Chikungunya Diagnostics

Chikungunya virus is an alphavirus transmitted by Aedes aegypti and Aedes albopictus mosquitoes. Diagnosis uses RT-PCR for viral RNA in serum or whole blood during the first 5 to 7 days (viraemic phase), and IgM and IgG serology by ELISA or immunofluorescence from day 4 to 5 onward. Neutralisation (plaque reduction) tests confirm specificity because of cross-reaction with other alphaviruses (o'nyong nyong, Ross River, Mayaro). Rapid lateral flow tests exist but have limited accuracy.

The virus has caused epidemics across Africa, the Indian Ocean islands, South and Southeast Asia, the Americas and parts of Europe, with millions of cases. After an incubation of 3 to 7 days, abrupt high fever, severe symmetrical polyarthralgia (often disabling), rash, headache and myalgia develop.

Acute illness lasts 1 to 2 weeks, but joint pain persists for over 3 months in 25 to 60% and for years in some. Severe disease (neurological, cardiac, hepatic, renal and bullous skin disease) and deaths occur in neonates, older adults and people with comorbidity. Mother-to-child transmission at delivery causes severe neonatal disease in about 50% of infants born to viraemic mothers.

Indications. Acute fever with severe arthralgia in residents of or travellers from endemic regions. Differential diagnosis of dengue, Zika, malaria, leptospirosis, rickettsial infection and rheumatic fever. Neonates of mothers with fever near delivery. Chronic inflammatory arthritis after travel. Outbreak surveillance. Encephalitis or Guillain-Barre syndrome in an endemic setting.

Specimen. Serum 1 to 2 mL (RT-PCR within 7 days of onset, serology after day 5 to 7). Whole blood in EDTA for PCR. CSF 0.5 to 1 mL in neurological disease. Paired serum samples 10 to 14 days apart for IgG rise.

Reference values (assay dependent). RT-PCR: not detected. IgM and IgG: negative (index under 0.8 or under 9 U/mL), equivocal, positive (over 1.1 index).

Interpretation.

• RT-PCR is positive from day 0 to about day 5 to 7 (viral loads up to 10^9 copies/mL) and is the test of choice in the first week.
• IgM appears from day 2 to 7 and persists for 3 to 6 months (rarely longer), and IgG appears by day 7 to 10 and persists for years or life.
• A fourfold rise in IgG in paired sera, or IgM seroconversion, confirms acute infection. IgM positive with a negative PCR after the first week is probable infection and is confirmed by neutralisation.
• Laboratory findings: lymphopenia (nadir in the first days), mild thrombocytopenia (less common and less marked than dengue), raised transaminases, raised C-reactive protein, mildly raised creatinine kinase.
• Persistent arthralgia after acute infection occurs with normal rheumatoid factor and anti-CCP in most, though a minority develop true inflammatory arthritis mimicking rheumatoid arthritis, with positive tests.
• Co-infection with dengue or Zika occurs in outbreaks where the vectors overlap.

Critical values and findings needing immediate action.

• Neonate with fever, poor feeding, seizures, rash or haemorrhagic signs after delivery to a mother with fever around the time of birth: neonatal chikungunya, urgent intensive care and PCR of blood and CSF.
• Encephalitis, seizures, altered consciousness, Guillain-Barre syndrome or myelitis: admission, CSF PCR and supportive care.
• Hypotension, myocarditis, arrhythmia or heart failure: cardiac monitoring.
• Older patient with comorbidity, renal failure, bleeding or shock: severe disease, fluid support, admission.
• Patient with fever and thrombocytopenia in dengue endemic areas: dengue testing and warning signs are checked at the same time, because the two cannot be told apart clinically.

Interferences and pitfalls.

• A negative PCR after day 7 does not exclude infection, and serology must be done.
• IgM can cross-react with other alphaviruses (o'nyong nyong, Mayaro, Ross River, Sindbis) and rarely flaviviruses, and confirmation uses neutralisation in endemic multi-virus regions.
• Rapid tests have poor sensitivity early in disease, and rates of false positives and negatives vary.
• Persistent IgM beyond 3 to 6 months occurs in chronic arthritis and should not be mistaken for new infection.
• Rheumatoid factor and autoantibodies can be transiently positive after infection.
• Non-steroidal anti-inflammatory drugs and aspirin are avoided until dengue is excluded, because of bleeding risk.
• Chronic post-viral arthritis is managed with analgesia, physiotherapy and in refractory cases disease modifying drugs, and early treatment with corticosteroids may worsen rebound.
• Differential diagnosis includes dengue, Zika, malaria, rubella, parvovirus B19, rheumatic fever, reactive arthritis and early rheumatoid arthritis.

Special groups.

• Neonates: perinatal transmission causes encephalopathy and long term neurodevelopmental delay in about half of those with severe disease.
• Pregnancy: infection in the first trimester is not clearly linked to foetal malformation, and the peripartum viraemic period carries the main risk. Delivery timing is individualised.
• Children: more often present with fever, rash and neurological features, and fewer chronic joint symptoms.
• Older adults: more severe acute disease and chronic arthritis.
• Regions: urban epidemics follow Aedes mosquito abundance, rainfall and travel, and diagnosis in resource limited settings is clinical, with PCR in reference laboratories.

Follow up tests. RT-PCR for chikungunya, dengue and Zika, paired serology, plaque reduction neutralisation test, full blood count, liver function tests, creatinine, creatine kinase, C-reactive protein, malaria smear, leptospirosis tests, rheumatoid factor and anti-CCP in persistent arthritis, joint ultrasound or MRI, CSF analysis, and ECG with echocardiography when cardiac features are present.