Swine flu: how a new virus has taken over other genotypes in France
In 2020, a new genotype of swine influenza virus, responsible for swine flu, emerged in France and quickly replaced certain previous strains. Scientists at ANSES’s Ploufragan-Plouzané-Niort Laboratory conducted a study to understand how this rapid change could have occurred. The emergence of a new genotype poses a risk to the health of pigs and humans alike.
Serious clinical signs in pigs
The main genotypes of swine influenza viruses affecting pigs in France had not changed for 30 years when, in 2020, a new genotype, called H1avN2#E (referenced as H1N2 from clade 1C.2.4 in the international nomenclature), spread on pig farms within a period of just a few months. "We noticed this new genotype because it was associated with an increase in outbreaks and severe cases of flu in pigs, characterised by high fever, respiratory problems, coughing and also abortions in sows”, explains Gaëlle Simon, head of the Pig Immunology and Virology Unit and the National Reference Laboratory for swine influenza at ANSES.
A rapidly spreading virus
First detected in Brittany, the virus quickly spread throughout mainland France. Within just a few months, it became the predominant genotype on pig farms. In 2020, 661 outbreaks of swine flu were reported, which was far more than the 400 observed on average in previous years. To better understand this rapid emergence, scientists at ANSES analysed samples collected between January 2019 and December 2022. They had mainly been collected through Résavip, the national surveillance network for swine influenza virus coordinated by the French Agricultural Cooperation (La Coopération Agricole), in which ANSES participates.
The analysis of the viruses collected confirmed that they were genetically and antigenically different from those previously present in France. “This difference meant that they were able to evade the pre-existing immunity of pigs, resulting from previous infections or vaccination” explains the researcher.
Comparison with the other known swine influenza viruses showed that this genotype probably originated in Denmark. It most likely arrived in France through imports of infected animals, whether directly or via other European countries.
Stepping up measures to prevent the introduction of new viruses
In addition to the impact on the pig sector, the emergence of a new variant may also increase the risk of transmission to other animal species and to humans. “The H1avN2#E virus has caused several outbreaks of infection on turkey farms since 2020 and was responsible for a serious human case of swine flu in 2021. Human exposure to swine influenza viruses increases the risk of reassortment with a human flu virus, which could lead to the emergence of a virus that is better adapted to humans. As pigs are also susceptible to human and avian influenza viruses, these animals can end up being mixing vessels for viruses. The last flu pandemic, which occurred in 2009, was caused by a swine influenza virus” underlines the scientist.
Since 2022, the H1avN2#E virus has established itself on French pig farms, where it remains predominant. However, its impact is now less severe, indicating that animals have developed immunity to this genotype.
The analysis of this introduction highlighted the urgent need to consolidate biosecurity measures to prevent the importation and spread of new viruses. The study’s authors emphasise the importance of strengthening quarantine measures when introducing new animals onto farms and encouraging the surveillance of pigs infected with swine influenza virus, even though swine flu is not a notifiable disease.