Detection of Macrobrachium rosenbergii golda virus (MrGV) in giant river prawn larvae across Asia through NCBI sequence read archive (SRA) data mining

Abstract

1Macrobrachium rosenbergii golda virus (MrGV) was first characterised in Macrobrachium rosenbergii larvae in 2020, associated with mass mortalities in multiple Southern Bangladesh prawn hatcheries. MrGV has since been detected in two metatranscriptomic datasets from M. rosenbergii in China and in relation to a larval mortality event in India. The major objective of this study was to further characterise the geographical spread of the virus by mining the NCBI Sequence Read Archive (SRA) database. Utilising a new database, Logan, generated from assembling each SRA dataset, and a custom Snakemake pipeline, we discovered MrGV sequence data in M. rosenbergii SRA datasets from China, Thailand, and India, and determined that presence and relative abundance of MrGV is mostly associated with the larval life stage of M. rosenbergii. These results provide insights into the current prevalence of MrGV globally, suggest the life stages of prawn that should be screened to prevent spread of the virus, and demonstrate how the Logan database can be used to inform epidemiological studies.