PNAS: Evolution Of H9N2 And It’s Effect On The Genesis Of H7N9

Photo Credit – FAO

 

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We’ve a nifty piece of avian flu research which appears this week in PNAS, that looks at the continued evolution of H9N2 in Chinese poultry, and how that may have prompted  the emergence of the H7N9 virus during the spring of 2013.

 

A joint effort of several Chinese science institutions and the St. Jude Children's Research Hospital, this study features Jinhua Liu, Ph.D., of the College of Veterinary Medicine at the China Agricultural University, and Dr. Robert Webster as co-corresponding authors.

 

Regular readers of this blog are aware that the avian H9N2 virus – which has been rife in Asian poultry for the past couple of decades – has been a major contributor to the creation of new avian viruses. Of the viruses we are currently watching with the most concern – H5N1, H7N9, H5N6, and H10N8 – all  share several important features (see Study: Sequence & Phylogenetic Analysis Of Emerging H9N2 influenza Viruses In China):

• They all first appeared in  Mainland China
• They all  have come about through viral reassortment in poultry
• And most telling of all, while their HA and NA genes differ - they all carry the internal genes from the avian H9N2 virus

 

Last January, The Lancet carried a report entitled Poultry carrying H9N2 act as incubators for novel human avian influenza viruses by Chinese researchers Di Liu a, Weifeng Shi b & George F Gao that warned:

Several subtypes of avian influenza viruses in poultry are capable of infecting human beings, and the next avian influenza virus that could cause mass infections is not known. Therefore, slaughter of poultry carrying H9N2—the incubators for wild-bird-origin influenza viruses—would be an effective strategy to prevent human beings from becoming infected with avian influenza.

 

Last May, in EID Journal: H7N9 As A Work In Progress, we looked at a study that found the H7N9 avian virus continues to reassort with local H9N2 viruses, making the H7N9 viruses that circulated in wave 2 genetically distinct from those that were seen during the 1st wave.

Although categorized by their two surface proteins (HA & NA) Influenza A viruses have 8 gene segments (PB2, PB1, PA, HA, NP, NA, M1, M2, NS1, NS2).

H7N9 carries 6 genes from H9N2 – Credit Eurosurveillance

 

And while we have only seen a handful of human infections with H9N2 (see Hong Kong: Isolation & Treatment Of An H9N2 Patient), it is also true that in areas where this virus is most common, testing and surveillance for the virus is extremely limited.  Like so many other novel viruses, we can only guess at is true burden in the human population.

 

While it’s impact on emerging avian flu viruses has been well documented, the reasons behind it’s influence have been less than clear. 

 

Today, however, we have research that shows a new, better adapted genotype  (G57) of the H9N2 virus has emerged  – one that evades the poultry vaccines currently in use – and that it has become widespread among vaccinated Chinese poultry since 2010.

 

This spread has provided more opportunities for reassortment, and so we see more avian viruses emerging.

 

First the Abstract from the study, followed by some excerpts from a St. Jude Children’s Research Hospital press release, after which I’ll return with a bit more.

 

Evolution of the H9N2 influenza genotype that facilitated the genesis of the novel H7N9 virus

Juan Pu^a,^b,¹, Shuoguo Wang^c,¹, Yanbo Yin^d,¹, Guozhong Zhang^a, Robert A. Carter^c, Jinliang Wang^a, Guanlong Xu^a, Honglei Sun^a, Min Wang^a, Chu Wen^a, Yandi Wei^a, Dongdong Wang^d, Baoli Zhu^e, Gordon Lemmon^c, Yuannian Jiao^c, Susu Duan^b, Qian Wang^a, Qian Du^a, Meng Sun^a, Jinnan Bao^a, Yipeng Sun^a, Jixun Zhao^a, Hui Zhang^f, Gang Wu^c, Jinhua Liu^a,², and Robert G. Webster^b,²

 

Significance

The emergence of human infection with a novel H7N9 avian influenza reassortant in China raises a pandemic concern. However, it is not fully understood how these H9N2 chicken viruses facilitated the genesis of the novel H7N9 viruses. Here we show that a “fittest” genotype (G57) emerged with changed antigenicity and improved adaptability in chickens. It became predominant in vaccinated farm chickens and caused widespread outbreaks before the H7N9 virus emergence, increasing reassortment between H9N2 and other subtype viruses and finally providing all of their internal genes to the novel H7N9 viruses. The prevalence and variation of H9N2 influenza virus in farmed poultry could provide an important early warning of the emergence of novel reassortants with pandemic potential.

