (if other options unavailable/not tolerated) | 42% lower risk of adverse pregnancy outcomes vs. quinine; CDC recommends if no alternatives |
| 2nd–3rd trimester | Artemether-lumefantrine | Preferred; well-studied safety profile |
| All trimesters | Chloroquine (sensitive areas), quinine + clindamycin | Alternative options |
| Any trimester — AVOID | Doxycycline/tetracycline, primaquine, tafenoquine, halofantrine | Teratogenic or hemolytic risk |
Important
For hypnozoite clearance in pregnancy: Delay primaquine/tafenoquine until after delivery and cessation of breastfeeding. Administer weekly chloroquine suppression until delivery.
| Timing | Likely Cause | Action |
|---|---|---|
| <14 days | Recrudescence (resistance or inadequate Rx) | Switch to a different ACT |
| 14–28 days | Probable recrudescence | Switch ACT; consider PCR genotyping |
| >28 days | Likely reinfection (endemic areas) | First-line ACT again |
| Any time (P. vivax/ovale) | Relapse from hypnozoites | Repeat blood-stage Rx + add antirelapse therapy |
Note
Add single low-dose primaquine (0.25 mg base/kg) to ACT treatment for uncomplicated P. falciparum in areas approaching elimination, to reduce onward transmission.
At this dose, G6PD testing is NOT required (hemolysis risk negligible).
| Drug Class | Lifecycle Stage Targeted |
|---|---|
| ACTs | Asexual blood stages (rings → schizonts) |
| Primaquine/tafenoquine (14d) | Hypnozoites (liver) |
| Single low-dose primaquine | Stage V gametocytes |
| Chloroquine | Asexual blood stages (CQ-sensitive only) |
| Drug | Coverage | Adult Dose | Pediatric Dose | Timing | Key AEs / Contraindications |
|---|---|---|---|---|---|
| Atovaquone-proguanil | All areas | 250/100 mg (1 tab) daily | 62.5/25 mg (¼ tab) daily (11–20 kg); 125/50 mg (½ tab) 21–30 kg; 187.5/75 mg (¾ tab) 31–40 kg; adult dose >40 kg | 1–2 d before → 7 d after | GI upset; take with food; not in pregnancy or <5 kg |
| Doxycycline | All areas | 100 mg daily | 2.2 mg/kg/day (≥8 years only) | 1–2 d before → 4 wk after | Photosensitivity; esophagitis; not in pregnancy or <8 y |
| Mefloquine | All areas except SE Asia | 228 mg base weekly | 5 mg base/kg weekly (≥5 kg); max 228 mg | 1–2 wk before → 4 wk after | Neuropsych AEs; seizure hx; cardiac conduction defects |
| Tafenoquine (Arakoda) | All areas; esp. P. vivax | 200 mg daily × 3 d load → 200 mg weekly | Not approved <18 y | 3 d before → 7 d after | G6PD testing required; pregnancy; psychosis hx |
| Chloroquine | CQ-sensitive only | 300 mg base weekly | 5 mg base/kg weekly | 1–2 wk before → 4 wk after | Retinal toxicity (prolonged use); pruritus; only CQ-sensitive areas |
| Primaquine | P. vivax areas | 30 mg base daily | 0.5 mg base/kg daily (≥6 mo) | 1–2 d before → 7 d after | G6PD testing required; not in pregnancy |
| Drug | Common Side Effects | Serious / Rare Reactions | Counseling Points |
|---|---|---|---|
| Artemether-lumefantrine | Headache, dizziness, nausea | QT prolongation (avoid with other QT-prolonging drugs) | Take with fatty food (↑ lumefantrine absorption by 2–3×) |
| Atovaquone-proguanil | GI upset, headache | Rare: Stevens-Johnson syndrome | Take with food; avoid in severe renal failure (CrCl <30) |
| Doxycycline | Photosensitivity, GI upset, esophagitis | Rare: pseudotumor cerebri | Take upright with full glass of water; sunscreen essential |
| Mefloquine | Vivid dreams, dizziness, insomnia | Neuropsych: anxiety, psychosis, seizures (1:10,000–1:13,000) | Screen for psych history; give test dose 2 wk before travel |
| Primaquine | GI upset, methemoglobinemia | Hemolytic anemia (G6PD-deficient) | Always check G6PD; take with food |
| Tafenoquine | Headache, dizziness | Hemolytic anemia (G6PD-deficient); vortex keratopathy | Quantitative G6PD required; long half-life = sustained hemolysis |
| Chloroquine | Pruritus (esp. dark skin), GI upset | Retinopathy (long-term use), cardiomyopathy | Annual eye exam if prolonged use (>5 years) |
| IV Artesunate | Post-artesunate delayed hemolysis (PADH) | Transient neutropenia | Monitor CBC weekly × 4 weeks post-treatment |
Important
IPTp is one of the most cost-effective maternal health interventions in sub-Saharan Africa.
