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Volume 41 Issue 2
April 2026
    Citation: Yutong Wei, Qiyan Liu, Zhen Gong, Guan-Zhu Han. Unveiling the cryptic diversity and distribution of elements related to virophage mavirus through deep mining of pPolB proteins .VIROLOGICA SINICA, 2026, 41(2) : 371-381.  http://dx.doi.org/10.1016/j.virs.2026.03.009
    shu

    Unveiling the cryptic diversity and distribution of elements related to virophage mavirus through deep mining of pPolB proteins

    • College of Life Sciences, Nanjing Normal University, Nanjing 210023, China

    • Virophages are unique double-stranded DNA (dsDNA) viruses that parasitize viruses of Nucleocytoviricota (NCVs). While conventionally viewed as a viral group, growing evidence suggests that “virophage” is better understood as a parasitic lifestyle, rather than a natural group. Despite this conceptual shift, their diversity and evolution remain largely obscure and contentious. Through deep mining of protein-primed type B DNA polymerase (pPolB) in 7041 eukaryotic genomes and 12,053 metagenomes sampled globally, we expand the diversity of pPolB-carrying mavirus virophage-related elements (pMVREs), which include virophages, transpovirons, and Polinton-like viruses (PLVs). Our phylogenomic and metagenomic mining reveals the widespread distribution of pMVREs in eukaryotic genomes (97/7041, 1.38%) and global environments (2450/12053, 20.33%). pMVREs possess genome architectures of high plasticity and promiscuity. The presence of pMVREs and NCVs is statistically correlated in both eukaryotic genomes and global metagenomes, supporting a specific co-occurrence association between pMVREs and NCVs. Moreover, pMVRE diversity and composition exhibit strong heterogeneity across global ecosystems. Together, this study unveils a vast diversity of virophage-related elements and provides insights into the intricate relationship among virophages, transpovirons, PLVs, pMVREs, and NCVs.
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      1. Altschul, S.F., Wootton, J.C., Gertz, E.M., Agarwala, R., Morgulis, A., Schaffer, A.A., Yu, Y.K., 2005. Protein database searches using compositionally adjusted substitution matrices. FEBS J 272, 5101-5109.

      2. Aylward, F.O., Moniruzzaman, M., Ha, A.D., Koonin, E.V., 2021. A phylogenomic framework for charting the diversity and evolution of giant viruses. PLoS Biol 19, e3001430.

      3. Barreat, J.G.N., Katzourakis, A., 2023. A billion years arms-race between viruses, virophages, and eukaryotes. Elife 12, RP86617.

      4. Bastian, M., Heymann, S., Jacomy, M., 2009. Gephi: an Open Source Software for Exploring and Manipulating Networks. Third International AAAI Conference on Weblogs and Social Media 3, 361-362.

      5. Bellas, C., Hackl, T., Plakolb, M.S., Koslova, A., Fischer, M.G., Sommaruga, R., 2023. Large-scale invasion of unicellular eukaryotic genomes by integrating DNA viruses. Proc Natl Acad Sci USA 120, e2300465120.

      6. Bellas, C.M., Sommaruga, R., 2021. Polinton-like viruses are abundant in aquatic ecosystems. Microbiome 9, 13.

      7. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E., 2000. The Protein Data Bank. Nucleic Acids Res 28, 235-242.

      8. Blanc, G., Gallot-Lavallee, L., Maumus, F., 2015. Provirophages in the Bigelowiella genome bear testimony to past encounters with giant viruses. Proc Natl Acad Sci USA 112, E5318-E5326.

      9. Bulzu, P.A., Henriques Vieira, H., Ghai, R., 2025. Lineage-specific expansions of polinton-like viruses in photosynthetic cryptophytes. Microbiome 13, 154.

      10. Desnues, C., La Scola, B., Yutin, N., Fournous, G., Robert, C., Azza, S., Jardot, P., Monteil, S., Campocasso, A., Koonin, E.V., Raoult, D., 2012. Provirophages and transpovirons as the diverse mobilome of giant viruses. Proc Natl Acad Sci USA 109, 18078-18083.

      11. Eddy, S.R., 1998. Profile hidden Markov models. Bioinformatics 14, 755-763.

      12. Fischer, M.G., Hackl, T., 2016. Host genome integration and giant virus-induced reactivation of the virophage mavirus. Nature 540, 288-291.

