{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T08:51:43Z","timestamp":1773996703124,"version":"3.50.1"},"reference-count":55,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T00:00:00Z","timestamp":1773792000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009060","name":"SIDACTION","doi-asserted-by":"crossref","award":["12676"],"award-info":[{"award-number":["12676"]}],"id":[{"id":"10.13039\/100009060","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003323","name":"Agence Nationale de Recherches sur le Sida et les H\u00e9patites Virales","doi-asserted-by":"crossref","award":["ECTZ243867"],"award-info":[{"award-number":["ECTZ243867"]}],"id":[{"id":"10.13039\/501100003323","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004794","name":"Centre National de la Recherche Scientifique","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004794","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Human Immunodeficiency Virus Type 1 (HIV-1), the causative agent of the acquired immune deficiency syndrome (AIDS), originated from zoonotic transmissions of simian immunodeficiency viruses (SIVs) infecting African great apes, following complex cross-species transmission events and virus\u2013host co-evolution. These processes were accompanied by multiple viral adaptations, particularly within structural and accessory genes, enabling evasion of host restriction factors and long-term viral persistence. In 1988, an antisense open reading frame (ORF) overlapping the env gene was proposed and subsequently confirmed by the identification of antisense transcripts and the antisense protein (ASP). An \u201cintact\u201d ASP ORF (defined as &gt;150 codons) is predominantly conserved in pandemic HIV-1 group M viruses and shows evidence of positive selection, suggesting a selective advantage. Increasing evidence supports the hypothesis that the asp gene emerged de novo during the evolution of group M and contributed to viral adaptation and global spread in humans. This review combines a narrative review of the literature with original in silico analyses of HIV-1 and SIV sequences retrieved from the Los Alamos National Laboratory database. We systematically reassessed the distribution, length variability and conservation of the ASP ORF across HIV-1 groups (M, N, O, P), subtypes, circulating recombinant forms (CRFs), unique recombinant forms (URFs) and related SIV lineages. Our updated analyses confirmed the strong association between the presence of an \u201cintact\u201d ASP ORF and pandemic HIV-1 group M lineages, while revealing rare but notable antisense ORFs in selected SIVcpz and SIVgor strains. By integrating evolutionary, epidemiological and sequence-based evidence, we aim to clarify the origin and maintenance of the ASP ORF and to contextualize its emergence within the broader framework of overlapping gene evolution, de novo gene birth and the selective pressures shaping viral fitness and pandemic potential.<\/jats:p>","DOI":"10.3390\/v18030381","type":"journal-article","created":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T14:14:05Z","timestamp":1773843245000},"page":"381","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The Gene Encoding the Antisense Protein ASP of HIV-1: Origin, Distribution and Maintenance"],"prefix":"10.3390","volume":"18","author":[{"given":"Myriam Abla","family":"Houmey","sequence":"first","affiliation":[{"name":"Institut de Recherche en Infectiologie de Montpellier (IRIM), Universit\u00e9 de Montpellier, Centre National de la Recherche Scientifique, 1919 Route de Mende, 34293 Montpellier, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sara","family":"Sadek","sequence":"additional","affiliation":[{"name":"Institut de Recherche en Infectiologie de Montpellier (IRIM), Universit\u00e9 de Montpellier, Centre National de la Recherche Scientifique, 1919 Route de Mende, 34293 Montpellier, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3677-1280","authenticated-orcid":false,"given":"Coralie F.","family":"Daussy","sequence":"additional","affiliation":[{"name":"Institut de Recherche en Infectiologie de Montpellier (IRIM), Universit\u00e9 de Montpellier, Centre National de la Recherche Scientifique, 1919 Route de Mende, 34293 Montpellier, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1528-9607","authenticated-orcid":false,"given":"Nathalie","family":"Chazal","sequence":"additional","affiliation":[{"name":"Institut de Recherche en Infectiologie de Montpellier (IRIM), Universit\u00e9 de Montpellier, Centre National de la Recherche Scientifique, 1919 Route de Mende, 34293 Montpellier, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1126\/science.6189183","article-title":"Isolation of a T-Lymphotropic Retrovirus from a Patient at Risk for Acquired Immune Deficiency Syndrome (AIDS)","volume":"220","author":"Chermann","year":"1983","journal-title":"Science"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"a006841","DOI":"10.1101\/cshperspect.a006841","article-title":"Origins of HIV and the AIDS Pandemic","volume":"1","author":"Sharp","year":"2011","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1097\/00002030-199704000-00013","article-title":"Geographical Distribution of HIV-1 Group O Viruses in Africa","volume":"11","author":"Peeters","year":"1997","journal-title":"AIDS"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1016\/j.chom.2014.10.002","article-title":"Nef Proteins of Epidemic HIV-1 Group O Strains Antagonize Human Tetherin","volume":"16","author":"Kluge","year":"2014","journal-title":"Cell Host Microbe"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.chom.2018.12.002","article-title":"Key Viral Adaptations Preceding the AIDS Pandemic","volume":"25","author":"Sauter","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1097\/00126334-200306010-00020","article-title":"High Genetic Diversity of HIV-1 Strains in Chad, West Central Africa","volume":"33","author":"Vidal","year":"2003","journal-title":"J. Acquir. Immune Defic. Syndr."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1126\/science.288.5463.55d","article-title":"HIV-1 Nomenclature Proposal","volume":"288","author":"Robertson","year":"2000","journal-title":"Science"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1016\/j.molmed.2011.12.001","article-title":"The Origin and Diversity of the HIV-1 Pandemic","volume":"18","author":"Hemelaar","year":"2012","journal-title":"Trends Mol. Med."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"100912","DOI":"10.1016\/S2666-5247(24)00151-4","article-title":"Global and Regional Genetic Diversity of HIV-1 in 2010\u201321: Systematic Review and Analysis of Prevalence","volume":"5","author":"Nair","year":"2024","journal-title":"Lancet Microbe"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1126\/science.3347840","article-title":"Human Immunodeficiency Virus May Encode a Novel Protein on the Genomic DNA plus Strand","volume":"239","author":"Miller","year":"1988","journal-title":"Science"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Gholizadeh, Z., Iqbal, M.S., Li, R., and Romerio, F. (2021). The HIV-1 Antisense Gene ASP: The New Kid on the Block. Vaccines, 9.","DOI":"10.3390\/vaccines9050513"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Savoret, J., Mesnard, J.-M., Gross, A., and Chazal, N. (2021). Antisense Transcripts and Antisense Protein: A New Perspective on Human Immunodeficiency Virus Type 1. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.625941"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Miller, R., Zimmer, A., Moutot, G., Mesnard, J.-M., and Chazal, N. (2021). Retroviral Antisense Transcripts and Genes: 33 Years after First Predicted, a Silent Retroviral Revolution?. Viruses, 13.","DOI":"10.3390\/v13112221"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"5089","DOI":"10.1128\/JVI.00225-13","article-title":"Detection of the HIV-1 Minus-Strand-Encoded Antisense Protein and Its Association with Autophagy","volume":"87","author":"Torresilla","year":"2013","journal-title":"J. Virol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e00574-19","DOI":"10.1128\/JVI.00574-19","article-title":"The HIV-1 Antisense Protein ASP Is a Transmembrane Protein of the Cell Surface and an Integral Protein of the Viral Envelope","volume":"93","author":"Affram","year":"2019","journal-title":"J. Virol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1089\/aid.1990.6.425","article-title":"Plus Strand of the HIV Provirus DNA Is Expressed at Early Stages of Infection","volume":"6","author":"Bukrinsky","year":"1990","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1016\/S0042-6822(95)80034-4","article-title":"A Natural Antisense RNA Derived from the HIV-1 Env Gene Encodes a Protein Which Is Recognized by Circulating Antibodies of HIV+ Individuals","volume":"206","author":"Thoreau","year":"1995","journal-title":"Virology"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1128\/jvi.68.2.979-987.1994","article-title":"Negative-Strand RNA Transcripts Are Produced in Human Immunodeficiency Virus Type 1-Infected Cells and Patients by a Novel Promoter Downregulated by Tat","volume":"68","author":"Michael","year":"1994","journal-title":"J. Virol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/1742-4690-4-71","article-title":"Detection, Characterization and Regulation of Antisense Transcripts in HIV-1","volume":"4","author":"Landry","year":"2007","journal-title":"Retrovirology"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/1742-4690-9-38","article-title":"HIV-1-Encoded Antisense RNA Suppresses Viral Replication for a Prolonged Period","volume":"9","author":"Yamagishi","year":"2012","journal-title":"Retrovirology"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1038\/mt.2014.29","article-title":"An HIV-Encoded Antisense Long Noncoding RNA Epigenetically Regulates Viral Transcription","volume":"22","author":"Saayman","year":"2014","journal-title":"Mol. Ther. J. Am. Soc. Gene Ther."