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Comparative Analysis of B.1.617.2 (Delta) Variant of SARS-CoV-2

Year 2022, , 38 - 51, 15.03.2022
https://doi.org/10.5799/jmid.1086226

Abstract

ABSTRACT
The emergence of numerous variants of SARS-CoV-2 has caused massive setbacks and prolonged the COVID-19 pandemic. Some of the variants are still under investigation, while some have become a reason of grave concern. One such variant is B.1.617.2, known as the Delta variant, which was first detected in India. A comprehensive analysis and comparison of this particular variant have been done to the original Wuhan strain, and the possible reasons behind rapid mutation have also been discussed.
A comprehensive literature search was done to summarize the information on the variants of SARS-CoV-2 and the reasons behind their mutation, with a significant focus on the B.1.617.2 variant. Data were collected from various online sources such as PubMed, Google Scholar, MEDLINE, Worldometer, WHO, CDC, and GISAID. In addition, 3D structures of spike proteins were obtained from Protein Data Bank (PDB).
The data shows that the spike protein of the B.1.617.2 strain is highly mutated and has accumulated eight amino acid changes. Besides spike protein, changes in non-structural proteins (nsP2, nsP3, nsP4, nsP12, and nsP15), other structural proteins (nucleocapsid and membrane protein), and accessory proteins (ns3, ns7a) have been observed as well. Furthermore, in almost all the variants of SARS-CoV-2, D614G mutation occurs, suggesting its role in increased infectivity and transmission.
New variants are continuously emerging on which we have no control. Spike mutations are more favored and essential in the evolution of new variants because it increases the transmissibility and infectivity of the virus. Therefore, to maximally protect public health, knowledge of different variants is essential. J Microbiol Infect Dis 2022; 12(1):38-51.

References

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Year 2022, , 38 - 51, 15.03.2022
https://doi.org/10.5799/jmid.1086226

