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. 2022 Jun 7;12:9377. doi: 10.1038/s41598-022-13113-4

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Conceptual design of the approach to identify co-infection by SARS-CoV-2 VOCs. Samples with two distinct VOCs (X and Y) of the SARS-CoV-2 virus are sequenced (A). Using a strategy for the whole-genome assembly, a single and misclassified sequence is obtained (B). In contrast, the correct identification of the two VOCs is achieved when an ASV inference is implemented, with the use of a custom database of SARS-CoV-2 for the taxonomy assignment. In this process, specific ASV are recognized for the VOCs, while shared ASVs among all the genomes are assigned to other sequences.