2026-08-29T14:12:21Zhttps://repisalud.isciii.es/rest/oai/requestoai:repisalud.isciii.es:20.500.12105/260222025-12-18T13:00:48Zcom_20.500.12105_2052com_20.500.12105_2051col_20.500.12105_19609
Repisalud
author
Guerrero-Tamayo, Ana
author
Sanz Urquijo, Borja
author
Olivares, Isabel
author
Moragues Tosantos, María-Dolores
author
Casado, Concepcion
author
Pastor-López, Iker
funder
Universidad de Deusto (España)
2025-01-15T10:25:52Z
2025-01-15T10:25:52Z
2024
Guerrero-Tamayo A, Sanz Urquijo B, Olivares I, Moragues Tosantos MD, Casado C, Pastor-López I. Classification of SARS-CoV-2 sequences as recombinants via a pre-trained CNN and identification of a mathematical signature relative to recombinant feature at Spike, via interpretability. PLoS One. 2024 Aug 26;19(8):e0309391.
10.1371/journal.pone.0309391
1932-6203
PloS one
39186542
https://hdl.handle.net/20.500.12105/26022
The global impact of the SARS-CoV-2 pandemic has underscored the need for a deeper understanding of viral evolution to anticipate new viruses or variants. Genetic recombination is a fundamental mechanism in viral evolution, yet it remains poorly understood. In this study, we conducted a comprehensive research on the genetic regions associated with genetic recombination features in SARS-CoV-2. With this aim, we implemented a two-phase transfer learning approach using genomic spectrograms of complete SARS-CoV-2 sequences. In the first phase, we utilized a pre-trained VGG-16 model with genomic spectrograms of HIV-1, and in the second phase, we applied HIV-1 VGG-16 model to SARS-CoV-2 spectrograms. The identification of key recombination hot zones was achieved using the Grad-CAM interpretability tool, and the results were analyzed by mathematical and image processing techniques. Our findings unequivocally identify the SARS-CoV-2 Spike protein (S protein) as the pivotal region in the genetic recombination feature. For non-recombinant sequences, the relevant frequencies clustered around 1/6 and 1/12. In recombinant sequences, the sharp prominence of the main hot zone in the Spike protein prominently indicated a frequency of 1/6. These findings suggest that in the arithmetic series, every 6 nucleotides (two triplets) in S may encode crucial information, potentially concealing essential details about viral characteristics, in this case, recombinant feature of a SARS-CoV-2 genetic sequence. This insight further underscores the potential presence of multifaceted information within the genome, including mathematical signatures that define an organism's unique attributes.
eng
Classification of SARS-CoV-2 sequences as recombinants via a pre-trained CNN and identification of a mathematical signature relative to recombinant feature at Spike, via interpretability
research article
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