Microbiology chapters
Influenza, SARS-CoV-2 and dengue
Three viruses that cause epidemics: influenza (haemagglutinin, neuraminidase, antigenic drift and shift, complications, oseltamivir, vaccine), SARS-CoV-2 (spike protein, ACE2, transmission, COVID-19 illness, testing and vaccines) and dengue (Aedes mosquitoes, the four serotypes, warning signs, plasma leakage and fluid management, NS1 and IgM tests), with the dengue fluid and haematocrit calculations.
- Influenza is an orthomyxovirus with segmented negative-sense RNA; its spikes are haemagglutinin (attaches to sialic acid) and neuraminidase (releases new virions; blocked by oseltamivir); antigenic drift (point mutations) causes yearly epidemics (A and B), and antigenic shift (reassortment of segments between human and animal strains, influenza A only) causes pandemics; complications include secondary bacterial pneumonia (S. aureus, pneumococcus) and Reye syndrome with aspirin in children; a new vaccine is made each year.
- SARS-CoV-2 is an enveloped positive-sense RNA coronavirus whose spike protein binds ACE2 (with TMPRSS2); it spreads by droplets and aerosols, incubates about 2–14 days (shorter with recent variants), ranges from no symptoms to pneumonia, ARDS, thrombosis and cytokine storm, and is diagnosed by RT-PCR (gold standard) or rapid antigen tests; vaccines target the spike.
- Dengue is a flavivirus spread by day-biting Aedes aegypti (also A. albopictus) with four serotypes; a second infection with a different serotype raises the risk of severe dengue (antibody-dependent enhancement); illness has febrile, critical (around days 3–7, when fever falls: plasma leakage, rising haematocrit, falling platelets, shock) and recovery phases; NS1 antigen (first 5 days) and IgM (after day 5) confirm it; treat with paracetamol and careful fluids, avoid NSAIDs and aspirin.
On this page
Influenza
The virus
- Orthomyxovirus: enveloped, helical, negative-sense ssRNA in 8 segments (influenza A and B); replicates in the nucleus.
- Types: A (humans, birds, pigs, horses; epidemics and pandemics; subtyped by H and N), B (humans; epidemics), C (mild).
- Surface spikes:
- Haemagglutinin (HA): binds sialic acid receptors on respiratory cells; agglutinates red cells; main target of neutralising antibodies; 18 known H subtypes.
- Neuraminidase (NA): cleaves sialic acid to release new virions and move through mucus; target of oseltamivir and zanamivir.
- M2 ion channel (uncoating; amantadine target, now widespread resistance).
Antigenic variation
| Feature | Antigenic drift | Antigenic shift |
|---|---|---|
| Mechanism | Point mutations in HA and NA genes | Reassortment of gene segments between different strains (human and avian/swine) in a co-infected host (often pigs) |
| Change | Minor | Major: a new subtype (new H and/or N) |
| Types | A and B | A only |
| Result | Seasonal epidemics; vaccine updated every year | Pandemics (little population immunity): 1918 (H1N1), 1957 (H2N2), 1968 (H3N2), 2009 (H1N1 "swine flu") |
Avian influenza (H5N1, H7N9): severe disease with high mortality in people with close poultry contact; little human-to-human spread so far.
Clinical features and complications
- Spread by droplets, aerosols and hands; incubation 1–4 days; shed from just before symptoms.
- Sudden high fever, chills, myalgia, headache, sore throat, dry cough, prostration; recovery in about a week (cough lingers).
- Complications: primary viral pneumonia; secondary bacterial pneumonia (S. aureus, S. pneumoniae, H. influenzae), myocarditis, myositis, encephalitis, worsening of asthma, COPD and heart failure; Reye syndrome (acute encephalopathy and fatty liver) in children given aspirin (especially with influenza B and varicella).
- High risk: elderly, very young, pregnant women, chronic heart, lung, kidney and metabolic disease, immunosuppression.
Diagnosis, treatment and prevention
- RT-PCR on nasopharyngeal swabs (best); rapid antigen tests (less sensitive); culture.
- Oseltamivir (oral) or zanamivir (inhaled): neuraminidase inhibitors; most effective within 48 hours; used for high-risk and severe cases.
- Vaccine: inactivated injectable (most) or live attenuated nasal; reformulated each year (WHO recommends strains); priority groups: elderly, health workers, pregnant women, chronic disease. Contains egg protein in many formulations.
- Hand hygiene, masks, staying home when ill.
SARS-CoV-2 (COVID-19)
The virus
- Coronavirus (betacoronavirus): enveloped, positive-sense ssRNA (one of the largest RNA genomes), with club-shaped spike (S) proteins ("crown").
- Spike binds ACE2 receptors (lungs, nose, gut, heart, kidney, blood vessels); cell entry helped by the protease TMPRSS2.
