In the present study, we have developed a TFF-based method allowing purification and concentration of OsHV-1 infectious particles from infected oyster tissues and we have evaluated the long-reads Nanopore sequencing in front of the state of the art short-read Illumina sequencing. Our results show that TFF purification of OsHV-1 viral particle coupled with ONT sequencing is a promising strategy to decipher genetic diversity and evolution of OsHV-1 populations.