Genomic evolution of SARS-CoV-2 variants of concern underin vitroneutralising selection pressure following two doses of the Pfizer-BioNTech BNT162b2 COVID-19 vaccine
Authors: Basile Kerri , Agius Jessica E. , Fong Winkie , McPhie Kenneth , Fennel Michael , Ko Danny , Heuston Linda , Lam Connie , Arnott Alicia , Chen Sharon C-A , Maddocks Susan , O’Sullivan Matthew V. N. , Dwyer Dominic E. , Sintchenko Vitali , Kok Jen , Rockett Rebecca J. ,   the CIDMLS COVID-19 Study Group
Published: September 2023

Aims

To explore viral evolution duringin vitroneutralisation using next generation sequencing, and to determine whether sera from individuals immunised with two doses of the Pfizer-BioNTech vaccine (BNT162b2) are as effective at neutralising the SARS-CoV-2 variant of concern (VOC) Delta (B 1.617.2) compared to the earlier lineages Beta (B.1.351) and wild-type (A.2.2) virus.

Methods

Using a live-virus SARS-CoV-2 neutralisation assay in Vero E6 cells we determined neutralising antibody titres (nAbT) in 14 participants (vaccine-naïve (n=2) and post-second dose of BNT162b2 vaccination (n=12), median age 45 years [IQR 29–65], median time after second dose = 21 days [IQR 19–28] against three SARS-CoV-2 strains: wild-type, Beta and Delta. The determination of nAbT was performed by visual inspection of cytopathic effect (CPE) and in-house quantitative reverse transcriptase real time quantitative polymerase chain reaction (RT-qPCR) to confirm SARS-CoV-2 replication. A total of 110 representative samples including inoculum, neutralisation breakpoints at 72 hrs, negative and positive controls underwent genome sequencing using the Respiratory Viral Oligo Panel version 2 (RVOP) (Illumina Inc. (San Diego, United States of America)) viral enrichment and short read sequencing using (Illumina Inc.San Diego, United States of America)(Figure 1).

Results

There was a significant reduction in nAbT observed against the Delta and Beta VOC compared with wild-type, 4.4-fold (p= >0.0006) and 2.3-fold (p= 0.0140), respectively (Figure 2). Neutralizing antibodies were not detected in one vaccinated immunosuppressed participant nor the vaccine-naïve participants (n=2). The highest nAbT against the SARS-CoV-2 variants investigated was obtained from a participant who was vaccinated following SARS-CoV-2 infection 12 months prior (Table S1). Limited consensus level mutations occurred in the SARS-CoV-2 genome of any lineage duringin vitroneutralisation, however, consistent minority allele frequency variants (MFV) were detected in the SARS-CoV-2 polypeptide, spike (S) and membrane protein.

Discussion

Significant reductions in nAbT post-vaccination were identified, with Delta demonstrating a 4.4-fold reduction. The reduction in nAbT for the VOC Beta has been previously documented, however, limited data is available on vaccine evasion for the Delta VOC, the predominant strain currently circulating worldwide at the time. Studies in high incidence countries may not be applicable to low incidence settings such as Australia as nAbT may be significantly higher in vaccine recipients previously infected with SARS-CoV-2, as seen in our cohort. Monitoring viral evolution is critical to evaluate the impact of novel SARS-CoV-2 variants on vaccine effectiveness as mutational profiles in the sub-consensus genome could indicate increases in transmissibility, virulence or allow the development of antiviral resistance.