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.virol.2017.03.002","article-title":"The Human Immunodeficiency Virus 1 ASP RNA Promotes Viral Latency by Recruiting the Polycomb Repressor Complex 2 and Promoting Nucleosome Assembly","volume":"506","author":"Zapata","year":"2017","journal-title":"Virology"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1099\/jgv.0.001244","article-title":"Detection of Antisense Protein (ASP) RNA Transcripts in Individuals Infected with Human Immunodeficiency Virus Type 1 (HIV-1)","volume":"100","author":"Mancarella","year":"2019","journal-title":"J. Gen. Virol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"4015","DOI":"10.1128\/JVI.03435-14","article-title":"Immune Screening Identifies Novel T Cell Targets Encoded by Antisense Reading Frames of HIV-1","volume":"89","author":"Berger","year":"2015","journal-title":"J. Virol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s12977-015-0135-y","article-title":"The HIV-1 Antisense Protein (ASP) Induces CD8 T Cell Responses during Chronic Infection","volume":"12","author":"Bet","year":"2015","journal-title":"Retrovirology"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Savoret, J., Chazal, N., Moles, J.-P., Tuaillon, E., Boufassa, F., Meyer, L., Lecuroux, C., Lambotte, O., Van De Perre, P., and Mesnard, J.-M. (2020). A Pilot Study of the Humoral Response Against the AntiSense Protein (ASP) in HIV-1-Infected Patients. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.00020"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"11537","DOI":"10.1073\/pnas.1605739113","article-title":"Concomitant Emergence of the Antisense Protein Gene of HIV-1 and of the Pandemic","volume":"113","author":"Cassan","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_28","first-page":"2440","article-title":"OLGenie: Estimating Natural Selection to Predict Functional Overlapping Genes","volume":"37","author":"Nelson","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e03802-23","DOI":"10.1128\/spectrum.03802-23","article-title":"Creation of the HIV-1 Antisense Gene Asp Coincided with the Emergence of the Pandemic Group M and Is Associated with Faster Disease Progression","volume":"12","author":"Pavesi","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Pavesi, A. (2021). Origin, Evolution and Stability of Overlapping Genes in Viruses: A Systematic Review. Genes, 12.","DOI":"10.3390\/genes12060809"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Pavesi, A., and Romerio, F. (2025). Covariation of Amino Acid Substitutions in the HIV-1 Envelope Glycoprotein Gp120 and the Antisense Protein ASP Associated with Coreceptor Usage. Viruses, 17.","DOI":"10.1101\/2025.01.19.633671"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Houmey, M.A., Caico, I., Rivault, A., Espert, L., Mesnard, J.-M., Romerio, F., and Chazal, N. (2025). The Antisense Protein ASP of HIV-1 Enhances Viral Entry in CD4+ T Cells. Viruses, 17.","DOI":"10.3390\/v17101332"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1093\/bioinformatics\/bts091","article-title":"Unipro UGENE: A Unified Bioinformatics Toolkit","volume":"28","author":"Okonechnikov","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1097\/QAD.0b013e328342ff93","article-title":"Global Trends in Molecular Epidemiology of HIV-1 during 2000\u20132007","volume":"25","author":"Hemelaar","year":"2011","journal-title":"AIDS"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1089\/aid.1998.14.807","article-title":"HIV Type 1 Env Subtype A Variants in Taiwan","volume":"14","author":"Lee","year":"1998","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1089\/aid.1996.12.1413","article-title":"Genomic Structure and Nucleotide Sequence Analysis of a New HIV Type 1 Subtype A Strain from Nigeria","volume":"12","author":"Howard","year":"1996","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Abidi, S.H., Aibekova, L., Davlidova, S., Amangeldiyeva, A., Foley, B., and Ali, S. (2021). Origin and Evolution of HIV-1 Subtype A6. