Integration of bioinformatic tools for the detection of SARS-CoV-2 co-infection cases.

ABSTRACT: Co-infection with multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, though rare, may have clinical and public health implications, including facilitating variant recombination. Early detection of co-infections is, therefore, crucial. In this study, we report two probable cases of co-infection identified during routine genomic surveillance. Initially suspected as cross-contamination due to the presence of private mutations and nucleotide mixtures flagged by Nextclade and bammix, the samples were re-extracted and re-sequenced after workspace decontamination, yet the anomalies persisted. To investigate further, we developed a bioinformatics pipeline (Katmon) incorporating various tools such as Freyja, with lineage abundance results that illustrated the presence o

SUBMITTER: Realingo AML 

PROVIDER: S-EPMC12856159 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature