Delta variant - A new phase of COVID-19 in India
International Journal of Medical Science |
© 2021 by SSRG - IJMS Journal |
Volume 8 Issue 7 |
Year of Publication : 2021 |
Authors : S.S.Sreenivas |
How to Cite?
S.S.Sreenivas, "Delta variant - A new phase of COVID-19 in India," SSRG International Journal of Medical Science, vol. 8, no. 7, pp. 35-39, 2021. Crossref, https://doi.org/10.14445/23939117/IJMS-V8I7P105
Abstract:
SARS-CoV-2 virus first reported from Wuhan City of Hubei Province of China became COVID-19 pandemic throughout the world. A variant of SARS-CoV-2 was noticed in India in late 2020, spread throughout India and other countries. The variant became dominant in India and the United Kingdom. The delta variant is now present in almost 100 countries. This variant of SARS-CoV-2 was assigned sub-lineage B.1.617.2 (Delta), of B.1.617. Variant Delta has around nine critical mutations with altered amino-acid sequences of the proteins it encodes and linked to increased ACE2 binding and enhanced escape from neutralizing antibodies. The global emergence of L452R independently in several lineages since November/December 2020 suggests a role in immune-evasion as an adaptation. Delta variant with an additional K417N mutation resulted in a new variant B.1.617.2.1 (Delta plus). The impact of mutation E484Q in Delta plus is similar to that of E484K, which was reported to diminish antibody binding, including those elicited by vaccination.
Keywords:
COVID-19, SARS-CoV-2, Delta variant, mutation, Delta plus
References:
[1] G. Gabutti, E.d’Anchera, F.Sandri, et al. Coronavirus: update related to the current outbreak of COVID-19. Infect Dis Ther., 9(2020) 1–13.
[2] K.Yuki, M.Fujiogi and S. Koutsogiannaki. COVID-19 pathophysiology: a review. Clin. Immunol (2020) 215: 108427.
[3] WHO. Coronavirus disease 2019 (COVID-19): dashboard. World Health Organization. (2009) https://covid19.who.int/
[4] World Health Organization. Pneumonia of unknown cause–China. Geneva:WHO; (2020) 5thJan Available at:https://wwwwhoint/csr/don/05-january-2020-pneumonia-of-unkown-cause-china/en/">https://wwwwhoint/csr/don/05-january-2020-pneumonia-of-unkown-cause-china/en/.
[5] World Health Organization. Novel coronavirus (2019-nCoV) situation report – 11. Geneva: WHO; 2020. Jan 31, World Health Organization. Coronavirus disease 2019 (COVID-19) Situation Report – 28. Geneva: WHO; (2020).
[6] World Health Organization. Novel coronavirus – China. Available at: http://wwwwhoint/csr/don/12-january-(2020)novel-coronavirus-china/en/
[7] Coronavirus disease: What you need to know. Available at: https://wwwafrowhoint/news/coronavirus-disease-what-you- need-know, Available at>https://wwwafrowhoint/news/coronavirus-disease-what-you- need-know (2020).
[8] Lai, M. M. C., and S.A. Stohlman. RNA of mouse hepatitis virus. J. Virol.26 (1978) 236–242.
[9] Sturman, L. S., and Holmes, K. V. The molecular biology of coronaviruses. Adv.Virus Res. 28 (1983) 35–111.
[10] Siddell, S. G., (ed.)., The Coronaviridae., Plenum, New York (1995).
[11] Enjuanes, L., (ed.). Coronavirus replication and reverse genetics. In “Curr. Top. Microbiol. Immunol., 287 (2005).
[12] Richman DD, Whitley RJ, Hayden FG.Clinical Virology, 4th ed.Washington: ASM Press (2006).
[13] World Health Organization. Situation reports. Available at: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ (2019).
[14] H. Chen, C. Guo J, Wang, et al. Clinical characteristics and intrauterine vertical transmission potential of COVID-19 infection in nine pregnant women: a retrospective review of medical records. Lancet (2020) https://doi.org/10.1016/S0140-6736(20)30360-3.
[15] J.A.Plante, Y. Liu, J. Liu, et al. Spike mutation D614G alters SARS-CoV-2 fitness. Nature. Published online December 23(2020). doi:10.1038/s41586-020- 2895-3.
[16] Y.J. Hou, S. Chiba, P.Halfmann. et al..SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Science, 370(6523) (2020) 1464-1468. doi:10.1126/science.abe8499.
[17] B.Korber, W.M.Fischer, S.Gnanakaran. et al. Sheffield. 2020. COVID-19 Genomics Group. Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell..182(4):812-827.e19. doi:10.1016/j.cell.(2020).06.043.
[18] E.Volz, V.Hill, J.T.McCrone et al. COG-UK Consortium. Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity. Cell.; S0092867420315373(2020).
[19] Jennifer Gribble, J.S. Laura, Maria L. Agostini, et al. The coronavirus proofreading exoribonuclease mediates extensive viral recombination. https://doi.org/10.1371/journal.ppat.1009226 (2021).
