SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion methods
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Extended data figures and tables
Extended Data Table 4 Relative recei1 vaccine effectiveness against B1.617.2 v non- B1.617.2: Upper Table: Odds ratios for detection of B.1.617.2 relative to non-B.1.617.2 in vaccinated compared to unvaccinated individuals in multi-variable logistic regression
SARS-CoV-2 Delta variant replication
We first infected a lung epithelial cell line, Calu-3, comparing B.1.1.7 and B.1.617.2 (Fig. ). We observed a replication advantage for B.1.617.2 (Fig. ), as well as an increase in released virions from cells (Fig. ). Next we tested B.1.1.7 against two separate isolates of B.1.617.2 in a human airway epithelial (HAE) model. In this system we again observed that both B.1.617.2 isolates had a significant replication advantage over B.1.1.7 (Fig. ). Finally, we infected primary three-dimensional airway organoids (Fig. ) with B.1.617.2 and B.1.1.7 virus isolates, noting a significant replication advantage for B.1.617.2 over B.1.1.7. These data clearly support the higher replication rate and therefore transmissibility of B.1.617.2 over B.1.1.7. Fig. 2 Delta variant live virus replication kinetics and spike-mediated infectivity. a - d, Live virus replication comparing B.1.1.7 with B....
B.1.617.2 vaccine breakthrough infection
We hypothesized that vaccine effectiveness against B.1.617.2 would be compromised relative to that against other circulating variants. Vaccination of health care workers (HCWs) started in early 2021 with the ChAdOx1 vaccine (Covishield). During the wave of infections in March and April, symptomatic SARS-CoV-2 was confirmed in 30 vaccinated staff members among a workforce of 3,800 at a single tertiary centre in Delhi. Genomic data from India and Delhi suggested B.1.1.7 dominance (Fig. and Extended Data Fig. ), with growth of B.1.617 during March 2021. Short-read sequencing of symptomatic non-fatal infections in the HCW outbreak revealed that the majority were B.1.617.2 with a range of other B lineage viruses (Fig. ). Phylogenetic analysis demonstrated a group of highly related, and in some cases, genetically indistinct sequences that were sampled within 1 or 2 days of each other (Fig....
B.1.617.2 vaccine breakthrough infection
Across the three centres, we noted that the median age and duration of infection of those infected with B.1.617.2 versus non-B.1.617.2 were similar (Extended Data Table ), with no evidence that B.1.617.2 was associated with higher risk of hospitalization (Extended Data Table ). Next we evaluated the effect of B.1.617.2 on vaccine effectiveness against symptomatic infection in the HCWs, compared with other lineages. We used multivariable logistic regression to estimate the odds ratio of testing positive with B.1.617.2 versus non-B.1.617.2 in vaccinated relative to unvaccinated individuals, adjusting for age, sex and hospital. The adjusted odds ratio for B.1.617.2 relative to non-B.1.617.2 was 5.45 (95% confidence interval 1.39-21.4, P = 0.018) for two vaccine doses (Extended Data Table ).
Vaccine effectiveness
To estimate vaccine effectiveness for the B.1.617.2 variant relative to non-B.1.617.2 variants, we adopted a recently described approach. This method is based on the premise that if the vaccine is equally effective against B.1.617.2 and non-B.1.617.2 variants, a similar proportion of cases with each variant would be expected in both vaccinated and unvaccinated cases. This approach overcomes the issue of higher background prevalence of one variant over the other. We determined the proportion of individuals with the B.1.617.2 variant relative to all other circulating variants by vaccination status. We then used logistic regression to estimate the odds ratio of testing positive with B.1.617.2 in vaccinated compared with unvaccinated individuals. The final regression model was adjusted for age as a continuous variable, and sex and hospital as categorical variables. Model sensitivity and...
Standardization of virus input by SYBR Green-based product-enhanced PCR assay
The reverse transcriptase (RT) activity of virus preparations was determined by quantitative PCR (qPCR) using a SYBR Green-based product-enhanced PCR assay as previously described. In brief, tenfold dilutions of virus supernatant were lysed in a 1:1 ratio in a 2 × lysis solution (made up of 40% glycerol (v/v), 0.25% Triton X-100 (v/v), 100 mM KCl, RNase inhibitor 0.8 U ml -1, Tris HCl 100 mM, buffered to pH 7.4) for 10 min at room temperature.
Viral isolate comparison between B.1.617.1 and B.1.617.2
Vero E6 TMPRSS2 cells (an African green monkey ( Chlorocebus sabaeus ) kidney cell line; JCRB1819) were maintained in DMEM (low glucose) (Wako, catalogue no. 041-29775) containing 10% FCS, G418 (1 mg ml -1; Nacalai Tesque, catalogue no. G8168-10ML) and 1% antibiotics (penicillin and streptomycin (P/S)).
Viral isolate comparison between B.1.617.1 and B.1.617.2
Calu-3 cells (a human lung epithelial cell line; ATCC HTB-55) were maintained in minimum essential medium Eagle (Sigma-Aldrich, catalogue no. M4655-500ML) containing 10% FCS and 1% PS.
