Genetic Adaptation of Influenza A Viruses in Domestic Animals and Their Potential Role in Interspecies Transmission: A Literature Review

Abstract

In December 2011, the European Food Safety Authority awarded a Grant for the implementation of the FLURISK project. The main objective of FLURISK was the development of an epidemiological and virological evidence-based influenza risk assessment framework (IRAF) to assess influenza A virus strains circulating in the animal population according to their potential to cross the species barrier and cause infections in humans. With the purpose of gathering virological data to include in the IRAF, a literature review was conducted and key findings are presented here. Several adaptive traits have been identified in influenza viruses infecting domestic animals and a significance of these adaptations for the emergence of zoonotic influenza, such as shift in receptor preference and mutations in the replication proteins, has been hypothesized. Nonetheless, and despite several decades of research, a comprehensive understanding of the conditions that facilitate interspecies transmission is still lacking. This has been hampered by the intrinsic difficulties of the subject and the complexity of correlating environmental, viral and host factors. Finding the most suitable and feasible way of investigating these factors in laboratory settings represents another challenge. The majority of the studies identified through this review focus on only a subset of species, subtypes and genes, such as influenza in avian species and avian influenza viruses adapting to humans, especially in the context of highly pathogenic avian influenza H5N1. Further research applying a holistic approach and investigating the broader influenza genetic spectrum is urgently needed in the field of genetic adaptation of influenza A viruses.

Protective Measures for Humans against Avian Influenza A(H5N8) Outbreaks in 22 European Union/European Economic Area Countries and Israel, 2016–17

“…Although rapid sequencing of these viruses might identify markers for transmissibility to humans, uncertainty regarding the risk to human health might persist until sufficient data for human exposures and outcomes have been collected. International organizations have developed tools to assess such risk: these tools include the FluRisk project of the European Food Safety Authority ( 11 ), the Tool for Influenza Pandemic Risk Assessment of the World Health Organization ( 12 ), and the Influenza Risk Assessment Tool of the US Centers for Disease Control and Prevention ( 13 ). However, how these risks are managed locally might vary.…”

H1N1 Swine Influenza Viruses Differ from Avian Precursors by a Higher pH Optimum of Membrane Fusion

“…These viruses occasionally infect other avian and mammalian species, such as aquatic and terrestrial poultry, sea mammals, horses, and pigs. On rare occasions they adapt to and establish stable lineages in new species (2,3). Documented transmissions of avian and swine influenza viruses to men are typically restricted to individual, often severe, cases of infection (for recent reviews, see references 4 and 5).…”

Assessment of low pathogenic avian influenza virus transmission via raw poultry meat and raw table eggs

“…In general, avian influenza viruses lack sufficient adaptation for the efficient infection of, replication in and excretion from human respiratory tissue (Munoz et al, 2016). Avian influenza viruses which cause infection in humans are generally those which have an affinity for human cell surface receptors, and this is driven by several different amino acid substitutions which are involved in the polymerase activity and receptor binding necessary for replication and transmission of avian influenza viruses in mammals (Hill et al, 2015;Xiang et al, 2018).…”