Monthly SP + amodiaquine for children 3–59 months during rainy/transmission season
3–4 monthly cycles per season
WHO-recommended in Sahel sub-region of Africa
Efficacy: >75% reduction in uncomplicated malaria episodes; >50% reduction in mortality
>45 million children treated in 2022
Timing Matters
G6PD activity is falsely elevated during acute hemolysis or reticulocytosis. Test before treatment or wait until hematologic recovery to get accurate results.
Clinical pearl
Never assume a single diagnosis in a febrile returned traveler. Blood cultures, dengue serology, and malaria testing should often be sent simultaneously.
RTS,S/AS01 (Mosquirix)
R21/Matrix-M
| Approach | Stage | Target | Key Feature |
|---|---|---|---|
| PfSPZ Vaccine (Sanaria) | Phase 2 | Whole sporozoites | Attenuated radiation; requires IV route and cold chain |
| PfSPZ-CVac | Phase 2 | Live sporozoites + CQ | Controlled human malaria infection approach |
| mRNA-CSP vaccines | Phase 1 | CSP | Moderna, BioNTech platforms; rapid manufacturing |
| Blood-stage vaccines | Phase 1–2 | RH5, PfAMA1 | Reduce parasite density; anti-disease |
| TBV (Pfs25, Pfs230) | Phase 1–2 | Gametocyte surface | Transmission-blocking; altruistic vaccine |
| WHO Region | First-Line ACT | Key Considerations |
|---|---|---|
| Sub-Saharan Africa | AL or ASAQ | K13 mutations emerging in East Africa (Rwanda, Uganda) |
| Southeast Asia | DHA-PPQ or AL | Highest rates of artemisinin + partner drug resistance |
| South Asia | AL or ASAQ | Generally good ACT efficacy |
| South America | AL or ASAQ | CQ+PQ still used for P. vivax |
| Oceania/Pacific | AL | CQ-resistant P. vivax in PNG, Indonesia |
Abbreviations
AL = artemether-lumefantrine; ASAQ = artesunate-amodiaquine; DHA-PPQ = dihydroartemisinin-piperaquine; ASPY = artesunate-pyronaridine; CQ = chloroquine; PQ = primaquine
Stalled progress
Global malaria cases increased from 2019–2023, partly due to COVID-19 disruptions, humanitarian crises, and the funding shortfall. The 2030 targets of 90% reduction are unlikely to be met without accelerated action.
The 3-Month Rule
All febrile travelers returning from a malaria-endemic area within the past 3 months have malaria until proven otherwise. Beyond 3 months, still consider malaria — particularly for P. vivax (relapses) and P. malariae (chronic infection).
The Golden Rule
Fever in any traveler returning from a malaria-endemic area = malaria until proven otherwise. Test immediately, treat promptly, hospitalize non-immune patients.
| Year | Discovery |
|---|---|
| 17th c. | Peruvian bark (Cinchona) used for fever |
| 1820 | Quinine isolated (Pelletier & Caventou) |
| 1880 | Plasmodium identified (Laveran) |
| 1897 | Anopheles as vector (Ross) |
| 1928 | Pamaquine (first synthetic antimalarial) |
| 1944 | Chloroquine synthesized |
| 1957 | Global eradication campaign launched |
| 1969 | Eradication campaign abandoned |
| 1972 | Artemisinins discovered (Tu Youyou) |
| 2000 | ~2 million deaths/year (peak) |
| 2015 | Nobel Prize in Medicine — Tu Youyou |
| 2021 | RTS,S vaccine recommended by WHO |
| 2023 | R21/Matrix-M vaccine recommended by WHO |
Nobel Laureate connection
Tu Youyou received the Nobel Prize in Physiology or Medicine (2015) for discovering artemisinin. Her team found it by systematically testing over 2,000 traditional Chinese medicine preparations.
A 35-year-old woman presents with 3 days of high fever (40°C), headache, myalgia, and vomiting. She returned from Kenya 2 weeks ago, where she visited family for 3 weeks. She states she “took some malaria pills but stopped after a week because she felt fine.”
Vital signs: HR 118, BP 95/60, RR 24, SpO₂ 94% on room air
Lab: Hgb 8.2 g/dL, platelets 42,000, creatinine 2.1 mg/dL (baseline 0.8), bilirubin 4.2 mg/dL
Blood smear: Multiple ring forms per RBC, some with banana-shaped gametocytes, parasitemia estimated at 8%
Parikh S, Taylor T. Chapter 280: Malaria (Plasmodium Species). In: Bennett JE, Dolin R, Blaser MJ, eds. Mandell, Douglas, and Bennett’s Principles and Practice of Infectious Diseases, 9th ed. Elsevier; 2025. Pages 3308–3345.