Surveillance of Seasonal Influenza Viruses in Switzerland

In Switzerland, epidemiological and virological surveillance of the influenza virus (flu) is provided by the Sentinella reporting system (1986) and the mandatory reporting system. A third system, targeting the monitoring of influenza in hospitalized patients, has also been in the testing phase since 2018.
Of the primary care physicians (general practitioners, internists and pediatricians) participating in the Sentinella reporting system, around a half address nasopharyngeal swabs taken from some of their patients with influenza-like illness (ILI)(fever >38°C, and coughing or sore throat in the absence of another diagnosis) to the National Reference Center of Influenza (NRCI) during each influenza season (week 40 from one year to week 16 of the following year). The latter performs the diagnosis for influenza A and B. For samples that are positive for influenza A and/or B, a detailed characterization of the influenza viruses present in the sample will be performed (subtyping, antigenic proximity to vaccine strains, genotyping and identification of  mutations associated with antiviral resistance).
On this page, you will find a report of the number of samples tested by the NRCI; as well as the results relative to viral characterization.
We invite you to consult the website of the Federal Office of Public Health, if you are interested in an overview of the current situation relative to the epidemiology of influenza-like illness cases in Switzerland. The annual epidemic threshold is of 69 cases of influenza illness per 100'000 inhabitants. It was exceeded on week 02/2020.

Report on the activity of influenza viruses (NRCI data)

Week 13/2020
Last update 3 April 2020 
During week 13/2020,  7 samples were tested by the NRCI. None was positive for influenza but 2 were positiv for SARS-CoV-2. Since week 40/19, a total of 1095 samples have been tested for influenza. Since week 12/2020, a total of 114 samples have been tested for SARS-CoV-2.(Table 1 and charts 1-3).
Table 1. Report of influenza and SARS-CoV-2 viruses activity in the Sentinella population 

Chart 1: Overview of the activity of human influenza and SARS-CoV-2 viruses in the Sentinella population and incidence (‰) of influenza-like illness in the Swiss population
Chart 2: Percent positive and negative samples for influenza A and B. Since week 40/19 (left). During the week 13/2020 (right).
Of the 487 influenza  viruses tested since week 40/19, 205 were identified as A(H1N1)pdm09 strains and 97 as A (H3N2) strains; 178 Influenza B virus were also detected among which 177 bolonged to the Victoria-lineage (Charts 1 and 3). 
Chart 3: Number of negative and positive influenza A subtypes / B lineages since week 40/19
Influenza viruses characterisation (last updated 13.03.2020)
The 26 A(H1N1) pdm09 viruses tested are well recognized by the reference antiserum produced against the vaccine strain A/ Brisbane/02/2018. Similarly, 3 out of 4 A(H3N2) viruses tested  show reactivity with the reference antiserum against the vaccine strain A/ Kansas/14/2017 (Table 2).
The 20 influenza B viruses tested are weakly recognized by the antiserum produced against the vaccine strain B/Colorado/06/2017. All viruses are better recognized by the antiserum against B/Washington/02/2019 strain.
The antigenic proximity is determined on the basis of the haemagglutination inhibition test. The viruses and antisera (ferret) reference are provided by the Worldwide Influenza Center in London (Francis Crick Institute). Yamagata B strain is not present in trivalent influenza vaccines.
Table 2. Antigenic proximity between CNRI-characterized viruses and vaccine strains recommended by the World Health Organization for the 2019/2020 season

Twenty-two  A(H1N1)pdm09 viruses analyzed by hemagglutinin sequencing are genetically related to the strain A/Switzerland/3847/2019 (clade 6B.1A5A). Two are genetically related to the strain A/Switzerland/3330/2018 (clade 6B.1A5B). Although the A(H1N1)pdm09 viruses from clade 6B.1A5 are different from that of the vaccine virus A/Brisbane/02/2018 (clade 6B.1A1), it is expected that immunity induced by the vaccine strain will be effective against circulating viruses (based on hemagglutination inhibition tests).

Four genotyped A(H3N2) viruses belong to two subgroups of clade 3C.2a1b (Table 3). They are genetically distinct from the vaccine strain A/Kansas/14/2017 (clade 3C.3a) and may be less well covered by the human immune responses induced by the vaccine strain. Five viruses belong the vaccine strain A/Kansas/14/2017 clade (3C.3a).

The 18 influenza B viruses tested belong to clade 1A(del3)B characterized by a triple deletion (1A (del 162-164)). No virus containing a double deletion like the vaccine virus B/Colorado/ 06/2017 (1A (del 162-163)) has been detected in Switzerland so far. 

Table 3. Genetic Classification of Viruses Characterized at NCRI for the 2019/2020 Season  


None of the viruses tested for antiviral resistance exibited mutations in the neuraminidase gene associated with a reduced sencitivity to neuraminidase inhibitors.

Reduced influenza vaccine efficacy against influenza A(H3N2) viruses has been demonstrated during several consecutive seasons. This could be explained to some extent by:
Influenza A(H3N2) viruses are more variable than influenza A(H1N1)pdm09 and B viruses. Each modification/mutation in a virus is likely to cause differences between the vaccine strain and the influenza viruses circulating during the season. These are antigenic modifications; and for yet unknown reasons, they are more frequent in influenza A(H3N2) viruses than in the other two strains. From the time the influenza vaccine strain is recommended to the actual vaccination event (more than 6 months delay), A(H3N2) viruses are more likely to have undergone mutations, which may result in an antigenic drift potentialy impacting the vaccine effectiveness.
The main mode of production of vaccine strains remains their amplification in chicken eggs. But while all influenza viruses undergo mutations induced by this mode of production, changes in influenza A(H3N2) viruses have an increased tendency to result in antigenic modifications than those of A(H1N1)pdm09 and B viruses. Other production methods exist but are still not widely used.
Contact :
For further information on the activity of human influenza viruses in Switzerland and on the different tests and methods used to characterize them contact Ana Rita Gonçalves, 022 372 40 81 ou
Useful links (accessed 03.04.2020):
Valuable information on the vaccine and influenza vaccination in Switzerland is available on the website
Centers for Disease Control and Prevention:


Last update : 03/04/2020