class: center, middle, inverse, title-slide # Infectious Diseases Epidemiology ## Research from the population to the individual level ### ### 2021 - Oct --- class: middle, center ### Yang Ge #### University of Georgia #### Infectious Diseases Epidemiology #### Epidemiology (PhD), Biostatistics (MS) </br> </br> </br> <img src="uga cph logo.png" width="35%" style="display: block; margin: auto;" /> --- ### Research experience Infectious Diseases Epidemiology + Disease outbreak control, high-risk population protection and modeling: - Outbreak Epidemiology - Emerging and New Infectious Diseases - Infectious Disease Dynamics - The Immune System and Host Defense - Vaccines --- ### Projects Population level `\(\rightarrow\)` Individual level + Population level: prevention and control of emerging infectious diseases 1. <span style="color:grey">Screening for infectious diseases</span> 1. <span style="color:grey">Real-time estimation of COVID-19 mortality</span> 1. <span style="color:grey">Assessment of people at high risk of COVID-19 death</span> 1. <span style="color:blue">COVID-19 transmission dynamics and prevention and control strategies</span> 1. <span style="color:grey">Risk assessment of COVID-19 contacts</span> </br> + Individual level: Modeling responses after infection (Norovirus, influenza) 1. <span style="color:blue">Dose relationship between virus exposure and transmission ability</span> 1. <span style="color:grey">The relationship between virus exposure and the dose of antibodies</span> --- class: middle, inverse, center ## Population level: Prevention and control of emerging infectious diseases (COVID-19) --- ### COVID-19 transmission dynamics and prevention and control strategies <div class="figure" style="text-align: center"> <img src="npi1.png" alt="SEIR" width="80%" /> <p class="caption">SEIR</p> </div> --- ### COVID-19 transmission dynamics and prevention and control strategies Social contacts `$$cnt1_{ji} - (cnt1_{ji} - cnt2_{ji})\cdot w(t)$$` `$$w(t) = \frac{1}{1 + \exp(-a(t-b))}$$` <div class="figure" style="text-align: center"> <img src="wt.png" alt="y = w(t,a,b)" width="50%" /> <p class="caption">y = w(t,a,b)</p> </div> --- ### COVID-19 transmission dynamics and prevention and control strategies `\begin{aligned} \text{ODEs} & : \\ \lambda & = \sum\limits_{j=1}^{14}\beta \cdot \Big(cnt1_{ji} - (cnt1_{ji} - cnt2_{ji})\cdot w(t)\Big) \cdot (P_j + C_j) \\ \dot S_i & = - S_i \lambda \\ \dot E_i & = S_i \lambda - E/\gamma \\ \dot P_i & = (1-p)E/\gamma - P_i/\delta \\ \dot C_i & = P_i/\delta - C_i/\epsilon \\ \dot Q_{pi} & = pE/\gamma - Q_{pi}/\delta \\ \dot Q_{ci} & = Q_{pi}/\delta - Q_{ci}/\theta \\ \dot R_i & = C_i/\epsilon + Q_{ci}/\theta \end{aligned}` --- ### COVID-19 transmission dynamics and prevention and control strategies <img src="npi2.png" width="90%" style="display: block; margin: auto;" /> --- ### COVID-19 transmission dynamics and prevention and control strategies <img src="npi3.png" width="85%" style="display: block; margin: auto;" /> --- class: middle, inverse, center ## Individual level: post-infection response modeling </br> (Norovirus) --- ### Dose relationship between virus exposure and transmission ability <img src="noro_shed_raw.png" width="100%" style="display: block; margin: auto;" /> --- ### Dose relationship between virus exposure and transmission ability + Methods - LOD - Holder, 2011 `$$V_{(t)} = \frac{2 V_p}{\exp(\lambda_g(t - t_p)) + \exp(\lambda_d(t - t_p))}$$` - Mixed effect model $$ `\begin{aligned} V_p \sim \alpha + \gamma_{(id)} + \beta_{dose} X_{dose} \\ \lambda_g \sim \alpha + \gamma_{(id)} + \beta_{dose} X_{dose} \\ t_p \sim \alpha + \gamma_{(id)} + \beta_{dose} X_{dose} \\ \lambda_d \sim \alpha + \gamma_{(id)} + \beta_{dose} X_{dose} \\ \end{aligned}` $$ --- ### Dose relationship between virus exposure and transmission ability <img src="holder_curves_id.png" width="100%" style="display: block; margin: auto;" /> --- ### Dose relationship between virus exposure and transmission ability <img src="feces_vshed_mean_curve1.png" width="100%" style="display: block; margin: auto;" /> --- ### Dose relationship between virus exposure and transmission ability <img src="coef_plot.png" width="100%" style="display: block; margin: auto;" /> --- ### Publication and presentation - **Yang Ge**, et al.. (2021). Estimation of case-fatality rate in COVID-19 patients with hypertension and diabetes mellitus in the New York state: A preliminary report. *Epidemiology & Infection*, 149. - **Yang Ge**, et al.. (2020). Estimation of Coronavirus Disease Case-Fatality Risk in Real Time. *Emerging Infectious Diseases*, 26(8), 1922–1923. - **Yang Ge**, et al.. (2021). The impact of social distancing, contact tracing, and case isolation interventions to suppress the COVID-19 epidemic: A modeling study. *Epidemics*, 36, 100483–100483. - **Yang Ge**, et al.. (2021). COVID-19 Transmission Dynamics Among Close Contacts of Index Patients With COVID-19: A Population-Based Cohort Study in Zhejiang Province, China. *JAMA Internal Medicine*. - **Yang Ge**, et al.. (2021). “Impact of seasonal influenza vaccine dose on homologous and heterologous immunity”. 2nd Annual CIVICs Network Meeting. - **Yang Ge**, et al.. (2021). “A comparison of high‐dose and regular‐dose seasonal influenza vaccines toward eliciting homologous and heterologous immunity”. 18th Ecology and Evolution of Infectious Diseases meeting. - **Yang Ge**, et al.. (2021). “The association between norovirus infection outcomes and inoculum dose”. 2021 MIDAS Network Annual Meeting. --- class: middle, inverse, center # Thanks ### https://yangepi.github.io/ ### yang.ge@uga.edu