**9. Adaptive immune response**

The importance of humoral response in recovery from encephalitis is demonstrated by several studies showing that administration of antibody during early infection can pro‐ tect against JE. Studies of the entry process of JEV using electron and confocal microsco‐ py techniques showed that neutralizing mAb strongly inhibits JEV-induced fusion and internalization into cells, but not binding of virus to cells. T cells are of crucial impor‐ tance for the recovery from most virus infections and individuals deficient in T cells are unable to control virus infections. T cells are necessary for recovery and protection after JEV infection and also their depletion affects the humoral and cellular, immune defence against flavivirus infections (Müllbacher et al., 2003).

sponses via its roles in activation and maturation of antigen-presenting cells. The ability of the individual non-structural proteins to antagonize JAK-STAT signaling has been studied and results indicated that NS5 blocked STAT1 phosphorylation in response to ei‐ ther IFN-α or IFN-β which highlights the function of NS5 to have a critical role in virus

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**Figure 5.** Displaying the JAK STAT Pathway. JAK STAT signaling pathway is important for transduction of information between cells carrying information for cellular differentiation and homeostasis. Cytokines and their receptors are the major activator of JAK/STAT pathway. IFN are antiviral cytokines produced by cells as soon as the onset of viral infec‐ tion. IFN-α and IFN-β bind to different receptors and, play important role in recovery from flaviviral infections. Howev‐

Serology is an important tool for the diagnosis of JE since the virus is difficult to isolate from clinical samples. The hemagglutination inhibition assay also is used but it has prac‐ tical limitations as it requires paired serum samples from the acute and convalescent phases. The IgM antibody capture ELISA for CSF and serum samples is currently the standard test for diagnosis of JE but still has the drawback of not being able to diagnose about the infection in early stage. Molecular methods using reverse-transcriptase (RT) - PCR techniques have proved to be highly effective for diagnosing infection by RNA vi‐ ruses. JE viral genome sequences have been detected by RT-PCR in CSF from acute encephalitis cases from several places around the globes. The conventional RT-PCR has

er, they fail sometimes due to ability of JEV to inhibit the JAK-STAT pathway.

**12. Diagnosis**

pathogenesis (Best et al., 2005).
