Identification of combinatorial host-specific signatures with a potential to affect host adaptation in influenza A H1N1 and H3N2 subtypes

Abstract

Background: The underlying strategies used by influenza A viruses (IAVs) to adapt to new hosts while crossing the species barrier are complex and yet to be understood completely. Several studies have been published identifying singular genomic signatures that indicate such a host switch. The complexity of the problem suggested that in addition to the singular signatures, there might be a combinatorial use of such genomic features, in nature, defining adaptation to hosts.

Results: We used computational rule-based modeling to identify combinatorial sets of interacting amino acid (aa) residues in 12 proteins of IAVs of H1N1 and H3N2 subtypes. We built highly accurate rule-based models for each protein that could differentiate between viral aa sequences coming from avian and human hosts. We found 68 host-specific combinations of aa residues, potentially associated to host adaptation on HA, M1, M2, NP, NS1, NEP, PA, PA-X, PB1 and PB2 proteins of the H1N1 subtype and 24 on M1, M2, NEP, PB1 and PB2 proteins of the H3N2 subtypes. In addition to these combinations, we found 132 novel singular aa signatures distributed among all proteins, including the newly discovered PA-X protein, of both subtypes. We showed that HA, NA, NP, NS1, NEP, PA-X and PA proteins of the H1N1 subtype carry H1N1-specific and HA, NA, PA-X, PA, PB1-F2 and PB1 of the H3N2 subtype carry H3N2-specific signatures. M1, M2, PB1-F2, PB1 and PB2 of H1N1 subtype, in addition to H1N1 signatures, also carry H3N2 signatures. Similarly M1, M2, NP, NS1, NEP and PB2 of H3N2 subtype were shown to carry both H3N2 and H1N1 host-specific signatures (HSSs).

Conclusions: To sum it up, we computationally constructed simple IF-THEN rule-based models that could distinguish between aa sequences of avian and human IAVs. From the rules we identified HSSs having a potential to affect the adaptation to specific hosts. The identification of combinatorial HSSs suggests that the process of adaptation of IAVs to a new host is more complex than previously suggested. The present study provides a basis for further detailed studies with the aim to elucidate the molecular mechanisms providing the foundation for the adaptation process.

Keywords: Combinatorial signatures; Host adaptation; Host-specific signatures; Influenza A virus; MCFS; Rosetta; Rough sets.

Fig. 1

Ciruvis diagrams of combinations from the rules of H1N1 models. Models having at least three combinations are shown. The outer circle shows the positions. The inner circle shows the position or positions to which the position of the outer circle is connected. The edges show these connections. The width and color of the edges are related to the connection score (low = yellow and thin, high = red and thick). The width of an outer position is the sum of all connections to it, scaled so that all positions together cover the whole circle [26]

Fig. 2

Ciruvis diagrams of combinations from the rules of H3N2 models. Models having at least three combinations are shown. The outer circle shows the positions. The inner circle shows the position or positions to which the position of the outer circle is connected. The edges show these connections. The width and color of the edges are related to the connection score (low = yellow and thin, high = red and thick). The width of an outer position is the sum of all connections to it, scaled so that all positions together cover the whole circle [26]

Fig. 3

Phylogeny of PB2 H3N2 protein of avian hosts annotated with top 5 avian rules form the PB2 H3N2 model. Each sequences is represented by its GeneBank accession. The violet nodes mark the sequences that supports rule 1,2,3,4 and 5, which are 91.4 % of the total sequences. Similarly the DarkViolet nodes mark the sequences that support rule 1, 2, 3 and 4 but lacks support for rule 5, which are 2.2 % of the total sequences. The nodes with a LightBlue background are the new, unseen sequences. The unmarked nodes do not support the top 5 rules, and were either supporting rules other than the top 5 or were not classified by the models

Fig. 4

Phylogenetic tree of the M1 protein from sequences of both subtypes and both hosts. Both the subtypes and the hosts are combined into a single tree. It can be seen that human sequences of both the subtypes form their own distinct clades. The avian sequences, on the other hand, fell into a single clade