Neutralization assays for SARS-CoV-2: Implications for assessment of protective efficacy of COVID-19 vaccines

The WHO emergency use-listed (EUL) COVID-19 vaccines were developed against early strains of SARS-CoV-2. With the emergence of SARS-CoV-2 variants of concern (VOCs) - Alpha, Beta, Gamma, Delta and Omicron, it is necessary to assess the neutralizing activity of these vaccines against the VOCs. PubMed and preprint platforms were searched for literature on neutralizing activity of serum from WHO EUL vaccine recipients, against the VOCs, using appropriate search terms till November 30, 2021. Our search yielded 91 studies meeting the inclusion criteria. The analysis revealed a drop of 0-8.9-fold against Alpha variant, 0.3-42.4-fold against Beta variant, 0-13.8-fold against Gamma variant and 1.35-20-fold against Delta variant in neutralization titres of serum from the WHO EUL COVID-19 vaccine recipients, as compared to early SARS-CoV-2 isolates. The wide range of variability was due to differences in the choice of virus strains selected for neutralization assays (pseudovirus or live virus), timing of serum sample collection after the final dose of vaccine (day 0 to 8 months) and sample size (ranging from 5 to 470 vaccinees). The reasons for this variation have been discussed and the possible way forward to have uniformity across neutralization assays in different laboratories have been described, which will generate reliable data. Though in vitro neutralization studies are a valuable tool to estimate the performance of vaccines against the backdrop of emerging variants, the results must be interpreted with caution and corroborated with field-effectiveness studies.

Whole-genome sequencing of SARS-CoV-2 Gamma variant first discovered in Chinese mainland / 中华微生物学和免疫学杂志

Objective:To investigate the whole genome of SARS-CoV-2 causing COVID-19 in Rongcheng city of Shandong Province in May 2022 and to further analyze the nucleotide and amino acid variations for source tracing.Methods:High-throughput sequencing was used to sequence the SARS-CoV-2 genome in 15 nasopharyngeal swab samples from COVID-19 cluster infections and three environmental samples related to an aquatic product import company. Whole-genome sequence splicing, variant site analysis and sequence typing were performed on the raw sequencing data using virus sequence and variant analysis software. A phylogenetic tree was constructed by evolutionary analysis software. Epidemiological investigation was used to trace the potential source of infection.Results:Thirteen whole genome sequences of SARS-CoV-2 with the length ranging from 29 653 bp to 29 780 bp were successfully obtained from the nasopharyngeal swab samples. The average sequencing depth was 1 756-6 565 X and the genome coverage was 99.20%-99.63%. The results of Pangolin typing showed that the 13 genomes belonged to the VOC/Gamma (P.1.15) evolutionary branch. Compared with the Wuhan reference strain (NC_045512.2), the 13 genome sequences had 40-41 nucleotide mutation sites. There were 23-24 amino acid variation sites in seven protein domains (ORF1a, ORF1b, S, ORF3a, ORF8, ORF9b and N proteins). Evolutionary analysis showed that the viral sequence was grouped to the same subclade as the reference strain from Argentina (EPI_ISL_4082233).Conclusions:In this study, the whole genome sequences of 13 Gamma variant strains were obtained from COVID-19 cluster infections associated with imported cold-chain aquatic products in Rongcheng city, and the imported seafood from South America in 2021 was found to be the source of the virus in a timely manner. This study provided reference for the SARS-CoV-2 variant analysis and case tracing and also suggested that the survival and transmission ability of SARS-CoV-2 on the surface of cold-chain products should not be underestimated and needed further investigation.

