Like all influenza viruses (also called influenza), those responsible for influenza in swine are constantly evolving. Pigs can be infected by swine influenza viruses but also by human or avian influenza viruses. It can therefore become an intermediate host for the transmission of avian influenza viruses to humans, but also serve as a “crucible”, where, thanks to co-infections, new so-called reassortant viruses can emerge (reassortant viruses have genes from influenza viruses of different origins). Thus, a large number of different strains have been isolated over the years through surveillance carried out in pig farms. Overall, viruses of three subtypes (H1N1, H3N2 and H1N2) circulate in the pig population, but many genetic lineages (or genotypes) are distinguished within each of these subtypes, depending on the origin of each of the viral genes.
Monitoring pig health to anticipate pandemics in humans
Type A swine influenza viruses (or swIAV for swine influenza A virus) have zoonotic potential, and can therefore be transmitted to humans. In 2009, the H1N1pdm09 virus, which caused a pandemic in humans, was the result of a reassortment of several swIAVs. Its emergence recalled the need to monitor and study influenza viruses in pigs, both from an animal health and human health point of view. This virus then spread to many pig populations around the world from 2009. Through co-infections with other swIAVs, the H1N1pdm09 virus has been responsible for the emergence of new reassortant viruses, including some have also disseminated in some pig populations. Among them, a few have been responsible for cases of human infections.
ANSES, reference laboratory for swine flu
The Agency’s Ploufragan-Plouzané-Niort laboratory has been the national reference laboratory for swine influenza (NRL IP) since August 2009. This NRL is hosted by the Swine Virology Immunology Unit (VIP). As such, the VIP Unit develops, validates and controls diagnostic tools for detecting and identifying influenza A virus subtypes and lines in pigs. It coordinates the network of veterinary laboratories approved for the molecular diagnosis of these infections. In particular, it verifies the maintenance of their aptitude by organizing inter-laboratory tests. It provides reference reagents (which make it possible to detect viruses or antibodies directed against these viruses) and offers technical support to characterize the identified viruses more precisely.
Active monitoring of virus strains present in France
Although it has a significant economic and health impact for the pig industry, and it can affect humans, swine flu is not a regulated disease and there are few formalized and long-lasting surveillance systems. Knowledge of the viruses circulating in a territory varies according to the country, and is often scattered or incomplete. In France, the Swine Virology Immunology (VIP/LNR IP) and Health and Well-Being Epidemiology (EPISABE) units of the Ploufragan-Plouzané-Niort laboratory have been actively contributing to the surveillance of swine influenza viruses since 2005. This is was amplified from 2011, with the establishment of the national monitoring network ” Résavip “. The surveillance carried out by this network makes it possible to describe the genetic diversity and geographical distribution of swine influenza viruses.
In addition, ANSES develops or contributes to specific surveillance programs on certain farms, or even certain regions, depending on particular epidemiological contexts. Occasional surveys are also carried out on wild boars. Prospective work also concerns influenza viruses of types B, C and D, which are much less pathogenic or less frequent in pigs than influenza viruses of type A.
An activity that takes place internationally
The Agency is represented within the international network OFF, a joint OIE-FAO network for animal influenza viruses, which allows exchanges on viruses circulating beyond European borders. More specifically, the VIP Unit is an active member of the “Swine Influenza Virus Technical Group” of this network. The results exchanged make it possible to inform the World Health Organization (WHO) of the emergence of swine influenza viruses which could present pandemic risks. The objective is to select strains for the development of new vaccines when necessary.
Research activities to better understand the virus, its transmission factors and its effects on pigs
The Agency is carrying out several research projects on swine flu:
Monitoring the genetic and antigenic evolution of swine influenza viruses
The viruses identified in France within the framework of epidemiological surveillance are the subject of in-depth studies at the level of their genes and their antigens (the antigens being viral molecules recognized by the immune system of the infected animal). These studies aim to improve knowledge on the evolution of swIAVs in France, their diversity and the contexts of emergence of new virus lines. The in-depth analysis of the genetic sequences of viruses aims to identify molecular determinants of virulence as well as characteristics that could contribute to facilitating the transmission of porcine viruses to other animal species, and in particular to humans. These properties are studied via bioinformatics analyses, in cell culture, and when necessary on animals.
This knowledge contributes to supporting the expertise, and makes it possible to inform the French authorities of any new emergence at risk, both for animal health and human health.
Study the dynamics of swine influenza viruses and their pathogenicity
Influenza infection in pigs generally results in mild clinical manifestations and only affects some of the pigs on the same farm. However, the infection can take a more severe and almost general turn, depending on the virulence of the strain involved and the breeding practices. Concomitant infections with other pathogens affecting the respiratory system can lead to complications. Other unfavorable conditions, still poorly defined, could also influence the severity of the disease.
Moreover, while influenza infection is usually responsible for a temporary (episodic) flu syndrome, a recurrent form of the disease has become more pronounced in farms in recent years. These repeated influenza episodes lead to a destabilization of infected farms and could promote co-infections by several strains of influenza virus, and therefore viral reassortment. Research work is carried out on farms (observational epidemiological studies) and in silico (epidemiological modelling), in order to better understand the determinants of virus persistence in pig farms
Studying the role of influenza viruses in respiratory syndromes in pigs
The Agency is studying the dynamics of strains in farming and the factors associated with the different severities and epidemiological forms of the disease. Experimental and modeling work focuses on the characteristics of the transmission of swine influenza viruses from one animal to another. The modes of airborne transmission are also studied, taking into account the different ventilation conditions in farms. swIAV infections are sometimes associated with infections by other pathogens, bacteria or viruses. This double infection can lead to complications for the health of the animal. Experimental studies are carried out on pigs with a high health status (pigs free of specified pathogenic organisms, SPF), in order to study the mechanisms underlying the synergy or, on the contrary, the interference between these pathogens of the respiratory system of the pig. Together, the results of epidemiological surveys, experimental research work and modeling work make it possible to better understand the disease and to propose prevention and control measures to veterinarians and breeders.
The research work carried out on swine influenza viruses at the Agency is shared within the Influenza Virus Research Group, created by the CNRS on 1is January 2020 and named RésaFLU. Its mission is to promote an interdisciplinary network, which brings together French teams working on the influenza viruses responsible for influenza in humans and animals. Its scientific axes relate to the understanding of the mechanisms of emergence of new influenza viruses, the identification of the determining factors of the pathophysiology of influenza virus infections, or the development of new preventive and therapeutic strategies.