The highly pathogenic H7N3 avian influenza strain from July 2012 in Mexico acquired an extended cleavage site through recombination with host 28S rRNA

Abstract

Background: A characteristic difference between highly and non-highly pathogenic avian influenza strains is the presence of an extended, often multibasic, cleavage motif insertion in the hemagglutinin protein. Such motif is found in H7N3 strains from chicken farm outbreaks in 2012 in Mexico.

Methods: Through phylogenetic, sequence and structural analysis, we try to shed light on the role, prevalence, likelihood of appearance and origin of the inserted cleavage motifs in these H7N3 avian influenza strains.

Results: The H7N3 avian influenza strain which caused outbreaks in chicken farms in June/July 2012 in Mexico has a new extended cleavage site which is the likely reason for its high pathogenicity in these birds. This cleavage site appears to have been naturally acquired and was not present in the closest low pathogenic precursors. Structural modeling shows that insertion of a productive cleavage site is quite flexible to accept insertions of different length and with sequences from different possible origins. Different from recent cleavage site insertions, the origin of the insert here is not from the viral genome but from host 28S ribosomal RNA (rRNA) instead. This is a novelty for a natural acquisition as a similar insertion has so far only been observed in a laboratory strain before. Given the abundance of viral and host RNA in infected cells, the acquisition of a pathogenicity-enhancing extended cleavage site through a similar route by other low-pathogenic avian strains in future does not seem unlikely. Important for surveillance of these H7N3 strains, the structural sites known to enhance mammalian airborne transmission are dominated by the characteristic avian residues and the risk of human to human transmission should currently be low but should be monitored for future changes accordingly.

Conclusions: This highly pathogenic H7N3 avian influenza strain acquired a novel extended cleavage site which likely originated from recombination with 28S rRNA from the avian host. Notably, this new virus can infect humans but currently lacks critical host receptor adaptations that would facilitate human to human transmission.

Figure 1

Frequency of occurrence of H7N3 strains with and without extended cleavage site. 257 HAs from H7N3 strains since the year 2000 were downloaded from GISAID and their absolute numbers per year shown as bar plot (values on left axis). The orange curve shows the percentage of sequences with extended cleavage site as defined by a consensus motif of R-x-x-R (where the final R is the normal cleavage site without insertion).

Figure 2

Phylogenetic relationship between 205 H7N3 full-length HA nucleotide sequences collected from 2000 till 2012. Strains with extended cleavage sites representing high pathogenic avian influenza (HPAI) strains as reported in the literature were separated by geographical regions and different years of outbreak and were highlighted with 5 different colors indicated in the legend. The recent 2012 Mexican chicken farm outbreak arose from a cluster of originally low pathogenic strains and therefore independently acquired the extended cleavage site which likely switched the strain to highly pathogenic.

Figure 3

Structure of the Influenza A hemagglutinin monomer showing a representative extended cleavage site. A) The crystal structure representation of an uncleaved hemagglutinin HA0 precursor from subtype H3 (PDBID: 1HA0 [6], cleavage region green) overlaid with a structure of a cleaved HA1/HA2 heterodimer from a highly pathogenic H7 virus (PDBID: 4DJ6 [40], cleavage region blue) and an energy-minimized average representation of the cleavage loop for the highly pathogenic H7 with the new insertion modelled in YASARA Structure (yellow). Cleavage site indicated with dashed box at the stem region. B) Detailed structure of hemagglutinin cleavage site. Uncleaved loop (PDBID: 1HA0, green) shown with cleaved ends (PDBID: 4DJ6, blue) Glu317 of HA1 and Gly1 of HA2 connected with pink dots representative of the cleaved loop fragment. Basic arginine residues at positions 323, 326, 328 and 329 in the loop model are indicated.