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. 2021 Jun 10;13(6):1116.
doi: 10.3390/v13061116.

Field and Molecular Epidemiology: How Viral Sequencing Changed Transmission Inferences in the First Portuguese SARS-CoV-2 Infection Cluster

Nicole Pedro  1   2   3 , Veronica Fernandes  1   2 , Bruno Cavadas  1   2 , João Tiago Guimarães  4   5   6 , Henrique Barros  5   6 , Margarida Tavares  4   5   6 , Luisa Pereira  1   2
Affiliations

Field and Molecular Epidemiology: How Viral Sequencing Changed Transmission Inferences in the First Portuguese SARS-CoV-2 Infection Cluster

Nicole Pedro et al. Viruses. .

Abstract

Field epidemiology and viral sequencing provide a comprehensive characterization of transmission chains and allow a better identification of superspreading events. However, very few examples have been presented to date during the COVID-19 pandemic. We studied the first COVID-19 cluster detected in Portugal (59 individuals involved amongst extended family and work environments), following the return of four related individuals from work trips to Italy. The first patient to introduce the virus would be misidentified following the traditional field inquiry alone, as shown by the viral sequencing in isolates from 23 individuals. The results also pointed out family, and not work environment, as the primary mode of transmission.

Keywords: COVID-19; epidemiological survey; family versus work environment; infection cluster; viral sequencing.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Representation of the studied SARS-CoV-2 in the 59-individual cluster in the diverse environments (at home, factory, two distinct family gatherings and external events). Date of diagnosis is represented in the lateral bar. The code of colours mean: in yellow individuals infected by the 20B+A3660G+T11194C viral haplotype; in gold the 20B haplotype; in blue the 20A+G24077T haplotype; in grey the symptomatic individuals, not sequenced; in green the not-infected/asymptomatic; the red outline indicates the individuals who went to Italy. Besides the family and factory, other close contacts were established based on the epidemiological survey: friends of P1 (P35–P36–P37); family of the girlfriend of P22 (P33–P34); family of a friend of P21 (P31–P32); other family members of P29 (P38–P39).
Figure 2
Figure 2
Phylogenetic tree of the SARS-CoV-2 whole sequences isolated from the samples analysed here and other sequences from GenBank.
Figure 3
Figure 3
The geographic distance between individuals infected by the SARS-CoV-2 20A+G24077T lineage, including the 18 belonging to the studied infectious cluster (in red) and 11 other individuals (in grey) out of 150 Covid-19 Northern Portuguese cases identified during the same period (till 16 March 2020). The size of the circle is proportional to the effective size observed at a specific point, while lines represent the linear geographic distance from the bulk of the infectious cluster.
See this image and copyright information in PMC

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