UNCOVERING THE EPIDEMIOLOGY OF COVID-19: JUST-IN-TIME SCIENCE IN A PANDEMIC
Embargo until
2021-12-01
Date
2020-10-30
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Johns Hopkins University
Abstract
COVID-19 pandemic has led to over 30 million reported cases 10 month after it was first detected. This dissertation presents results generated as the pandemic emerged to better understand the epidemiology of the disease, it’s clinical trajectory and the effectiveness of testing and screening strategies.
In Shenzhen, China, contact tracing reduced time from symptom onset to isolation by 1.9 days from 4.6 day. Household contacts (OR=6.3) were at higher risk of infection than other close contacts. The household secondary attack rate was 11.2%, and children were as likely to be infected as adults (infection rate 7.4% in children <10 years vs population average of 6·6%). The observed reproductive number (R) was 0·4, with a mean serial interval of 6.3 days.
We quantified the timing of and overall time patients diagnosed with COVID-19 in Shenzhen spend in each clinical stage, including mild cases. Using machine learning algorithms for analysis of survival data, we show that characteristics observed near symptom onset with and without lab results are highly predictive of clinical progression of COVID-19.
Serological testing using total Ab ELISA was conducted among PCR-negative patients in Shenzhen 2-15 weeks after initial testing. The adjusted seropositivity rate among these PCR-negative close-contacts was 4.1%, significantly higher than among residents without known exposure to cases (0.0%). PCR-positive cases were 8.0 times more likely to report symptoms than the PCR-negative individuals who were seropositive, but otherwise similar. RT-PCR missed 36% of infected close-contacts, and false negative rates appear to be highly dependent on stage of infection.
Using data from a household-based population serosurvey in Geneva, Switzerland, we estimated that the cumulative risk of infection from extra-household sources was 5.1% over the course of the first wave of the epidemic. The chance of being infected by a single infected household member was 17.3%, and the risk increased with age. Seropositive household members not reporting symptoms had 0.27 times the odds of infecting another household member and were responsible for 20.0% of all household infections.
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Keywords
COVID-19, SARS-CoV-2, transmission, surveillance, RT-PCR, serology