Generation of neutralizing antibodies against Omicron, Gamma and Delta SARS-CoV-2 variants following CoronaVac vaccination

ABSTRACT Vaccination is a fundamental tool to prevent SARS-CoV-2 infection and to limit the COVID-19 pandemic. The emergence of SARS-CoV-2 variants with multiple mutations has raised serious concerns about the ability of neutralizing antibody responses elicited by prior vaccination to effectively combat these variants. The neutralizing capacity against the Gamma, Delta and Omicron variants of sera from individuals immunized with the CoronaVac vaccine remains incompletely determined. The present study evaluated 41 health care workers at the Faculdade de Medicina of the Universidade de Sao Paulo, in Sao Paulo, Brazil, naive to previous SARS- CoV-2 infection, who were vaccinated with two doses of the CoronaVac SARS-CoV-2 vaccine 28 days apart. Neutralizing antibody levels against the Gamma, Delta, and Omicron variants were measured at 32 and 186 days after the second vaccination. We also measured neutralizing antibodies against Omicron in 34 of these individuals following a subsequent booster immunization with the Pfizer vaccine. Quantification of neutralizing antibodies was performed using the Cytopathic Effect-based Virus Neutralization test. Neutralization antibody activity against the Gamma, Delta and Omicron variants was observed in 78.0%, 65.9% and 58.5% of serum samples, respectively, obtained at a mean of 32 days after the second immunization. This decreased to 17.1%, 24.4% and 2.4% of sera having activity against Delta, Gamma and Omicron, respectively, at 186 days post-vaccination. The median neutralizing antibody titers at 32 days were 1:40, 1:20 and 1:20 against Gamma, Delta and Omicron, respectively, and decreased to an undetectable median level against all variants at the later time. A booster immunization with the Pfizer vaccine elicited neutralizing antibodies against Omicron in 85% of subjects tested 60 days after vaccination. We conclude that two doses of the CoronaVac vaccine results in limited protection of short duration against the Gamma, Delta and Omicron SARS-CoV-2 variants. A booster dose with the Pfizer vaccine induced antibody neutralizing activity against Omicron in most patients which was measurable 60 days after the booster.

Absence of neutralizing antibodies against the Omicron SARS-CoV-2 variant in convalescent sera from individuals infected with the ancestral SARS-CoV-2 virus or its Gamma variant

Abstract Objectives: The aim of the present study was to evaluate if neutralizing antibody responses induced by infection with the SARS-CoV-2 strain that was dominant at the beginning of the pandemic or by the Gamma variant was effective against the Omicron variant. Methods: Convalescent sera from 109 individuals, never exposed to a SARS-CoV-2 vaccine, who had mild or moderate symptoms not requiring hospitalization following either a documented SARS-CoV-2 ancestral strain infection or a Gamma variant infection, were assayed for in vitro neutralizing antibody activity against their original strains and the Omicron variant. Results: Following an infection with the ancestral strain, 56 (93.3%), 45 (77.6%) and 1 (1.7%) serum sample were positive for neutralizing antibodies against the ancestral, Gamma variant, and Omicron variant, respectively. After infection with the Gamma variant, 43 (87.8%) and 2 (4.1%) sera were positive for neutralizing antibodies against the Gamma and Omicron variants, respectively. Conclusions: Neutralizing antibodies generated following mild or moderate infection with the SARS-CoV-2 ancestral strain or the Gamma variant are not protective against the Omicron variant. HIGHLIGHTS Individuals previously infected with SARS-CoV-2 ancestral strain do not develop neutralizing antibodies against the Omicron variant. Omicron variant escapes immune response after SARS CoV-2 previous infection with the SARS CoV-2 Gamma variant. Individuals previously infected with SARS-CoV-2 ancestral strain or with SARS-CoV-2 Gamma variant will likely have little protection if subsequently exposed to the Omicron variant.

Analytical evaluation of thirty-two severe acute respiratory syndrome 2 lateral flow antigen tests demonstrates sensitivity remains with the SARS-CoV-2 Gamma lineage

ABSTRACT Background: The emergence of variants of concern (VOCs) requires an ongoing assessment of the performance of antigen lateral flow tests (Ag-RDTs). The limit of detection (LOD) of 32 Ag-RDTs was evaluated using the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma variant. Methods: Ag-RDTs were performed according to the manufacturer's instructions with a clinical isolate of the Gamma variant. Results: Twenty-eight of the 32 Ag-RDTs exceeded the World Health Organization criteria. Conclusions: This comprehensive analytical evaluation of Ag-RDTs demonstrated that the test performance was maintained with Gamma VOC.