Study: Adaptation Of H6N1 From Avian To Human Receptor-Binding

Flu Virus binding to Receptor Cells – Credit CDC

 

# 10,019

 

A couple of days ago in EID Journal: Seropositivity For H6 Influenza Viruses In China, we looked at a study that found a low, but significant level of antibodies – particularly among live bird handlers – to the avian H6 virus in China.  This study was published not quite two years after the Taiwan CDC Reported the Human Infection With Avian H6N1.

 

The H6N1 virus has been around for decades in Chinese poultry - it possesses similar internal genes to H5N1 and H9N2 (cite 2002 J Virol  Molecular evolution of H6 influenza viruses from poultry in Southeastern China by Webster, Webby, Shortridge  et al.) - and it has been speculated that it may have been involved in the genesis of H5N1 in Hong Kong in 1997.

 

While viewed with some suspicion by virologists 15 years ago, once H5N1 emerged into the limelight again in 2003, H6N1 as a possible human threat receded back into the shadows.  It was still studied as an avian threat, of course (see 2007’s Establishment of influenza A virus (H6N1) in minor poultry species in southern China), as it continued to spread (and reassort) across Southeast Asia.

 

The discovery of the virus in a 20 year-old woman with pneumonia in Taiwan two years ago has, understandably, renewed interest in this viral contender, and we’ve seen a flurry of new studies as a result.

 

• Last March, in Avian Flu Antibody Survey In Poultry Workers – Taiwan 2012, we looked at a study that looked for antibodies to H5N2, H6N1, H7N3 and H7N9 among hundreds of subjects, and while they found a fairly low incidence of antibodies overall (max 2.99% for H5N2 in poultry vendors), only found one positive for H6N1.
• Also last March, in TSRI: H10N8 and H6N1 Bind Poorly To Human Receptor Cells - while ostensibly good news – researchers warned that both of these viruses bind differently than other avian viruses we’ve seen, and that our understanding of how these viruses mutate isn’t complete enough to warrant complacency.
• And in late 2013, the Taiwan CDC: Epidemiological Analysis Of Human H6N1 Infection, warned that a (emphasis mine)  “unique clade of H6N1 viruses with a G228S substitution of haemagglutinin have circulated persistently in poultry in Taiwan. These viruses continue to evolve and accumulate changes, increasing the potential risk of human-to-human transmission.”

 

While one (known) human infection pales against the hundreds of H5N1 and H7N9 infections we’ve see over the past decade – it is one more than we’ve seen from H5N8, H5N2, and H5N3 - and it hints as to what is possible down the road.  

 

To this mix we add a new study, published in the EMBO Journal, that finds recent and worrisome changes in the receptor binding characteristics of the H6N1 virus.  Changes they maintain have steadily moved the virus towards an affinity towards human receptor cells instead of avian receptor cells.

 

Note: The G228S substitution mentioned in the Taiwan CDC report above plays heavily in this study.

 

First the abstract, then I’ll return with a bit more:

 

Adaptation of avian influenza A (H6N1) virus from avian to human receptor-binding preference

Fei Wang^1,2,†, Jianxun Qi^2,3,†, Yuhai Bi^2,3, Wei Zhang^2,3, Min Wang^1,2, Baorong Zhang^4,5, Ming Wang¹, Jinhua Liu¹, Jinghua Yan^2,3, Yi Shi^2,3,4 and George F Gao^{1,2,3,4,6,7,*}

Article first published online: 4 MAY 2015

Abstract

The receptor-binding specificity of influenza A viruses is a major determinant for the host tropism of the virus, which enables interspecies transmission. In 2013, the first human case of infection with avian influenza A (H6N1) virus was reported in Taiwan. To gather evidence concerning the epidemic potential of H6 subtype viruses, we performed comprehensive analysis of receptor-binding properties of Taiwan-isolated H6 HAs from 1972 to 2013. We propose that the receptor-binding properties of Taiwan-isolated H6 HAs have undergone three major stages: initially avian receptor-binding preference, secondarily obtaining human receptor-binding capacity, and recently human receptor-binding preference, which has been confirmed by receptor-binding assessment of three representative virus isolates. Mutagenesis work revealed that E190V and G228S substitutions are important to acquire the human receptor-binding capacity, and the P186L substitution could reduce the binding to avian receptor. Further structural analysis revealed how the P186L substitution in the receptor-binding site of HA determines the receptor-binding preference change. We conclude that the human-infecting H6N1 evolved into a human receptor preference.