- Related to SARS-CoV (2002–3) and MERS-CoV (camels, Middle East). Thought to have come from bats.
- Variants (Alpha, Delta, Omicron and its sub-lineages) differ in transmissibility and immune escape, mostly through spike mutations.
Transmission and clinical features
- Respiratory droplets and aerosols (especially indoors, poor ventilation), close contact; contaminated surfaces less important; spread from people before symptoms and without symptoms.
- Incubation: about 2–14 days (median about 5 days; shorter with Omicron).
- Spectrum: asymptomatic → mild (fever, cough, sore throat, fatigue, loss of smell and taste, myalgia, diarrhoea) → pneumonia (bilateral peripheral ground-glass shadows) → ARDS, cytokine storm (high IL-6, ferritin, CRP, D-dimer), thrombosis (venous and arterial), myocarditis, multi-organ failure.
- Risk factors for severe disease: older age, diabetes, obesity, hypertension, heart and lung disease, chronic kidney disease, immunosuppression, being unvaccinated.
- Long COVID: symptoms lasting months (fatigue, breathlessness, brain fog).
- Children: usually mild; rare multisystem inflammatory syndrome (MIS-C).
Diagnosis
| Test | Notes |
|---|---|
| RT-PCR (nasopharyngeal swab) | Gold standard; detects viral RNA; may stay positive after recovery (non-infectious RNA) |
| Rapid antigen test | Quick, cheap; best when viral load is high (early symptomatic); less sensitive |
| Antibody tests | Past infection or vaccination; not for acute diagnosis |
| Blood tests and imaging | Lymphopenia, raised CRP, D-dimer, ferritin; CT chest ground-glass opacities |
Treatment and prevention
- Mild: rest, fluids, paracetamol; antivirals (nirmatrelvir-ritonavir, remdesivir) for high-risk patients early.
- Severe: oxygen, dexamethasone (reduces mortality in patients needing oxygen), anticoagulation prophylaxis, IL-6 blockade (tocilizumab) in selected cases, proning, ventilation.
- Vaccines: mRNA (Pfizer-BioNTech, Moderna), viral vector (AstraZeneca, CanSino), inactivated (Sinopharm, Sinovac); all target the spike protein; reduce severe disease and death.
- Masks, ventilation, hand hygiene, isolation, testing and contact tracing.
Dengue
The virus and vector
- Flavivirus: enveloped, positive-sense ssRNA; four serotypes (DENV-1 to DENV-4).
- Spread by female Aedes aegypti mosquitoes (also A. albopictus): day-biting (early morning and late afternoon), breed in clean, stored water (containers, tyres, flower pots, water tanks, coolers), in and around homes; not person to person.
- Same vector spreads chikungunya, Zika and yellow fever.
- Pakistan: large outbreaks after the monsoon (often September to November), notably in Lahore (2011), Karachi, Rawalpindi, Peshawar (2017) and nationwide (2019 and later years).
Immunity and pathogenesis
- Infection gives lifelong immunity to that serotype but only short-lived cross-protection.
- A second infection with a different serotype carries a higher risk of severe dengue: non-neutralising antibodies from the first infection help the virus enter macrophages via Fc receptors (antibody-dependent enhancement) → more virus, more cytokines → endothelial dysfunction → plasma leakage.
- Infants born to immune mothers can develop severe primary dengue for the same reason.
Clinical course
| Phase | Timing | Features |
|---|---|---|
| Febrile phase | Days 1–3 (2–7) | Sudden high fever, severe headache, retro-orbital pain, myalgia and arthralgia ("breakbone fever"), flushing, rash, nausea; positive tourniquet test, petechiae; leucopenia; falling platelets |
| Critical phase | Around days 3–7, as the fever falls (defervescence), lasts 24–48 hours | Plasma leakage: rising haematocrit, falling platelets, pleural effusion and ascites, low albumin; risk of shock (narrow pulse pressure, cold extremities), bleeding, organ impairment |
| Recovery phase | After the critical phase | Fluid reabsorbed (watch for fluid overload), appetite returns, bradycardia, convalescent rash ("isles of white in a sea of red"), platelets rise |
Warning signs (WHO 2009; need admission): abdominal pain or tenderness, persistent vomiting, clinical fluid accumulation (ascites, pleural effusion), mucosal bleeding, lethargy or restlessness, liver enlargement over 2 cm, rising haematocrit with a rapid fall in platelets.
Severe dengue: severe plasma leakage (shock: dengue shock syndrome, or fluid accumulation with respiratory distress), severe bleeding, or severe organ involvement (liver AST/ALT ≥ 1000, encephalopathy, myocarditis).
The danger time is when the fever settles (critical phase); a falling temperature does not mean recovery.
