Journal of medical virology · 2025
Deep Sequencing Reveals Dual Evolution of SARS-CoV-2: Insights Into Defective Genomes From Wuhan-Hu-1 Variants to Omicron Subvariants.
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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
Аннотация
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.