Synopsis

Historical analysis of influenza H6N1 isolates from 1972 until 2013, when the first human infection occurred, reveals amino acid changes that change receptor binding preference from birds to humans and therefore virus ability to cross the species barrier.

• Human-infecting avian influenza H6N1 has gained human receptor binding preference.
• H6N1 HA has changed binding preference in at least two steps.
• First, E190V and G228S substitutions provide human receptor binding ability.
• Subsequently, P186L substitution reduces avian receptor binding, and provides human receptor binding preference.

 

For an influenza virus to infect a host, the virus must bind (attach) itself to the surface of a cell.  To do that 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 host’s receptor cells.

 

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 α2-6 receptor cell found in the upper airway (trachea).

 

Although a preferential binding to human receptor cells is considered perhaps the biggest obstacle for an avian virus to successfully jump species – it isn’t the only one.

 

Another major requirement is the ability to replicate efficiently at the lower temperatures found in the upper respiratory system of humans, as opposed to the hotter gastrointestinal system of birds.  There are other factors – some we know about, others we don’t – that must come together properly to allow an avian virus to jump species successfully.

 

All of which means that even with an improved receptor binding ability, the H6N1 virus may be far from being ready for prime time.

 

But it does mean that H6N1 is legitimately a virus worth watching, both for further evolutionary changes, and for how it behaves in poultry and in humans.

TSRI: H10N8 and H6N1 Bind Poorly To Human Receptor Cells

Flu Virus binding to Receptor Cells – Credit CDC

 

# 9818

 

Considering the recent spate of worrisome H5 and H7N9 bird flu news, I’m happy to report that at least two recently emerged avian viruses haven’t yet acquired one of the main traits that would allow them to become serious pandemic threats; the ability to bind preferentially to human receptor cells.

While our gaze has been focused primarily on H5N1 and H7N9, in the summer of 2013 Taiwan reported the first known human infection with an avian H6N1 virus, and a few months later mainland China reported the first three cases of H10N8 (two fatal). 

 

While only four cases were recorded, they – along with H5N6, and the globe-trotting H5N8 avian virus and its descendents – have shown just how quickly new subtypes can emerge.

 

Luckily, turning up in a small handful of cases is a far cry from being ready for prime time.

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.

 

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

Although 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 able to bind to the a 2,6 receptor cell.  

 

There are other requirements – some we know about, others we don’t – that determine how well a virus can infect, replicate, and transmit in humans.  The ability to replicate at the lower temperatures found in the upper respiratory system is one of them. 

 

But first, and foremost, the virus must be able to bind to human receptor cells.

 

And here, the news on these two viruses remains encouraging.  

 

The journal Cell, Host & Microbe carries a pair of studies this week that look at the binding properties of these viruses, and both find they fall short.  While behind a pay wall,  we do have a press release from the The Scripps Research Institute (TSRI)  which provides some welcome details.

Links to the studies, and excerpts from the press release, follow:

 

Structure and Receptor Binding of the Hemagglutinin from a Human H6N1 Influenza Virus

Netanel Tzarum, Robert P. de Vries, Xueyong Zhu, Wenli Yu, Ryan McBride, James C. Paulson, Ian A. Wilson

Highlights

• The human H6N1 HA receptor binding site is distinct from other avian and human HAs
• The HA of a human H6N1 influenza virus retains avian receptor specificity
• The interactions of H6 HA with avian receptor analogs differ from other HAs
• Additional mutations are required to switch H6 HA to human receptor specificity

(Continue . . .)