      13. Fischer, M.G., Suttle, C.A., 2011. A virophage at the origin of large DNA transposons. Science 332, 231-234.

      14. Fritz, S.A., Purvis, A., 2010. Selectivity in mammalian extinction risk and threat types: a new measure of phylogenetic signal strength in binary traits. Conserv Biol 24, 1042-1051.

      15. Gaia, M., Benamar, S., Boughalmi, M., Pagnier, I., Croce, O., Colson, P., Raoult, D., La, Scola, B., 2014. Zamilon, a novel virophage with Mimiviridae host specificity. PLoS One 9, e94923.

      16. Gao, Y., Wang, W., Zhang, T., Gong, Z., Zhao, H., Han, G.Z., 2018. Out of Water: The Origin and Early Diversification of Plant R-Genes. Plant Physiol 177, 82-89.

      17. Gremme, G., Steinbiss, S., Kurtz, S., 2013. GenomeTools: a comprehensive software library for efficient processing of structured genome annotations. IEEE/ACM Trans Comput Biol Bioinform 10, 645-656.

      18. Gong, Z., Zhang, Y., Han, G.Z., 2020. Molecular fossils reveal ancient associations of dsDNA viruses with several phyla of fungi. Virus evolution 6, veaa008.

      19. Hoang, D.T., Chernomor, O., von Haeseler, A., Minh, B.Q., Vinh, L. S., 2018. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol Biol Evol 35, 518-522.

      20. Hsieh, T.C., Ma, K.H., Chao, A., 2020. iNEXT: an R package for rarefaction and extrapolation of species diversity. R package version 2.0.20.

      21. Kahle, D., Wickham, H., 2013. ggmap: Spatial Visualization with ggplot2. The R Journal 5, 144-161.

      22. Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., von Haeseler, A., Jermiin, L.S., 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 14, 587-589.

      23. Katoh, K., Standley, D.M., 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30, 772-780.

      24. Kolde, R., 2019. pheatmap: Pretty Heatmaps. R package version 1.0.12.

      25. Koonin, E.V., Krupovic, M., 2017. Polintons, virophages and transpovirons: a tangled web linking viruses, transposons and immunity. Curr Opin Virol 25, 7-15.

      26. Koslova, A., Hackl, T., Bade, F., Sanchez Kasikovic, A., Barenhoff, K., Schimm, F., Mersdorf, U., Fischer, M.G., 2024. Endogenous virophages are active and mitigate giant virus infection in the marine protist Cafeteria burkhardae. Proc Natl Acad Sci USA 121, e2314606121.

      27. Krupovic, M., Koonin, E.V., 2015. Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution. Nat Rev Microbiol 13, 105-115.

      28. Krupovic, M., Kuhn, J.H., Fischer, M.G., Koonin, E.V., 2024. Natural history of eukaryotic DNA viruses with double jelly-roll major capsid proteins. Proc Natl Acad Sci USA 121, e2405771121.

      29. Krupovic, M., Kuhn, J.H., Fischer, M.G., 2016. A classification system for virophages and satellite viruses. Arch Virol 161, 233-247.

      30. Krupovic, M., Yutin, N., Koonin, E.V., 2016. Fusion of a superfamily 1 helicase and an inactivated DNA polymerase is a signature of common evolutionary history of Polintons, polinton-like viruses, Tlr1 transposons and transpovirons. Virus Evol 2, vew019.

      31. Kumar, S., Suleski, M., Craig, J.M., Kasprowicz, A.E., Sanderford, M., Li, M., Stecher, G., Hedges, S.B., 2022. TimeTree 5: An Expanded Resource for Species Divergence Times. Mol Biol Evol 39, msac174.

      32. La Scola, B., Desnues, C., Pagnier, I., Robert, C., Barrassi, L., Fournous, G., Merchat, M., Suzan-Monti, M., Forterre, P., Koonin, E., Raoult, D., 2008. The virophage as a unique parasite of the giant mimivirus. Nature 455, 100-104.

      33. Letunic, I., Bork, P., 2019. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 47, W256-W259.

      34. Lu, S., Wang, J., Chitsaz, F., Derbyshire, M.K., Geer, R.C., Gonzales, N.R., Gwadz, M., Hurwitz, D.I., Marchler, G.H., Song, J.S., Thanki, N., Yamashita, R.A., Yang, M., Zhang, D., Zheng, C., Lanczycki, C.J., Marchler-Bauer, A., 2020. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res 48, D265-D268.

