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

Authors

  • Hayder O. Hashim Department of Clinical Laboratory Sciences, College of Pharmacy, University of Babylon, Babil 51001 http://orcid.org/0000-0001-8933-0994
  • Mudher K. Mohammed Department of Pharmacy, Al-Manara College of Medical Science
  • Mazin J. Mousa Department of Clinical Laboratory Sciences, College of Pharmacy, University of Babylon, Babil 51001
  • Hadeer H. Abdulameer University of Kufa/Faculty of Education for Girls
  • Alaa T.S. Alhassnawi Department of Biology, College of Science, University of Babylon, Babil 51001
  • Safa A. Hassan Alfadhel for training and development company / Babylon branch
  • Mohamed Baqur S. Al-Shuhaib Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil 51001 http://orcid.org/0000-0002-6458-2068

DOI:

https://doi.org/10.2298/ABS201024051H

Keywords:

co-infection, SARS-CoV-2, spike glycoprotein, stop mutations

Abstract

Paper description:

  • We examined the biological diversity of SARS-CoV-2 infection by investigating possible genetic variations of the spike glycoprotein in Iraqi patients with COVID-19.
  • A 795 bp coding region within the viral spike (S) gene was amplified from 19
  • Nucleic acid variations showed co-infection with two different viral strains. Most samples had three nonsense single nucleotide polymorphisms (SNPs). Network and phylogenetic analyses indicated that all viral infections exhibited mixed evolutionary origins represented by multiple viral sources.
  • Our findings indicate that defective SARS-CoV-2 relied on helper strains with intact spikes for infection. An alternative putative ACE2-independent viral infection route is also suggested.

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.

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References

Fauver JR, Petrone ME, Hodcroft EB, Shioda K, Ehrlich HY, Watts AG, Vogels CB, Brito AF, Alpert T, Muyombwe A, Razeq J. Coast-to-coast spread of SARS-CoV-2 during the early epidemic in the United States. Cell. 2020;181(5):990-6.e5.

Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH, Pei YY, Yuan ML. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(7798):265-9.

Cohen J. “Were behind the curve”: US hospitals confront the challenges of large-scale coronavirus testing. Science. 2020;3:4.

Hu Y, Riley LW. Dissemination and co-circulation of SARS-CoV2 subclades exhibiting enhanced transmission associated with increased mortality in Western Europe and the United States. medRxiv 20152959 [Preprint]. 2020 [cited 2020 Jul 13]. Available from: https://doi.org/10.1101/2020.07.13.20152959

Phan T. Genetic diversity and evolution of SARS-CoV-2. Infect Genet Evol. 2020;81:104260.

Korber B, Fischer W, Gnanakaran SG, Yoon H, Theiler J, Abfalterer W, Foley B, Giorgi EE, Bhattacharya T, Parker MD, Partridge DG. Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2. bioRxiv 069054 [Preprint]. 2020 [cited 2020 Apr 29]. Available from: https://doi.org/10.1101/2020.04.29.069054

Bhattacharyya C, Das C, Ghosh A, Singh AK, Mukherjee S, Majumder PP, Basu A, Biswas NK. Global Spread of SARS-CoV-2 Subtype with Spike Protein Mutation D614G is Shaped by Human Genomic Variations that Regulate Expression of TMPRSS2 and MX1 Genes. bioRxiv 075911 [Preprint]. 2020 [cited 2020 May 4]. Available from: https://doi.org/10.1101/2020.05.04.075911

Zheng S, Fan J, Yu F, Feng B, Lou B, Zou Q, Xie G, Lin S, Wang R, Yang X, Chen W. Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China, January-March 2020: retrospective cohort study. BMJ-Brit Med J. 2020;369:m1443.

Robson B. Bioinformatics studies on a function of the SARS-CoV-2 spike glycoprotein as the binding of host sialic acid glycans. Comput. Biol Med. 2020;122:103849.

Wang K, Chen W, Zhou YS, Lian JQ, Zhang Z, Du P, Gong L, Zhang Y, Cui HY, Geng JJ, Wang B. SARS-CoV-2 invades host cells via a novel route: CD147-spike protein. BioRxiv 988345 [Preprint]. 2020 [cited 2020 Mar 14]. Available from: https://doi.org/10.1101/2020.03.14.988345

Jeffers SA, Tusell SM, Gillim-Ross L, Hemmila EM, Achenbach JE, Babcock GJ, Thomas WD, Thackray LB, Young MD, Mason RJ, Ambrosino DM. CD209L (L-SIGN) is a receptor for severe acute respiratory syndrome coronavirus. Proc Natl Acad Sci USA. 2004;101(44):15748-53.

Wang H, Yang P, Liu K, Guo F, Zhang Y, Zhang G, Jiang C. SARS coronavirus entry into host cells through a novel clathrin-and caveolae-independent endocytic pathway. Cell Res. 2008;18(2):290-301.

Tang X, Wu C, Li X, Song Y, Yao X, Wu X, Duan Y, Zhang H, Wang Y, Qian Z, Cui J. On the origin and continuing evolution of SARS-CoV-2. Natl Sci Rev. 2020;7(6):1012-23.

Essa S, Owayed A, Altawalah H, Khadadah M, Behbehani N, Al-Nakib W. Mixed viral infections circulating in hospitalized patients with respiratory tract infections in Kuwait. Adv Virol. 2015;2015:714062.

Li J, Kou Y, Yu X, Sun Y, Zhou Y, Pu X, Jin T, Pan J, Gao GF. Human co-infection with avian influenza and seasonal influenza viruses, China. Emerg Infect Dis. 2014;20:1953-5.