[20] J.Shang, K. Ye G, Shi. et al. Structural basis of receptor recognition by SARS-CoV-2. Nature. Nature Publishing Group. 581(7807)(2020):221–224.
[21] Y. Wan, J.Shang, R.Graham, R.S.Baric, Li F. Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus. J Virol. (2020) 94(7):e00127-20, /jvi/94/7/JVI.00127-20.atom.
[22] Andersen, K. G. et al. The proximal origin of SARS-CoV-2. Nat. Med. 26 (2020) 450–452.
[23] Yi, C. et al. Key residues of the receptor-binding motif in the spike protein of SARS-CoV-2 that interact with ACE2 and neutralizing antibodies. Cell Mol. Immunol. 17(2020) 621–630.
[24] Y. Wang, M. Liu and J. Gao. Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions.
Proc. Natl Acad. Sci. The USA. 117 (2020) 13967–13974.
[25] K. Wu K, A.P. Werner, J.I.Moliva, et al. mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants. BioRxiv (2021). doi: https://doi.org/10.1101/01.25.427948external icon
[26] B. Zhou, T.Thi Nhu Thao, D.Hoffmann. et al. SARS-CoV-2 spike D614G change enhances replication and transmission. Nature. https://doi.org/10.1038/s41586-021-03361-1external icon (2021).
[27] Fact Sheet For Health Care Providers Emergency Use Authorization (EUA) of Bamlanivimab And Etesevimab 02092021 (fda.gov) external icon (2021).
[28] Fact Sheet for Health Care Providers Emergency Use Authorization (EUA) of Regen-COV (fda.gov)external icon (2021). SARS-CoV-2 variants of concern as of 3 June 2021 – ECDC https://www.ecdc.europa.eu › covid-19 › variants-concern (2021)
[30] IDSA Contributor (2 February 2021). COVID "Mega-variant" and eight criteria for a template to assess all variants" Science Speaks:
Global ID News (2021).
[31] Tracking of Variants., gisaid.org. GISAID. 26 April (2021).
[32] "Expert reaction to cases of variant B.1.617 (the 'Indian variant') being investigated in the UK., Science Media Centre.
[33] Thiagarajan, K. Why is India having a covid-19 surge? BMJ 373, n1124. (2021).
[34] Campbell, F., Archer, B., Laurenson-Schafer, H., Jinnai, Y. et al. Increased transmissibility and global spread of SARS-CoV-2 variants of concern as of June 2021. Euro Surveill, 26. (2021).
[35] J. Singh, S.A. Rahman, N.Z. Ehtesham et al., SARS-CoV-2 variants of concern are emerging in India. Nat Med. (2021).
[36] "Covid: WHO renames the UK and other variants with Greek letters". BBC News. 31 May (2021).
[37] Rambaut A, Holmes EC, O’Toole Á, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology. Nature Publishing Group; 5(11) (2020) 1403–1407.
[38] Eurosurveillance. European Centre for Disease Prevention and Control (2021) 26(1):2002106. https://www.gov.uk/government/publications/phe-monitoring-ofthe-effectiveness-of-covid-19-vaccination.
[39] Expert reaction to cases of variant B.1.617 (the 'Indian variant') being investigated in the UK., Science Media Centre. Retrieved 20 April (2021).
[40] Shang, Jian; Yushun, Wan Lou, et al., Cell entry mechanisms of SARS-CoV-2. Proceedings of the National Academy of Sciences. 117 (21)(2020)11727– 11734. doi:10.1073/pnas.2003138117. PMC 7260975. PMID 32376634.
[41] expert reaction to VUI-21APR-02/B.1.617.2 being classified by PHE as a variant of concern., sciencemediacentre.org. 7(2021).
[42] S.Elbe, G. Buckland_Merrett G. Data, disease, and diplomacy: GISAID’s innovative contribution to global health. Global Challenges. Wiley Online Library; (2017) 1(1):33–46.
[43] B. Korber, W.M.Fischer,S. Gnanakaran. et al. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell., 182(4) (2020) 812- 827.e19.
[44] E.Volz, V. Hill, J.T.McCrone. et al. Evaluating the Effects of SARSCoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell. 184(1) (2021) 64-75.e11.
[45] Z.Liu, L.A Vanblargan. Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Cell Host Microbe, 29 (2021) 477-488 e4.,
[46] M. Mccallum, A. De Marco, F.A. Lempp, et al. N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell, 184 (2021) 2332-2347 e16.
[47] N. Suryadevara,S. Shrihari, P.Gilchuk. et al.Neutralizing and protective human monoclonal antibodies are recognizing the N-512 terminal domain of the SARS-CoV-2 spike protein. Cell, 184 (2021) 2316-2331 e15.
[48] X. Chi, R. Yan, J. Zhang. et al.A neutralizing human antibody binds to the N-terminal domain of the Spike protein of 396 SARS-CoV-2. Science, 369 (2020) 650-655.
[49] M.South, Andrew, I. Diz, Debra, C. Chappell, Mark., COVID-19, ACE2, and the cardiovascular consequences., American Journal of Physiology-Heart and Circulatory Physiology. 318 (5) H1084–H1090. doi:10.1152/ajpheart.00217.2020. (2020).