      35. Markowitz, V. M., Chen, I. M., Chu, K., Szeto, E., Palaniappan, K., Grechkin, Y., Ratner, A., Jacob, B., Pati, A., Huntemann, M., Liolios, K., Pagani, I., Anderson, I., Mavromatis, K., Ivanova, N. N., Kyrpides, N. C., 2012. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic acids research 40, D123-D129.

      36. Minh, B.Q., Schmidt, H.A., Chernomor, O., Schrempf, D., Woodhams, M.D., von Haeseler, A., Lanfear, R., 2020. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol Biol Evol 37, 1530-1534.

      37. Moniruzzaman, M., Martinez-Gutierrez, C.A., Weinheimer, A.R., Aylward, F.O., 2020. Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses. Nat Commun 11, 1710.

      38. Moniruzzaman, M., Weinheimer, A.R., Martinez-Gutierrez, C.A., Aylward, F.O., 2020. Widespread endogenization of giant viruses shapes genomes of green algae. Nature 588, 141-145.

      39. Nayfach, S., Paez-Espino, D., Call, L., Low, S.J., Sberro, H., Ivanova, N.N., Proal, A.D., Fischbach, M.A., Bhatt, A.S., Hugenholtz, P., Kyrpides, N.C., 2021. Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nat Microbiol 6, 960-970.

      40. vegan: Community Ecology Package.

      41. Paez-Espino, D., Zhou, J., Roux, S., Nayfach, S., Pavlopoulos, G.A., Schulz, F., McMahon, K.D., Walsh, D., Woyke, T., Ivanova, N.N., Eloe-Fadrosh, E.A., Tringe, S.G., Kyrpides, N.C., 2019. Diversity, evolution, and classification of virophages uncovered through global metagenomics. Microbiome 7, 157.

      42. Pagel, M., Meade, A., 2006. Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. Am Nat 167, 808-825.

      43. Price, M.N., Dehal, P.S., Arkin, A.P., 2010. FastTree 2--approximately maximum-likelihood trees for large alignments. PloS one 5, e9490.

      44. Roitman, S., Rozenberg, A., Lavy, T., Brussaard, C.P.D., Kleifeld, O., Beja, O., 2023. Isolation and infection cycle of a polinton-like virus virophage in an abundant marine alga. Nat Microbiol 8, 332-346.

      45. Roux, S., Chan, L.K., Egan, R., Malmstrom, R.R., McMahon, K.D., Sullivan, M.B., 2017. Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. Nat Commun 8, 858.

      46. Sarre, L.A., Kim, I.V., Ovchinnikov, V., Olivetta, M., Suga, H., Dudin, O., Sebe-Pedros, A., de Mendoza, A., 2024. DNA methylation enables recurrent endogenization of giant viruses in an animal relative. Sci Adv 10, eado6406.

      47. Sayers, E. W., Beck, J., Bolton, E. E., Brister, J. R., Chan, J., Comeau, D. C., Connor, R., DiCuccio, M., Farrell, C. M., Feldgarden, M., Fine, A. M., Funk, K., Hatcher, E., Hoeppner, M., Kane, M., Kannan, S., Katz, K. S., Kelly, C., Klimke, W., Kim, S., Sherry, S. T., 2024. Database resources of the National Center for Biotechnology Information. Nucleic acids research 52, D33-D43.

      48. Schulz, F., Roux, S., Paez-Espino, D., Jungbluth, S., Walsh, D.A., Denef, V.J., McMahon, K.D., Konstantinidis, K.T., Eloe-Fadrosh, E.A., Kyrpides, N.C., Woyke, T., 2020. Giant virus diversity and host interactions through global metagenomics. Nature 578, 432-436.

      49. Sheng, Y., Wu, Z., Xu, S., Wang, Y., 2022. Isolation and Identification of a Large Green Alga Virus (Chlorella Virus XW01) of Mimiviridae and Its Virophage (Chlorella Virus Virophage SW01) by Using Unicellular Green Algal Cultures. J Virol 96, e0211421.

