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.

Ongoing Recombination in SARS-CoV-2 Revealed through Genealogical Reconstruction

“…Recombination can occur when the same host is coinfected by two different strains, which has been noted to occur in COVID-19 patients ( Samoilov et al 2021 ), and could become more likely with the emergence of more transmissible variants. We note that the potential mosaic sequences we identified in the South Africa sample from November are represented only once in the data.…”

Strain Wars: Competitive interactions between SARS-CoV-2 strains are explained by Gibbs energy of antigen-receptor binding

“…Moreover, dual SARS-CoV-2 infection has been studied with two phylogenetically distant strains. The initially dominant strain belonged to GH clade and was suppressed by another strain from the GR clade, in only eight days ( Samoilov et al, 2021 ). The initial ratio of the GH to GR strain was 70:30, while 8 days later it became 3:97, obviously as a result of interference ( Samoilov et al, 2021 ).…”

“…The initially dominant strain belonged to GH clade and was suppressed by another strain from the GR clade, in only eight days ( Samoilov et al, 2021 ). The initial ratio of the GH to GR strain was 70:30, while 8 days later it became 3:97, obviously as a result of interference ( Samoilov et al, 2021 ). Thus, we have observed interference between various strains of SARS-CoV-2 ( Korber et al, 2020 ).…”

VirStrain: a strain identification tool for RNA viruses

“…A recent study [ 48 ] reported a case where one patient was infected by 2 different SARS-CoV-2 strains simultaneously. According to the authors, two samples (Sample1 and Sample2) were obtained from the same patient 8 days apart and both samples were found to contain two highly similar SARS-CoV-2 strains from different clades.…”

“…All SARS-CoV-2 single-strain sequencing datasets used in this manuscript can be downloaded from the NCBI SRA database ( https://www.ncbi.nlm.nih.gov/sra ) [ 61 ] with accession numbers: SRR10971381, SRR11593364, SRR11880659, SRR13644068, SRR12546786, ERR4387386, SRR12528370, SRR11513776, SRR11570921, SRR13634208, SRR11593362, SRR11593358, SRR13574086, SRR13574250, SRR13574082, SRR13644095, SRR13718002, SRR13684392, SRR13644074, SRR13681138, SRR13684393, SRR13499395, SRR13499389, SRR13499360, SRR11968882, SRR12316191, SRR12588591, SRR12598969, SRR12598968, SRR12352751, SRR12352750, and SRR11587603. The SARS-CoV-2 mix-strain sequencing datasets are downloaded from [ 48 ] (SRA accession number: SRR14142136 and SRR14142137). The HIV 5-strain mock data is downloaded from [ 49 ] (SRA accession number: SRR961514).…”