Comparative genomic segmental abundance of southern rice black-streaked dwarf virus in rice and weeds reveals host-dependent accumulation and variation post first outbreak in India

Southern rice black-streaked dwarf virus (SRBSDV), a member of the Fijivirus genus, is an emerging threat to rice production in Asia. Since its first outbreak in 2022, the virus has raised concerns due to its potential impact on rice ecosystems in India. However, limited genomic data exist on its establishment, ecology and evolution, particularly in alternative hosts. In this study, high-throughput sequencing (HTS) and RT-PCR were used to perform a comparative genomic segmental analysis of SRBSDV in symptomatic rice ( Oryza sativa ) and asymptomatic monocot weeds from the vicinity of rice fields in North India. Complete SRBSDV genomes (segments S1-S10) were recovered from rice samples, while seven near-complete segments were identified in the monocot weeds during the two subsequent rice growing seasons. Viral segment accumulation, copy number and FPKM analyses revealed significantly higher SRBSDV loads in rice than in weeds. SNV profiling indicated active viral replication and intra-host evolution in rice, whereas limited SNV in weeds suggested viral stability and a reservoir role. Phylogenetic analysis of SRBSDV segments S8 and S10 confirmed close relatedness to Chinese isolates. Diversity analysis of the S8 segment using DNAsp demonstrated high haplotype richness, moderate nucleotide diversity, and strong purifying selection, with Indian isolates forming a low-diversity subgroup relative to highly polymorphic Chinese populations. RT-PCR validation across additional samples supported HTS findings and segment-specific variability in detection. This study provides the first genomic evidence of SRBSDV establishment in weed hosts in Indian rice agroecosystem post its first outbreak and highlights the role of asymptomatic weeds as potential reservoirs. Furthermore, the detection of all ten SRBSDV genomic segments in the white-backed planthopper (WBPH) vector collected from these fields confirms its role in viral transmission. These findings provide the first genomic evidence of SRBSDV persistence in weed hosts in India and underscore the importance of integrated disease and vector management strategies to safeguard rice productivity, contributing to sustainable agriculture. • First genomic evidence of SRBSDV establishment in India post-2022 outbreak • Complete SRBSDV genomes recovered from rice; partial genomes from monocot weeds • Rice shows higher viral load and active replication compared to weeds • Weeds act as asymptomatic reservoirs with low viral variation and stability • WBPH vector confirmed to carry all SRBSDV segments, enabling transmission