Zika virus outbreak in Rajasthan, India in 2018 was caused by a virus endemic to Asia.

Zika virus (ZIKV) infection in human has been reported from Gujarat and Tamil Nadu states during the year 2016 and 2017 respectively. In paucity of complete genome data of ZIKV, the analysis and prediction were not possible. Zika cases were reported in Jaipur city, Rajasthan, India during the period of 21 September 2018 to 29 October 2018. In order to understand the circulating ZIKV strain in Rajasthan state about ten human serum samples from the positive cases of Jaipur city, Rajasthan state considering the locality and clustering variations were sequenced using next-generation sequencing (NGS) platform. Complete genome phylogenetic analysis of Jaipur city sequences with known GenBank ZIKV sequences revealed that the outbreak in Jaipur city was being caused by ZIKV belonging to Asian lineage. Partial genome sequencing revealed the presence of a pre-outbreak strain of ZIKV in Gujarat and current outbreak strain of Asian lineage in Tamil Nadu. Further sequence analysis of the five ZIKV positive samples of Jaipur revealed that the S139N and A188V mutations, linked to enhanced neurovirulence and transmission in animal models, were not found in the current outbreak strain. Whether this strain can cause birth defects and cause large outbreaks is not currently known, but they should be treated as such until more is known. With the identification of ZIKV in Gujarat, Tamil Nadu, and recent outbreaks of ZIKV in Rajasthan and Madhya Pradesh states alarm for India to enhance surveillance in other states and monitor the mutation and evolutionary changes in circulating Zika strains.