 

A Human-Infecting H10N8 Influenza Virus Retains a Strong Preference for Avian-type Receptors

Heng Zhang, Robert P. de Vries, Netanel Tzarum, Xueyong Zhu, Wenli Yu, Ryan McBride, James C. Paulson, Ian A. Wilson

Highlights

• Human influenza H10N8 HA has negligible binding to human-like receptors
• Human influenza H10N8 HA retains strong binding to avian-like receptors
• The human receptor orientation in H10 HA differs from most human HA complexes
• Mutations that switch specificity in pandemic viruses do not alter H10 specificity

          (Continue . . .)

 

While ostensibly good news, the press release from Scripps warns that both of these viruses bind differently than other avian viruses we’ve seen, and that our understanding of how these viruses mutate isn’t complete enough to warrant complacency.

 

Scripps Research Institute Study Shows Two New Flu Strains Do Not Yet Easily Infect Humans

But Great Versatility of Viruses Suggests Continued Caution

LA JOLLA, CA—March 11, 2015—Scientists at The Scripps Research Institute (TSRI) have analyzed a key protein from two influenza strains that recently began causing sporadic infections among people in China and Taiwan.

The analyses suggest that the flu viruses, variants of subtypes H10N8 and H6N1, have not acquired changes that would allow them to infect people easily and cause a much-feared pandemic.

Yet the studies also highlight the versatility that bird flu viruses apparently have in attaching to host cells.

“These bird flu viruses seem able to bind to receptors on host cells in different ways and thus can probably mutate in different ways to jump to humans—so we shouldn’t be complacent about our ability to predict the viral changes required to get a pandemic,” said Ian A. Wilson, Hansen Professor of Structural Biology and chair of TSRI’s Department of Integrative Structural and Computational Biology.

<SNIP>

Difficult to Predict

How did such bird viruses end up causing infections of people? “We suspect that sporadic cases of human infection by a bird flu virus can occur, even without a change in the receptor specificity, if the dose of the viral exposure is high enough and/or it gets deep into the lungs, where there are some flu-virus receptors like those found in birds,” said Tzarum, a research associate in the Wilson laboratory who was first author of the H6N1 paper.

Flu viruses with these HAs thus remain essentially bird viruses, with limited ability to infect humans. Yet further mutations that would enable a switch in preference to human receptors—and a potential global pandemic—are still possible.

The new TSRI analyses also show that, at the atomic scale, these new bird flu HAs bind to host-cell receptors in ways not observed in studies of other bird flu viruses—implying that the mutations required for the switch to human receptors may be different for different strains and inherently hard to know in advance.

“There appear to be no general rules for this switch among bird flu viruses,” said Tzarum.

Determining whether a bird flu strain has truly jumped the species barrier will therefore continue to require detailed receptor-binding and structural studies like these, Wilson said.

(Continue . . . )

TSRI: H7N9 Virus Still Binds Preferentially to Avian Receptors

Binding of H7N9 to Avian Receptors

Credit: Rui Xu, The Scripps Research Institute

 

# 8045

 

Research over the summer has repeatedly suggested that the newly emerging H7N9 virus in China is better adapted to mammalian hosts than many other avian influenza viruses we’ve previously seen (see Science: H7N9 Transmissibility Study In Ferrets & Nature: Limited Airborne Transmission Of H7N9 Between Ferrets), giving rise to the concern that this virus might be close to sparking a pandemic.

 

Yet, despite these findings, only a handful of small clusters of human infection have been documented, and the vast majority of contacts of known cases never become infected.

 

While the virus appears more readily transmitted from birds to humans than say, the H5N1 virus . . .  it has not yet shown the crucial ability to transmit efficiently from one human to another.   

 

Viruses constantly change, of course, and no one is entirely sure what change (or more likely, what combination of changes) are needed to fully `humanize’ this virus.

 

Influenza viruses have an RBD - Receptor Binding Domain (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 their preferential host.

 

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 `humanized’ flu viruses have an affinity for the alpha 2,6 receptor cells most commonly found in the human respiratory system. .

