{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T13:06:16Z","timestamp":1789995976938,"version":"4.0.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T00:00:00Z","timestamp":1788393600000},"content-version":"vor","delay-in-days":245,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>RNA viruses form genetically diverse populations structured as mutant spectra, or quasispecies, whose internal organization influences their evolutionary and adaptive dynamics. While genetic diversity has been extensively characterized, the structural organization of viral populations in sequence space remains less explored. Here, we compare genotype network architectures in two RNA viruses with markedly different evolutionary contexts: bacteriophage $Q\\beta$ evolving in controlled laboratory conditions and severe acute respiratory syndrome coronavirus 2 evolving within infected human hosts. Using deep sequencing data, we reconstruct the genotype network of mutationally coupled variants within viral populations and analyse their topological properties. Despite large differences in genome size, mutation rate, and ecological setting, both viruses exhibit a common organization: a highly abundant central haplotype surrounded by layers of variants of diminishing abundance as Hamming distance to the central haplotype increases. All reconstructed networks share qualitative and quantitative topological features, displaying a hierarchical structure. The robust organization of both populations under multiple conditions suggests that RNA viruses may share a common genotype network architecture governed by fundamental properties of sequence space and the generic mechanisms of replication and mutation. Genotype networks provide a unifying framework to describe viral population structure beyond conventional diversity measures and, by revealing how local constraints shape mutational search, offers insights into the predictability of viral evolution.<\/jats:p>","DOI":"10.1093\/ve\/veag053","type":"journal-article","created":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T11:44:57Z","timestamp":1787312697000},"source":"Crossref","is-referenced-by-count":0,"title":["Shared quasispecies architecture in experimental and natural RNA virus populations"],"prefix":"10.1093","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-2024-2427","authenticated-orcid":false,"given":"Samuel","family":"Mart\u00ednez-Alcal\u00e1","sequence":"first","affiliation":[{"name":"Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC) , c\/ Jos\u00e9 Guti\u00e9rrez Abascal 2, E-28006 Madrid ,","place":["Spain"]},{"name":"Grupo Interdisciplinar de Sistemas Complejos (GISC) , E-28911 Madrid ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5941-4775","authenticated-orcid":false,"given":"Iker","family":"Atienza-Diez","sequence":"additional","affiliation":[{"name":"Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC) , c\/ Jos\u00e9 Guti\u00e9rrez Abascal 2, E-28006 Madrid ,","place":["Spain"]},{"name":"Grupo Interdisciplinar de Sistemas Complejos (GISC) , E-28911 Madrid ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8368-3641","authenticated-orcid":false,"given":"Pilar","family":"Somovilla","sequence":"additional","affiliation":[{"name":"Centro de Astrobiolog\u00eda (CAB), CSIC-INTA , Carretera de Ajalvir Km 4, E-28850 Torrej\u00f3n de Ardoz, Madrid ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4482-5181","authenticated-orcid":false,"given":"Brenda","family":"Mart\u00ednez-Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Microbes in Health and Welfare Program , Centro de Biolog\u00eda Molecular Severo Ochoa (CSIC-UAM), C\/ Nicol\u00e1s Cabrera, 1, Campus de Cantoblanco, E-28049 Madrid ,","place":["Spain"]},{"name":"Department of Clinical Microbiology , Instituto de Investigaci\u00f3n Sanitaria-Fundaci\u00f3n Jim\u00e9nez D\u00edaz University Hospital (UAM), Av. de los Reyes Cat\u00f3licos, 2, E-28040 Madrid ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1618-1937","authenticated-orcid":false,"given":"Celia","family":"Perales","sequence":"additional","affiliation":[{"name":"Microbes in Health and Welfare Program , Centro de Biolog\u00eda Molecular Severo Ochoa (CSIC-UAM), C\/ Nicol\u00e1s Cabrera, 1, Campus de Cantoblanco, E-28049 Madrid ,","place":["Spain"]},{"name":"Department of Clinical Microbiology , Instituto de Investigaci\u00f3n Sanitaria-Fundaci\u00f3n Jim\u00e9nez D\u00edaz University Hospital (UAM), Av. de los Reyes Cat\u00f3licos, 2, E-28040 Madrid ,","place":["Spain"]},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Infecciosas (CIBERINFEC) , C\/ de Melchor Fern\u00e1ndez Almagro, 3, E- 28029 Madrid ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0045-8145","authenticated-orcid":false,"given":"Luis F","family":"Seoane","sequence":"additional","affiliation":[{"name":"BIT Lab , Complexity of Life program, Institut de Biologia Evolutiva (CSIC-UPF), Pg. Mar\u00edtim de la Barceloneta, 37, 08003 Barcelona ,","place":["Spain"]},{"name":"Theoretical Sciences Visiting Program , Okinawa Institute of Science and Technology Graduate University, Onna 904-0495 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7477-7822","authenticated-orcid":false,"given":"Ester","family":"L\u00e1zaro","sequence":"additional","affiliation":[{"name":"Centro de Astrobiolog\u00eda (CAB), CSIC-INTA , Carretera de Ajalvir Km 4, E-28850 Torrej\u00f3n de Ardoz, Madrid ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0134-2785","authenticated-orcid":false,"given":"Susanna","family":"Manrubia","sequence":"additional","affiliation":[{"name":"Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC) , c\/ Jos\u00e9 Guti\u00e9rrez Abascal 2, E-28006 Madrid ,","place":["Spain"]},{"name":"Grupo 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