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oai:recercat.cat:20.500.12327/47102025-10-22T11:05:43Zcom_2072_4428com_2072_4427col_2072_487898

Deep Sequencing Reveals Dual Evolution of SARS-CoV-2: Insights Into Defective Genomes From Wuhan-Hu-1 Variants to Omicron Subvariants Campos, Carolina Ibañez-Lligoña, Marta Colomer‑Castell, Sergi Gregori, Josep Garcia‑Cehic, Damir Andrés, Cristina Piñana, Maria González‑Sánchez, Alejandra Rando‑Segura, Ariadna Esperalba, Juliana Saubí, Narcis Cortese, Maria Francesca Tabernero, David Rodriguez-Frias, Francisco Ferrer, Roser Esteban, Juan Ignacio Kakze-van der Honing, Renate W. Kampfraath, Andries A. Vergara-Alert, Júlia Segalés, Joaquim van der Poel, Wim H. M. Pumarola, Tomàs Antón, Andrés Quer, Josep Producció Animal Sanitat Animal SARS‐CoV‐2 has evolved from early variants dominating the first (B.1.5, B.1.1) and second (B.1.177) pandemic waves, which exhibited a higher frequency of minority mutants with deletions leading to Defective Viral Genomes (DVGs) in the spike region near the S1/S2 cleavage site than the Alpha, Beta, and Delta variants. The emergence of Omicron has significantly altered the dominant variant profile, with Omicron subvariants now representing 100% of circulating viruses. To monitor the evolution and adaptation of Omicron in the human population, a deep‐sequencing study was performed in RNA samples of BA.1, BA.1.1, BA.2, BA.5, BQ.1.1, XBB.1.5 and BA.2.86 Omicron subvariants. The findings reveal two occurrences of similar evolutionary patterns within SARS‐CoV‐2 characterized by a shift from a significant to a very low production of DVGs. This event suggests that DVGs might play a role in the virus's spread and adaptation for persistence in infected humans. 2025-10-22T11:05:43Z 2025-10-22T11:05:43Z 2025-10-22T11:05:43Z 2025-06-30 info:eu-repo/semantics/article Campos, Carolina, Marta Ibañez‐Lligoña, Sergi Colomer‑Castell, Josep Gregori, Damir Garcia‑Cehic, Cristina Andrés, Maria Piñana, Júlia Vergara, et al. 2025. “Deep Sequencing Reveals Dual Evolution of SARS‐CoV‐2: Insights Into Defective Genomes From Wuhan‐Hu‐1 Variants to Omicron Subvariants.” Journal of Medical Virology 97 (7). https://doi.org/10.1002/jmv.70476. 0146-6615 http://hdl.handle.net/20.500.12327/4710 https://doi.org/10.1002/jmv.70476 eng Journal of Medical Virology MICINN/Programa Estatal para impulsar la investigación científico-técnica y su transferencia/PID2021‐126447OB‐I00/ES/Estrategias de terapia génica para controlar la infección por los virus de la hepatitis B y Delta basada en el estudio de las cuasiespecies virales por secuenciación masiva/ ISCIII/Programa Estatal de I+D+I orientada a los retos de la sociedad/PI19-00533/ES/Cambios dinámicos en la respuesta inmunitaria específica de VHC durante y después del tratamiento con DAAS para desentrañar nuevos enfoques para el desarrollo de vacunas profilácticas/ FEDER/ / /EU/ / CIBER/ / /ES/ / CDTI/IDI-20200297/ES/ / / http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess Attribution 4.0 International Wiley