Introduction

Influenza viruses are negative-sense, single-stranded, segmented RNA viruses within the family Orthomyxoviridae. Influenza A and influenza B viruses cause seasonal epidemics of influenza, commonly known as “the flu”, a highly contagious respiratory disease characterized by symptoms such as fever, cough, sore throat, body aches, and fatigue but diarrhea and vomiting can also occur. Influenza A virus is widespread in water birds but also infects other birds and various mammals, including humans and pigs, while influenza B virus primarily infects humans. Influenza viruses mutate rapidly, leading to different strains and seasonal outbreaks. Both influenza A and influenza B viruses can cause seasonal outbreaks, but only influenza A is known to cause pandemics due to its broad host range and resulting potential for interspecies genetic reassortment. Globally the “seasonal flu” is estimated to be responsible for 290,000–645,000 deaths/year.

The data presented on this page is generated in the SLU (Swedish University of Agricultural Sciences) laboratories of SEEC (Swedish Environmental Epidemiology Center). The project is part of SciLifeLab’s Pandemic Laboratory Preparedness (PLP) Program, and is led by Anna J. Székely (Dep. of Aquatic Sciences and Assessment, SLU). Wastewater analyses are overseen by Anna J. Székely, Javier Vargas and Maja Malmberg (Virology unit of Department of Biomedical Science and Veterinary Public Health, SLU). This page pertains to the quantification of the levels of influenza A and B viruses in multiple cities across Sweden. This project currently has the broadest geographic coverage across Sweden; generating data for 43% of the Swedish population.

The data and visualisation on this page are usually updated weekly, typically on Mondays. Please note that the scores provided in the dataset and depicted in plot below are preliminary, so corrections and changes may occur. Data and information about the group on this dashboard are updated frequently, so please check back regularly to stay up to date.

Visualisations

Before we proceed with the visualizations of Influenza A and B virus levels in wastewater, it’s important to understand the methodologies used in this process. These methods ensure the accuracy and reliability of the data presented in the graphs. For a comprehensive understanding, please refer to the Methods section.

Important note: Please note that although the same methods are used for all cities shown on this tab, differences in the wastewater collection systems and populations of different cities might bias direct comparisons between cities.

Influenza A

Code used to produce plot: Script to produce plot.

Influenza B

Code used to produce plot: Script to produce plot.

Commentary from the research group

Reports from the research group

The group provide reports to summarise their latest findings. The latest report is available here (only available in Swedish).

Dataset

Contact: anna.szekely@slu.se and javier.vargas@slu.se

Download the data: Respiratory virus gene copy numbers normalised per PMMoV gene copy number.CSV file. Data are available for Influenza A from week 42 of 2022 and for Influenza B from week 12 of 2023; updated weekly.

How to cite the dataset:

Székely, A. J., Malmberg, M., Vargas, J., Mohamed, N., Dafalla, I., Petrini, F., Davies, L. (2023). Dataset of SARS-CoV-2, influenza A and influenza B virus content in wastewater samples from wastewater treatment plants in Sweden. https://doi.org/10.17044/scilifelab.14256317.

Methods

For most cities represented on this page, raw, untreated wastewater samples that are representative of a single day are collected by flow compensated samplers at the wastewater treatment plants (WWTP). Uppsala is the exception, where samples are collected daily, and then combined flow-proportionally into one composite weekly sample for the purpose of analyses.

The viral genomic material from the freshly collected samples is extracted by the direct capture method, using the Maxwell RSC Enviro TNA kit (Promega).

Absolute quantification of the copy numbers of the genome of influenza A and B viruses is performed by One-Step RT-qPCR using the Flu SC2 Multiplex Assay from the Centers for Disease Control and Prevention (CDC). To correct for variations in population size and wastewater flow, pepper mild mottle virus (PMMoV) is quantified using a modified version of the assay of Zhang et al. (2006). PMMoV is an abundant RNA virus in human faeces and serves as an estimator of human faecal content (Symonds et al., 2019).

The data in the graphs and datafile is presented in three different formats:

• PMMoV normalised Influenza content represents the ratio of the copy numbers of influenza and PMMoV measured by the influenza assay and PMMoV-assays, respectively, multiplied by 1000. As the influenza assay provides proxies for influenza virus content in the wastewater and PMMoV is a proxy of the faecal content (which is related to the contributing population), the ratio of the two can be considered to be a proxy for the prevalence of influenza infections in the population of the wastewater catchment area.
• Influenza genome copies concentration presents the influenza copy number concentration measured in the wastewater. These data is influenced by the setup of the different wastewater collection nsystems and is therefore not suitable for comparison betwwen sites. The virus concentrations in the wastewater are also influenced by the weather events that impact wastewater flow (e.g., heavy rain or snow melt).
• Influenza genome copies/day/inhabitant represents the daily virus amount estimated in the wastewater normalized for the number of inhabitants connected to the system. These data allows for comparison of different sites but some delays in the presentation of these data may occur compared to the other.

How to cite the method:

Isaksson, F., Lundy, L., Hedström, A., Székely, A. J., Mohamed, N. (2022). Evaluating the Use of Alternative Normalization Approaches on SARS-CoV-2 Concentrations in Wastewater: Experiences from Two Catchments in Northern Sweden. Environments, 9, 39. https://doi.org/10.3390/environments9030039.

Wastewater collection sites

SLU-SEEC collects and analyses samples for influenza A and B viruses from multiple areas. The below table shows details about each of these sites. The table lists the towns/cities monitored, wastewater treatment plants (WWTP) that samples were collected from, the number of people in the catchment area (Number of people), and the dates that monitoring by SLU-SEEC started and ended monitoring (Start and End date, respectively). Please note that ‘Start date’ refers to the first date of monitoring for influenza A, but that the start date for influenza B is always later. A value of ’null’ for the end date indicates that collection is ongoing. An asterisk (*) next to the number of people indicates that the value is a BOD-7 value (an estimate of the people connected), rather than the number of people physically connected to each WWTP. Two asterisks (**) next to the Town/City indicates that data is only available for influenza A, not influenza B. The information in the below table is available for download as an excel file.