Diagnosis
| Test | Best timing |
|---|---|
| NS1 antigen (rapid or ELISA) | Days 1–5 of fever |
| RT-PCR | Days 1–5 (identifies serotype) |
| IgM ELISA | After day 5; IgM appears earlier in primary infection |
| IgG | High early IgG suggests secondary infection |
| Full blood count | Leucopenia, thrombocytopenia (< 100,000/µL in severe disease), haematocrit rise |
| Tourniquet test | BP cuff at midpoint between systolic and diastolic for 5 minutes; 10 or more petechiae per square inch (2.5 × 2.5 cm) = positive |
Management
- No specific antiviral. Paracetamol for fever and pain (within daily limits); avoid NSAIDs, aspirin and IM injections (bleeding).
- Oral fluids; daily FBC and haematocrit monitoring; teach warning signs.
- Warning signs or shock: IV isotonic crystalloid guided by haematocrit and vital signs; colloids for refractory shock; avoid fluid overload (effusions, pulmonary oedema) especially in the recovery phase.
- Platelet transfusion is not given just for a low count; transfuse blood for significant bleeding.
Haemoconcentration % = (current Hct − baseline Hct) ÷ baseline Hct × 100
Baseline Hct 40%, now 48%:
(48 − 40) ÷ 40 × 100 = 8 ÷ 40 × 100 = 20% rise → significant plasma leakage
Adult 60 kg with warning signs, not in shock:
start crystalloid 5–7 mL/kg/h for 1–2 h
5 × 60 = 300 mL/h to 7 × 60 = 420 mL/h
then reduce stepwise (3–5, then 2–3 mL/kg/h) as Hct and vital signs improve
Maintenance check (Holliday-Segar, 24 h) for 60 kg:
100 mL/kg for first 10 kg = 1000 mL
50 mL/kg for next 10 kg = 500 mL
20 mL/kg for remaining 40 kg = 800 mL
Total = 2300 mL/day ≈ 96 mL/h
Fluid rates follow WHO dengue guidance; always follow the current national dengue protocol and the patient's response.
Prevention
- Vector control: remove standing water weekly (cover tanks, empty containers, discard tyres), larvicides, fogging in outbreaks, community clean-up campaigns.
- Personal protection: long sleeves, repellents (DEET), screens, nets (including daytime rest).
- Vaccines: Dengvaxia (only for people with previous dengue, because of enhancement risk in seronegative people), TAK-003 (Qdenga); not part of Pakistan's routine programme.
Expect: influenza structure (segmented negative RNA, HA and NA), drift vs shift and epidemics vs pandemics, influenza A vs B, oseltamivir mechanism and timing, secondary S. aureus pneumonia, Reye syndrome; SARS-CoV-2 genome, spike and ACE2, incubation, clinical spectrum, RT-PCR as gold standard, dexamethasone, vaccine types; dengue vector and its habits, four serotypes and secondary infection risk (ADE), the three phases and when the critical phase occurs, warning signs, NS1 vs IgM timing, tourniquet test, haematocrit rise, fluid principles, and avoiding NSAIDs.
Quick revision
- Influenza: segmented (−) RNA; HA (sialic acid), NA (oseltamivir).
- Drift = point mutations = epidemics (A, B). Shift = reassortment = pandemics (A only).
- Influenza complications: S. aureus pneumonia, Reye syndrome (aspirin).
- SARS-CoV-2: (+) RNA coronavirus; spike → ACE2; RT-PCR; dexamethasone if on oxygen.
- Dengue: flavivirus, Aedes aegypti (day-biting, clean water), 4 serotypes.
- Secondary infection with another serotype → severe dengue (ADE).
- Critical phase days 3–7 as fever falls: leakage, Hct ↑ ≥ 20%, platelets ↓.
- NS1 days 1–5; IgM after day 5. Paracetamol; no NSAIDs/aspirin; careful fluids.
Written by The House Job from standard microbiology references (Levinson's Review of Medical Microbiology and Immunology) and WHO dengue guidance.
FAQ
What is the difference between antigenic drift and antigenic shift?
Drift is gradual change from point mutations in haemagglutinin and neuraminidase, causing yearly epidemics; shift is a sudden major change from reassortment of gene segments between different strains, producing a new subtype that can cause a pandemic (influenza A only).
Which enzyme does oseltamivir inhibit?
Neuraminidase, which influenza needs to release new virus particles from infected cells.
Which receptor does SARS-CoV-2 use?
Angiotensin-converting enzyme 2 (ACE2), with help from the protease TMPRSS2.
Why is a second dengue infection more dangerous?
Antibodies from a first infection with a different serotype bind the new virus without neutralising it and help it enter immune cells (antibody-dependent enhancement), increasing viral load and the risk of plasma leakage and shock.