      50. Steinegger, M., Soding, J., 2017. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol 35, 1026-1028.

      51. Tokarz-Deptula, B., Chrzanowska, S., Gurgacz, N., Stosik, M., Deptula, W., 2023. Virophages-Known and Unknown Facts. Viruses 15, 1321.

      52. Van Dongen, S., 2008. Graph Clustering Via a Discrete Uncoupling Process. SIAM Journal on Matrix Analysis and Applications 30, 121-141.

      53. Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., Zidek, A., Green, T., Tunyasuvunakool, K., Petersen, S., Jumper, J., Clancy, E., Green, R., Vora, A., Lutfi, M., Figurnov, M., Velankar, S., 2022. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res 50, D439-D444.

      54. Wei, Y., Gong, Z., Han, G.Z., 2023. Plants acquired mitochondrial linear plasmids horizontally from fungi likely during the conquest of land. Mob DNA 14, 15.

      55. Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, D.L., Francois, R., Grolemund, G., Hayes, A., Henry, L., Hester, J., Kuhn, M., Pedersen, L.T., Miller, E., Bache, M.S., Muller, K., Ooms, J., Robinson, D., Seidel, P.D., Spinu, V., Takahashi, K., Vaughan, D., Wilke, C., Woo, K., Yutani, H., 2019. Welcome to the Tidyverse. Journal of open source software 4, 1686.

      56. Wickham, H., 2016. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York.

      57. Xie, W., Lewis, P.O., Fan, Y., Kuo, L., Chen, M.H., 2011. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst Biol 60, 150-160.

      58. Yu, G., 2023. scatterpie: Scatter Pie Plot. R package version 0.2.1.

      59. Yutin, N., Kapitonov, V.V., Koonin, E.V., 2015. A new family of hybrid virophages from an animal gut metagenome. Biol Direct 10, 19.

      60. Yutin, N., Shevchenko, S., Kapitonov, V., Krupovic, M., Koonin, E.V., 2015. A novel group of diverse Polinton-like viruses discovered by metagenome analysis. BMC Biol 13, 95.

      61. Zablocki, O., van Zyl, L., Adriaenssens, E.M., Rubagotti, E., Tuffin, M., Cary, S.C., Cowan, D., 2014. High-level diversity of tailed phages, eukaryote-associated viruses, and virophage-like elements in the metaviromes of antarctic soils. Appl Environ Microbiol 80, 6888-6897.

      62. Zhou, J., Sun, D., Childers, A., McDermott, T.R., Wang, Y., Liles, M.R., 2015. Three novel virophage genomes discovered from Yellowstone Lake metagenomes. J Virol 89, 1278-1285.

      63. Zhou, J., Zhang, W., Yan, S., Xiao, J., Zhang, Y., Li, B., Pan, Y., Wang, Y., 2013. Diversity of virophages in metagenomic data sets. J Virol 87, 4225-4236.

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      Unveiling the cryptic diversity and distribution of elements related to virophage mavirus through deep mining of pPolB proteins

      • Received Date: 22 December 2025
      • Accepted Date: 20 March 2026

      Abstract: Virophages are unique double-stranded DNA (dsDNA) viruses that parasitize viruses of Nucleocytoviricota (NCVs). While conventionally viewed as a viral group, growing evidence suggests that “virophage” is better understood as a parasitic lifestyle, rather than a natural group. Despite this conceptual shift, their diversity and evolution remain largely obscure and contentious. Through deep mining of protein-primed type B DNA polymerase (pPolB) in 7041 eukaryotic genomes and 12,053 metagenomes sampled globally, we expand the diversity of pPolB-carrying mavirus virophage-related elements (pMVREs), which include virophages, transpovirons, and Polinton-like viruses (PLVs). Our phylogenomic and metagenomic mining reveals the widespread distribution of pMVREs in eukaryotic genomes (97/7041, 1.38%) and global environments (2450/12053, 20.33%). pMVREs possess genome architectures of high plasticity and promiscuity. The presence of pMVREs and NCVs is statistically correlated in both eukaryotic genomes and global metagenomes, supporting a specific co-occurrence association between pMVREs and NCVs. Moreover, pMVRE diversity and composition exhibit strong heterogeneity across global ecosystems. Together, this study unveils a vast diversity of virophage-related elements and provides insights into the intricate relationship among virophages, transpovirons, PLVs, pMVREs, and NCVs.

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