Volume 6, Issue 4 (Journal of Clinical and Basic Research (JCBR) 2022)
jcbr 2022, 6(4): 13-18 |
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Mohebbi A. Analysis of the RNA-Seq Data of Solanum tuberosum Revealed Viral Sequence Reads of a Severe Laboratory-Developed Strain of SARS-CoV-2 Containing Novel Substitutions. jcbr 2022; 6 (4) :13-18
URL: http://jcbr.goums.ac.ir/article-1-391-en.html
URL: http://jcbr.goums.ac.ir/article-1-391-en.html
Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran , Mohebbi-a@goums.ac.ir
Abstract: (1582 Views)
Background: Metagenomics is a promising approach to discovering novel sequences of microorganisms in environmental samples. A recently published RNA-Seq data of Solanum tuberosum from China was used for a metavirome study.
Methods: RNA-seq data of a BioSample project of S. tuberosum containing sequence read archive (SRA) of six plant samples were imported into the Galaxy server. Transcriptome data were de novo assembled for viral sequences with rnaviralSPAdes. The contig files were further organized by VirHunter and Kraken tools. Raw SRA data were trimmed and assembled for severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) genome by coronaSPAdes. The scaffolds were arranged by pairwise alignment against the SARS-CoV-2 reference genome (NC_045512.2). Coronavirus Typing Tool, Nextstrain, and Pangolin platforms were used to further investigate the SARS-CoV-2 genotype, phylogenetic analysis, and mutation estimations.
Results: Several environmentally related non-intact virus sequence reads from forest animals, moths, bacteria, and amoeba were detected. Further investigation resulted in non-indigenous sequences of SARS-CoV-2 genomes of lineage B with novel substitutions. Three polymorphisms, including A22D and A36V in the envelope protein, and Q498H in the spike (S) glycoprotein that were recently reported from a mice-adopted strain of SARS-CoV-2 with enhanced virulence were detected in all samples. Further novel substitutions at ORF1ab were also uncovered. These were L1457V, D4553N, W6538S, I1525T, D1585Y, D6928G, N3414K, and T3432S. Two unexpected frameshifts, ORF1a:2338-4401 and ORF1a:3681-4401, were also detected.
Conclusion: The findings of the presented study highlight the threats of the emerged potentially severe genotypes of SARS-CoV-2 bearing substitutions that are not yet clinically reported.
Methods: RNA-seq data of a BioSample project of S. tuberosum containing sequence read archive (SRA) of six plant samples were imported into the Galaxy server. Transcriptome data were de novo assembled for viral sequences with rnaviralSPAdes. The contig files were further organized by VirHunter and Kraken tools. Raw SRA data were trimmed and assembled for severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) genome by coronaSPAdes. The scaffolds were arranged by pairwise alignment against the SARS-CoV-2 reference genome (NC_045512.2). Coronavirus Typing Tool, Nextstrain, and Pangolin platforms were used to further investigate the SARS-CoV-2 genotype, phylogenetic analysis, and mutation estimations.
Results: Several environmentally related non-intact virus sequence reads from forest animals, moths, bacteria, and amoeba were detected. Further investigation resulted in non-indigenous sequences of SARS-CoV-2 genomes of lineage B with novel substitutions. Three polymorphisms, including A22D and A36V in the envelope protein, and Q498H in the spike (S) glycoprotein that were recently reported from a mice-adopted strain of SARS-CoV-2 with enhanced virulence were detected in all samples. Further novel substitutions at ORF1ab were also uncovered. These were L1457V, D4553N, W6538S, I1525T, D1585Y, D6928G, N3414K, and T3432S. Two unexpected frameshifts, ORF1a:2338-4401 and ORF1a:3681-4401, were also detected.
Conclusion: The findings of the presented study highlight the threats of the emerged potentially severe genotypes of SARS-CoV-2 bearing substitutions that are not yet clinically reported.
Article Type: Research |
Subject:
Microbiology
References
1. Zhang YZ, Shi M, Holmes EC. Using Metagenomics to Characterize an Expanding Virosphere. Cell. 2018; 172(6):1168-72. [View at Publisher] [DOI] [PubMed] [Google Scholar]
2. Aevarsson A, Kaczorowska AK, Adalsteinsson BT, Ahlqvist J, Al-Karadaghi S, Altenbuchner J, et al. Going to extremes - a metagenomic journey into the dark matter of life. FEMS Microbiol Lett. 2021; 368(12). [View at Publisher] [DOI] [PubMed] [Google Scholar]
3. Yin H, Dong Z, Wang X, Lu S, Xia F, Abuduwaili A, et al. Metagenomic Analysis of Marigold: Mixed Infection Including Two New Viruses. Viruses. 2021; 13(7):1254. [View at Publisher] [DOI] [PubMed] [Google Scholar]
4. Lappe RR, Elmore MG, Lozier ZR, Jander G, Miller WA, Whitham SA. Metagenomic identification of novel viruses of maize and teosinte in North America. BMC Genomics. 2022; 23(1):1-15. [View at Publisher] [DOI] [PubMed] [Google Scholar]
5. Damian D, Maghembe R, Damas M, Wensman JJ, Berg M. Application of viral metagenomics for study of emerging and reemerging tick-borne viruses. Vector Borne Zoonotic Dis. 2020; 20(8):557-65. [View at Publisher] [DOI] [PubMed] [Google Scholar]
