Unraveling the hurdles of a large COVID-19 epidemiological investigation by viral genomics

•Increasing dimension of the clusters triggered the misidentification of links.•Densely populated settings mislead the identification of epidemiological links.•Epidemiological investigation had a sensitivity of 80% to detect transmission chains. COVID-19 local outbreak response relies on subjective...

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Bibliographic Details
Published in:The Journal of infection 2022-07, Vol.85 (1), p.64-74
Main Authors: Sá, Regina, Isidro, Joana, Borges, Vítor, Duarte, Sílvia, Vieira, Luís, Gomes, João P, Tedim, Sofia, Matias, Judite, Leite, Andreia
Format: Article
Language:English
Subjects:
Disease outbreaks
Epidemics
Genomics
Public health
SARS-CoV-2
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Summary:•Increasing dimension of the clusters triggered the misidentification of links.•Densely populated settings mislead the identification of epidemiological links.•Epidemiological investigation had a sensitivity of 80% to detect transmission chains. COVID-19 local outbreak response relies on subjective information to reconstruct transmission chains. We assessed the concordance between epidemiologically linked cases and viral genetic profiles, in the Baixo Vouga Region (Portugal), from March to June 2020. A total of 1925 COVID-19 cases were identified, with 1143 being assigned to 154 epiclusters. Viral genomic data was available for 128 cases. Public health authorities identified two large epiclusters (280 and 101 cases each) with a central role on the spread of the disease. Still, the genomic data revealed that each epicluster included two distinct SARS-CoV-2 genetic profiles and thus more than one transmission network. We were able to show that the initial transmission dynamics reconstruction was most likely accurate, but the increasing dimension of the epiclusters and its extension to densely populated settings (healthcare and nursing home settings) triggered the misidentification of links. Genomics was also key to resolve some sporadic cases and misidentified direction of transmission. The epidemiological investigation showed a sensitivity of 70%–86% to detect transmission chains. This study contributes to the understanding of the hurdles and caveats associated with the epidemiological investigation of hundreds of community cases in the context of a massive outbreak caused by a highly transmissible and new respiratory virus. [Display omitted]
ISSN:0163-4453
1532-2742
1532-2742
DOI:10.1016/j.jinf.2022.05.013