Outbreak report of SARS-CoV-2 infection by airborne transmission: Epidemiologic and molecular evidence

Abstract

Introduction: It has been shown that the transmission of SARS-CoV-2 occurs mainly by air, and the risk of infection is greater in closed spaces.

Objective: To describe the epidemiology, virology and molecular characterization of a COVID-19 outbreak at a closed vaccination point during the third wave of SARS-CoV-2 in Colombia.

Materials and methods: Diagnostic tests, interviews, sampling, cell cultures and viral sequencing were carried out, the latter being molecular characterization and lineage identification.

Results: Seven workers were positive for SARS-CoV-2; among these, 3 samples were analyzed, plus an additional sample belonging to the mother of the presumed index case; all samples were identified with lineage B.1.625, with a maximum of 2 nucleotides difference between them.

Conclusions: Variant B.1.625 was identified as the cause of the COVID-19 outbreak, and a co-worker was also identified as the index case. Unexpectedly, attending a vaccination day became a risk factor for acquiring the infection.

Keywords: SARS-CoV-2; COVID-19; disease outbreaks; vaccination; Colombia.

Figure 1. Schematic diagram of vaccination appointment location. The distribution of the study population during the vaccination appointment, the distance between rows and chairs, and the location of the index and source person are presented in this figure. The rectangles correspond to each one of the people present in the room: health personnel highlighted in red, coordinator of vaccination appointment in yellow, index case in green, co-workers who were infected in this outbreak in blue and other co-workers in brown. The double arrows indicate the distance between each attendee and the dotted arrows indicate the contagion link between index case and those affected.

Figure 2. Contagion timeline of the indoor vaccination appointment outbreak in Medellín, Colombia. The timeline describes the most important events associated with the viral outbreak, the data was collected through interviews as described in the materials and methods section.

Figure 3. Phylogenetic tree of the sequences obtained in this study and other reference sequences. The different variants, lineages and cases were colored according to the key in the left panel. The four sequences associated with the outbreak are indicated as green stars. The sequence B.1 corresponds to the first isolation of SARS-CoV-2 in Colombia . The size of the gray circles indicates the strength of the branch support according to the upper right panel. The boxes on the outside of the circle indicate the country of origin according to the colors in the lower right panel. The analysis was performed by the maximum likelihood method in the IQ-Tree server.

Figure 4. Frequency of the reported genomes of the alpha, gamma and mu variants and the B.1.625 lineage in Antioquia from February to September 2021. Frequency is based on genomes reported on the GISAID platform, the time frame corresponds to the first and last reported date of lineage B.1.625, and the frequencies of alpha, gamma and mu variants were added as they are the most reported during the time frame. The dotted line indicates the date of the outbreak.