Infection with different strains of SARS-COV-2 in patients with COVID-19

Abstract

The biological diversity of SARS-CoV-2 was assessed by investigating the genetic variations of the spike glycoprotein of patients with COVID-19 in Iraq. Sequencing identified fifteen novel nucleic acid variations with a variety of distributions within the investigated samples. The electropherograms of all identified variations showed obvious co-infections with two different viral strains per sample. Most samples exhibited three nonsense single nucleotide polymorphism (SNPs), p.301Cdel, p.380Ydel and p.436del, which yielded three truncated spike glycoproteins, respectively. Network and phylogenetic analyses indicated that all viral infections were derived from multiple viral origins. Results inferred from the specific clade-based tree showed that some viral strains were derived from European G-clade sequences. Our data demonstrated the absence of single-strain infection among all investigated samples in the studied area, which entails a higher risk of SARS-CoV-2 in this country. The identified high frequency of truncated spike proteins suggests that defective SARS-CoV-2 depend on helper strains possessing intact spikes during infection. Alternatively, another putative ACE2-independent route of viral infection is suggested. To the best of our knowledge, this is the first report to describe co-infection with multiple strains of SARS-CoV- 2 in patients with COVID-19.

Isolation of Viable SARS-CoV-2 Virus from Feces of an Immunocompromised Patient Suggesting a Possible Fecal Mode of Transmission

“…Genome sequence differences were probably not related to subcultures as the comparison of more than 50 SARS-CoV-2 full-length genomes sequenced in our laboratory showed no significant differences between the sequences from isolates or samples. Genome sequences of the two strains were sufficiently different to hypothesize a dual SARS-CoV-2 infection as it has already been reported [ 18 , 19 ], rather than genome variants related to ongoing evolution of SARS-CoV-2 in the human body [ 20 ].…”

Change of dominant strain during dual SARS-CoV-2 infection

“…Meanwhile, despite a rapidly growing body of articles, there is almost no information about dual SARS-CoV-2 infection. To our knowledge, the possibility of SARS-CoV-2 double infection or within-patient genetic diversity was discussed in two works [9, 10]. Authors of both provided no information about patients’ medical history, viral subpopulation dynamics during disease progression, and almost no information about clade classification of SARS-CoV-2 analyzed strains.…”

“…Hashim et al [9] utilized Sanger sequencing and found double peaks in short (795 bp) fragments of spike protein gene and interpreted it as the presence of double infection in all of the 19 analyzed samples. Unfortunately, the authors’ interpretation of Sanger sequencing data is questionable.…”

“…Unfortunately, the authors’ interpretation of Sanger sequencing data is questionable. Most of the electropherograms presented in the manuscript [9] undoubtedly consist of double peaks, but the authors also present too many electropherograms with low intensity of the minor peak. In conventional Sanger sequencing analysis, it is challenging to interpret the data when there is a low level of the second peak at the same nucleotide position.…”

“…The findings of dual infections were reported for influenza viruses [4], the Epstein-Barr virus [5], and other viruses. Cases of SARS-CoV-2 reinfection are described in the scientific literature [6 - 8]; however, there are almost no reports of double infection with SARS-CoV-2 with the exceptions of in two works from Iraq [9] and Switzerland [10]. Here, we present a case report of an individual with two genetically distinct SARS-CoV-2 strains during the same illness manifestation.…”