Friday, April 12, 2013

Eurosurveillance: Genetic Analysis Of Novel H7N9 Virus


The H7N9 Reassortment – Credit Eurosurveillance


# 7118


Less than two weeks after the announcement from China that they had isolated a novel H7N9 virus from a handful of patients, we are seeing a flood of scientific analyses describing the virus and its impact.


A few examples from the past two days include:


NEJM On The H7N9 Virus
OIE: H7N9 Represents An `Exceptional Situation’
Eurosurveillance: The Implications Of H7N9 For Europe


Adding to this growing knowledge base is an exploration of the genetic makeup of this viral hybrid, produced  by researchers primarily based in Japan. 


Attached to this research you’ll find such familiar names as Yoshihiro Kawaoka and Masato Tashiro. 


Eurosurveillance, Volume 18, Issue 15, 11 April 2013

Rapid communications

Genetic analysis of novel avian A(H7N9) influenza viruses isolated from patients in China, February to April 2013

T Kageyama, S Fujisaki, E Takashita, H Xu, S Yamada, Y Uchida, G Neumann, T Saito, Y Kawaoka, M Tashiro


Novel influenza viruses of the H7N9 subtype have infected 33 and killed nine people in China as of 10 April 2013. Their haemagglutinin (HA) and neuraminidase genes probably originated from Eurasian avian influenza viruses; the remaining genes are closely related to avian H9N2 influenza viruses. Several characteristic amino acid changes in HA and the PB2 RNA polymerase subunit probably facilitate binding to human-type receptors and efficient replication in mammals, respectively, highlighting the pandemic potential of the novel viruses.


The abstract above is both brief and simplified, but be assured you’ll find ample details in the main body of the paper, which is well worth reading in its entirety.


Briefly, researchers found several worrying genetic changes, including the discovery of mammalian-adapting mutations in the RBS (receptor-binding site) of the surface HA protein. 


The authors describe their findings:


The amino acid sequence of the receptor-binding site (RBS) of HA determines preference for human- or avian-type receptors.


At this site, A/Shanghai1/2013 encodes an S138A mutation (H3 numbering; Figure 4, Table 3), whereas A/Shanghai/2/2013, A/Anhui/1/2013, the two avian isolates, and the virus from the environmental sample encode G186V and Q226L mutations; any of these three mutations could increase the binding of avian H5 and H7 viruses to human-type receptors [12-14].


The finding of mammalian-adapting mutations in the RBS of these novel viruses is cause for concern. The A/Hangzhou/1/2013 isolate encodes isoleucine at position 226, which is found in seasonal influenza A(H3N2) viruses.


In addition, all seven influenza A(H7N9) viruses possess a T160A substitution (H3 numbering; Table 3) in HA, which is found in recently circulating H7 viruses; this mutation leads to the loss of an N-glycosylation site at position 158 (H3 numbering; position 149 in H7 numbering), which results in increased virus binding to human-type receptors [15].


We’ve discussed receptor binding often in the past (see Study: Dual Receptor Binding H5N1 Viruses In China & PLoS: Human-Type H5N1 Receptor Binding In Egypt) but to review:



Flu Virus binding to Receptor Cells – Credit CDC


Human adapted influenza viruses have an RBS - Receptor Binding Site (the area of its genetic sequence that allows it to attach to, and infect, host cells) that – like a key slipping into a padlock -`fit’ the receptor cells commonly found in the human upper respiratory tract; the alpha 2,6 receptor cell.


Avian adapted flu viruses, like the H5N1 virus, bind preferentially to the alpha 2,3 receptor cells found in the gastrointestinal tract of birds.


While there are some alpha 2,3 cells deep in the lungs of humans, for an influenza to be successful in a human host, most researchers believe it needs to a able to bind to the a 2,6 receptor cell.


Another item generating concern is finding the (E627K) substitution in the (PB2) protein; The swapping out of the amino acid Glutamic acid (E) at position 627 for Lysine (K).


Glutamic acid (E) at this position is a hallmark of avian influenza viruses, and is believed to make the virus better adapted to replicate at the higher temperatures commonly found in birds (41C).


Human flu viruses normally have Lysine (K) at position 627.  That mutation supposedly makes the virus better adapted to replicate at the lower temperatures (roughly 33C) normally found in the upper human respiratory tract.


Again, the authors write:


Lysine at position 627 of the polymerase PB2 protein is essential for the efficient replication of avian influenza viruses in mammals [16] and has been detected in highly pathogenic avian influenza A(H5N1) viruses and in the influenza A(H7N7) virus isolated from the fatal case in the Netherlands in 2003 [17]. PB2-627K is rare among avian H9N2 PB2 proteins (i.e. it has been found in only five of 827 isolates). In keeping with this finding, the avian and environmental influenza A(H7N9) viruses analysed here encode PB2-627E. By contrast, all four human H7N9 viruses analysed here encode PB2-627K.


Antiviral susceptibility can often be inferred from various genetic changes, although this is an imprecise science. All 7 viruses showed signs of resistance to the older Amantadine-type ion channel inhibitors, while one had changes often associated with oseltamivir (Tamiflu ®) resistance. 


The authors write:


Based on the sequences of their NA proteins, all H7N9 viruses analysed here, with the exception of A/Shanghai/1/2013, should be sensitive to neuraminidase inhibitors (Table 3).


However, the R294K mutation in the NA protein of A/Shanghai/1/2013 is known to confer resistance to NA inhibitors in N2 and N9 subtype viruses [20], and is therefore of great concern.



There is a good deal more to be gleaned from this paper, but in conclusion the authors write:


In conclusion, we here present a biological evaluation of the sequences of the avian influenza A(H7N9) viruses that caused fatal human infections in China.


These viruses possess several characteristic features of mammalian influenza viruses, which are likely to contribute to their ability to infect humans and raise concerns regarding their pandemic potential.