Assessment of the Biological Impact of SARS-CoV-2 Genetic Variation Using an Authentic Virus Neutralisation Assay with Convalescent Plasma, Vaccinee Sera, and Standard Reagents

Overview

Journal Viruses

Publisher MDPI

Specialty Microbiology

Date 2023 Mar 30

PMID 36992342

Authors

Naomi S Coombes

Kevin R Bewley

Yann Le Duff

Matthew Hurley

Lauren J Smith

Thomas M Weldon

Karen Osman

Steven Pullan

Neil Berry

Bassam Hallis

Sue Charlton

Yper Hall

Simon G P Funnell

Affiliations

Soon will be listed here.

Abstract

In the summer of 2020, it became clear that the genetic composition of SARS-CoV-2 was changing rapidly. This was highlighted by the rapid emergence of the D614G mutation at that time. In the autumn of 2020, the project entitled "Agility" was initiated with funding from the Coalition for Epidemic Preparedness Innovations (CEPI) to assess new variants of SARS-CoV-2. The project was designed to reach out and intercept swabs containing live variant viruses in order to generate highly characterised master and working stocks, and to assess the biological consequences of the rapid genetic changes using both in vitro and in vivo approaches. Since November 2020, a total of 21 variants have been acquired and tested against either a panel of convalescent sera from early in the pandemic, and/or a panel of plasma from triple-vaccinated participants. A pattern of continuous evolution of SARS-CoV-2 has been revealed. Sequential characterisation of the most globally significant variants available to us, generated in real-time, indicated that the most recent Omicron variants appear to have evolved in a manner that avoids immunological recognition by convalescent plasma from the era of the ancestral virus when analysed in an authentic virus neutralisation assay.

Citing Articles

The Omicron Sub-Variant BA.4 Displays a Remarkable Lack of Clinical Signs in a Golden Syrian Hamster Model of SARS-CoV-2 Infection.

Davies E, Ryan K, Bewley K, Coombes N, Salguero F, Carnell O Viruses. 2023; 15(5).

PMID: 37243219 PMC: 10224153. DOI: 10.3390/v15051133.

References

Dupont L, Snell L, Graham C, Seow J, Merrick B, Lechmere T . Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern. Nat Microbiol. 2021; 6(11):1433-1442. PMC: 8556155. DOI: 10.1038/s41564-021-00974-0. View

Bekliz M, Adea K, Vetter P, Eberhardt C, Hosszu-Fellous K, Vu D . Neutralization capacity of antibodies elicited through homologous or heterologous infection or vaccination against SARS-CoV-2 VOCs. Nat Commun. 2022; 13(1):3840. PMC: 9253337. DOI: 10.1038/s41467-022-31556-1. View

Wratil P, Stern M, Priller A, Willmann A, Almanzar G, Vogel E . Three exposures to the spike protein of SARS-CoV-2 by either infection or vaccination elicit superior neutralizing immunity to all variants of concern. Nat Med. 2022; 28(3):496-503. DOI: 10.1038/s41591-022-01715-4. View

Arya R, Kumari S, Pandey B, Mistry H, Bihani S, Das A . Structural insights into SARS-CoV-2 proteins. J Mol Biol. 2020; 433(2):166725. PMC: 7685130. DOI: 10.1016/j.jmb.2020.11.024. View

Khoury D, Cromer D, Reynaldi A, Schlub T, Wheatley A, Juno J . Neutralizing antibody levels are highly predictive of immune protection from symptomatic SARS-CoV-2 infection. Nat Med. 2021; 27(7):1205-1211. DOI: 10.1038/s41591-021-01377-8. View

Ren W, Ju X, Gong M, Lan J, Yu Y, Long Q . Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. mBio. 2022; 13(2):e0009922. PMC: 9040861. DOI: 10.1128/mbio.00099-22. View

Bewley K, Coombes N, Gagnon L, McInroy L, Baker N, Shaik I . Quantification of SARS-CoV-2 neutralizing antibody by wild-type plaque reduction neutralization, microneutralization and pseudotyped virus neutralization assays. Nat Protoc. 2021; 16(6):3114-3140. DOI: 10.1038/s41596-021-00536-y. View

Grant O, Montgomery D, Ito K, Woods R . Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition. Sci Rep. 2020; 10(1):14991. PMC: 7490396. DOI: 10.1038/s41598-020-71748-7. View

Zhou P, Yang X, Wang X, Hu B, Zhang L, Zhang W . A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; 579(7798):270-273. PMC: 7095418. DOI: 10.1038/s41586-020-2012-7. View

10.

