Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Unexpected Co-infection with Different Strains of SARS-CoV-2 in Patients with COVID-19

Version 1 : Received: 15 September 2020 / Approved: 17 September 2020 / Online: 17 September 2020 (05:33:59 CEST)

How to cite: Hashim, H.O.; Mohammed, M.K.; Mousa, M.J.; Abdulameer, H.H.; Alhassnawi, A.T.; Hassan, S.A.; Al-Shuhaib, M.B.S. Unexpected Co-infection with Different Strains of SARS-CoV-2 in Patients with COVID-19. Preprints 2020, 2020090375 (doi: 10.20944/preprints202009.0375.v1). Hashim, H.O.; Mohammed, M.K.; Mousa, M.J.; Abdulameer, H.H.; Alhassnawi, A.T.; Hassan, S.A.; Al-Shuhaib, M.B.S. Unexpected Co-infection with Different Strains of SARS-CoV-2 in Patients with COVID-19. Preprints 2020, 2020090375 (doi: 10.20944/preprints202009.0375.v1).

Abstract

There is a rising global concern for the ongoing outbreak of SARS-CoV-2 due to its high transmission rate and unavailability of treatment. Through the binding of its spike glycoprotein with angiotensin type 2 (ACE2), SARS-CoV-2 can efficiently get in the cells of patients and start its pandemic cycle. Herein, the biological diversity of SARS-CoV-2 infection was assessed in Babylon province of Iraq by investigating the possible genetic variations of the spike glycoprotein. A specific coding region of 795 bp within the viral spike (S) gene was amplified from 19 patients who suffered from obvious symptoms of SARS-CoV-2 infection. Sequencing results identified fifteen novel nucleic acid variations with a variety of distributions within the investigated samples. The electropherograms of all the identified variations showed obvious co-infections with at least two different viral strains per sample. Within these co-infections, the majority of samples exhibited three nonsense single nucleotide polymorphism (SNP)s, p.301Cdel, p.380Ydel, and p.436del, which yielded three truncated SARS-CoV-2 spike glycoproteins of 301, 380, and 436 amino acids length, respectively. The network and phylogenetic analyses indicated that for all viral infections were derived from multi-ancestral origins. Results inferred from the specific clade-based tree entailed that some viral strains were derived from European G-clade sequences. In conclusion, our data demonstrated the absence of any single strain infection among all investigated viral samples in the studied area, which may entail a higher risk of SARS-CoV-2 in this country. Through the identified high frequency of truncated spike proteins, we suggest that defective SARS-CoV-2 may depend on helper strains having intact spikes in its infection. Alternatively, another putative ACE2-independent route of viral infection way also suggested. To the best of our knowledge, this is the first report to describe the co-infection of multiple strains of SARS-CoV-2 in patients with COVID-19.

Subject Areas

co-infection; SARS-CoV-2; pike glycoprotein; stop mutations

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