Liu Y, Ning Z, Chen Y, Guo M, Liu Y, Gali NK, Sun L, Duan Y, Cai J, Westerdahl D, Liu X. Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals. Nature. 2020;582(7813):557-60.

Zhang XS. Strain interactions as a mechanism for dominant strain alternation and incidence oscillation in infectious diseases: seasonal influenza as a case study. PLoS ONE. 2015;10(11):e0142170.

Brundage JF. Interactions between influenza and bacterial respiratory pathogens: implications for pandemic preparedness. Lancet Infect Dis. 2006;6:303-12.

Goldstein E, Cobey S, Takahashi S, Miller JC, Lipsitch M. Predicting the epidemic sizes of Influenza A/H1N1, A/H3N2, and B: A Statistical Method. PLoS Med. 2011;8(7):e1001051.

Tsuchihashi Y, Sunagawa T, Yahata Y, Takahashi H, Toyokawa T, Odaira F, Ohyama T, Taniguchi K, Okabe N. Association between seasonal influenza vaccination in 2008-2009 and pandemic influenza A(H1N1) 2009 infection among school students from Kobe, Japan, April-June 2009. Clin Infect Dis. 2012;54:381-3.

Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden T. Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics. 2012;13:134.

Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003;31(13):3784-8.

Morgat A, Lombardot T, Coudert E, Axelsen K, Neto TB, Gehant S, Bansal P, Bolleman J, Gasteiger E, De Castro E, Baratin D. Enzyme annotation in UniProtKB using Rhea. Bioinformatics. 2020;36(6):1896-901.

Ng PC, Henikoff S. Predicting the effects of amino acid substitutions on protein function. Annu Rev Genom Hum Genet. 2006;22(7):61-80.

Choi Y, Sims GE, Murphy S, Miller JR, Chan AP. Predicting the functional effect of amino acid substitutions and indels. PLoS ONE. 2012;7:e46688.

Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7(4):248-9.

Smigielski EM, Sirotkin K, Ward M, Sherry ST. dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res. 2000;28:352-5.

Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucl Acids Res. 2010;38:W529-33.

Pires DEV, Ascher DB, Blundell TL. mCSM: predicting the effects of mutations in proteins using graph-based signatures. Bioinformatics. 2012;30:335-42.

Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25:1451-2.

French N, Yu S, Biggs P, Holland B, Fearnhead P, Binney B, Fox A, Grove-White D, Leigh JW, Miller W, Muellner P. Evolution of Campylobacter species in New Zealand. In: Sheppard SK, Méric G, editors. Campylobacter ecology and evolution. Caister Academic Press; 2014. p. 221-40.

Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Glob Chall. 2017;1:33-46.

Letunic I, Bork P. Interactive tree of life (iTOL) v4: recent updates and new developments. Nucl Acids Res. 2019;47(W1):W256-9.

Barrett JC, Fry B, Maller JDM J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005;21(2):263-265.

Memish ZA, Aljerian N, Ebrahim SH. Tale of three seeding patterns of SARS-CoV-2 in Saudi Arabia. Lancet Infect Dis. 2020;https://doi.org/10.1016/S1473-3099(20)30425-4.

Ghinai I, McPherson TD, Hunter JC, Kirking HL, Christiansen D, Joshi K, Rubin R, Morales-Estrada S, Black, SR, Pacilli M, Fricchione MJ. First known person-to-person transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the USA. Lancet Infect Dis. 2020;395(10230):1137-44.

Mercatelli D, Giorgi FM. Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Front Microbiol. 2020;22;11:1800.

Ceraolo C, Giorgi FM. Genomic variance of the 2019‐nCoV coronavirus. J Med Virol. 2020;92(5):522-8.

Sanche S, Lin Y, Xu C, Romero-Severson E, Hengartner N, Ke R. High Contagiousness and Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2. Emerg Infect Dis. 2020;26(7):1470-7.

Duffy S. Why are RNA virus mutation rates so damn high? PLoS Biol. 2018;16(8):e3000003.

Andersen KG, Rambaut A Lipkin, WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nat Med. 2020;26:450-2.

Brufsky, A. Distinct viral clades of SARS-CoV-2: implications for modeling of viral spread. J Med Virol. 2020;92(9):1386-90.

Morniroli D, Giannì ML, Consales A, Pietrasanta C, Mosca F. Human Sialome and Coronavirus Disease-2019 (COVID-19) Pandemic: An Understated Correlation? Front Immunol. 2020;11:1480.

Cox MJ, Loman N, Bogaert D, O'grady J. Co-infections: potentially lethal and unexplored in COVID-19. Lancet Microbe. 2020;1(1):e11.

Liu W, Li Z-D, Tang F, Wei M-T, Tong Y-G, Zhang L, Xin ZT, Ma MJ, Zhang XA, Liu LJ, Zhan L. Mixed infections of pandemic H1N1 and seasonal H3N2 viruses in 1 outbreak. Clin Infect Dis. 2010;50:1359-65.

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Published

2020-12-25

How to Cite

1.
Hashim HO, Mohammed MK, Mousa MJ, Abdulameer HH, Alhassnawi AT, Hassan SA, Al-Shuhaib MBS. Infection with different strains of SARS-CoV-2 in patients with COVID-19. Arch Biol Sci [Internet]. 2020Dec.25 [cited 2024Dec.22];72(4):575-8. Available from: https://serbiosoc.org.rs/arch/index.php/abs/article/view/5973

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Vol. 72 No. 4 (2020)

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