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Software Identifies Potential for Co-Infection with Two Coronavirus Variants
VICOS tool aids in understanding co-infections with existing strains.
Argentine researchers, who are part of the public consortium Proyecto País, developed an algorithm that allows them to identify whether a person contracted two types of SARS-CoV-2 coronavirus.
The tool is called VICOS (Viral COinfection Surveillance) and was used to detect SARS-CoV-2 coinfections in data from 1,097 complete genomes collected between March 2020 and August 2021 in Argentina.
According to the work, published in the journal Virus Research, 23 cases (2%) of different SARS-CoV-2 coinfections were detected. If the results are broken down, three of these cases were due to two viruses of the same lineage, two were due to viruses of different genetic lineages, 13 were compatible with both coinfection and intra-host evolution, and 5 cases were probably the product of laboratory contamination.
Since 2020, researchers from Proyecto País – a consortium of the Ministry of Science, Technology and Innovation of the Nation – began to sequence coronavirus genomes from samples of patients with Covid-19.
The new VICOS computer pipeline revealed 2% of SARS-CoV-2 coinfections during the first wave of COVID-19 in Argentina.
VICOS output along with additional metadata helps differentiate between 2 SARS-CoV-2 co-infection, within-host evolution, or sequencing contamination.
Interlineage and intralineage SARS-CoV-2 co-infections should be monitored as the driving force of recombination and evolution.
Coinfection with two SARS-CoV-2 viruses remains a very little studied 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.
VICOS (Viral COinfection Surveillance), a new bioinformatic filtering and statistical analysis algorithm, has been developed to identify samples suspected of being mixed populations of SARS-CoV-2 from a large data set within the framework of community genomic surveillance. VICOS was used to detect SARS-CoV-2 coinfections in a set of record data from 1097 whole genomes collected between March 2020 and August 2021 in Argentina.
23 cases (2%) of SARS-CoV-2 coinfections were detected. Detailed study of the VICOS 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 probably laboratory contamination product.
Viral diversity within the sample provides important information to understand the transmission dynamics of SARS-CoV-2. Advanced bioinformatics tools, such as VICOS, are a necessary resource to help reveal the hidden plurality of SARS-CoV-2.
Working algorithm used by VICOS to identify and report the number, frequency and position of iSNVs in SARS-CoV-2 genomes obtained with Illumina technology. The pipeline requires a set of BAM files as input.
