Examining the Impact of Increasing Vaccine Coverage and Nonpharmaceutical Interventions against Coronavirus Disease 2019 In Ghana using Mathematical Modeling (preprint)

Seroprevalence studies assessing community exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Ghana concluded that population-level immunity remained low as of February 2021. Thus, it is important to demonstrate how increasing vaccine coverage reduces the economic and public health impacts associated with transmission of the novel coronavirus. To that end, this study used a Susceptible-Exposed-Presymptomatic-Symptomatic-Asymptomatic-Recovered-Dead-Vaccinated compartmental model to simulate coronavirus disease 2019 (COVID-19) transmission and the role of public health interventions in Ghana. The impact of increasing vaccination rate and decline in transmission rates due to nonpharmaceutical interventions (NPIs) on cumulative infections and deaths averted was explored under different scenarios. Latin hypercube sampling-partial rank correlation coefficient (LHS-PRCC) was used to investigate uncertainty and sensitivity of the outcomes to the parameters. Simulation results suggest that increasing the vaccination rate to achieve 50% coverage was associated with almost 30,000 deaths and 25 million infections averted. In comparison, a 50% decrease in the transmission coefficient was associated with about 50 million infections and 120,000 deaths averted. The LHS-PRCC results also found that cumulative infections and deaths averted were most sensitive to three model parameters: Transmission rate, vaccination rate, and waning immunity rate from infection. There is a need to increase vaccination coverage by ensuring an increased supply. Adherence to NPIs and increased vaccine uptake would successfully mitigate the impact of COVID-19 in Ghana.

Modeling infections and deaths averted due to COVID-19 vaccination strategies in Ghana (preprint)

This study assessed the impact of various COVID-19 vaccination strategies on health outcomes in Ghana using an age-stratified compartmental model. The population was stratified into three age groups: <25 years, 25-64 years, and 65+ years. Five vaccination optimization scenarios were explored, assuming that one million persons could be vaccinated in three versus six months. We also performed uncertainty analysis by assuming that the available doses were halved and doubled. The vaccine optimization strategies were assessed for the initial strain, followed by a sensitivity analysis for the delta variant by varying the reproduction number and vaccine efficacy. The results showed that vaccinating individuals <65 years was associated with the lowest cumulative infections when one million persons were vaccinated over three months for both the initial strain and the delta variant. On the contrary, prioritizing the elderly (65+) was associated with the lowest cumulative deaths for both strains.

A pharmacoepidemiological study of myocarditis and pericarditis following mRNA COVID-19 vaccination in Europe (preprint)

ABSTRACT Purpose To assess myocarditis and pericarditis reporting rate as adverse drug reactions (ADRs) for the messenger ribonucleic acid (mRNA) coronavirus disease 2019 (COVID-19) vaccines authorized in Europe. Methods Data on myocarditis and pericarditis related to mRNA COVID-19 vaccines (period: January 1, 2021 - February 11, 2022) were collected from the EudraVigilance database and combined with the European Centre for Disease Prevention and Control’s (ECDC) vaccination tracker database. The reporting rate was expressed as 1 million individual vaccinated-days with a corresponding 95% confidence interval (CI), and an observed-to-expected (OE) analysis was performed to check if there was an excess risk for myocarditis or pericarditis following mRNA COVID-19 vaccination. Results The reporting rate of myocarditis per 1 million individual vaccinated-days in the study period was 17.27 (95% CI, 16.34-18.26) for the CX-024414 vaccine and 8.44 (95% CI, 8.18-8.70) for TOZINAMERAN vaccine. The reporting rate for pericarditis per 1 million individual vaccinated-days in the study period was 9.76 (95% CI, 9.06-10.51) for the CX-024414 vaccine and 5.79 (95% CI, 5.56-6.01) for TOZINAMERAN vaccine. The OE analysis showed that both vaccines produced a myocarditis standardized morbidity ratio (SMR) greater than 1, with the CX-024414 vaccine having a greater SMR than TOZINAMERAN. Regarding TOZINAMERAN, SMR for pericarditis was greater than 1 when considering the lowest background incidence, but smaller than 1 when considering the highest background incidence. Conclusions Our results suggest an excess risk of myocarditis following the first dose of mRNA COVID-19 vaccine, but the relationship between pericarditis and mRNA COVID-19 vaccine remains unclear.

Elevated COVID-19 Case Rates of Government Employees, District of Columbia, 2020-22 (preprint)

The rate ratios of COVID-19 cases among 5 District of Columbia departments' personnel with reference to D.C. residents were found greater than one from March 2020 to early January 2022, suggesting higher case rates for emergency responders and frontline personnel than for general population. Vaccination is highly recommended.

