Impact of public health policy and mobility change on transmission potential of severe acute respiratory syndrome coronavirus 2 in Rhode Island, March 2020 - November 2021.

To study the SARS-CoV-2 transmission potential in Rhode Island (RI) and its association with policy changes and mobility changes, the time-varying reproduction number, Rt, was estimated. The daily incident case counts (16 March 2020, through 30 November 2021) were bootstrapped within a 15-day sliding window and multiplied by Poisson-distributed multipliers (λ = 4, sensitivity analysis: 11) to generate 1000 estimated infection counts, to which EpiEstim was applied to generate Rt time series. The median Rt percentage change when policies changed was estimated. The time lag correlations were assessed between the 7-day moving average of the relative changes in Google mobility data in the first 90 days, and Rt and estimated infection count, respectively. There were three major pandemic waves in RI in 2020-2021: spring 2020, winter 2020-2021 and fall-winter 2021. The median Rt fluctuated within the range of 0.5-2 from April 2020 to November 2021. Mask mandate (18 April 2020) was associated with a decrease in Rt (-25.99%, 95% CrI: -37.42%, -14.30%). Termination of mask mandates on 6 July 2021 was associated with an increase in Rt (36.74%, 95% CrI: 27.20%, 49.13%). Positive correlations were found between changes in grocery and pharmacy, Rt retail and recreation, transit, and workplace visits, for both Rt and estimated infection count, respectively. Negative correlations were found between changes in residential area visits for both Rt and estimated infection count, respectively. Public health policies enacted in RI were associated with changes in the pandemic trajectory. This ecological study provides further evidence of how non-pharmaceutical interventions and vaccination slowed COVID-19 transmission in RI.

SARS-CoV-2 transmission potential and rural-urban disease burden disparities across Alabama, Louisiana, and Mississippi, March 2020 - May 2021.

PURPOSE: To quantify and compare SARS-CoV-2 transmission potential across Alabama, Louisiana, and Mississippi and selected counties. METHODS: To determine the time-varying reproduction number Rt of SARS-CoV-2, we applied the R package EpiEstim to the time series of daily incidence of confirmed cases (mid-March 2020 - May 17, 2021) shifted backward by 9 days. Median Rt percentage change when policies changed was determined. Linear regression was performed between log10-transformed cumulative incidence and log10-transformed population size at four time points. RESULTS: Stay-at-home orders, face mask mandates, and vaccinations were associated with the most significant reductions in SARS-CoV-2 transmission in the three southern states. Rt across the three states decreased significantly by ≥20% following stay-at-home orders. We observed varying degrees of reductions in Rt across states following other policies. Rural Alabama counties experienced higher per capita cumulative cases relative to urban ones as of June 17 and October 17, 2020. Meanwhile, Louisiana and Mississippi saw the disproportionate impact of SARS-CoV-2 in rural counties compared to urban ones throughout the study period. CONCLUSION: State and county policies had an impact on local pandemic trajectories. The rural-urban disparities in case burden call for evidence-based approaches in tailoring health promotion interventions and vaccination campaigns to rural residents.

Spatially refined time-varying reproduction numbers of SARS-CoV-2 in Arkansas and Kentucky and their relationship to population size and public health policy, March - November 2020.

PURPOSE: To examine the time-varying reproduction number, Rt, for COVID-19 in Arkansas and Kentucky and investigate the impact of policies and preventative measures on the variability in Rt. METHODS: Arkansas and Kentucky county-level COVID-19 cumulative case count data (March 6-November 7, 2020) were obtained. Rt was estimated using the R package 'EpiEstim', by county, region (Delta, non-Delta, Appalachian, non-Appalachian), and policy measures. RESULTS: The Rt was initially high, falling below 1 in May or June depending on the region, before stabilizing around 1 in the later months. The median Rt for Arkansas and Kentucky at the end of the study were 1.15 (95% credible interval [CrI], 1.13, 1.18) and 1.10 (95% CrI, 1.08, 1.12), respectively, and remained above 1 for the non-Appalachian region. Rt decreased when facial coverings were mandated, changing by -10.64% (95% CrI, -10.60%, -10.70%) in Arkansas and -5.93% (95% CrI, -4.31%, -7.65%) in Kentucky. The trends in Rt estimates were mostly associated with the implementation and relaxation of social distancing measures. CONCLUSIONS: Arkansas and Kentucky maintained a median Rt above 1 during the entire study period. Changes in Rt estimates allow quantitative estimates of potential impact of policies such as facemask mandate.

Time-varying Reproduction Numbers of COVID-19 in Georgia, USA, March 2, 2020 to November 20, 2020.

BACKGROUND: In 2020, Severe Acute Respiratory Syndrome Coronavirus 2 impacted Georgia, USA. Georgia announced a state-wide shelter-in-place on April 2 and partially lifted restrictions on April 27. We estimated the time-varying reproduction numbers (Rt) of COVID-19 in Georgia, Metro Atlanta, and Dougherty County and environs from March 2, 2020, to November 20, 2020. METHODS: We analyzed the daily incidence of confirmed COVID-19 cases in Georgia, Metro Atlanta, and Dougherty County and its surrounding counties, and estimated Rt using the R package EpiEstim. We used a 9-day correction for the date of report to analyze the data by assumed date of infection. RESULTS: The median Rt estimate in Georgia dropped from between 2 and 4 in mid-March to < 2 in late March to around 1 from mid-April to November. Regarding Metro Atlanta, Rt fluctuated above 1.5 in March and around 1 since April. In Dougherty County, the median Rt declined from around 2 in late March to 0.32 on April 26. Then, Rt fluctuated around 1 in May through November. Counties surrounding Dougherty County registered an increase in Rt estimates days after a superspreading event occurred in the area. CONCLUSIONS: In Spring 2020, Severe Acute Respiratory Syndrome Coronavirus 2 transmission in Georgia declined likely because of social distancing measures. However, because restrictions were relaxed in late April and elections were conducted in November, community transmission continued, with Rt fluctuating around 1 across Georgia, Metro Atlanta, and Dougherty County as of November 2020. The superspreading event in Dougherty County affected surrounding areas, indicating the possibility of local transmission in neighboring counties.

Spatially Refined Time-Varying Reproduction Numbers of COVID-19 by Health District in Georgia, USA, March-December 2020.

This study quantifies the transmission potential of SARS-CoV-2 across public health districts in Georgia, USA, and tests if per capita cumulative case count varies across counties. To estimate the time-varying reproduction number, Rt of SARS-CoV-2 in Georgia and its 18 public health districts, we apply the R package 'EpiEstim' to the time series of historical daily incidence of confirmed cases, 2 March-15 December 2020. The epidemic curve is shifted backward by nine days to account for the incubation period and delay to testing. Linear regression is performed between log10-transformed per capita cumulative case count and log10-transformed population size. We observe Rt fluctuations as state and countywide policies are implemented. Policy changes are associated with increases or decreases at different time points. Rt increases, following the reopening of schools for in-person instruction in August. Evidence suggests that counties with lower population size had a higher per capita cumulative case count on June 15 (slope = -0.10, p = 0.04) and October 15 (slope = -0.05, p = 0.03), but not on August 15 (slope = -0.04, p = 0.09), nor December 15 (slope = -0.02, p = 0.41). We found extensive community transmission of SARS-CoV-2 across all 18 health districts in Georgia with median 7-day-sliding window Rt estimates between 1 and 1.4 after March 2020.