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 of 68 cases of influenza illness per 100'000 inhabitants was crossed in week 2/2019.

Report on the activity of influenza viruses (NRCI data)

Week 16/2019
Last update 10.05.2019 (last update for the 2018/19 influenza season)
Next update on September 30, 2019
Since week 40/18, 1001 samples have been tested by the NRCI. Of these 401 were positive for influenza. During the 16th week of 2019, the NRCI received 11 samples; one sample was positive for influenza A. No influenza B was detected. (Table 1, Charts 1 and 2).
Table 1. Report of human influenza virus activity in the Sentinella population
Chart 1: Overview of the activity of human influenza 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. a) since week 40/18. b) during the week 16/19.
Of the 399 influenza A viruses tested since week 40/18, 176 were identified as A(H1N1)pdm09 strains and 216 as A(H3N2) strains; only 2 Influenza B viruses were detected. (Charts 1 and 3)
Chart 3: Number of negative and positive influenza A subtypes / B lineages since week 40/18

The majority of the A(H1N1)pdm09 viruses, we tested by hemagglutination inhibition, were well recognized by the reference antiserum produced against the corresponding vaccine strain (A/Michigan/45/2015). Of note, recent data from hemagglutination inhibition tests, performed with panels of human sera collected from individuals vaccinated with either triavalent or quadrivalent inactivated influenza vaccines, show a decrease in the recognition of A(H1N1)pdm09 viruses bearing the S183P mutation in hemagglutinin 1. The exact impact of this reduced recognition on vaccine efficiency is yet unknown. However, given the increasing number of recent viruses carrying the S183P substitution,  A/Brisbane/strain 02/2018 strain should replace  A/Michigan/45/2015 strain in the 2019-2020 Northern Hemisphere influenza vaccines.
All A(H3N2) viruses showed good reactivity with the reference antiserum raised against the corresponding vaccine strain (A/Singapore/INFIMH-160019/2016-cell) (Table 2). But as shown for A/H1N1pdm09 viruses, human serology data suggested that the vaccine efficiency against some of the circulating A(H3N2) viruses may be suboptimal.
Table 2. Antigenic proximity between NRCI-characterized viruses and vaccine strains recommended by the World Health Organization for the 2018/19 season
The 51 A (H1N1)pdm09 viruses analyzed by hemagglutinin sequencing were genetically related to vaccine strain A/ Michigan/45/2015 (clade 6B.1). Most of them carried the S183P substitution in the hemagglutinin. 41 of the A(H3N2) viruses genotyped belonged to the clade 3C.2a1b and were therefore genetically similar to the vaccine strain A/Singapore/INFIMH-16-0019/2016 (3C.2a1) (Table 3). Four A(H3N2) viruses were genetically related to group 3C.2a2 viruses corresponding to one of the recommended vaccine strains (A/Switzerland/8060/2017) for the 2019 southern hemisphere vaccines. Finally, 6 A(H3N2) viruses were genetically related to clade 3C.3a recent viruses (sub-clade: A/England/538/2018).
Table 3. Genetic Classification of Viruses Characterized at NRCI for the 2018/19 Season
The identification of resistance mutations to neuraminidase inhibitors (oseltamivir and zanamivir) is performed either by sequencing the neuraminidase gene or using a neuraminidase  inhibition assay (MUNANA test) or both. Of the 51 A (H1N1)pdm09 viruses and the 50 A(H3N2) viruses analyzed by sequencing, none had known mutations associated with a reduced inhibition by neuraminidase inhibitors. One non-Sentinella isolate originating from an oseltamivir treated patient presented the H275Y mutation associated with a highly reduced sensitivity to oseltamivir.
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 10.05.2019):
Influenza virus surveillance in Switzerland, Season 2017-2018: link
Valuable information on the vaccine and influenza vaccination in Switzerland is available on the website
Francis Crick Institute, Worldwide Influenza Centre :      
Centers for Disease Control and Prevention:


Last update : 16/05/2019