Neutralisation of SARS-CoV-2 lineage P.1 by antibodies elicited through natural SARS-CoV-2 infection or vaccination with an inactivated SARS-CoV-2 vaccine: an immunological study

Abstract

Background: Mutations accrued by SARS-CoV-2 lineage P.1-first detected in Brazil in early January, 2021-include amino acid changes in the receptor-binding domain of the viral spike protein that also are reported in other variants of concern, including B.1.1.7 and B.1.351. We aimed to investigate whether isolates of wild-type P.1 lineage SARS-CoV-2 can escape from neutralising antibodies generated by a polyclonal immune response.

Methods: We did an immunological study to assess the neutralising effects of antibodies on lineage P.1 and lineage B isolates of SARS-CoV-2, using plasma samples from patients previously infected with or vaccinated against SARS-CoV-2. Two specimens (P.1/28 and P.1/30) containing SARS-CoV-2 lineage P.1 (as confirmed by viral genome sequencing) were obtained from nasopharyngeal and bronchoalveolar lavage samples collected from patients in Manaus, Brazil, and compared against an isolate of SARS-CoV-2 lineage B (SARS.CoV2/SP02.2020) recovered from a patient in Brazil in February, 2020. Isolates were incubated with plasma samples from 21 blood donors who had previously had COVID-19 and from a total of 53 recipients of the chemically inactivated SARS-CoV-2 vaccine CoronaVac: 18 individuals after receipt of a single dose and an additional 20 individuals (38 in total) after receipt of two doses (collected 17-38 days after the most recent dose); and 15 individuals who received two doses during the phase 3 trial of the vaccine (collected 134-230 days after the second dose). Antibody neutralisation of P.1/28, P.1/30, and B isolates by plasma samples were compared in terms of median virus neutralisation titre (VNT50, defined as the reciprocal value of the sample dilution that showed 50% protection against cytopathic effects).

Findings: In terms of VNT50, plasma from individuals previously infected with SARS-CoV-2 had an 8·6 times lower neutralising capacity against the P.1 isolates (median VNT50 30 [IQR <20-45] for P.1/28 and 30 [<20-40] for P.1/30) than against the lineage B isolate (260 [160-400]), with a binominal model showing significant reductions in lineage P.1 isolates compared with the lineage B isolate (p≤0·0001). Efficient neutralisation of P.1 isolates was not seen with plasma samples collected from individuals vaccinated with a first dose of CoronaVac 20-23 days earlier (VNT50s below the limit of detection [<20] for most plasma samples), a second dose 17-38 days earlier (median VNT50 24 [IQR <20-25] for P.1/28 and 28 [<20-25] for P.1/30), or a second dose 134-260 days earlier (all VNT50s below limit of detection). Median VNT50s against the lineage B isolate were 20 (IQR 20-30) after a first dose of CoronaVac 20-23 days earlier, 75 (<20-263) after a second dose 17-38 days earlier, and 20 (<20-30) after a second dose 134-260 days earlier. In plasma collected 17-38 days after a second dose of CoronaVac, neutralising capacity against both P.1 isolates was significantly decreased (p=0·0051 for P.1/28 and p=0·0336 for P.1/30) compared with that against the lineage B isolate. All data were corroborated by results obtained through plaque reduction neutralisation tests.

Interpretation: SARS-CoV-2 lineage P.1 might escape neutralisation by antibodies generated in response to polyclonal stimulation against previously circulating variants of SARS-CoV-2. Continuous genomic surveillance of SARS-CoV-2 combined with antibody neutralisation assays could help to guide national immunisation programmes.

Funding: São Paulo Research Foundation, Brazilian Ministry of Science, Technology and Innovation and Funding Authority for Studies, Medical Research Council, National Council for Scientific and Technological Development, National Institutes of Health.

Translation: For the Portuguese translation of the abstract see Supplementary Materials section.

Conflict of interest statement

MSD is a consultant for Inbios, Vir Biotechnology, NGM Biopharmaceuticals, and Carnival Corporation, and on the Scientific Advisory Boards of Moderna and Immunome. MSD is the principal investigator of a laboratory that has received funding support in sponsored research agreements from Moderna, Vir Biotechnology, and Emergent BioSolutions.