Abstract

References

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  • 2. Sharma B, Shahanshah MF, Gupta S, Gupta V. Recent advances in the diagnosis of COVID-19: A bird’s eye view. Expert Rev Mol Diagn. 2021;21(5):475-491. doi:10.1080/14737159.2021.1874354
  • 3. Worldometer. COVID live update: 168,291,956 cases and 3,493,098 deaths from the Coronavirus. Available: https://www.worldometers.info/coronavirus/. (Accessed on May 25, 2021).
  • 4. WHO Coronavirus (COVID-19) Dashboard. Available: https://covid19.who.int/. (Accessed on May 25, 2021).
  • 5. Wu C, Liu Y, Yang Y, et al. Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharm Sin B. 2020;10(5):766-788. doi:10.1016/j.apsb.2020.02.008
  • 6. Wu A, Peng Y, Huang B, et al. Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China. Cell Host Microbe 2020; 27(3):325-328. doi:10.1016/j.chom.2020.02.001
  • 7. Giovanetti M, Benedetti F, Campisi G, et al. Evolution patterns of SARS-CoV-2: Snapshot on its genome variants. Biochem Biophys Res Commun 2021; 538;88-91. doi:10.1016/j.bbrc.2020.10.102
  • 8. Singh A, Gupta V. SARS-CoV-2 therapeutics: how far do we stand from a remedy? Pharmacol Rep 2021;73(3):750-768. doi:10.1007/s43440-020-00204-0
  • 9. Dolan PT, Whitfield ZJ, Andino R. Mechanisms and Concepts in RNA Virus Population Dynamics and Evolution. Annu Rev Virol 2018; 5(1):69-92. doi:10.1146/annurev-virology-101416-041718
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  • 14. Annavajhala MK, Mohri H, Zucker JE, et al. A Novel SARS-CoV-2 Variant of Concern, B.1.526, Identified in New York. medRxiv. February 2021. doi:10.1101/2021.02.23.21252259
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  • 18. Cherian S, Potdar V, Jadhav S, et al. Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India. bioRxiv.2021:440932. doi:10.1101/2021.04.22.440932
  • 19. Yadav PD, Sapkal GN, Abraham P, et al. Neutralization of variant under investigation B.1.617 with sera of BBV152 vaccinees. bioRxiv.2021:441101. doi:10.1101/2021.04.23.441101
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  • 23. Wang P, Casner RG, Nair MS, et al. Increased resistance of SARS-CoV-2 variant P. 1 to antibody neutralization. Cell Host & Microbe 2021; 29(5):747-751. doi:10.1101/2021.01.25.428137
  • 24. Shen X, Tang H, McDanal C, Wagh K, Fischer W, Theiler J, Yoon H, Li D, Haynes BF, Sanders KO, Gnanakaran S. SARS-CoV-2 variant B. 1.1. 7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines. Cell host & microbe. 2021; 29(4):529-539. doi:10.1101/2021.01.27.428516
  • 25. Edara VV, Floyd K, Lai L, et al. Infection and mRNA-1273 vaccine antibodies neutralize SARS-CoV-2 UK variant. medRxiv. 2021.doi:10.1101/2021.02.02.21250799
  • 26. Wang P, Casner RG, Nair MS, et al. Increased resistance of SARS-CoV-2 variant P. 1 to antibody neutralization. Cell host & microbe. 2021;29(5):747-51.doi:10.1101/2021.03.01.433466
  • 27. Planas D, Bruel T, Grzelak L, et al. Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies. Nat Med. 2021;27(5):917-924. doi:10.1038/s41591-021-01318-5
  • 28. Deng X, Garcia-Knight MA, Khalid MM, et al. Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. MedRxiv. 2021.doi:10.1101/2021.03.07.21252647
  • 29. Doucleff M. People Are Talking About A “Double Mutant” Variant In India. What Does That Mean? NPR 2021. Available: https://www.npr.org/sections/goatsandsoda/2021/04/24/988744811/people-are-talking-about-a-double-mutant-variant-in-india-what-does-that-mean.. (Accessed May 16, 2021).
  • 30. SARS-CoV-2 variants of concern as of 29 November 2021. ECDC 2021. Available: https://www.ecdc.europa.eu/en/covid-19/variants-concern. (Accessed November 30, 2021).
  • 31. Callaway E., Heavily mutated Omicron variant puts scientists on alert. Nature. 2021.DOI: https://doi.org/10.1038/d41586-021-03552-w (Accessed on 29 November 2021)
  • 32. Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern. World Health Organisation.2021. https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern (Accessed on 29 November 2021)
  • 33. Implications of the emergence and spread of the SARS-CoV-2 B.1.1.529 variant of concern (Omicron) for the EU/EEA. Threat Assessment Brief, European Center for Disease Prevention and Control. 2021. Available: https://www.ecdc.europa.eu/
  • 34. Jerusalem Post Staff. New coronavirus variant identified in Europe. The Jerusalem Post 2021. Available: https://www.jpost.com/. (Accessed May 25, 2021).
  • 35. GitHub. cov-lineages/pango-designation. 2021. Available: https://github.com/cov-lineages/pango-designation.(Accessed May 25, 2021).
  • 36. Jangra S, Ye C, Rathnasinghe R, et al. SARS-CoV-2 spike E484K mutation reduces antibody neutralisation. The Lancet Microbe 2021.doi:10.1016/S2666-5247(21)00068-9
  • 37. Bugembe DL, Phan MV, Ssewanyana I, et al. A SARS-CoV-2 lineage A variant (A. 23.1) with altered spike has emerged and is dominating the current Uganda epidemic. MedRxiv. 2021.doi:10.1101/2021.02.08.21251393
  • 38. A coronavirus variant, with a “similar change” to the fast-spreading variant in the UK and US, has emerged in Uganda. Business Insider India 2021. Available: https://www.businessinsider.in/science/health/news/a-coronavirus-variant-with-a-similar-change-to-the-fast-spreading-variant-in-the-uk-and-us-has-emerged-in-uganda/articleshow/80881380.cms.(Accessed May 25, 2021).
  • 39. Mallm JP, Bundschuh C, Kim H, et al. Local emergence and decline of a SARS-CoV-2 variant with mutations L452R and N501Y in the spike protein. medRxiv. 2021.doi:10.1101/2021.04.27.21254849
  • 40. SARS-CoV-2 variants of concern and variants under investigation in England. PHE 2021. Available: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/984274/Variants_of_Concern_VOC_Technical_Briefing_10_England.pdf.(Accessed May 25, 2021).
  • 41. C.37, the new variant of COVID-19 that spreads in Peru and Chile | coronavirus | INS | UPCH | PERU. ARCHYDE 2021. Available: https://www.archyde.com/c-37-the-new-variant-of-covid-19-that-spreads-in-peru-and-chile-coronavirus-ins-upch-peru/. (Accessed May 25, 2021).
  • 42. Tegally H, Wilkinson E, Giovanetti M, et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature. 2021;592(7854):438-443. doi:10.1038/s41586-021-03402-9
  • 43. Cele S, Gazy I, Jackson L, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021;593(7857):142-146. doi:10.1038/s41586-021-03471-w
  • 44. Estimates of severity and transmissibility of novel South Africa SARS-CoV-2 variant 501Y.V2. GitHub 2021. Available: https://cmmid.github.io/topics/covid19/reports/sa-novel-variant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA. (Accessed May 25, 2021).
  • 45. Davies NG, Abbott S, Barnard RC, et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science. 2021;372(6538). doi:10.1126/science.abg3055
  • 46. Davies NG, Jarvis CI, CMMID COVID-19 Working Group, et al. Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. Nature. 2021;593(7858):270-274. doi:10.1038/s41586-021-03426-1
  • 47. CoVsurver Analysis of the sequences. GISAID. Available: https://www.gisaid.org/. (Accessed Nov 29, 2021).
There are 47 citations in total.

