Assessing the hidden diversity underlying consensus sequences of SARS-CoV-2 using VICOS, a novel bioinformatic pipeline for identification of mixed viral populations.

GOYA, STEPHANIE; SOSA, EZEQUIEL; NABAES JODAR, MERCEDES S.; TORRES, CAROLINA; KÖNIG, GUIDO; ACUÑA, DOLORES; CEBALLOS, SANTIAGO; DISTÉFANO, ANA; DOPAZO, HERNÁN; DUS SANTOS, MARÍA JOSÉ; FASS, MÓNICA; FERNÁNDEZ DO PORTO, DARÍO; FERNÁNDEZ, AILÉN; GALLEGO, FERNANDO; GISMONDI, MARÍA INÉS; GRAMUNDI, IVAN; LUSSO, SILVINA B.; MARTÍ, MARCELO; MAZZEO, MELINA; MISTCHENKO ALICIA SUSANA; MUÑOZ HIDALGO, MARIANNE; NATALE, MONICA I; NARDI, CRISTINA; OUSSET, JULIA; PERALTA, ANDREA P; PINTOS, CAROLINA; PUEBLA, ANDREA F; PIANCIOLA, LUIS; RIVAROLA, MÁXIMO; TURJANSKI, ADRIÁN; VALINOTTO, LAURA E.; VERA, PABLO V; ZAIAT, JONATHAN; ZUBRYCKI, JEREMIAS; PROYECTO PAIS; AULICINO, PAULA; VIEGAS, MARIANA

VIRUS RESEARCH

ELSEVIER SCIENCE BV

Año: 2023 vol. 325

0168-1702

Introduction: Coinfection with two SARS-CoV-2 viruses is still a very understudied phenomenon. Although nextgeneration sequencing methods are very sensitive to detect heterogeneous viral populations in a sample, there isno 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 forvariant 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 detectSARS-CoV-2 coinfections in a dataset of 1,097 complete genomes collected between March 2020 and August2021 in Argentina.Results: We detected 23 cases (2%) of SARS-CoV-2 coinfections. Detailed study of VICOS’s results together withadditional 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 5cases were likely a product of laboratory contamination.Discussion: Intra-sample viral diversity provides important information to understand the transmission dynamicsof SARS-CoV-2. Advanced bioinformatics tools, such as VICOS, are a necessary resource to help unveil the hiddendiversity of SARS-CoV-2.