Abstract

The emergence of human infection with a novel H7N9 influenza virus in China raises a pandemic concern. Chicken H9N2 viruses provided all six of the novel reassortant’s internal genes. However, it is not fully understood how the prevalence and evolution of these H9N2 chicken viruses facilitated the genesis of the novel H7N9 viruses. Here we show that over more than 10 y of cocirculation of multiple H9N2 genotypes, a genotype (G57) emerged that had changed antigenicity and improved adaptability in chickens. It became predominant in vaccinated farm chickens in China, caused widespread outbreaks in 2010–2013 before the H7N9 viruses emerged in humans, and finally provided all of their internal genes to the novel H7N9 viruses. The prevalence and variation of H9N2 influenza virus in farmed poultry could provide an important early warning of the emergence of novel reassortants with pandemic potential.

 

Tracing evolution of chicken flu virus yields insight into origins of deadly H7N9 strain

Memphis, Tennessee, December 29, 2014

An international research team has shown how changes in a flu virus that has plagued Chinese poultry farms for decades helped create the novel avian H7N9 influenza A virus that has sickened more than 375 people since 2013. The research appears in the current online early edition of the scientific journal Proceedings of the National Academy of Sciences.

The results underscore the need for continued surveillance of flu viruses circulating on poultry farms and identified changes in the H9N2 virus that could serve as an early warning sign of emerging flu viruses with the potential to trigger a pandemic and global health emergency. The work focused on the H9N2 chicken virus, which causes egg production to drop and leaves chickens vulnerable to deadly co-infections. Scientists at St. Jude Children’s Research Hospital and the China Agricultural University, Beijing, led the study.

Researchers used whole genome sequencing to track the evolution of the H9N2 chicken virus between 1994 and 2013. The analysis involved thousands of viral sequences and showed that the genetic diversity of H9N2 viruses fell sharply in 2009. From 2010 through 2013 an H9N2 virus emerged as the predominant subtype thanks to its genetic makeup that allowed it to flourish despite widespread vaccination of chickens against H9N2 viruses.

Evidence in this study suggests the eruptions set the stage for the emergence of the H7N9 avian virus that has caused two outbreaks in humans since 2013, with 115 confirmed deaths. The H9N2 infected chickens likely served as the mixing vessel where H9N2 and other avian flu viruses from migratory birds and domestic ducks swapped genes, researchers noted. The resulting H7N9 virus included six genes from the H9N2.

"Sequencing the viral genome allowed us to track how H9N2 evolved across time and geography to contribute to the H7N9 virus that emerged as a threat to human health in 2013," said Robert Webster, Ph.D., a member of the St. Jude Department of Infectious Diseases. He and Jinhua Liu, Ph.D., of the College of Veterinary Medicine at the China Agricultural University, are co-corresponding authors.

"The insights gained from this collaboration suggest that tracking genetic diversity of H9N2 on poultry farms could provide an early warning of emerging viruses with the potential to spark a pandemic," Webster said.

(Continue . . .)

 

If all of this sounds vaguely familiar, last April in Study: Sequence & Phylogenetic Analysis Of Emerging H9N2 influenza Viruses In China, we saw H9N2 viruses collected from two Chinese Provinces (Zhejiang & Guangdong) in late 2011 showed signs of evolving antigenically away from the vaccine strain, with a majority of isolates (14 out of 18) showing an amino acid change in the receptor binding site suggestive of an enhanced ability to bind to human receptor cells.

 

While poultry vaccination has been adopted by a number of countries to control their avian flu problems, there are distinct downsides to relying on vaccines for the control of avian viruses (for earlier blogs see OIE: Countries That Vaccinate Poultry Need An `Exit Strategy' & Food Insecurity, Economics, And The Control Of H7N9).

 

While vaccines can often protect poultry against illness - with increasingly diverse and rapidly evolving avian flu viruses - they can’t always prevent infection.  Particularly if they aren’t updated often.

 

The end result being that subclinical infections can go undetected, viruses continue to circulate unnoticed, and new variants or reassortants continue to emerge. These failures are not limited to the H9N2 vaccines, as we’ve seen similar results with H5 vaccines as well (see EID Journal: Subclinical HPAI In Vaccinated Poultry – China &  Egypt: A Paltry Poultry Vaccine). 

 

There are, unfortunately, no simple solutions.

