Case report: change of dominant strain during dual SARS-CoV-2 infection

Abstract

Background: The dual infection with SARS-CoV-2 is poorly described and is currently under discussion. We present a study of two strains of SARS-CoV-2 detected in the same patient during the same disease presentation.

Case presentation: A patient in their 90 s was hospitalised with fever. Oropharyngeal swab obtained on the next day (sample 1) tested positive for SARS-CoV-2. Five days later, the patient was transferred to the ICU (intensive care unit) of the hospital specialising in the treatment of COVID-19 patients, where the patient's condition progressively worsened and continuous oxygen insufflation was required. Repeated oropharyngeal swab (sample 2), which was taken eight days after the first one, also tested positive for SARS-CoV-2. After 5 days of ICU treatment, the patient died. The cause of death was a coronavirus infection, which progressed unfavourably due to premorbid status. We have performed sequencing of full SARS-CoV-2 genomes from oropharyngeal swabs obtained eight days apart. Genomic analysis revealed the presence of two genetically distant SARS-CoV-2 strains in both swabs. Detected strains belong to different phylogenetic clades (GH and GR) and differ in seven nucleotide positions. The relative abundance of strains was 70% (GH) and 30% (GR) in the first swab, and 3% (GH) and 97% (GR) in the second swab.

Conclusions: Our findings suggest that the patient was infected by two genetically distinct SARS-CoV-2 strains at the same time. One of the possible explanations is that the second infection was hospital-acquired. Change of the dominant strain ratio during disease manifestation could be explained by the advantage or higher virulence of the GR clade strain.

Keywords: COVID-19; Case report; Dual infection; High-throughput sequencing; SARS-CoV-2.

Fig. 1

Relative coverage of SARS-CoV-2 genomic variants, which differentiate strains 1 and 2. Genomic positions are at the X-axis, their relative frequencies are at Y-axis. A Sample 1, sequencing using genome fragments amplification (SCV-2000 bp protocol); B Sample 1, sequencing using total RNA library; C Sample 2 (collected eight days later), sequencing using genome fragments amplification (SCV-2000 bp protocol)

Fig. 2

Phylogenetic tree of all of the available SARS-CoV-2 strains isolated in Russia (as of 11 November 2020). GISAID clade classification is represented by colour. Tip labels mark positions of strain 1 (MW305251.1) and strain 2 (MW305250.1). Closely related to SARS-CoV-2 virus strain bat/Yunnan/RmYN02/2019 (GISAID ID EPI_ISL_412977) was used as a root (not shown)