© 2021 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY-NC-ND 4.0 license.

Figures

Figure 1

Immunofluorescent staining with commercial antibodies against SARS-CoV-2 proteins Images show staining of mock-infected Vero cells and of Vero cells inoculated with a SARS-CoV-2 lineage B isolate or a SARS-CoV-2 lineage P.1 isolate (P.1/28 or P.1/30). Cells were stained with antibodies against SARS-CoV-2 nucleocapsid protein (red fluorescence, columns 1, 3, and 4) and spike protein (green fluorescence, columns 2–4) and phalloidin for visualisation of F-actin filaments (pink fluorescence, column 4). Nuclei were labelled with 4′,6-diamidino-2-phenylindole dihydrochloride (blue fluorescence). Slides were analysed by confocal microscopy and images were merged with ImageJ.

Figure 2

Neutralisation of SARS-CoV-2 lineages B and P.1 by plasma from previously infected or vaccinated individuals, according to VNT50 Plasma samples were incubated with Vero cells infected with a SARS-CoV-2 lineage B isolate (SARS.CoV2/SP02.2020) or one of two lineage P.1 isolates (P.1/28 and P.1/30) to assess VNT50 (defined as the reciprocal value of the plasma sample dilution that showed 50% protection against cytopathic effects). (A) Plasma from blood donors previously infected with SARS-CoV-2 (n=21). (B) Plasma from individuals vaccinated with a single dose of CoronaVac vaccine during the Brazilian vaccination programme (n=18), collected at a median 21 days (IQR 21–21; range 20–23) after receipt of the first dose. (C) Plasma from individuals vaccinated with two doses of CoronaVac vaccine during the Brazilian vaccination programme (n=38), collected at a median 21 days (IQR 20–23; range 17–38) after receipt of the second dose. (D) Plasma from individuals vaccinated with two doses of CoronaVac vaccine in the Sinovac phase 3 trial (n=15), collected at a median 158 days (IQR 156–170; range 134–260) after receipt of the second dose. Dashed lines indicate the lower LOD of the VNT50 assay for samples with low or absent virus neutralisation capacity. Black circles indicate group medians for each isolate, with bars showing IQRs. Each data point is the average of a duplicate assay for each plasma sample, and two independent assays were done for all groups (except the group of participants who received a single dose of vaccine, panel B). LOD=limit of detection (VNT50 titre <20). ND=not detected (below LOD). VNT50=median virus neutralisation titre.

Figure 3

Neutralisation of SARS-CoV-2 lineages B and P.1 by plasma from previously infected or vaccinated individuals, according to PRNT50 Plasma samples were tested by PRNT in Vero cells after incubation with 100 plaque-forming units of different isolates of SARS-CoV-2 (B and two isolates of P.1 lineages). PRNT50 represents the sample dilution that showed a 50% reduction in plaque formation compared with a control well inoculated with SARS-CoV-2 alone (without plasma), after linear regression analysis. Each data point represents the mean of all plasma samples for each group at each dilution level (shown as log2 serum dilution) and error bars represent SD. (A) Plasma from blood donors previously infected with SARS-CoV-2 (n=21). (B) Plasma from individuals vaccinated with a single dose of CoronaVac vaccine during the Brazilian vaccination programme (n=18), collected at a median 21 days (IQR 21–21; range 20–23) after receipt of the first dose. (C) Plasma from individuals vaccinated with two doses of CoronaVac vaccine during the Brazilian vaccination programme (n=38), collected at a median 21 days (IQR 20–23; range 17–38) after receipt of the second dose. (D) Plasma from individuals vaccinated with two doses of CoronaVac vaccine in the Sinovac phase 3 trial (n=15), collected at a median 158 days (IQR 156–170; range 134–260) after receipt of the second dose. All PRNT curves for each sample used in the study are shown in appendix 2 (pp 4–7). PRNT=plaque reduction neutralisation test.