#18,725
China's EA H1N1 `G4' swine influenza virus leads the CDC's IRAT list of riskiest zoonotic influenza viruses (see CDC Selected Swine-Variant EA H1N1 Virus For The Top Of Their IRAT List), but for the past 5+ years we've been closely following the evolution of another `avian-like' 1C genotype of swine influenza A virus (swIAV) in Europe.The ECDC maintains a Swine influenza Factsheet, which describes the introduction and spread of influenza viruses in European pigs where they describe this (H1N1/H1N2) lineage:
The first significant outbreak of an avian A(H1N1) influenza virus lineage occurred in 1979 and led to the establishment of an ‘avian-like’ A(H1N1) virus lineage in European pigs. This virus, referred to as Eurasian avian-like 1C lineage, rapidly established itself in Europe and has continued to circulate in swine until the present day.
In 2020 (see Genetic and Antigenic Evolution of European Swine Influenza A Viruses of HA-1C (Avian-Like) and HA-1B (Human-Like) Lineages in France from 2000 to 2018) we saw a noticeable shift from H1N1 to H1N2 in France and other parts of Europe.
We also began to see sporadic spillovers of related H1N2v 1C virus to humans (see Eurosurveillance: Human Infections with Eurasian Avian-like Swine Influenza Virus Detected by Coincidence Via Routine Respiratory Surveillance Systems, the Netherlands, 2020 to 2023).
Five weeks ago, in Emerg. Microbes & Inf.: Eurasian 1C Swine Influenza A Virus Exhibits High Pandemic Risk Traits, we looked at a cautionary report which found that the Eurasian 1C swine influenza virus has significant pandemic potential.
Abstract
Recent surveillance has identified an expansion of swine H1 1C influenza viruses in Eurasian swine. Since 2010, at least twenty-one spillover events of 1C virus into humans have been detected and three of these occurred from July to December of 2023.
Pandemic risk assessment of H1 1C influenza virus revealed that individuals born after 1950 had limited cross-reactive antibodies, confirming that they are antigenically novel viruses. The 1C virus exhibited phenotypic signatures similar to the 2009 pandemic H1N1 virus, including human receptor preference, productive replication in human airway cells, and robust environmental stability.
Efficient inter- and intraspecies airborne transmission using the swine and ferret models was observed, including efficient airborne transmission to ferrets with pre-existing human seasonal H1N1 immunity. Together our data suggest H1 1C influenza virus pose relatively high pandemic risk.
Five months ago the Journal Virus Evolution carried a report from ANSES (the French Agency for Food, Environmental and Occupational Health & Safety) describing the rise of H1N2 1C in France:
Major change in swine influenza virus diversity in France owing to emergence and widespread dissemination of a newly introduced H1N2 1C genotype in 2020
Gautier Richard , Séverine Hervé , Amélie Chastagner , Stéphane Quéguiner , Véronique Beven , Edouard Hirchaud , Nicolas Barbier , Stéphane Gorin , Yannick Blanchard , Gaëlle Simon
While one might quibble over the term `new', earlier this month ANSES published the following update on their website, which includes quotes from the lead author of the above report. I'll have a postscript after the break.
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.
The last line of this report is a stark reminder how much of our surveillance for zoonotic diseases is passive, and dependent more on luck than skill. While veterinarians may submit respiratory samples to testing labs in response to clinical signs, those signs are often absent in IAV infected swine.
Our USDA’s Influenza A Virus in Swine (IAV-S) Surveillance Program is voluntary, and we've seen reluctance on the part of pig farmers to have their herds tested (see Swine Flu: Don’t Test, Don’t Tell), despite more than 500 spillover infections in humans in the United States over the past 15 years.
We've seen the similar hesitance from Dairy farmers over HPAI H5, Last summer the USDA set up a voluntary dairy herd testing program, and as of the last update just 100 herds have been enrolled. That's 1 in 360 herds in the country, or just 0.27%.
While we might go years - or even decades - before any of these viral contenders finds the right genetic combination to spark the next pandemic, it could just as easily happen tomorrow.
But at least with our current surveillance system, our leaders can honestly say `they never saw it coming'.
