Genome mutations in novel human H7N9 influenza virus

We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiFlu™ Database on which this analysis is based. A list of the sequences, their submitting labs and GISAID links is provided on this page.


This page presents the analysis of mutations in the virus genomes occurred before and during the emergence of human H7N9 in China. 

Segment 1 - PB2 gene

Mutation: E627K

PB2_minus627_17.phyml.tree.png

Maximum likelihood tree of available PB2 outbreak sequences (as of 2013-05-01) omitting the 627 codon to avoid biasing the tree if this has convergent mutations.

Now there are many more sequences from the outbreak, a clearer pattern of the E627K mutation in PB2 appears. The 627K is only found in human cases and even then not all of them. This would appear to mean that these mutations are occuring de novo in each human case. This may be due to the fact that these are severe, hospitalized cases which can be associated with a longer infection period giving the virus time to adapt to the human host. This would also suggest this mutation is not involved in the increased human-susceptability that seems to be associated with this virus. All the human cases with 627K involve a GAG -> AAG codon mutation (i.e., a G to A transition in the first codon position) but as both glutamic acid and lysine are both encoded by only 2 codons, this is the only available path between these amino acids.

Previous notes from Tommy Lam (see revisions for full details).

In summary, there are a number of distinctive mutations. (1) A short deletion (69-73aa) in stalk region of NA protein. (2) 627 E > K mutation in PB2 sequence, indicative of mammalian adaptation. (3) Quite a few amino acid substitutions in NP protein. Interestingly, a recent paper (Bogs et al. 2011) suggests PB2 627 mutation depends on the origin of NP protein.   

Points to note - whether these substitutions on the 'pre-emergence' branch did actually occur before the human H7N9 lineage relies on the assumption that the same mutation has not independently occurred during the infections (or tranmissions to) of the H7N9 patients. Even this assumption holds, it is expected that the most recent common ancestor (e.g. red dot) carry these mutations; Addressing whether these mutations occurred in the source animal population or just during the cross-species infection in the human requires the further understanding of the number of such inter-species transmissions that have led to this H7N9 emergence, as well as the genome sequences of the direct virus precursors from the animal population.           

It is especially controversial as to whether PB2 627 E > K mutation occurred before or after (or during) jumping to human. Previous experiments have demonstrated this mutation could be volatile during cell passage. It is also noteworthy that most of the 627K mutations in H5N1 have occurred in mammalian hosts (but not solely - some bird H5N1 viruses do carry that mutation).   

 

 

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Comments

Jesse Bloom's picture

The two newest sequences, A/Zhejiang/1/2013 and A/Zhejiang/2/2013, have possible human-adaptation polymorphisms in NP. Both of these sequences have nucleotide ambiguity codes (such as R or K) at a few sites. These sites include the codons for amino acids M352 and V353. Recent work has shown that mutation V353I increases the resistance of pandemic H1N1 to the human anti-viral restriction factor MxA (http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1003279). With regards to the ambiguity codes in the two most recent human H7N9 NP sequences, I suppose it is possible to make a couple of interpretations:

1) During the course of infection both of these isolates have independently acquired polymorphisms that might increase MxA resistance.

2) The virus acquired polymorphism in the first individual, which was then maintained during transmission to the second individual.

3) There was some consistent technical problem with the sequencing reactions used to obtain both of these sequences, such that they both gave the same ambiguous nucleotide pairs at several sites.

Just to point out that I in my early comment, just when sequences from chicken became available, pointed out that the PB2 E627K appeared to happen de novo in the humans and may be linked to the NP sequence as shown for H5N1 in mice by the FLI folks (Bogs in al.). It is correct that the varian of H5N1 may be seen in birds, but according to the FLI work this may not be selected for nor directly against, so when first introoduced, most likely in a mammalian host, and transmitted back to birds it may not necessarily revert. That is at least how I read the data based on H5N1.