I found multiple entries of Zika virus in Pubmed. You can align these sequences to determine the highly conserved region of genome and then design PCR primers targeting that region. I found a few articles describing Zika virus specific antibodies in patients, but cross-reactivity with other flaviviruses could be a potential problem.  In short, qPCR-based detection of viral RNA in the clinical specimens is the way to go. Please make sure that your primers don't bind with the other flaviviruses. 

Thanks Dr. Mohsan Saeed for your suggestion. We also need good controls...

Zika virus has a rapid growing CPE that causes cell sloughing, unlike DENG CPE that is slow growing and doesn´t cause cell sloughing, can you take a picture of your cells and post it here ? 

Hi Mohammad,

The easiest way to screen samples is with qRT-PCR. The best method i have tested is http://www.ncbi.nlm.nih.gov/pubmed/?term=18680646 (Lanciotti et al) - 1086 assay. The problem with qPCR is that viraemia for Zika infection is highly transient - even samples taken 72 hrs post onset have screened negative while some have still been positive 10+ days post onset. 

Serology is the typical first alert system as most labs already run dengue IgM/IgG. Zika cross-reacts on these assays so any dengue positive that this DENV PCR negative is a good candidate for ZIKV screening

We have had success with PRNT however you'll need the virus to perform this. CDC will be able to provide however I think they classify as BSL3. Positive serum controls are few and far between I am afraid!

There are interesting data for ZIKV persistence in urine and semen so it is worth considering these in highly probably cases where serum samples are negative

Hi Mohammad,

You can also try to detect ZIKV in saliva samples collected on dry cotton swab then immersed and vortexed in lysis buffer before extraction