Deep Sequencing Reveals Dual Evolution of SARS‐CoV‐2: Insights Into Defective Genomes From Wuhan‐Hu‐1 Variants to Omicron Subvariants
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.
Authors
- Ariadna Rando‐Segura (ORCID: https://orcid.org/0000-0003-4555-7286)
- David Tabernero (ORCID: https://orcid.org/0000-0002-1146-4084)
- María Francesca Cortese (ORCID: https://orcid.org/0000-0002-4318-532X)
- Juliana Esperalba (ORCID: https://orcid.org/0000-0003-1326-1341)
- Damir García‐Cehic (ORCID: https://orcid.org/0000-0002-0009-038X)
- Sergi Colomer‐Castell (ORCID: https://orcid.org/0000-0002-0307-7455)
- Narcı́s Saubi (ORCID: https://orcid.org/0000-0001-5493-1044)
- Renate W. Hakze‐van der Honing (ORCID: https://orcid.org/0000-0001-7621-2729)
- María Piñana (ORCID: https://orcid.org/0000-0002-4766-2613)
- Alejandra Gónzalez‐Sánchez (ORCID: https://orcid.org/0000-0002-1809-3415)
- Josep Quer (ORCID: https://orcid.org/0000-0003-0014-084X)
- Francisco Rodríguez‐Frias (ORCID: https://orcid.org/0000-0002-9128-7013)
- Cristina Andrés (ORCID: https://orcid.org/0000-0002-3200-0895)
- Juan Ignacio Esteban (ORCID: https://orcid.org/0000-0001-5085-917X)
- Andrés Antón (ORCID: https://orcid.org/0000-0002-1476-0815)
- Andries A. Kampfraath (ORCID: https://orcid.org/0000-0002-2556-0608)
- Roser Ferrer (ORCID: https://orcid.org/0000-0002-8925-3172)
- Joaquím Segalés (ORCID: https://orcid.org/0000-0002-1539-7261)
- Júlia Vergara‐Alert (ORCID: https://orcid.org/0000-0001-7484-444X)
- Carolina Campos (ORCID: https://orcid.org/0000-0002-0132-7027)
- Marta Ibañez‐Lligoña (ORCID: https://orcid.org/0000-0003-3428-2168)
- Josep Gregori (ORCID: https://orcid.org/0000-0002-4253-8015)
- Tomàs Pumarola (ORCID: https://orcid.org/0000-0002-3434-7585)
- Wim H. M. van der Poel (ORCID: https://orcid.org/0000-0002-7498-8002)
Institutions
- Universitat Autònoma de Barcelona (ES)
- Instituto de Salud Carlos III (ES)
- Universitat Internacional de Catalunya (ES)
- Centre de Recerca en Sanitat Animal (ES)
- Vall d'Hebron Institut de Recerca (ES)
- Vall d'Hebron Hospital Universitari (ES)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (ES)
- Wageningen University & Research (NL)
- University of Cincinnati Medical Center (US)
Publication Details
- Journal
- Journal of Medical Virology
- Published
- 2025-06-30
- DOI
- https://doi.org/10.1002/jmv.70476
- Primary Topic
- SARS-CoV-2 and COVID-19 Research
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- European Commission
- Centro para el Desarrollo Tecnológico Industrial
- Ministerio de Economía y Competitividad
- Ministerio de Ciencia e Innovación
- Fundació Institut de Recerca Hospital Universitari Vall d’Hebron
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas
- Fundación Bancaria Caixa d'Estalvis i Pensions de Barcelona
- Instituto de Salud Carlos III
- European Regional Development Fund
- Agencia Estatal de Investigación