On the Origins of Omicron’s Unique Spike Gene Insertion
Abstract
:1. Introduction
2. Methods
2.1. Analysis of Mutations Defining the Omicron Lineage
2.2. Nucleotide 9-mer Search to Identify Candidate Viral and Human Templates for ins214EPE
2.3. Assessment of Homology between Regions Flanking Insertion and Origin Sites
2.4. Single-Cell Analysis of Coronavirus Receptor Co-Expression
3. Results
3.1. Comparison of Mutations in Omicron to Previous SARS-CoV-2 Lineages Shows the Presence of a Unique Insertion Mutation in Omicron’s Spike Protein
3.2. Template Switching Is a Plausible Mechanism for the Origin of ins214EPE in Omicron
3.3. Candidate Templates for the Origin of ins214EPE in Omicron
3.4. Consideration of Local Homology for the Candidate Templates
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Candidate Insertion Sequence | Human Transcriptome | SARS-CoV-2 Genomes from GISAID | Human Coronaviridae Genomes | |||
---|---|---|---|---|---|---|
Transcripts (Genes) | Total (Non-Omicron) | Any (Seasonal or Enteric) | ||||
Forward | Reverse-Complement | Forward | Reverse-Complement | Forward | Reverse-Complement | |
5′-GAGCCAGAA-3′ | 4677 (1534) | 3264 (1220) | 2100 (931) | 27 (27) | 18 (8) | 17 (6) |
5′-AGCCAGAAG-3′ | 6190 (2008) | 4293 (1591) | 1275 (106) | 269 (269) | 3 (0) | 12 (0) |
5′-GCCAGAAGA-3′ | 5210 (1564) | 3146 (1144) | 1319 (150) | 201,632 (201,632) | 13 (7) | 4 (2) |
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Venkatakrishnan, A.J.; Anand, P.; Lenehan, P.J.; Suratekar, R.; Raghunathan, B.; Niesen, M.J.M.; Soundararajan, V. On the Origins of Omicron’s Unique Spike Gene Insertion. Vaccines 2022, 10, 1509. https://doi.org/10.3390/vaccines10091509
Venkatakrishnan AJ, Anand P, Lenehan PJ, Suratekar R, Raghunathan B, Niesen MJM, Soundararajan V. On the Origins of Omicron’s Unique Spike Gene Insertion. Vaccines. 2022; 10(9):1509. https://doi.org/10.3390/vaccines10091509
Chicago/Turabian StyleVenkatakrishnan, A. J., Praveen Anand, Patrick J. Lenehan, Rohit Suratekar, Bharathwaj Raghunathan, Michiel J. M. Niesen, and Venky Soundararajan. 2022. "On the Origins of Omicron’s Unique Spike Gene Insertion" Vaccines 10, no. 9: 1509. https://doi.org/10.3390/vaccines10091509
APA StyleVenkatakrishnan, A. J., Anand, P., Lenehan, P. J., Suratekar, R., Raghunathan, B., Niesen, M. J. M., & Soundararajan, V. (2022). On the Origins of Omicron’s Unique Spike Gene Insertion. Vaccines, 10(9), 1509. https://doi.org/10.3390/vaccines10091509