Genomic evolution of SARS-CoV-2 variants of concern under in vitro neutralising selection pressure following two doses of the Pfizer-BioNTech BNT162b2 COVID-19 vaccine

摘要: Aims To explore viral evolution during in vitro neutralisation 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 SARSCoV2 variant of concern (VOC) Delta (B 1.617.2) compared to the earlier lineages Beta (B.1.351) and wildtype (lineage A.2.2) virus. Methods Using a live virus SARSCoV2 neutralisation assay in Vero E6 cells we determined neutralising antibody titres (nAbT) in 14 participants (vaccine naive (n=2) and post second dose of BNT162b2 vaccination (n=12), median age 45 years [IQR 29 to 65], median time after second dose = 21 days [IQR 19 to 28] against three SARSCoV2 strains: wild-type, Beta and Delta. The determination of nAbT was performed by visual inspection of cytopathic effect (CPE) and inhouse quantitative reverse transcriptase real time quantitative polymerase chain reaction (RTqPCR) 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 wildtype, 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 …