[50] Zhang, Wenjuan, Davis, D.Brian, Chen, S. Stephanie, Sincuir Martinez, M.Jorge, Plummer, T. Jasmine, Vail, Eric., Emergence of a Novel SARS-CoV-2 Variant in Southern California., JAMA. 325 (13) 1324–1326. doi:10.1001/jama.2021.1612. PMC 7879386. PMID 33571356. (2021)
[51] Koshy, Jacob., Coronavirus | Indian 'double mutant' strain named B.1.617, The Hindu. Retrieved 19 April 2021. Though these mutations have individually been found in several other coronavirus variants, the presence of both these mutations together has been first found in some coronavirus genomes from India. (2021).
[52] X.Deng, M.Garcia-Knight.Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell. (2021).
[53] J.Liu, Y.Liu, H.Xia, J.Zou. et al. Bnt162b2-elicited neutralization of B.1.617 and other SARS-CoV-2 variants. Nature. (2021).
[54] Sample, Ian., Nepal Covid variant: does it exist and should we be concerned?., The Guardian. (2021).
[55] Z. Wang. et al. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. bioRxiv, (2021).2001.2015.426911.
[56] D.A. Collier. et al. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature 593, 136-141 (2021)SARS-CoV-2
variants of concern and variants under investigation in England, technical briefing 16 (PDF) (Briefing).
[57] Petra Mlcochova, Steven Kemp, Mahesh Shanker Dhar, et al. SARS-CoV-2 B.1.617.2 Delta variant emergence and vaccine breakthrough. Research Square DOI: https://doi.org/10.21203/rs.3.rs-637724/v1 (2021).
[58] A. Malani. et al.Seroprevalence of SARS-CoV-2 in slums versus non-slums in Mumbai, India. Lancet Glob Health 9, e110-e111, doi:10.1016/S2214-109X(20)30467-8 (2021).
[59] Sarah Cherian1, Varsha Potdar, Santosh Jadhav et al. Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q, and P681R, in the second wave of COVID-19 in Maharashtra, IndiabioRxiv preprint doi: https://doi.org/10.1101/2021.04.22.440932; CC-BY-NC-ND (2021).
[60] L. Liu, P. Wang et al. Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike. Nature, 450-456. (2020) .
[61] Z. Liu, L.A. Vanblargan, L.M. Bloyet, P.W. Rothlauf et al. Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Cell Host Microbe, 29 (2021) 477-488 e4.
[62] E.C. Wall, M. Wu, R. Harvey, Kelly et al. Measuring Sars-Cov-2 Neutralizing Antibody Activity Using Pseudotyped And Chimeric Viruses. J Exp Med, 217 (2020).
[63] Delta plus: New Covid variant identified; experts say no cause of concern for now., The Indian Express. Press Trust of India. 14(2021).
[64] SARS-CoV-2 variants of concern as of 24 May 2021. European Centre for Disease Prevention and Control (2021).
[65] Sample, Ian (3 June 2021). Nepal Covid variant: does it exist, and should we be concerned? The Guardian (2021).
[66] Prerna Arora, Amy Kempf, Inga Nehlmeier, et al. Increased lung cell entry of B.1.617.2 and evasion of antibodies induced by infection and Bnt162b2 vaccination. doi: https://doi.org/10.1101/2021.06.23.449568 bioRxiv preprint. CCBY-NC-ND 4.0 (2021).
[67] J.L.Bernal et al. Effectiveness of COVID-19 vaccines against the B.1.617.2 variant. medRxiv, 2021.2005.2022.21257658 (2021).
[68] T.P. Peacock et al.The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets. Nat Microbiol, doi:10.1038/s41564-021-00908-w (2021).
[69] S.A. Kemp et al. Recurrent emergence and transmission of a SARSCoV-2 spike deletion H69/V70. bioRxiv, 2020.2012.2014.422555,
doi:10.1101/2020.12.14.422555 (2021).
[70] D.S.Khoury et al. Neutralizing antibody levels are highly predictive of immune protection from symptomatic SARS-CoV-2 infection Nature Medicine, https://doi.org/10.1038/s41591-021-01377-8(2021).
[71] Delphine Planas, David Veyer, et al. Benhassine. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization Nature. https://doi.org/10.1038/s41586-021-03777-9 (2021).
[72] Public Health England. PHE monitoring of the effectiveness of covid-19 vaccination. 26 May (2021).
[73] V. Tchesnokova et al. Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-Cov-2 variants. bioRxiv, 2021.2002.2022.432189 (2021).
[74] F. Gallais et al. Anti-SARS-CoV-2 Antibodies Persist for up to 13 Months and Reduce Risk of Reinfection. medRxiv, 2021.2005.2007.21256823,
https://doi.org/10.1101/2021.05.07.21256823 (2021).
[75] F. Krammer et al. Antibody Responses in Seropositive Persons after a Single Dose of SARS-CoV-2 mRNA Vaccine. New England Journal of Medicine 384, 1372-1374 (2021).