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. 2022 Jun;19(191):20210900.
doi: 10.1098/rsif.2021.0900. Epub 2022 Jun 6.

COVID-19 pandemic dynamics in India, the SARS-CoV-2 Delta variant and implications for vaccination

Wan Yang  1 , Jeffrey Shaman  2
Affiliations

COVID-19 pandemic dynamics in India, the SARS-CoV-2 Delta variant and implications for vaccination

Wan Yang et al. J R Soc Interface. 2022 Jun.

Abstract

The Delta variant is a major SARS-CoV-2 variant of concern first identified in India. To better understand COVID-19 pandemic dynamics and Delta, we use multiple datasets and model-inference to reconstruct COVID-19 pandemic dynamics in India during March 2020-June 2021. We further use the large discrepancy in one- and two-dose vaccination coverage in India (53% versus 23% by end of October 2021) to examine the impact of vaccination and whether prior non-Delta infection can boost vaccine effectiveness (VE). We estimate that Delta escaped immunity in 34.6% (95% CI: 0-64.2%) of individuals with prior wild-type infection and was 57.0% (95% CI: 37.9-75.6%) more infectious than wild-type SARS-CoV-2. Models assuming higher VE among non-Delta infection recoverees, particularly after the first dose, generated more accurate predictions than those assuming no such increases (best-performing VE setting: 90/95% versus 30/67% baseline for the first/second dose). Counterfactual modelling indicates that high vaccination coverage for first vaccine dose in India combined with the boosting of VE among recoverees averted around 60% of infections during July-mid-October 2021. These findings provide support to prioritizing first-dose vaccination in regions with high underlying infection rates, given continued vaccine shortages and new variant emergence.

Keywords: COVID-19; Delta SARS-CoV-2 variant; India; boosting; prior infection; vaccine effectiveness.

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Figures

Figure 1.
Figure 1.
Model-inference estimates and validation. (a) Model fit. (b) Model validation. (c) Observed relative mobility and estimated disease seasonal trend, compared with case and death rates over time. Key model-inference estimates are shown for (d) the real-time reproduction number Rt, (e) transmissibility RTX and (f) population susceptibility, expressed relative to the population size (i.e. St/N × 100%). Blue lines and surrounding areas show the estimated mean, 50% (dark) and 95% (light) CrIs. Boxes and whiskers show the estimated mean, 50% and 95% CrIs for weekly cases and deaths in (a) and infection rates in (d–f). Grey shaded areas indicate the timing of national lockdowns (darker) or local restrictions (lighter); horizontal arrows indicate the timing of variant identification and vaccination rollout. In (c), for mobility (blue line; y-axis), values below 1 (dashed horizontal line) indicate reductions due to public health interventions. For the disease seasonal trend (orange line; y-axis), values above 1 indicate weather conditions more conducive for transmission than the yearly average and vice versa. Note that the transmissibility estimates have removed the effects of changing population susceptibility, NPIs and disease seasonality; thus, the trends are more stable than the reproduction number (Rt in d) and reflect changes in variant-specific properties.
Figure 2.
Figure 2.
Impact of vaccination. Model projections of weekly number of reported cases (a) and reported deaths (b) for India during July–mid-October 2021, compared with reported data. Crosses (x) show reported data (left y-axis). Red dashed lines show median counterfactual model projections assuming no further vaccination uptake during the 16-week period. Blue dashed lines show median model projections using reported vaccination rates and assuming 90%/95% VE for individuals with prior non-Delta infection after the first/second vaccine dose. Shaded areas with the same colour show projected interquartile ranges. For comparison, estimated seasonality (orange lines), reported mobility (dark-blue lines) and cumulative vaccination uptake (full bar for first dose and filled section for second dose) are overlaid (see right y-axis scale). All numbers are scaled per one million people.
Figure 3.
Figure 3.
Impact of prior non-Delta infection on immune boosting. Model projections under different VE settings are used to examine the most plausible VE for individuals with prior non-Delta infection, based on projection accuracy: (a) the RRMSE and (c) correlation between the projected and observed values for cases and deaths, respectively. The size of the dots represents VE for recoverees after the first vaccine dose and the colour represents VE after the second vaccine dose. The dots with the black circles represent the baseline VE setting (i.e. 30%/67% for the first/second dose). For comparison, projected weekly numbers of reported cases (b) and reported deaths (d) under different VE settings are plotted along with the weekly actuals. For clarity, only median projections are shown here; see example projections including interquartile ranges in figure 2.
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