{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:19:58Z","timestamp":1760059198798,"version":"build-2065373602"},"reference-count":36,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2025,5,28]],"date-time":"2025-05-28T00:00:00Z","timestamp":1748390400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["2023-04770"],"award-info":[{"award-number":["2023-04770"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Retroviruses insert DNA copies of themselves into the chromosomes of their hosts forming proviruses that can synthesize new transmissible viruses. Exogenous retroviruses (XRVs) insert into the DNA of somatic cells and are transmitted infectiously. Endogenous retroviruses (ERVs) become inserted in the DNA of germline cells and are transmitted genetically. ERVs can spread through the genome by transposition. ERVs originate from an initial copy of an XRV inserted into the genome of an organism infected by the XRV. Many XRVs are transmitted maternally as well as horizontally; therefore, we consider the effect of maternal transmission on the evolution of virulence of an XRV. Our model shows that the XRV either evolves high virulence with low maternal transmission, or vice versa. We then consider the spread of ERV genes in conjunction with the infectious spread of an XRV. Beginning from a single copy of an ERV, we calculate the probability that it spreads to fixation (i.e., the state where all individuals contain ERV genes). This depends on its virulence and transposition rate. If the XRV is present, the fixation probability also depends on the virulence of the XRV and whether the ERV provides resistance to the XRV. An ERV with only a small deleterious effect on host fitness has a high fixation probability, particularly if it provides resistance to the XRV. We also show that, if an ERV does not spread to fixation, it can still cause elimination of the XRV, with the end result that the population is cleared of both XRV and ERV.<\/jats:p>","DOI":"10.3390\/v17060770","type":"journal-article","created":{"date-parts":[[2025,5,29]],"date-time":"2025-05-29T04:46:38Z","timestamp":1748493998000},"page":"770","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The Spread of Endogenous Retroviruses in Populations Infected by Exogenous Viruses"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-2859-1240","authenticated-orcid":false,"given":"Hyunjin","family":"Park","sequence":"first","affiliation":[{"name":"Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4L8, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5220-9760","authenticated-orcid":false,"given":"Paul G.","family":"Higgs","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4L8, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,5,28]]},"reference":[{"key":"ref_1","unstructured":"Coffin, J.M., Hughes, S.H., and Varmus, H.E. (1997). Retroviruses, Cold Spring Harbor Laboratory Press."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1146\/annurev-virology-100114-054945","article-title":"Endogenous Retroviruses in the Genomics Era","volume":"2","author":"Johnson","year":"2015","journal-title":"Annu. Rev. Virol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/nrg3199","article-title":"Endogenous viruses: Insights into viral evolution and impact on host biology","volume":"13","author":"Feschotte","year":"2012","journal-title":"Nat. Rev. Genet."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1038\/nature04841","article-title":"Retroviral invasion of the koala genome","volume":"442","author":"Tarlinton","year":"2006","journal-title":"Nature"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"e00044-17","DOI":"10.1128\/MMBR.00044-17","article-title":"Transmission, Evolution, and Endogenization: Lessons Learned from Recent Retroviral Invasions","volume":"82","author":"Greenwood","year":"2017","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1590\/S0074-02762001000100001","article-title":"Vertical Human Immunodeficiency Virus Type 1-HIV-1-Transmission. A Review","volume":"96","author":"Bongertz","year":"2001","journal-title":"Mem. Inst. Oswaldo Cruz"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Cardenas, M.C., Farnan, S., Hamel, B.L., Plazas, M.C.M., Sintim-Aboagye, E., Johnson, E., Littlefield, D.R., Behl, S., Punia, S., and Enninga, E.A.L. (2023). Prevention of the Vertical Transmission of HIV; A Recap of the Journey so Far. Viruses, 15.","DOI":"10.3390\/v15040849"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"S24","DOI":"10.1093\/jpids\/piu070","article-title":"Mother-to-Child Transmission of Human T-Cell Lymphotropic Viruses-1\/2: What We Know, and What Are the Gaps in Understanding and Preventing This Route of Infection","volume":"3","author":"Bastos","year":"2014","journal-title":"J. Pediatr. Infect. Dis. Soc."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Kemeter, L.M., Birzer, A., Heym, S., and Thoma-Kress, A.K. (2023). Milk Transmission of Mammalian Retroviruses. Microorganisms, 11.","DOI":"10.3390\/microorganisms11071777"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1093\/ps\/77.8.1204","article-title":"Retrovirus-induced disease in poultry","volume":"77","author":"Payne","year":"1998","journal-title":"Poult. Sci."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/0966-842X(94)90537-1","article-title":"The evolution of virulence","volume":"2","author":"Read","year":"1994","journal-title":"Trends Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1098\/rspb.1995.0099","article-title":"The population dynamics of vertically and horizontally transmitted parasites","volume":"260","author":"Lipsitch","year":"1995","journal-title":"Proc. R. Soc. Lond. B"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1729","DOI":"10.2307\/2410731","article-title":"The evolution of virulence in pathogens with vertical and horizontal transmission","volume":"50","author":"Lipsitch","year":"1996","journal-title":"Evolution"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1093\/genetics\/101.3-4.519","article-title":"Selfish DNA: A sexually-transmitted nuclear parasite","volume":"101","author":"Hickey","year":"1982","journal-title":"Genetics"},{"key":"ref_15","first-page":"1","article-title":"Interactions between Exogenous and Endogenous Retroviruses","volume":"4","author":"Rasmussen","year":"1997","journal-title":"J. Biomed. Sci."