6. Souza JVC, Santos H de O, Leite AB, Giovanetti M, Bezerra R dos S, Carvalho E de, et al. Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification. Viruses. 2022; 14(9):1933. [View at Publisher] [DOI] [PubMed] [Google Scholar]
7. Mohsin H, Asif A, Fatima M, Rehman Y. Potential role of viral metagenomics as a surveillance tool for the early detection of emerging novel pathogens. Arch Microbiol. 2021; 203(3):865-72. [View at Publisher] [DOI] [PubMed] [Google Scholar]
8. Slavov SN. Viral Metagenomics for Identification of Emerging Viruses in Transfusion Medicine. Viruses. 2022; 14(11):2448. [View at Publisher] [DOI] [PubMed] [Google Scholar]
9. Erratum: Correction to "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update". Nucleic Acids Res. 2022; 50(15):w345-w3551. [View at Publisher] [DOI] [Google Scholar]
10. Antipov D, Korobeynikov A, McLean JS, Pevzner PA. HYBRIDSPADES: an algorithm for hybrid assembly of short and long reads. Bioinformatics. 2016; 32(7):1009-15. [View at Publisher] [DOI] [PubMed] [Google Scholar]
11. Prjibelski AD, Vasilinetc I, Bankevich A, Gurevich A, Krivosheeva T, Nurk S, et al. ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics. 2014; 30(12):i293-301. [View at Publisher] [DOI] [PubMed] [Google Scholar]
12. Vasilinetc I, Prjibelski AD, Gurevich A, Korobeynikov A, Pevzner PA. Assembling short reads from jumping libraries with large insert sizes. Bioinformatics. 2015; 31(20):3262-8. [View at Publisher] [DOI] [PubMed] [Google Scholar]
13. Sukhorukov G, Khalili M, Gascuel O, Candresse T, Marais-Colombel A, Nikolski M. VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data. Front Bioinform. 2022;2:38. [View at Publisher] [DOI] [PubMed] [Google Scholar]
14. Wood DE, Salzberg SL. Kraken: Ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15(3):1-2. [View at Publisher] [DOI] [PubMed] [Google Scholar]
15. Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. [View at Publisher] [DOI] [PubMed] [Google Scholar]
16. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9. [View at Publisher] [DOI] [PubMed] [Google Scholar]
17. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10(3):1-10. [View at Publisher] [DOI] [PubMed] [Google Scholar]
18. Meleshko D, Hajirasouliha I, Korobeynikov A. coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies. Bioinformatics. 2021;38(1):1-8. [View at Publisher] [DOI] [PubMed] [Google Scholar]
19. Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, et al. RaGOO: Fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 2019; 20(1):1-7. [View at Publisher] [DOI] [Google Scholar] [ISI]
20. Maan H, Mbareche H, Raphenya AR, Banerjee A, Nasir JA, Kozak RA, et al. Genotyping SARS-CoV-2 through an interactive web application. Lancet Digit Heal. 2020; 2(7):e340-1. [View at Publisher] [DOI] [PubMed] [Google Scholar]
21. O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, et al. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch. Wellcome Open Res. 2021; 6:121. [View at Publisher] [DOI] [PubMed] [Google Scholar]
22. O'Toole Á, Scher E, Underwood A, Jackson B, Hill V, McCrone JT, et al. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evol. 2021; 7(2):veab064. [View at Publisher] [DOI] [PubMed] [Google Scholar]
23. Rambaut A, Holmes E, O'Toole Á, VH-N, 2020 undefined. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5(11):1403-7. [View at Publisher] [DOI] [PubMed] [Google Scholar]
24. Aksamentov I, Roemer C, Hodcroft EB, Neher RA. Nextclade: clade assignment, mutation calling and quality control for viral genomes. JOSS. 2021;6(67):3773. [View at Publisher] [DOI] [Google Scholar]
25. Yan F, Li E, Wang T, Li Y, Liu J, Wang W, et al. Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. Front Immunol. 2022; 13: 821664. [View at Publisher] [DOI] [PubMed] [Google Scholar]
26. Shannon A, Fattorini V, Sama B, Selisko B, Feracci M, Falcou C, et al. A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase. Nat Commun. 2022; 13(1):621. [View at Publisher] [DOI] [PubMed] [Google Scholar]
27. Watanabe C, Okiyama Y, Tanaka S, Fukuzawa K, Honma T. Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. Chem Sci. 2021; 12(13):4722-39. [View at Publisher] [DOI] [PubMed] [Google Scholar]
28. Mou K, Abdalla M, Wei DQ, Khan MT, Lodhi MS, Darwish DB, et al. Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. Inform Med Unlocked. 2021; 25:100675. [View at Publisher] [DOI] [PubMed] [Google Scholar]
29. Bamford CGG, Broadbent L, Aranday-Cortes E, McCabe M, McKenna J, Courtney DG, et al. Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Viruses. 2022; 14(2):325. [View at Publisher] [DOI] [PubMed] [Google Scholar]
30. Dieterle ME, Haslwanter D, Bortz RH, Wirchnianski AS, Lasso G, Vergnolle O, et al. A Replication-Competent Vesicular Stomatitis Virus for Studies of SARS-CoV-2 Spike-Mediated Cell Entry and Its Inhibition. Cell Host Microbe. 2020; 28(3):486-496.e6. [View at Publisher] [DOI] [PubMed] [Google Scholar]
31. Carrazco-Montalvo A, Herrera-Yela A, Alarcón-Vallejo D, Gutiérrez-Pallo D, Armendáriz-Castillo I, Andrade-Molina D, et al. Omicron sublineages current status in Ecuador. Preprints [V1]. 2022. [View at Publisher] [DOI] [Google Scholar]
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