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; TORRES, CAROLINA; KÖNIG, GUIDO; ACUÑA, DOLORES; CEBALLOS, SANTIAGO; DISTÉFANO, ANA J; DOPAZO, HERNÁN; DUS SANTOS, MARÍA; FASS, MÓNICA; FERNÁNDEZ DO PORTO, DARÍO; FERNÁNDEZ, AILEN; GALLEGO, FERNANDO; GISMONDI, MARÍA I; GRAMUNDI, IVAN; LUSSO, SILVINA; MARTÍ, MARCELO; MAZZEO, MELINA; MISTCHENKO, ALICIA S.; MUÑOZ HIDALGO, MARIANNE; NATALE, MÓNICA; NARDI, CRISTINA; OUSSET, JULIA; PERALTA, ANDREA V; PINTOS, CAROLINA; PUEBLA, ANDREA F; PIANCIOLA, LUIS; RIVAROLA, MÁXIMO; TURJANSKI, ADRIAN; VALINOTTO, LAURA; VERA, PABLO A; ZAIAT, JONATHAN; ZUBRYCKI, JEREMÍAS; 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 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.