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/S0966-842X(97)01086-X","article-title":"Endogenous retroviruses and the evolution of resistance to retroviral infection","volume":"5","author":"Best","year":"1997","journal-title":"Trends Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1742-4690-3-41","article-title":"Identification of the hASCT2-binding domain of the Env ERVWE1\/syncytin-1 fusogenic glycoprotein","volume":"3","author":"Cheynet","year":"2006","journal-title":"Retrovirology"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"e00649-18","DOI":"10.1128\/JVI.00649-18","article-title":"Feline Leukemia Virus (FeLV) Disease Outcomes in a Domestic Cat Breeding Colony: Relationship to Endogenous FeLV and Other Chronic Viral Infections","volume":"92","author":"Powers","year":"2018","journal-title":"J. Virol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e02299-20","DOI":"10.1128\/JVI.02299-20","article-title":"Switching sides: How endogenous retroviruses protect us from viral infections","volume":"95","author":"Sauter","year":"2021","journal-title":"J. Virol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1128\/JVI.77.1.749-753.2003","article-title":"Receptor usage and fetal expression of ovine endogenous betaretroviruses: Implications for coevolution of endogenous and exogenous retroviruses","volume":"77","author":"Spencer","year":"2003","journal-title":"J. Virol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2429","DOI":"10.1128\/JVI.01926-08","article-title":"Mobilization of endogenous retroviruses in mice after infection with an exogenous retrovirus","volume":"83","author":"Evans","year":"2009","journal-title":"J. Virol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1128\/jvi.15.6.1367-1377.1975","article-title":"Recombination between endogenous and exogenous RNA tumor virus genes as analyzed by nucleic acid hybridization","volume":"15","author":"Hayward","year":"1975","journal-title":"J. Virol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1021\/j100540a008","article-title":"Exact Stochastic Simulation of Coupled Chemical Reactions","volume":"81","author":"Gillespie","year":"1977","journal-title":"J. Phys. Chem."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.virol.2015.03.012","article-title":"APOBECs and virus restriction","volume":"479\u2013480","author":"Harris","year":"2015","journal-title":"Virology"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1016\/j.tim.2008.08.013","article-title":"Restriction of retroviral replication by APOBEC3G\/F and TRIM5\u03b1","volume":"16","author":"Huthoff","year":"2008","journal-title":"Trends Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"e1555","DOI":"10.1002\/wrna.1555","article-title":"PIWI pathway against viruses in insects","volume":"10","author":"Kolliopoulou","year":"2019","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1095\/biolreprod.105.039776","article-title":"Sheep Endogenous Betaretroviruses (enJSRVs) and the Hyaluronidase 2 (HYAL2) Receptor in the Ovine Uterus and Conceptus","volume":"73","author":"Dunlap","year":"2005","journal-title":"Biol. Reprod."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1111\/j.1749-6632.2009.05002.x","article-title":"The Special Relationship between Endogenous Retroviruses and Their Host","volume":"1178","author":"Varela","year":"2009","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"R609","DOI":"10.1016\/j.cub.2012.06.002","article-title":"Retroviruses and the placenta","volume":"22","author":"Haig","year":"2012","journal-title":"Curr. Biol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1038\/35001608","article-title":"Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis","volume":"403","author":"Mi","year":"2000","journal-title":"Nature"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1093\/molehr\/gah070","article-title":"Endogenous retroviral syncytin: Compilation of experimental research on syncytin and its possible role in normal and disturbed human placentogenesis","volume":"10","author":"Knerr","year":"2004","journal-title":"Mol. Hum. Reprod."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1038\/nsmb.2799","article-title":"The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity","volume":"21","author":"Lu","year":"2014","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/nature13804","article-title":"Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells","volume":"516","author":"Wang","year":"2014","journal-title":"Nature"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.tig.2021.07.007","article-title":"The essential but enigmatic regulatory role of HERVH in pluripotency","volume":"38","author":"Sexton","year":"2022","journal-title":"Trends Genet."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1590\/S0036-46651998000400008","article-title":"Vertical transmission of HTLV-I\/II: A review","volume":"40","author":"Bittencourt","year":"1998","journal-title":"Rev. Inst. Med. Trop. Sao Paulo"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s12977-020-00525-1","article-title":"Frequent horizontal and mother-to-child transmission may contribute to high prevalence of STLV-1 infection in Japanese macaques","volume":"17","author":"Murata","year":"2020","journal-title":"Retrovirology"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/6\/770\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:42:38Z","timestamp":1760031758000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/6\/770"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,28]]},"references-count":36,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2025,6]]}},"alternative-id":["v17060770"],"URL":"https:\/\/doi.org\/10.3390\/v17060770","relation":{},"ISSN":["1999-4915"],"issn-type":[{"type":"electronic","value":"1999-4915"}],"subject":[],"published":{"date-parts":[[2025,5,28]]}}}