Surveillance of European Domestic Pig Populations Identifies an Emerging Reservoir of Potentially Zoonotic Swine Influenza A Viruses

Abstract

Swine influenza A viruses (swIAVs) can play a crucial role in the generation of new human pandemic viruses. In this study, in-depth passive surveillance comprising nearly 2,500 European swine holdings and more than 18,000 individual samples identified a year-round presence of up to four major swIAV lineages on more than 50% of farms surveilled. Phylogenetic analyses show that intensive reassortment with human pandemic A(H1N1)/2009 (H1pdm) virus produced an expanding and novel repertoire of at least 31 distinct swIAV genotypes and 12 distinct hemagglutinin/neuraminidase combinations with largely unknown consequences for virulence and host tropism. Several viral isolates were resistant to the human antiviral MxA protein, a prerequisite for zoonotic transmission and stable introduction into human populations. A pronounced antigenic variation was noted in swIAV, and several H1pdm lineages antigenically distinct from current seasonal human H1pdm co-circulate in swine. Thus, European swine populations represent reservoirs for emerging IAV strains with zoonotic and, possibly, pre-pandemic potential. ll Resource

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

“…H1 av N1 was predominant in France between 2000 and 2018 (66.5%), as in most European countries except the United Kingdom and Denmark, according to the European studies conducted between 2010 and 2017 [12,13,21]. The H1 av Ny strains identified in pigs in France clustered mainly in the HA clade 1C.2.1, described in Europe and Russia [7].…”

“…In Denmark, the H1N1pdm and the local H1 av N2 viruses were also more frequently detected than the H1 av N1 virus in recent years [13,15]. In Germany and Italy, the frequency of reassortant viruses harboring at least one H1N1pdm segment has increased continuously from 2009 [16][17][18][19][20][21].…”

Zoonotic infection with swine A/H1avN1 influenza virus in a child, Germany, June 2020

“…Antibodies against influenza A/ sw/H1 av N1 viruses in the human population are rare [27,28]. On the other hand, sera of human volunteers collected 3-7 weeks after vaccination with the annual 2017/18 vaccine all reflected antibodies against influenza A/sw/H1 av N1 virus at varying microneutralisation titres and none was negative [15]. Although the family members of the zoonotic case had not been vaccinated, they may have been exposed to human and swine influenza A viruses before, potentially resulting in pre-existing immunity which might impair transmission of influenza A/sw/H1 av N1 influenza virus.…”

“…The genetic diversity of influenza A viruses in the European pig population is increasing [15][16][17]. A/sw/ H1 av N1 are the predominant swine influenza viruses in Germany [18].…”

“…Among them, the two most prevalent lineages are H1 av N1 1C.2.2 and H1 av N1 1C.2.1. Other swine influenza viruses include H1 hu N2 and H3N2 viruses as well as H1 pdm N1 and H1 pdm N2 viruses [15][16][17][18]. An increasing number of reassortments between these viruses augment the diversity of influenza virus populations in swine.…”