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0260604"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"e772","DOI":"10.1016\/S2352-3018(20)30252-6","article-title":"Global and Regional Epidemiology of HIV-1 Recombinants in 1990\u20132015: A Systematic Review and Global Survey","volume":"7","author":"Hemelaar","year":"2020","journal-title":"Lancet HIV"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"7013","DOI":"10.1128\/jvi.70.10.7013-7029.1996","article-title":"The Heterosexual Human Immunodeficiency Virus Type 1 Epidemic in Thailand Is Caused by an Intersubtype (A\/E) Recombinant of African Origin","volume":"70","author":"Gao","year":"1996","journal-title":"J. Virol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1006\/viro.1998.9211","article-title":"Full Genome Sequences of Human Immunodeficiency Virus Type 1 Subtypes G and A\/G Intersubtype Recombinants","volume":"247","author":"Carr","year":"1998","journal-title":"Virology"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1126\/science.1126531","article-title":"Chimpanzee Reservoirs of Pandemic and Nonpandemic HIV-1","volume":"313","author":"Keele","year":"2006","journal-title":"Science"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1038\/nm.2016","article-title":"A New Human Immunodeficiency Virus Derived from Gorillas","volume":"15","author":"Plantier","year":"2009","journal-title":"Nat. Med."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1114","DOI":"10.1089\/aid.2007.0071","article-title":"Sequence Diversity among Chimpanzee Simian Immunodeficiency Viruses (SIVcpz) Suggests That SIVcpz Pts Was Derived from SIVcpz Ptt through Additional Recombination Events","volume":"23","author":"Leitner","year":"2007","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1789","DOI":"10.1126\/science.288.5472.1789","article-title":"Timing the Ancestor of the HIV-1 Pandemic Strains","volume":"288","author":"Korber","year":"2000","journal-title":"Science"},{"key":"ref_45","first-page":"E1343","article-title":"Origin of the HIV-1 Group O Epidemic in Western Lowland Gorillas","volume":"112","author":"Ayouba","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Pavesi, A., and Romerio, F. (2022). Extending the Coding Potential of Viral Genomes with Overlapping Antisense ORFs: A Case for the De Novo Creation of the Gene Encoding the Antisense Protein ASP of HIV-1. Viruses, 14.","DOI":"10.3390\/v14010146"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1038\/444164a","article-title":"SIV Infection in Wild Gorillas","volume":"444","author":"Li","year":"2006","journal-title":"Nature"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1713","DOI":"10.1126\/science.1080657","article-title":"Hybrid Origin of SIV in Chimpanzees","volume":"300","author":"Bailes","year":"2003","journal-title":"Science"},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Bell, S.M., and Bedford, T. (2017). Modern-Day SIV Viral Diversity Generated by Extensive Recombination and Cross-Species Transmission. PLoS Pathog., 13.","DOI":"10.1101\/101725"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"10719","DOI":"10.1128\/JVI.00595-09","article-title":"Overlapping Genes Produce Proteins with Unusual Sequence Properties and Offer Insight into de Novo Protein Creation","volume":"83","author":"Rancurel","year":"2009","journal-title":"J. Virol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"3644","DOI":"10.1128\/JVI.01959-09","article-title":"Meta-Analysis To Test the Association of HIV-1 Nef Amino Acid Differences and Deletions with Disease Progression","volume":"84","author":"Pushker","year":"2010","journal-title":"J. Virol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"20140332","DOI":"10.1098\/rstb.2014.0332","article-title":"New Genes from Non-Coding Sequence: The Role of de Novo Protein-Coding Genes in Eukaryotic Evolutionary Innovation","volume":"370","author":"McLysaght","year":"2015","journal-title":"Philos. Trans. R. Soc. B Biol. Sci."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"102384","DOI":"10.1016\/j.mib.2023.102384","article-title":"The Power of the Small: The Underestimated Role of Small Proteins in Bacterial and Archaeal Physiology","volume":"76","author":"Jordan","year":"2023","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"e00826-24","DOI":"10.1128\/spectrum.00826-24","article-title":"Identification and Characterization of a Novel Small Viral Peptide (VSP59) Encoded by Bombyx Mori Cypovirus (BmCPV) That Negatively Regulates Viral Replication","volume":"12","author":"Cao","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"RP106484","DOI":"10.7554\/eLife.106484","article-title":"Coupled Equilibria of Dimerization and Lipid Binding Modulate SARS CoV 2 Orf9b Interactions and Interferon Response","volume":"14","author":"Felipe","year":"2025","journal-title":"eLife"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/3\/381\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T05:27:29Z","timestamp":1773984449000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/3\/381"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,18]]},"references-count":55,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,3]]}},"alternative-id":["v18030381"],"URL":"https:\/\/doi.org\/10.3390\/v18030381","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,18]]}}}