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He succeeds Justice S V Bhatti who was recently elevated to the post of Supreme Court judge.
Desai was serving as the acting Chief Justice of Gujarat High Court.
In a brief ceremony held at Raj Bhavan, Governor Arif Mohammed Khan administered the oath of office to Desai.
Besides Khan, Chief Minister Pinarayi Vijayan, Law Minister P Rajeeve, Chief Secretary V Venu and senior IAS and IPS officers were also present during the function.