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

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.

Immune escape of Omicron lineages BA.1, BA.2, BA.5.1, BQ.1, XBB.1.5, EG.5.1 and JN.1.1 after vaccination, infection and hybrid immunity

“…31,32 In comparison with the parent lineage BA.2.86, JN.1 has an additional L455S substitution in the spike protein that was described to be associated with increased escape from humoral immunity as well as transmissibility. 5,[11][12][13][14][15] However in contrast to its parental lineage BA.2.86, JN.1 showed a rapid increase in numbers of sequences in late 2023 and was then designated as a VOI. 22 Indeed, after a prolonged period of continuous co-circulation of multiple Omicron lineages for most of 2022 and 2023, JN.1 has largely outcompeted earlier variants and became dominant.…”

Evaluation of the cross reactivity of neutralising antibody response in vaccinated human and convalescent hamster sera against SARS-CoV-2 variants up to and including JN.1 using an authentic virus neutralisation assay

“…With no differences in the main viral proteins exposed to neutralising antibodies (spike, membrane, envelope), it appears that the sequence is not responsible for the variation in titres seen here. Other potential explanations were described in our previous paper and include the potential impact of secretion of free spike protein, defective interfering particles and differences in spike glycosylation [12, 42-46].…”

“…Sighting for each variant into the Focus Reduction Neutralisation Test (FRNT) to calculate dilution at which a median of 130 foci could be counted in non-neutralised control wells was performed. Whole genome sequencing (SISPA-Illumina) was performed on final virus assay banks, as described previously, to confirm presence of FCS S1/S2 boundary, check for mixed bases as well as confirm variant identity [12, 23-25].…”

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

“…The GISAID ID or source of the isolation swabs/ viruses used in this study are as follows: Ancestral (EPI_ISL_406844, [7]), BA.1 (EPI_ISL_7400555), BA.2 (not available), BA.2.12.1 (Gavin Screaton, University of Oxford), BA.4 (EPI_ISL_13157810), BA.5.2.1 (EPI_ISL_12810908), BQ.1.22 (EPI_ISL_15581064), XBB.1.1 (EPI_ISL_15682231). Viruses were isolated and propagated on Vero/hSLAM (ECACC 04091501, European Collection of Authenticated Cell Cultures (ECACC) UKHSA, Porton Down, UK) with quality control checks and whole genome sequencing performed as previously described [8]. Sequence data of the virus banks used in this study are available in Supplementary Data File S1.…”