Weisblum Y, Schmidt F, Zhang F, DaSilva J, Poston D, Lorenzi J . Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. Elife. 2020; 9. PMC: 7723407. DOI: 10.7554/eLife.61312. View

11.

Cureton D, Massol R, Whelan S, Kirchhausen T . The length of vesicular stomatitis virus particles dictates a need for actin assembly during clathrin-dependent endocytosis. PLoS Pathog. 2010; 6(9):e1001127. PMC: 2947997. DOI: 10.1371/journal.ppat.1001127. View

12.

Funnell S, Afrough B, Baczenas J, Berry N, Bewley K, Bradford R . A cautionary perspective regarding the isolation and serial propagation of SARS-CoV-2 in Vero cells. NPJ Vaccines. 2021; 6(1):83. PMC: 8211640. DOI: 10.1038/s41541-021-00346-z. View

13.

Caly L, Druce J, Roberts J, Bond K, Tran T, Kostecki R . Isolation and rapid sharing of the 2019 novel coronavirus (SARS-CoV-2) from the first patient diagnosed with COVID-19 in Australia. Med J Aust. 2020; 212(10):459-462. PMC: 7228321. DOI: 10.5694/mja2.50569. View

14.

Kuzmina A, Wattad S, Khalaila Y, Ottolenghi A, Rosental B, Engel S . SARS CoV-2 Delta variant exhibits enhanced infectivity and a minor decrease in neutralization sensitivity to convalescent or post-vaccination sera. iScience. 2021; 24(12):103467. PMC: 8591850. DOI: 10.1016/j.isci.2021.103467. View

15.

Zhu N, Zhang D, Wang W, Li X, Yang B, Song J . A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med. 2020; 382(8):727-733. PMC: 7092803. DOI: 10.1056/NEJMoa2001017. View

16.

Alharbi N, Padron-Regalado E, Thompson C, Kupke A, Wells D, Sloan M . ChAdOx1 and MVA based vaccine candidates against MERS-CoV elicit neutralising antibodies and cellular immune responses in mice. Vaccine. 2017; 35(30):3780-3788. PMC: 5516308. DOI: 10.1016/j.vaccine.2017.05.032. View

17.

Singanallur N, van Vuren P, McAuley A, Bruce M, Kuiper M, Gwini S . At Least Three Doses of Leading Vaccines Essential for Neutralisation of SARS-CoV-2 Omicron Variant. Front Immunol. 2022; 13:883612. PMC: 9152325. DOI: 10.3389/fimmu.2022.883612. View

18.

Kwilas S, Liesman R, Zhang L, Walsh E, Pickles R, Peeples M . Respiratory syncytial virus grown in Vero cells contains a truncated attachment protein that alters its infectivity and dependence on glycosaminoglycans. J Virol. 2009; 83(20):10710-8. PMC: 2753119. DOI: 10.1128/JVI.00986-09. View

19.

Dejnirattisai W, Huo J, Zhou D, Zahradnik J, Supasa P, Liu C . SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell. 2022; 185(3):467-484.e15. PMC: 8723827. DOI: 10.1016/j.cell.2021.12.046. View

20.

Beom Park W, Kwon N, Choi S, Kang C, Choe P, Kim J . Virus Isolation from the First Patient with SARS-CoV-2 in Korea. J Korean Med Sci. 2020; 35(7):e84. PMC: 7036342. DOI: 10.3346/jkms.2020.35.e84. View