For establish a diagnostic protocol of routine, but I am interested to in phylogenetic research in E1-E2 sequences, and maybe nsP2-nsP3
about the E1-E2 but for real time pcr use the system with described in 2010. Karine Labadie et al. JCI 2010 or Thon Hon et al. virology journal 2012
this protocol was used by numerous groups and widely analysed by the group of alain michault (see below)
for nsP2-nsP3 I'm not sure because the nsP3 is one of the most variable region in CHIKV (yes not to much compared to other viruses) but the protocole used by Thon Hon et al. virology
perhaps some primer from Niyas KP, et al. (2010). might be used Virol J 7, 189.
Laurent P, Le Roux K, Grivard P, Bertil G, Naze F, Picard M, Staikowsky F, Barau G, Schuffenecker I & Michault A (2007). Development of a sensitive real-time reverse transcriptase PCR assay with an internal control to detect and quantify chikungunya virus. Clin Chem 53, 1408–1414.
You could also use this system described here: Pastorino et al. J Virol
Methods, 2005; 124:65-71.
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