Zika virus positivity in Aedes aegypti mosquitoes and its genomic landscape from Pune, Western India.

Background and objectives Zika virus cases were confirmed from Pune, Western India, during an outbreak in June 2024. We conducted an entomological investigation in the Pune municipal corporation area and aimed to characterise the Zika virus from Aedes aegypti mosquitoes at the genomic level. Methods An entomological survey was conducted covering 16 locations in the Pune Municipal Corporation, between June and August 2024. Adult mosquitoes were collected using aspirators, while larvae were collected with the standard dipping and pipetting method. Aedes vector density was assessed, and samples were pooled. Zika virus positivity was assessed using real-time RT-qPCR. Genomic characterisation of the strains was achieved by whole-genome sequencing using the Oxford Nanopore technology platform. Results A high density of Aedes mosquitoes was revealed in the Pune area. Zika virus positivity was observed in 34/128 (26.5%) of Aedes aegypti mosquito pools. Full genome sequences of two ZIKV isolates were recovered from adult mosquito pools. Their time-scaled phylogenetic analysis showed grouping within the Asian lineage, having a recent ancestral time of evolution around 2014, indicating the introduction of newer virus strains in the recent past in India. Mutations E-V473M and motif E-VNDT, indicative of faster viral replication and higher mosquito infectivity, were noted in only one of the two isolates. Interpretation and conclusions With a high positivity of the Zika virus in Aedes aegypti, this study highlights the ongoing risk prevailing in the Pune municipal corporation area. Distinct characteristics of the circulating strains of the virus, and their evolutionary links to different global strains, underlines the importance of continuous genomic surveillance in vectors and hosts.