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To support COVID-19 pandemic planning, we develop a model-inference system to estimate epidemiological properties of new SARS-CoV-2 variants of concern using case and mortality data while accounting for under-ascertainment, disease seasonality, non-pharmaceutical interventions, and mass-vaccination. Applying this system to study three variants of concern, we estimate that B.1.1.7 has a 46.6% (95% CI: 32.3–54.6%) transmissibility increase but nominal immune escape from protection induced by prior wild-type infection; B.1.351 has a 32.4% (95% CI: 14.6–48.0%) transmissibility increase and 61.3% (95% CI: 42.6–85.8%) immune escape; and P.1 has a 43.3% (95% CI: 30.3–65.3%) transmissibility increase and 52.5% (95% CI: 0–75.8%) immunemore »escape. Model simulations indicate that B.1.351 and P.1 could outcompete B.1.1.7 and lead to increased infections. Our findings highlight the importance of preventing the spread of variants of concern, via continued preventive measures, prompt mass-vaccination, continued vaccine efficacy monitoring, and possible updating of vaccine formulations to ensure high efficacy.

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Background With the availability of multiple Coronavirus Disease 2019 (COVID-19) vaccines and the predicted shortages in supply for the near future, it is necessary to allocate vaccines in a manner that minimizes severe outcomes, particularly deaths. To date, vaccination strategies in the United States have focused on individual characteristics such as age and occupation. Here, we assess the utility of population-level health and socioeconomic indicators as additional criteria for geographical allocation of vaccines. Methods and findings County-level estimates of 14 indicators associated with COVID-19 mortality were extracted from public data sources. Effect estimates of the individual indicators were calculated withmore »univariate models. Presence of spatial autocorrelation was established using Moran’s I statistic. Spatial simultaneous autoregressive (SAR) models that account for spatial autocorrelation in response and predictors were used to assess (i) the proportion of variance in county-level COVID-19 mortality that can explained by identified health/socioeconomic indicators (R 2 ); and (ii) effect estimates of each predictor. Adjusting for case rates, the selected indicators individually explain 24%–29% of the variability in mortality. Prevalence of chronic kidney disease and proportion of population residing in nursing homes have the highest R 2 . Mortality is estimated to increase by 43 per thousand residents (95% CI: 37–49; p < 0.001) with a 1% increase in the prevalence of chronic kidney disease and by 39 deaths per thousand (95% CI: 34–44; p < 0.001) with 1% increase in population living in nursing homes. SAR models using multiple health/socioeconomic indicators explain 43% of the variability in COVID-19 mortality in US counties, adjusting for case rates. R 2 was found to be not sensitive to the choice of SAR model form. Study limitations include the use of mortality rates that are not age standardized, a spatial adjacency matrix that does not capture human flows among counties, and insufficient accounting for interaction among predictors. Conclusions Significant spatial autocorrelation exists in COVID-19 mortality in the US, and population health/socioeconomic indicators account for a considerable variability in county-level mortality. In the context of vaccine rollout in the US and globally, national and subnational estimates of burden of disease could inform optimal geographical allocation of vaccines.« less

As COVID-19 continues to pose significant public health threats, quantifying the effectiveness of different public health interventions is crucial to inform intervention strategies. Using detailed epidemiological and mobility data available for New York City and comprehensive modelling accounting for under-detection, we reconstruct the COVID-19 transmission dynamics therein during the 2020 spring pandemic wave and estimate the effectiveness of two major non-pharmaceutical interventions—lockdown-like measures that reduce contact rates and universal masking. Lockdown-like measures were associated with greater than 50% transmission reduction for all age groups. Universal masking was associated with an approximately 7% transmission reduction overall and up to 20% reductionmore »for 65+ year olds during the first month of implementation. This result suggests that face covering can substantially reduce transmission when lockdown-like measures are lifted but by itself may be insufficient to control SARS-CoV-2 transmission. Overall, findings support the need to implement multiple interventions simultaneously to effectively mitigate COVID-19 spread before the majority of population can be protected through mass-vaccination.« less

Improved understanding of the effects of meteorological conditions on the transmission of SARS-CoV-2, the causative agent for COVID-19 disease, is needed. Here, we estimate the relationship between air temperature, specific humidity, and ultraviolet radiation and SARS-CoV-2 transmission in 2669 U.S. counties with abundant reported cases from March 15 to December 31, 2020. Specifically, we quantify the associations of daily mean temperature, specific humidity, and ultraviolet radiation with daily estimates of the SARS-CoV-2 reproduction number (R_t) and calculate the fraction ofR_tattributable to these meteorological conditions. Lower air temperature (within the 20–40 °C range), lower specific humidity, and lower ultraviolet radiation weremore »significantly associated with increasedR_t. The fraction ofR_tattributable to temperature, specific humidity, and ultraviolet radiation were 3.73% (95% empirical confidence interval [eCI]: 3.66–3.76%), 9.35% (95% eCI: 9.27–9.39%), and 4.44% (95% eCI: 4.38–4.47%), respectively. In total, 17.5% ofR_twas attributable to meteorological factors. The fractions attributable to meteorological factors generally were higher in northern counties than in southern counties. Our findings indicate that cold and dry weather and low levels of ultraviolet radiation are moderately associated with increased SARS-CoV-2 transmissibility, with humidity playing the largest role.

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Assessing the effects of early nonpharmaceutical interventions on coronavirus disease 2019 (COVID-19) spread is crucial for understanding and planning future control measures to combat the pandemic. We use observations of reported infections and deaths, human mobility data, and a metapopulation transmission model to quantify changes in disease transmission rates in U.S. counties from 15 March to 3 May 2020. We find that marked, asynchronous reductions of the basic reproductive number occurred throughout the United States in association with social distancing and other control measures. Counterfactual simulations indicate that, had these same measures been implemented 1 to 2 weeks earlier, substantialmore »cases and deaths could have been averted and that delayed responses to future increased incidence will facilitate a stronger rebound of infections and death. Our findings underscore the importance of early intervention and aggressive control in combatting the COVID-19 pandemic.« less

In Spring 2021, the highly transmissible SARS-CoV-2 Delta variant began to cause increases in cases, hospitalizations, and deaths in parts of the United States. At the time, with slowed vaccination uptake, this novel variant was expected to increase the risk of pandemic resurgence in the US in summer and fall 2021. As part of the COVID-19 Scenario Modeling Hub, an ensemble of nine mechanistic models produced 6-month scenario projections for July–December 2021 for the United States. These projections estimated substantial resurgences of COVID-19 across the US resulting from the more transmissible Delta variant, projected to occur across most of themore »US, coinciding with school and business reopening. The scenarios revealed that reaching higher vaccine coverage in July–December 2021 reduced the size and duration of the projected resurgence substantially, with the expected impacts was largely concentrated in a subset of states with lower vaccination coverage. Despite accurate projection of COVID-19 surges occurring and timing, the magnitude was substantially underestimated 2021 by the models compared with the of the reported cases, hospitalizations, and deaths occurring during July–December, highlighting the continued challenges to predict the evolving COVID-19 pandemic. Vaccination uptake remains critical to limiting transmission and disease, particularly in states with lower vaccination coverage. Higher vaccination goals at the onset of the surge of the new variant were estimated to avert over 1.5 million cases and 21,000 deaths, although may have had even greater impacts, considering the underestimated resurgence magnitude from the model.« less