Positive-strand RNA viruses

Key pathogen: Norovirus (Norwalk virus).

• Transmission: faecal–oral, contaminated food/water, cruise ship outbreaks.
• Disease: acute non-inflammatory gastroenteritis – watery diarrhoea, vomiting, nausea; no blood/pus.
• Diagnosis: ELISA, RIA (stool or serology).
• Treatment: self-limiting; supportive care (hydration).
• Prevention: handwashing, isolation of cases.

Hepatitis E virus – faecal–oral transmission, endemic in developing regions.

• Acute self-limiting hepatitis, but can be severe in pregnant women (high mortality).
• No chronic infection (except in immunocompromised).
• Diagnosis: anti-HEV IgM; RT-PCR in stool/ serum.

Genera: Enteroviruses (acid-stable), Rhinoviruses (acid-labile), Heparnaviruses (HAV).

• St. Louis encephalitis (SLE) & West Nile (WNV): Culex mosquito; birds as reservoir; encephalitis.
• Dengue: Aedes mosquito; breakbone fever (myalgia, rash); second infection can cause haemorrhagic shock.
• Yellow fever: Aedes; visceral disease (liver, kidney, heart); black vomit; live attenuated vaccine.
• Zika: Aedes, vertical/sexual; mild febrile illness, but congenital microcephaly and fetal loss.
• Hepatitis C – chronic hepatitis, cirrhosis, HCC; treated with direct-acting antivirals.

Alphaviruses (arboviruses)

• EEE, WEE, VEE: mosquito-borne; birds/horses; encephalitis. Killed vaccines available for EEE/WEE.
• Chikungunya: Aedes; acute febrile illness with severe polyarthralgia/arthritis.

Rubivirus

• Rubella (German measles): respiratory transmission; maculopapular rash (face → trunk).
• Congenital rubella syndrome (first 16 weeks): cataracts, patent ductus arteriosus, pulmonary stenosis, deafness, microcephaly.
• Prevention: live attenuated MMR vaccine.

• SARS-CoV: zoonotic (civet cats), respiratory droplets; severe atypical pneumonia, winter/spring.
• SARS-CoV-2 (COVID-19): highly contagious; incubation 4–14 days; fever, cough, anosmia, GI symptoms; bilateral infiltrates. Severe in elderly/immunocompromised.
• MERS-CoV: camels/bats; similar to SARS, higher mortality.
• Diagnosis: RT-PCR (nasal swab), antigen tests, serology.
• Treatment: remdesivir (severe), dexamethasone (oxygen requirement), convalescent plasma.
• Prevention: mRNA vaccines (spike protein), adenovirus-vectored vaccines, recombinant protein vaccines.

Opportunistic infections prophylaxis

Diagnosis: 4th-gen immunoassay (screening), HIV-1/2 differentiation, RNA NAAT for confirmation/viral load. PCR for provirus in newborns.

• Measles: 3 Cs (cough, coryza, conjunctivitis), Koplik spots, rash (ears → downward). Warthin-Finkeldey giant cells. Complication: subacute sclerosing panencephalitis (SSPE) – slow virus, years later.
• Mumps: bilateral parotitis, orchitis (sterility), pancreatitis, aseptic meningitis. MMR vaccine.
• Parainfluenza: croup (barking cough), bronchiolitis, pneumonia.
• RSV: bronchiolitis in infants; palivizumab (fusion protein inhibitor) for prophylaxis.
• Human metapneumovirus: common cold, bronchiolitis, pneumonia.

• Zoonotic (bats, raccoons, foxes, dogs).
• Transmission: bite; virus travels retrograde to CNS.
• Clinical: prodrome → hydrophobia, hallucinations, coma, death (almost 100% fatal).
• Diagnosis: Negri bodies (cytoplasmic inclusions), DFA of corneal smears, PCR.
• Post-exposure: hRIG + 4 doses of vaccine (days 0,3,7,14).

• Zaire ebolavirus: high mortality (~70%).
• Transmission: direct contact with body fluids, blood, or infected animals.
• Pathogenesis: cytokine storm, vascular leak, multi-organ failure.
• Diagnosis: rapid antigen test (screen), RT-PCR (confirm).
• Supportive care; experimental antivirals (favipiravir), monoclonal antibodies (e.g., REGN-EB3).
• Vaccine: rVSV-ZEBOV (replication-competent, live attenuated).

• Antigenic drift: point mutations in H/N → epidemics (A & B).
• Antigenic shift: reassortment (influenza A only) → pandemics.
• Reservoir: aquatic birds (influenza A); humans (B).
• Clinical: sudden fever, myalgia, headache, cough; complications: pneumonia, Reye syndrome (aspirin), Guillain-Barré.
• Treatment: neuraminidase inhibitors (oseltamivir, zanamivir); amantadine/rimantadine resistance common.
• Vaccine: trivalent/quadrivalent inactivated or live attenuated (intranasal).

• California/La Crosse encephalitis: mosquito-borne; viral encephalitis.
• Hantavirus (Sin Nombre): rodent excreta; hantavirus pulmonary syndrome (cough, dyspnoea, pulmonary oedema, mortality ~50%).

• Lymphocytic choriomeningitis virus (LCMV): mice/hamsters; influenza-like with meningeal signs.
• Lassa fever: West Africa; haemorrhagic fever, 50% mortality; treatment with ribavirin.

• Rotavirus: major cause of infant gastroenteritis; faecal–oral; watery diarrhoea (no blood/pus). Diagnose by ELISA (stool). Oral live attenuated vaccine available.
• Reovirus: common cold, gastroenteritis; self-limiting.
• Colorado tick fever virus: tick-borne; fever, myalgia.

• PrP^C (normal) → PrP^Sc (pathogenic) via conformational change; accumulation leads to spongiform encephalopathy.
• Human: Kuru (cannibalism), Creutzfeldt-Jakob (sporadic, genetic, variant from BSE), Gerstmann-Sträussler-Scheinker, fatal familial insomnia.
• Animal: scrapie (sheep), bovine spongiform encephalopathy.
• Diagnosis: clinical, MRI, EEG, CSF 14-3-3 protein; brain biopsy (vacuolation).
• No treatment; prevention: avoid contaminated neural tissue.