SARS-CoV-2 dual infection with Delta and Omicron variants in an immunocompetent host: a case report

Abstract

Despite the high number of SARS-CoV-2 infections, only a few cases of dual infection have been reported. Here, we describe a case of COVID-19 caused simultaneously by Delta and Omicron variants in an immunocompetent individual during the early emergence of Omicron variant. A 73-year-old man was hospitalized with suspected acute coronary syndrome and a positive test result for SARS-CoV-2 RNA was received during routine testing at the hospital. He experienced mild symptoms of COVID-19 and was discharged on the ninth day. We sequenced the SARS-CoV-2 whole genome from the sample obtained on admission. The viral sequence was classified as PANGO lineage B.1.1.10 by the Galaxy pipeline; however, on detailed manual analysis, we identified the presence of both Delta and Omicron variants. After excluding the possibilities of a recombinant virus or contamination in the sample, we confirmed the presence of dual infection in this patient. We highlight that dual infections with SARS-CoV-2 may be more common than expected but are difficult to detect during the waves of one dominant variant.

Keywords: COVID-19; Dual infection; SARS-CoV-2; Single-genome sequencing.