SARS-CoV-2 Transmission Potential and Policy Changes in South Carolina, February 2020 - January 2021 (preprint)

IntroductionWe aimed to examine how public health policies influenced the dynamics of COVID-19 time-varying reproductive number (Rt) in South Carolina from February 26, 2020 to January 1, 2021. MethodsCOVID-19 case series (March 6, 2020 - January 10, 2021) were shifted by 9 days to approximate the infection date. We analyzed the effects of state and county policies on Rt using EpiEstim. We performed linear regression to evaluate if per-capita cumulative case count varies across counties with different population size. ResultsRt shifted from 2-3 in March to <1 during April and May. Rt rose over the summer and stayed between 1.4 and 0.7. The introduction of statewide mask mandates was associated with a decline in Rt (-15.3%; 95% CrI, -13.6%, -16.8%), and school re-opening, an increase by 12.3% (95% CrI, 10.1%, 14.4%). Less densely populated counties had higher attack rate (p<0.0001). ConclusionThe Rt dynamics over time indicated that public health interventions substantially slowed COVID-19 transmission in South Carolina, while their relaxation may have promoted further transmission. Policies encouraging people to stay home, such as closing non-essential businesses, were associated with Rt reduction, while policies that encouraged more movement, such as re-opening schools, were associated with Rt increase.

An investigation of spatial-temporal patterns and predictions of the COVID-19 pandemic in Colombia, 2020-2021 (preprint)

Colombia announced the first case of severe acute respiratory syndrome coronavirus 2 on March 6, 2020. Since then, the country has reported a total of 4,240,982 cases and 106,544 deaths as of June 30, 2021. This motivates an investigation of the SARS-CoV-2 transmission dynamics at the national and regional level using case incidence data. Mathematical models are employed to estimate the transmission potential and perform short-term forecasts of the COVID-19 epidemic trajectory in Colombia. Furthermore, geographic heterogeneity of COVID-19 in Colombia is examined along with the analysis of mobility and social media trends, showing that the increase in mobility in July 2020 and January 2021 were correlated with surges in case incidence. The estimation of national and regional reproduction numbers shows sustained disease transmission during the early phase of the pandemic, exhibiting sub-exponential growth dynamics. Moreover, most recent estimates of reproduction number are >1.0 at the national and regional levels as of May 30, 2021. Further, the 30-day ahead short-term forecasts obtained from Richards model present a sustained decline in case counts in contrast to the sub-epidemic and GLM model. Nevertheless, our spatial analysis in Colombia shows distinct variations in incidence rate patterns across different departments that can be grouped into four distinct clusters. Lastly, the correlation of social media trends and adherence to social distancing measures is observed by the fact that a spike in the number of tweets indicating the stay-at-home orders was observed in November 2020 when the case incidence had already plateaued. Author summary As the COVID-19 pandemic continues to spread across Colombia, studies highlighting the intensity of the pandemic become imperative for appropriate resource allocation and informing public health policies. In this study we utilize mathematical models to infer the transmission dynamics of SARS-CoV-2 at the regional and national level as well as short-term forecast the COVID-19 epidemic trajectory. Moreover, we examine the geographic heterogeneity of the COVID-19 case incidence in Colombia along with the analysis of mobility and social media trends in relation to the observed COVID-19 case incidence in the country. The estimates of reproduction numbers at the national and regional level show sustained disease transmission as of May 30, 2021. Moreover, the 30-day ahead short-term forecasts for the most recent time-period (June 1-June 30, 2021) generated from the mathematical models needs to be interpreted with caution as the Richards model point towards a sustained decline in case incidence contrary to the GLM and sub-epidemic wave model. Nevertheless, the spatial analysis in Colombia shows distinct variations in incidence rate patterns across different departments that can be grouped into four distinct clusters. Lastly, the social media and mobility trends explain the occurrence of case resurgences over the time.

Late surges in COVID-19 cases and varying transmission potential partially due to public health policy changes in 5 Western states, March 10, 2020-January 10, 2021 (preprint)

Objective: This study investigates how the SARS-CoV-2 transmission potential varied in North Dakota, South Dakota, Montana, Wyoming, and Idaho from March 2020 through January 2021. Methods: Time-varying reproduction numbers, Rt, of a 7-day-sliding-window and of non-overlapping-windows between policy changes were estimated utilizing the instantaneous reproduction number method. Linear regression was performed to evaluate if per-capita cumulative case-count varied across counties with different population size. Results: The median 7-day-sliding-window Rt estimates across the studied region varied between 1 and 1.25 during September through November 2020. Between November 13 and 18, Rt was reduced by 14.71% (95% credible interval, CrI, [14.41%, 14.99%]) in North Dakota following a mask mandate; Idaho saw a 1.93% (95% CrI [1.87%, 1.99%]) reduction and Montana saw a 9.63% (95% CrI [9.26%, 9.98%]) reduction following the tightening of restrictions. High-population counties had higher per-capita cumulative case-count in North Dakota at four time points (June 30, August 31, October 31, and December 31, 2020). In Idaho, North Dakota, and South Dakota, there was a positive correlation between population size and per-capita weekly incident case-count, adjusted for calendar time and social vulnerability index variables. Conclusions: Rt decreased after mask mandate during the region's case-count spike suggested reduction in SARS-CoV-2 transmission.