 

While there are some α2-3 cells deep in the lungs of humans – which may explain the high rate of pneumonia in the unlucky few who do contract avian flu -  for an influenza to be truly successful in a human host, it needs to a able to bind to the α2-6  receptor cells in the upper airway.

 

Today, The Scripps Research Institute (TSRI) has published their analysis of the receptor binding of the H7N9 virus to both human, and avian, receptor cells.  And while this virus does, indeed bind weakly to human α2-6 receptor cells, it still shows a strong preference to bind to avian α2-3 cells.

 

First a link to the study, then some excerpts from the press release.

Preferential Recognition of Avian-Like Receptors in Human Influenza A H7N9 Viruses

Rui Xu, Robert P. de Vries, Xueyong Zhu, Corwin M. Nycholat, Ryan McBride, Wenli Yu, James C. Paulson,Ian A. Wilson

Editor's Summary

The 2013 outbreak of avian-origin H7N9 influenza in eastern China has raised concerns about its ability to transmit in the human population. The hemagglutinin glycoprotein of most human H7N9 viruses carries Leu²²⁶, a residue linked to adaptation of H2N2 and H3N2 pandemic viruses to human receptors. However, glycan array analysis of the H7 hemagglutinin reveals negligible binding to humanlike α2-6–linked receptors and strong preference for a subset of avian-like α2-3–linked glycans recognized by all avian H7 viruses. Crystal structures of H7N9 hemagglutinin and six hemagglutinin-glycan complexes have elucidated the structural basis for preferential recognition of avian-like receptors. These findings suggest that the current human H7N9 viruses are poorly adapted for efficient human-to-human transmission.

(Continue . . . )

 

Scripps Research Institute

TSRI scientists: Emerging bird flu strain is still poorly adapted for infecting humans

LA JOLLA, CA—December 5, 2013—Avian influenza virus H7N9, which killed several dozen people in China earlier this year, has not yet acquired the changes needed to infect humans easily, according to a new study by scientists at The Scripps Research Institute (TSRI). In contrast to some initial studies that had suggested that H7N9 poses an imminent risk of a global pandemic, the new research found, based on analyses of virus samples from the Chinese outbreak, that H7N9 is still mainly adapted for infecting birds, not humans.

"Luckily, H7N9 viruses just don't yet seem well adapted for binding to human receptors," said Ian A. Wilson, the Hansen Professor of Structural Biology and chair of the Department of Integrative Structural and Computational Biology at TSRI.

"Because publications to date have implied that H7N9 has adapted to human receptors, we felt we should make a clear statement about this," said James C. Paulson, chair of TSRI's Department of Cell and Molecular Biology.

The Wilson and Paulson laboratories collaborated on the study, which is reported in the December 6, 2013 issue of the journal Science.

(Continue . . . )

 

MIT: Two Avian Flu Receptor Cell Binding Studies

 

 

# 7370

 

We’ve a pair of avian flu studies, published today in the online journal Cell, that look at the current ability of both the H7N9 and H5N1 viruses to bind to human receptor cells.

 

While there may be other factors at play, the primary barrier that prevents these viruses from sparking a pandemic appears to be their preferential binding to avian receptor cells.

 

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.

 

The $64 question that the research team lead by Ram Sasisekharan, the Alfred H. Caspary Professor of Biological Engineering at MIT, have endeavored to answer is: what type - and how many - changes would these viruses need in order to become more transmissible in humans?

And the authors suggest, it’s probably not a lot.

 

Particularly with the H7N9 virus. 

 

Quick links to the abstracts to these two studies (both studies are, alas, behind pay walls), and then a look at the press release, that describes their findings.