Details

Primary Language English
Subjects Health Care Administration
Journal Section Review
Authors

Mohd Fardeen Husain Shahanshah This is me

Saloni Jain This is me

Bhawna Sharma This is me

Ananya Grewall This is me

Shalini Swami This is me

Publication Date March 15, 2022
Published in Issue Year 2022

Cite

APA Shahanshah, M. F. H., Jain, S., Sharma, B., Grewall, A., et al. (2022). Comparative Analysis of B.1.617.2 (Delta) Variant of SARS-CoV-2. Journal of Microbiology and Infectious Diseases, 12(01), 38-51. https://doi.org/10.5799/jmid.1086226
AMA Shahanshah MFH, Jain S, Sharma B, Grewall A, Swami S. Comparative Analysis of B.1.617.2 (Delta) Variant of SARS-CoV-2. J Microbil Infect Dis. March 2022;12(01):38-51. doi:10.5799/jmid.1086226
Chicago Shahanshah, Mohd Fardeen Husain, Saloni Jain, Bhawna Sharma, Ananya Grewall, and Shalini Swami. “Comparative Analysis of B.1.617.2 (Delta) Variant of SARS-CoV-2”. Journal of Microbiology and Infectious Diseases 12, no. 01 (March 2022): 38-51. https://doi.org/10.5799/jmid.1086226.
EndNote Shahanshah MFH, Jain S, Sharma B, Grewall A, Swami S (March 1, 2022) Comparative Analysis of B.1.617.2 (Delta) Variant of SARS-CoV-2. Journal of Microbiology and Infectious Diseases 12 01 38–51.
IEEE M. F. H. Shahanshah, S. Jain, B. Sharma, A. Grewall, and S. Swami, “Comparative Analysis of B.1.617.2 (Delta) Variant of SARS-CoV-2”, J Microbil Infect Dis, vol. 12, no. 01, pp. 38–51, 2022, doi: 10.5799/jmid.1086226.
ISNAD Shahanshah, Mohd Fardeen Husain et al. “Comparative Analysis of B.1.617.2 (Delta) Variant of SARS-CoV-2”. Journal of Microbiology and Infectious Diseases 12/01 (March 2022), 38-51. https://doi.org/10.5799/jmid.1086226.
JAMA Shahanshah MFH, Jain S, Sharma B, Grewall A, Swami S. Comparative Analysis of B.1.617.2 (Delta) Variant of SARS-CoV-2. J Microbil Infect Dis. 2022;12:38–51.
MLA Shahanshah, Mohd Fardeen Husain et al. “Comparative Analysis of B.1.617.2 (Delta) Variant of SARS-CoV-2”. Journal of Microbiology and Infectious Diseases, vol. 12, no. 01, 2022, pp. 38-51, doi:10.5799/jmid.1086226.
Vancouver Shahanshah MFH, Jain S, Sharma B, Grewall A, Swami S. Comparative Analysis of B.1.617.2 (Delta) Variant of SARS-CoV-2. J Microbil Infect Dis. 2022;12(01):38-51.