Transmission dynamics of COVID-19 in Ghana and the impact of public health interventions (preprint)

The study characterized COVID-19 transmission in Ghana in 2020-21 by estimating the time-varying reproduction number (R t ) and exploring its association with various public health interventions at the national and regional levels. Ghana experienced four pandemic waves with epidemic peaks in July 2020, and January, August and December, 2021. The epidemic peak was the highest nationwide in December 2021 with R t ≥2. Throughout 2020-21, per-capita cumulative case count by region increased with population size. Mobility data suggested negative correlation between R t and staying home in the first 90 days of the pandemic. The relaxation of movement restrictions and religious gatherings were not associated with increased R t in the regions with lower case burdens. R t decreased from above 1 when schools reopened in January 2021 to below 1 after vaccination rollout in March 2021. Findings indicated most public health interventions were associated with R t reduction at the national and regional levels.

Pandemic fatigue impedes mitigation of COVID-19 in Hong Kong (preprint)

Community-wide social distancing has been a cornerstone of pandemic control prior to mass vaccinations. The extent to which pandemic fatigue is undermining adherence to such measures and accelerating transmission remains unclear. Using large-scale weekly telephone surveys and mobility data, we characterize the evolution of risk perception and protective behaviours in Hong Kong. We estimate a 1.5% to 5.5% reduction in population compliance with protective policies for the fourth wave (October 2020 to January 2021) versus the third wave (July to August 2020), inducing prolonged disease circulation with increased infections. Mathematical models incorporating population protective behaviours estimates that the fourth wave would have been 14% smaller if not for pandemic fatigue. Mitigating pandemic fatigue is essential in maintaining population protective behaviours for controlling COVID-19.

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 (preprint)

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 allows quantitative estimates of potential impact of policies such as facemask mandate.

SARS-CoV-2 Transmission in Alberta, British Columbia, and Ontario, Canada, January 1-July 6, 2020 (preprint)

ObjectiveTo investigate COVID-19 epidemiology in Alberta, British Columbia and Ontario, Canada. MethodsWe calculated the incidence rate ratio (January 1--July 6, 2020) between the 3 provinces, and estimated time-varying reproduction number, Rt, starting from March 1, using EpiEstim package in R. ResultsUsing British Columbia as a reference, the incidence rate ratios in Alberta and Ontario are 3.1 and 4.3 among females, and 3.4 and 4.0 among males. In Ontario, Rt fluctuated ~1 in March, reached values >1 in early and mid-April, then dropped <1 in late April and early May. Rt rose to ~1 in mid-May and then remained <1 from late May through early July. In British Columbia, Rt dropped <1 in early April, but it increased towards the end of April. Rt <1 in May while it fluctuated around 1.0 in June and early July. In Alberta, Rt > 1 in March; Rt dropped in early April and rose again in late April. In much of May, Rt <1, but Rt increases in early June and fluctuates ~1 since mid-June. ConclusionsRt wavering around 1.0 indicated that three provinces of Canada have managed to achieve limited onward transmission of SARS-CoV-2 as of early July 2020.

Transmission of SARS-CoV-2 in Georgia, USA, 2020 (preprint)

In 2020, SARS-CoV-2 impacted Georgia, USA. Georgia announced state-wide shelter-in-place on April 2 and partially lifted restrictions on April 27. We analyzed daily incidence of confirmed COVID-19 cases by reporting date, March 2-June 14, in Georgia, Metro Atlanta, and Dougherty County and estimate the time-varying reproduction number, Rt, using R package EpiEstim. The median Rt estimate in Georgia dropped from between 2 and 4 in mid-March, to <2 in late March, and around 1 from mid-April to mid-June. 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. In Spring 2020, SARS-CoV-2 transmission in Georgia declined likely because of social distancing measures. However, as restrictions were relaxed in late April, community transmission continued with Rt fluctuating around 1 across Georgia, Metro Atlanta, and Dougherty County as of mid-June.

If containment is not possible, how do we minimize mortality for COVID-19 and other emerging infectious disease outbreaks? (preprint)

If COVID-19 containment policies fail and social distancing measures cannot be sustained until vaccines becomes available, the next best approach is to use interventions that reduce mortality and prevent excess infections while allowing low-risk individuals to acquire immunity through natural infection until population level immunity is achieved. In such a situation, allowing some infections to occur in lower-risk groups might lead to an overall greater reduction in mortality than trying to protect everyone equally.

Transmission potential of COVID-19 in Iran (preprint)

We estimated the reproduction number of 2020 Iranian COVID-19 epidemic using two different methods: R0 was estimated at 4.4 (95% CI, 3.9, 4.9) (generalized growth model) and 3.50 (1.28, 8.14) (epidemic doubling time) (February 19 - March 1) while the effective R was estimated at 1.55 (1.06, 2.57) (March 6-19).

Epidemic doubling time of the 2019 novel coronavirus outbreak by province in mainland China (preprint)

COVID-19 epidemic doubling time by Chinese province was increasing from January 20 through February 9, 2020. The harmonic mean of the arithmetic mean doubling time estimates ranged from 1.4 (Hunan, 95% CI, 1.2-2.0) to 3.1 (Xinjiang, 95% CI, 2.1-4.8), with an estimate of 2.5 days (95% CI, 2.4-2.6) for Hubei.