 

Glycan Receptor Binding of the Influenza A Virus H7N9 Hemagglutinin

Cell, 06 June 2013
Copyright © 2013 Elsevier Inc. All rights reserved.
10.1016/j.cell.2013.05.034

Authors

Kannan Tharakaraman, Akila Jayaraman, Rahul Raman, Karthik Viswanathan, Nathan W. Stebbins, David Johnson, Zachary Shriver, V. Sasisekharan, Ram Sasisekharan

Highlights

• The hemagglutinin of H7N9 virus does not efficiently bind human receptors
• A single residue change in receptor binding site increases binding to human receptors
• Mutations on hemagglutinin may reduce the effectiveness of current H7 vaccines

(Continue . . . )

 

 

 

Structural Determinants for Naturally Evolving H5N1 Hemagglutinin to Switch Its Receptor Specificity

 

Cell, 06 June 2013
Copyright © 2013 Elsevier Inc. All rights reserved.
10.1016/j.cell.2013.05.035 

Authors

Kannan Tharakaraman, Rahul Raman, Karthik Viswanathan, Nathan W. Stebbins, Akila Jayaraman, Arvind Krishnan, V. Sasisekharan, Ram Sasisekharan

Highlights

• Hallmark mutations do not switch receptor preference of recent H5 strains
• Structural comparison of H5 and H2 hemagglutinin receptor complexes
• Determination of key H5Nl receptor-binding features needed for quantitative switch
• Recent strains may require a single base pair change to switch receptor preference

(Continue . . . )

 

While the full text of the articles are behind a pay wall, we do have a press release from MIT that tells us, in general terms, what these studies found. A few excerpts below, but follow the link to read it in its entirety.

 

 

Keeping an eye on bird flu

June 6, 2013

MIT studies of two influenza viruses reveal genetic mutations that could result in pandemic flu.

Anne Trafton, MIT News Office

 

(EXCERPTS)

New research from MIT shows that two recently emerged bird flu strains, which do not spread easily now, could become much more infectious with just one or a few genetic mutations.

 

The studies, which focused on the H5N1 and H7N9 flu strains, should help public health officials monitor evolving flu viruses for potential human-to-human transmission. They could also guide the development of new vaccines, says Ram Sasisekharan, the Alfred H. Caspary Professor of Biological Engineering and senior author of two papers appearing in the June 6 online edition of the journal Cell.

 

<SNIP>

 

H5N1

In the new Cell paper, the MIT team studied the structure of HA proteins from hundreds of H5N1 strains and identified three HA regions where one or two mutations would enable the HA to bind efficiently to human receptors. Most of these regions affect the base of the receptor-binding site.

 

The researchers also found that H5N1 has been evolving rapidly since 2005, but none of the current strains have all of the mutations needed to spread from human to human. However, the researchers found one strain that needs only a single amino-acid switch to become highly infectious, and several others that need only two. “There are multiple different ways that this can happen,” says Sasisekharan, who is also a member of MIT’s Koch Institute for Integrative Cancer Research.

 

Furthermore, because of all of the viral evolution that has occurred since 2005, the H5N1 vaccines that governments have stockpiled would probably no longer be effective, Sasisekharan says. “There is cause for concern,” he says. “Yet these findings open opportunities to make sure that some of these newer strains do become part of the stockpiling, because they are closer to human adaptation.”

 

H7N9

 

H7N9 has infected at least 132 people this year, mostly in China, and there have been 37 deaths, according to the World Health Organization — a lower fatality rate than that of the H5N1 virus.

The MIT researchers found that although the current circulating forms of H7N9 bind weakly to human receptors, a change in just one amino acid would dramatically increase the HA protein’s binding strength. “It was not a marginal increase; we saw a pretty significant increase in receptor binding,” Sasisekharan says.

 

“Our research provides insights to help keep track of potentially important mutations so that proactive steps can be taken to be better prepared against dangerous viruses.”

(Continue . . . )

 

 

Whether any avian influenza strain can make the right changes, and become a human pandemic strain, remains a mystery.

 

Yesterday, in a NEJM Perspective, David M. Morens, M.D., Jeffery K. Taubenberger, M.D., Ph.D., and Anthony S. Fauci, M.D. wrestled with this problem in:

 

Pandemic Influenza Viruses — Hoping for the Road Not Taken

This  remains one of the great debates in influenza science - and the question will likely only be settled after one finally does.