Large-scale inveLarge-scale investigation of a COVID-19 high-incidence region of Portugal : an outbreak analysis using genomic epidemiologystigation of a COVID-19 high-incidence region of Portugal : an outbreak analysis using genomic epidemiology
Year: 2021
Type: dissertation
Study design: Observational Study
Abstract: ABSTRACT - Background Local outbreak response is highly dependent on the epidemiologic investigation (EI), which relies on subjective information to reconstruct transmission chains. This study aims to describe COVID-19 transmission chains in the light of viral genomics. Additionally, it aims to estimate the sensitivity of the EI. Methods A combination of epidemiological and viral genomic data was performed to understand COVID-19 transmission chains, in Baixo Vouga, a region with a municipality in sanitary cordon and presenting one of the highest incidence rates during the first epidemic wave. Data previously collected by the public health authorities was used to reconstruct epidemiological clusters (epiclusters). The genome sequences were retrieved from the nationwide SARS-CoV-2 collection. Sensitivity was determined as the proportion of cases in each epicluster that belonged to the same main viral genetic profile. A metanalysis of epicluster-specific sensitivity was conducted. Findings A total of 1925 confirmed cases of COVID-19 were identified, from 8th March to 30th June 2020. From these, 128 cases had viral genomic data available. Two large epiclusters were identified (280 and 101 cases), presenting a central role on the spread of the disease. Genomics was also key to resolve some sporadic cases and misidentified direction of transmission. The sensitivity of epidemiological investigation to detect transmission chains was 80% (95% confidence interval: 70%-86%). Interpretation Epidemiological reconstruction of the transmission chains presented high sensitivity. However, high incidence and closed settings led to misidentification of links. This study contributes to understand the hurdles and caveats associated with the EI in the context of a massive outbreak of COVID-19.
Author: Sá, Ana Regina Serra
Language: English
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W7048447099