All that glitters is not gold--founder effects complicate associations of flu mutations to disease severity

Abstract

Background: The recent 2009 (H1N1) influenza A pandemic saw a rapid spread of the virus to essentially all parts of the world. In the course of its evolution, the virus acquired many mutations, some of which have been investigated in the context of increased severity due to high occurrences in fatal cases. For example, statements such as: "42.9% of individuals who died from laboratory-confirmed cases of the pandemic (H1N1) were infected with the hemagglutinin (HA) Q310 H mutant virus." give the impression that HA-Q310 H would be highly dangerous or important, while careful consideration of all available data suggests that this is unlikely to be the case.

Results: We compare the mutations HA-Q310 H, PB2-K340N, HA-D239N and HA-D239G using whole genome phylogenetic trees, structural modeling in their 3 D context and complete epidemiological data from sequences to clinical outcomes. HA-Q310 H and PB2-K340N appear as isolated subtrees in the phylogenetic analysis pointing to founder effects which is consistent with their clustered temporal appearance as well as the lack of an immediate structural basis that could explain a change of phenotypes. Considering the prevailing viral genomic background, shared origin of samples (all from the city of Sao Paulo) and narrow temporal window (all death case samples within 1 month), it becomes clear that HA-Q310 H was actually a generally common mutation in the region at that time which could readily explain its increased occurrence among the few analyzed fatal cases without requiring necessarily an association with severity. In further support of this, we highlight 3 mild cases with the HA-Q310 H mutation.

Conclusions: We argue that claims of severity of any current and future flu mutation need to be critically considered in the light of phylogenetic, structural and detailed epidemiological data to distinguish increased occurrence due to possible founder effects rather than real phenotypic changes.

Figure 1

Whole coding genome maximum likelihood phylogenetic tree with viral strains labeled according to mutations of interest to distinguish independent and cluster occurrences.

Figure 2

Temporal global appearance of mutations of interest shown as 28 days sliding window average of % sequences with the respective mutation.

Figure 3

Positions of discussed mutations in viral protein structures of hemagglutinin (HA) and polymerase basic protein 2 (PB2). Only HA-D239G and HA-D239N appear in a position that can be rationalized to directly alter the phenotypic properties of the virus.

Figure 4

Average monthly percentage of strains with the HA-Q310 H mutation compared between Brazil and the whole world. Clearly, HA-Q310 H appeared more frequently in Brazil in the months July and August which was the exact time frame of the analyzed death cases.