Hmmm that might be difficult. Are you trying to separate and purify virtosomes from cell cultures or tissue, or are you trying to actually separate the DNA from the complex? Virtosomes are notoriously fragile, so physically separating the DNA from the complex will be difficult. These problems of extraction are compounded by the highly heterogenous composition of virtosomes and fragmented nature of the DNA (especially when from cancer cells). I'm curious about this too and I've found a few papers that might interest you ...

contains an ultracentrifugation protocol for virtosome extraction from both tissue and cultured cells here...

Isolation of Lysosomes from Mammalian Tissues and Cultured Cells

10.1007/978-1-4939-3756-1_19

This paper did not specify the type of cfDNA being extracted from serum, but likely included virtosomes

Fong, S. L., Zhang, J. T., Lim, C. K., Eu, K. W., & Liu, Y. (2009). Comparison of 7 Methods for Extracting Cell-Free DNA from Serum Samples of Colorectal Cancer Patients. Clinical Chemistry, 55(3), 587–589. doi:10.1373/clinchem.2008.110122

This paper attempted to identify and characterize circulating nucleic acids (CNAs) differences in serum of pregnant/non-pregnant cows by tagging CNAs (Interestingly, some of the CNAs had were identified as retrotransposons)

Analysis of Circulating DNA Distribution in Pregnant and Nonpregnant Dairy Cowshttps://doi.org/10.1095/biolreprod.112.103168

These papers were involved in the sequencing of random cfDNA molecules from plasma and serum and have methods sections that may by useful to you, but they do not distinguish what type of cfDNA was isolated

Fan, H. C., Blumenfeld, Y. J., Chitkara, U., Hudgins, L., & Quake, S. R. (2008). Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proceedings of the National Academy of Sciences, 105(42), 16266–16271.

Beck J, Urnovitz HB, Riggert J, Clerici M, Schutz E. Profile of the circulating DNA in apparently healthy individuals. Clin Chem2009;55:730-738.

Hope that helps