Mapping Viral Landscapes: Genomic Surveillance of Aedes Mosquitoes From Central India

Mosquito-borne viral diseases pose a significant impact on human health, with the potential to cause widespread outbreaks of diseases. Monitoring viral genomes in mosquito populations can lead to informed risk assessment and promote early diagnosis. However, a standardized methodology is lacking to decipher circulating viral sequences in mosquito populations collected from human habitats. Our study aims to establish and evaluate a system of viral metagenomic analysis in the Aedes mosquito population.

Mosquitoes were collected using CDC-approved BG-Sentinel version 2 traps (Biogents AG, Regensburg, Germany) and battery-operated vacuum aspirators from different locations in the Bhopal region, India. They were sorted based on genus, gender, location, and collection date. The RNA was extracted from the homogenized mosquito pools and reverse transcribed. Complementary DNA (cDNA) was amplified using sequence-independent, single-prime amplification (SISPA). Further, polymerase chain reaction (PCR) products were sequenced using the Illumina NovaSeq 6000 platform (Illumina, Inc., San Diego, CA). Bioinformatic analysis of the reads was performed using Trimmomatic (Bolger AM, Lohse M, Usadel B (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data (Bioinformatics, btu170) for trimming low-quality raw reads. Later, Kraken2 and Bracken (Johns Hopkins University, Baltimore, MD) were used for the identification of viral sequences.

The study examined virus diversity and seasonal distribution in mosquito populations collected from 13 sites in Bhopal, India, over 15 months. A total of 31 mosquito pools of female Aedes mosquitoes were analyzed. Metagenomic analysis revealed viruses encompassing plant, animal, insect, fungal, and bacteriophage hosts. The highest mosquito catch was during the post-monsoon period, while virus diversity peaked during the monsoon. Seasonal variations showed a higher frequency and diversity of viruses during the monsoon than during pre- and post-monsoon periods. The findings highlight the importance of temporal and ecological factors in viral surveillance and mosquito-borne disease management.

Our findings demonstrate the potential of combining entomological and genomic surveillance for monitoring virus circulation in mosquito populations, which may be implemented as a routine surveillance tool for the timely detection of spikes in viruses with human pathogenic potential and thus inform targeted vector control measures to avert potential outbreaks in the future.