Assessing the hidden diversity underlying consensus sequences of SARS-CoV-2 using VICOS, a novel bioinformatic pipeline for identification of mixed viral populations
Introduction: Coinfection with two SARS-CoV-2 viruses is still a very understudied phenomenon. Although next generation sequencing methods are very sensitive to detect heterogeneous viral populations in a sample, there is no standardized method for their characterization, so their clinical and epidemiological importance is unknown. Material and methods: We developed VICOS (Viral COinfection Surveillance), a new bioinformatic algorithm for variant calling, filtering and statistical analysis to identify samples suspected of being mixed SARS-CoV-2 populations from a large dataset in the framework of a community genomic surveillance. VICOS was used to detect SARS-CoV-2 coinfections in a dataset of 1,097 complete genomes collected between March 2020 and August 2021 in Argentina. Results: We detected 23 cases (2%) of SARS-CoV-2 coinfections. Detailed study of VICOS's results together with additional phylogenetic analysis revealed 3 cases of coinfections by two viruses of the same lineage, 2 cases by viruses of different genetic lineages, 13 were compatible with both coinfection and intra-host evolution, and 5 cases were likely a product of laboratory contamination. Discussion: Intra-sample viral diversity provides important information to understand the transmission dynamics of SARS-CoV-2. Advanced bioinformatics tools, such as VICOS, are a necessary resource to help unveil the hidden diversity of SARS-CoV-2.
Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Format: | info:ar-repo/semantics/artículo biblioteca |
Language: | eng |
Published: |
Elsevier
2023-02
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Subjects: | Severe Acute Respiratory Syndrome Coronavirus 2, Bioinformatics, Viruses, Coronavirus del Síndrome Respiratorio Agudo Grave 2, Bioinformática, Virus, Coinfection, Intra-host Evolution, Coinfección, Evolución Intrahospedador, |
Online Access: | http://hdl.handle.net/20.500.12123/15828 https://www.sciencedirect.com/science/article/pii/S0168170222003641 https://doi.org/10.1016/j.virusres.2022.199035 |
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