Emergence of a Highly Pathogenic Avian Influenza Virus from a Low-Pathogenic Progenitor

Abstract

Avian influenza (AI) viruses of the H7 subtype have the potential to evolve into highly pathogenic (HP) viruses that represent a major economic problem for the poultry industry and a threat to global health. However, the emergence of HPAI viruses from low-pathogenic (LPAI) progenitor viruses currently is poorly understood. To investigate the origin and evolution of one of the most important avian influenza epidemics described in Europe, we investigated the evolutionary and spatial dynamics of the entire genome of 109 H7N1 (46 LPAI and 63 HPAI) viruses collected during Italian H7N1 outbreaks between March 1999 and February 2001. Phylogenetic analysis revealed that the LPAI and HPAI epidemics shared a single ancestor, that the HPAI strains evolved from the LPAI viruses in the absence of reassortment, and that there was a parallel emergence of mutations among HPAI and later LPAI lineages. Notably, an ultradeep-sequencing analysis demonstrated that some of the amino acid changes characterizing the HPAI virus cluster were already present with low frequency within several individual viral populations from the beginning of the LPAI H7N1 epidemic. A Bayesian phylogeographic analysis revealed stronger spatial structure during the LPAI outbreak, reflecting the more rapid spread of the virus following the emergence of HPAI. The data generated in this study provide the most complete evolutionary and phylogeographic analysis of epidemiologically intertwined high-and low-pathogenicity viruses undertaken to date and highlight the importance of implementing prompt eradication measures against LPAI to prevent the appearance of viruses with fitness advantages and unpredictable pathogenic properties. IMPORTANCEThe Italian H7 AI epidemic of 1999 to 2001 was one of the most important AI outbreaks described in Europe. H7 viruses have the ability to evolve into HP forms from LP precursors, although the mechanisms underlying this evolutionary transition are only poorly understood. We combined epidemiological information, whole-genome sequence data, and ultradeep sequencing approaches to provide the most complete characterization of the evolution of HPAI from LPAI viruses undertaken to date. Our analysis revealed that the LPAI viruses were the direct ancestors of the HPAI strains and identified low-frequency minority variants with HPAI mutations that were present in the LPAI samples. Spatial analysis provided key information for the design of effective control strategies for AI at both local and global scales. Overall, this work highlights the importance of implementing rapid eradication measures to prevent the emergence of novel influenza viruses with severe pathogenic properties.

First field evidence of the evolution from a non-virulent HPR0 to a virulent HPR-deleted infectious salmon anaemia virus

“…This is consistent with the hypothesis that these two mutations, the HPR deletion in the HE gene and the Q 266 L substitution in the F gene, represent necessary mutational steps for the transition to virulence in ISAV [18,22]. This is also in agreement with observations in avian influenza (AI) where highly pathogenic AI viruses (HPAIV) arise from low-pathogenic AI viruses (LPAIV) by mutations of specific virulence markers and where the acquisition and increase in virulence is a stepwise process [36][37][38][39][40][41]. Although the role of other proteins than HE and F in ISAV pathogenesis so far remains elusive, further mutations of other proteins are expected to increase virulence [11,22,42,43] as demonstrated in other members of the orthomyxovirus family, e.g.…”

“…The authors identified low-frequency HPR-deleted variants in HPR0-positive screening samples from healthy fish as well as lowfrequency HPR0 variants in subsequent HPR-deleted samples from ISA diseased fish [53]. Similar findings of low-frequency HPAIV in LPAIV and vice versa have been documented in samples from a natural outbreak of AI [40]. Therefore, it cannot be excluded that the FO/121/14 variant existed as a low-frequency minority variant in FO/07/12- [14].…”

Prevalence of the C-terminal truncations of NS1 in avian influenza A viruses and effect on virulence and replication of a highly pathogenic H7N1 virus in chickens

“…16 Genetic changes accompanying shift of the Italian LPAIV to HPAIV H7N1 have been well-defined. 17,18 Among other mutations, transformation of LPAIV to HPAIV has been also accompanied with alterations in NS1, where the contribution of these mutations in virulence remained indeterminate. 14 Truncation of 6 amino acids (aa) at the C-terminal end ( 225 RVESEV 230 ) of NS1 in the Italian HPAIV H7N1 vs. LPAIV is of special interest.…”

Next generation sequencing technologies: Tool to study avian virus diversity

“…NGS approaches have been approved for use in routine diagnostics to monitor the genomic diversity of AIV, early emergences and transmission of these viruses from waterfowl to domestic poultry (Croville et al, 2012). Based on ultra-deep sequencing approaches, evidence of emerging HPAIV from a LPAIV progenitor (H7N1) has been provided (Monne et al, 2014). USUV and WNV are members of Flavivirus genus belonging to the Japanese encephalitis antigenic complex and are phylogenetically closely related.…”