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Extended Data Table 4 Relative recei1 vaccine effectiveness against B1.617.2 v non- B1.617.2: Upper Table: Odds ratios for detection of B.1.617.2 relative to non-B.1.617.2 in vaccinated compared to unvaccinated individuals in multi-variable logistic regression
We first infected a lung epithelial cell line, Calu-3, comparing B.1.1.7 and B.1.617.2 (Fig. ). We observed a replication advantage for B.1.617.2 (Fig. ), as well as an increase in released virions from cells (Fig. ). Next we tested B.1.1.7 against two separate isolates of B.1.617.2 in a human airway epithelial (HAE) model. In this system we again observed that both B.1.617.2 isolates had a significant replication advantage over B.1.1.7 (Fig. ). Finally, we infected primary three-dimensional airway organoids (Fig. ) with B.1.617.2 and B.1.1.7 virus isolates, noting a significant replication advantage for B.1.617.2 over B.1.1.7. These data clearly support the higher replication rate and therefore transmissibility of B.1.617.2 over B.1.1.7. Fig. 2 Delta variant live virus replication kinetics and spike-mediated infectivity. a - d, Live virus replication comparing B.1.1.7 with B.1.617.2. Calu-3 cells were infected with variants at an MOI of 0.1. a, Viral loads measured by qPCR in cell lysates. b, Viral protein levels in cell lysates. c, d, Live virus produced from infected Calu-3 cell supernatants was collected and used to infect pe...
We hypothesized that vaccine effectiveness against B.1.617.2 would be compromised relative to that against other circulating variants. Vaccination of health care workers (HCWs) started in early 2021 with the ChAdOx1 vaccine (Covishield). During the wave of infections in March and April, symptomatic SARS-CoV-2 was confirmed in 30 vaccinated staff members among a workforce of 3,800 at a single tertiary centre in Delhi. Genomic data from India and Delhi suggested B.1.1.7 dominance (Fig. and Extended Data Fig. ), with growth of B.1.617 during March 2021. Short-read sequencing of symptomatic non-fatal infections in the HCW outbreak revealed that the majority were B.1.617.2 with a range of other B lineage viruses (Fig. ). Phylogenetic analysis demonstrated a group of highly related, and in some cases, genetically indistinct sequences that were sampled within 1 or 2 days of each other (Fig. and Extended Data Fig. ). We next looked in greater detail at the vaccination history of affected individuals. Nearly all had received two doses at least 21 days previously. We obtained similar data on vaccine breakthrough infections in two other health facilities in Delhi with 1,100 and 4,000 HCW s...
Across the three centres, we noted that the median age and duration of infection of those infected with B.1.617.2 versus non-B.1.617.2 were similar (Extended Data Table ), with no evidence that B.1.617.2 was associated with higher risk of hospitalization (Extended Data Table ). Next we evaluated the effect of B.1.617.2 on vaccine effectiveness against symptomatic infection in the HCWs, compared with other lineages. We used multivariable logistic regression to estimate the odds ratio of testing positive with B.1.617.2 versus non-B.1.617.2 in vaccinated relative to unvaccinated individuals, adjusting for age, sex and hospital. The adjusted odds ratio for B.1.617.2 relative to non-B.1.617.2 was 5.45 (95% confidence interval 1.39-21.4, P = 0.018) for two vaccine doses (Extended Data Table ).
To estimate vaccine effectiveness for the B.1.617.2 variant relative to non-B.1.617.2 variants, we adopted a recently described approach. This method is based on the premise that if the vaccine is equally effective against B.1.617.2 and non-B.1.617.2 variants, a similar proportion of cases with each variant would be expected in both vaccinated and unvaccinated cases. This approach overcomes the issue of higher background prevalence of one variant over the other. We determined the proportion of individuals with the B.1.617.2 variant relative to all other circulating variants by vaccination status. We then used logistic regression to estimate the odds ratio of testing positive with B.1.617.2 in vaccinated compared with unvaccinated individuals. The final regression model was adjusted for age as a continuous variable, and sex and hospital as categorical variables. Model sensitivity and robustness to inclusion of these covariates was tested by an iterative process of sequentially adding the covariates to the model and examining the impact on the odd ratios and confidence intervals until the final model was constructed (Extended Data Table ). The R 2 measure, as proposed by McFadden...
The reverse transcriptase (RT) activity of virus preparations was determined by quantitative PCR (qPCR) using a SYBR Green-based product-enhanced PCR assay as previously described. In brief, tenfold dilutions of virus supernatant were lysed in a 1:1 ratio in a 2 × lysis solution (made up of 40% glycerol (v/v), 0.25% Triton X-100 (v/v), 100 mM KCl, RNase inhibitor 0.8 U ml -1, Tris HCl 100 mM, buffered to pH 7.4) for 10 min at room temperature.
Vero E6 TMPRSS2 cells (an African green monkey ( Chlorocebus sabaeus ) kidney cell line; JCRB1819) were maintained in DMEM (low glucose) (Wako, catalogue no. 041-29775) containing 10% FCS, G418 (1 mg ml -1; Nacalai Tesque, catalogue no. G8168-10ML) and 1% antibiotics (penicillin and streptomycin (P/S)).
Calu-3 cells (a human lung epithelial cell line; ATCC HTB-55) were maintained in minimum essential medium Eagle (Sigma-Aldrich, catalogue no. M4655-500ML) containing 10% FCS and 1% PS.
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