Introduction

Surveillance of a viral pathogen is essential for minimising the impacts of that pathogen on society. Without surveillance, it is difficult to understand whether a given pathogen occurs in the area, whether new strains have appeared, or if an outbreak may be likely.

Throughout the pandemic and until present day, the section for Clinical Microbiology and Hospital Hygiene at Uppsala University Hospital have conducted surveillance for SARS-CoV-2 in Uppsala. To do this, they performed whole genome sequencing on samples from SARS-CoV-2 positive patients in the Uppsala region. Throughout the COVID-19 pandemic, they sequenced over 12,000 samples from Uppsala.

This dashboard includes two visualisations of the data from the section for Clinical Microbiology and Hospital Hygiene at Uppsala University Hospital. It also contains contact information for those behind the work, information about the code used to generate the graphs, and relevant publications. The data on this dashboard will be updated approximately monthly.

SARS-CoV-2 Sequence Visualisations

The sequences are presented according to their World Health Organisation (WHO) label (a greek letter) and/or their Pango lineage. The Pango lineage is determined using Pangolin, Nextclade, and an in-house annotation-based mutation analysis workflow.

Recent sequences with Pango lineage

In this subsection, there are two plots each showing the percentage of sequences that belonged to a given lineage in each week. Each plot represents a different level of granularity in the classification of lineages. The first shows the most granular level, and data is available from October 2023. The second has a slightly lower level of granularity and shows data from January 2023.

In both graphs, the date is allocated as the Monday of that week. The plots include multiple dynamic features that can be used to focus on certain subsets of the data.

Use the buttons on the top left of each plot to focus either on data from the Last 16 weeks or the whole time period (either Since October or January 2023). Use the ’Deselect all linages’ button on the right hand sides to clear data from all lineages from the graphs. It is possible to then view only certain lineages by clicking on them in the legend. You can then use the ’Select all lineages’ button to return to the view showing data from all lineages. The graphs also have many other interactive features. For example, it is possible to click and drag to focus on a certain part of the data. When you hover over the graph, further options will appear in the top right to e.g. zoom, download as a .png file, or reset the axes to the original view.

Code used to produce plots: Graph and data preparation script.

Code used to produce plots: Graph and data preparation script.

All sequences with WHO label/Pango lineage)

The below plot shows the percentage of sequences from each week belonged to a given lineage. The date is allocated as the Monday of the week that the samples were collected. The plot shows all of the data collected since 2021.

Use the ’Deselect all lineages’ button to clear data from all lineages from the graph. It is possible to then view only certain lineages by clicking on them in the legend. You can use the ’Select all lineages’ button to show data from all lineages. The graph also has many other interactive features. For example, it is possible to click and drag to focus on a certain part of the graph. When you hover over the graph, options will appear in the top right to e.g. zoom, download as a .png file, or reset the axes to the original view.

Code used to produce plots: Graph and data preparation script.

Commentary from the research group

Contact

Jonathan Haars, laboratory technician and PhD student at Uppsala University Hospital and Uppsala University. (jonathan.haars@akademiska.se)

René Kaden, microbiologist and researcher at Uppsala University Hospital and Uppsala University. (rene.kaden@akademiska.se)

Publications

Cumlin, T., Karlsson, I., Haars, J., Rosengren, M., Lennerstrand, J., Pimushyna, M., Feuk, L., Ladenvall, C., Kaden, R. (2024). SARS-CoV-2 to Global Preparedness: A Graphical Interface for Standardised High-Throughput Bioinformatics Analysis in Pandemic Scenarios and Surveillance of Drug Resistance. Int. J. Mol. Sci., 25, 6645. DOI: 10.3390/ijms25126645.

Haars, J., Palanisamy, N., Wallin, F., Mölling, P., Lindh, J., Sundqvist, M., Ellström, P., Kaden, R., Lennerstrand, J. (2023). Prevalence of SARS-CoV-2 Omicron Sublineages and Spike Protein Mutations Conferring Resistance against Monoclonal Antibodies in a Swedish Cohort during 2022–2023. Microorganisms, 11, 2417. DOI: 10.3390/microorganisms11102417.

Mannsverk, S., Bergholm, J., Palanisamy, N., Ellström, P., Kaden, R., Lindh, J., Lennerstrand, J. (2022). SARS-CoV-2 variants of concern and spike protein mutational dynamics in a Swedish cohort during 2021, studied by Nanopore sequencing. Virology Journal, 19, 164. DOI: 10.1186/s12985-022-01896-x.

Martinell, M., Andersson, T., Mannsverk, S., Bergholm, J., Ellström, P., Hill, A., Lindh, J., Kaden, R. (2022). In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. Viruses, 14, 504. DOI: 10.3390/v14030504.