 

Countries like China, Indonesia, Vietnam, and Egypt – places where avian flu viruses are well entrenched in both commercial and home raised poultry - rely heavily on poultry vaccines. They view the immediate culling of infected birds, the standard control practice for most of the rest of the world, as being impractical and fear the social and economic impacts of such a policy.

 

The problem is, as new avian flu subtypes, clades, and sub clades emerge, the vaccines in use inevitably lose the battle, and over time that can lead to a snowball effect where the number of viruses in circulation escalate rapidly.

 

Given the recent emergence of H7N9, H10N8, H5N6, H5N8 and H5N3, one has to wonder just how much faster this snowball will roll over the next few years.

PNAS: H5N1 Propagation Via Migratory Birds

Source - OIE 63 Countries Report H5N1 Avian Influenza in Domestic Poultry/Wildlife 2003-2010).

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Although migratory birds have been labeled a `convenient scapegoat’ by conservationists who instead point their finger at the poultry industry for the spread of avian flu (see this recent statement by the UN CMS/FAO Scientific Task Force on Avian Influenza and Wild Birds), a fair review of the data makes the wild bird connection difficult to ignore.

 

Not that migratory birds are the only factor, since evidence strongly suggests poultry operations (including legal and illegal trade & transportation) have contributed mightily to the evolution and spread of avian viruses as well.

 

This is an ongoing, and often bitter debate I covered at some length  last month in Bird Flu Spread: The Flyway Or The Highway?, and previously here, here, and here.

 

Yesterday, in EID Journal: A Proposed Strategy For Wild Bird Avian Influenza Surveillance, we looked at recommendations for a more consolidated and cost effective program to monitor avian flu viruses in birds, while previously (see The North Atlantic Flyway Revisited & Satellite Images Show Where The Wild Goose Goes) we’ve looked at some of the individual migratory bird studies.

 

With the recently emerged HPAI H5N8 avian virus showing up not only in Europe, but in North America this fall, and an upstart H5N6 making inroads in across China and Vietnam, defining the role of migratory birds in the spread of these viruses gains even more importance.

 

Today we’ve a report from PNAS that looks back over much of the data gathered since the emergence of H5N1 in Southeast Asia, and presents the case that migratory birds have play a significant role in its propagation.  Among other things, they cite that along migratory flyways, H5N1 outbreaks closely match the seasonal arrival of migratory flocks.

 

They are quick to clarify, however, that migratory birds are likely just one of several underlying transmission networks, and that in some cases where the virus was detected in wild birds, the virus may have transmitted from poultry to birds instead of the other way around. 

As with all studies, the authors list a number of limitations, and so you’ll probably want to read this report in its entirety.  I’ve only excepted a couple of highlights, so follow the link to read:

 

 

Avian influenza H5N1 viral and bird migration networks in Asia

Huaiyu Tian^a,¹, Sen Zhou^b,¹, Lu Dong^c,¹, Thomas P. Van Boeckel^d,¹, Yujun Cui^e,¹, Yarong Wu^e, Bernard Cazelles^f,^g, Shanqian Huang^a, Ruifu Yang^e, Bryan T. Grenfell^d,^h,², and Bing Xu^a,^b,ⁱ,²

 

Abstract

The spatial spread of the highly pathogenic avian influenza virus H5N1 and its long-term persistence in Asia have resulted in avian influenza panzootics and enormous economic losses in the poultry sector. However, an understanding of the regional long-distance transmission and seasonal patterns of the virus is still lacking. In this study, we present a phylogeographic approach to reconstruct the viral migration network. We show that within each wild fowl migratory flyway, the timing of H5N1 outbreaks and viral migrations are closely associated, but little viral transmission was observed between the flyways. The bird migration network is shown to better reflect the observed viral gene sequence data than other networks and contributes to seasonal H5N1 epidemics in local regions and its large-scale transmission along flyways. These findings have potentially far-reaching consequences, improving our understanding of how bird migration drives the periodic reemergence of H5N1 in Asia.

Significance

Highly pathogenic avian influenza virus H5N1 first emerged in Asia and subsequently unfolded into the first avian influenza panzootic, causing major economic losses in the poultry sector. However, we still do not understand the regional long-distance transmission and seasonal patterns of H5N1. In this study, we addressed this issue by combining H5N1 outbreak records, whole-genome sequences of viral samples, and satellite tracking data for four species of migratory birds in Asia. We show that timing of H5N1 outbreaks and viral migration are closely associated with known bird migration routes. The flyway is the major viral transmission barrier to the intracontinental spread of H5N1 by migratory birds in Asia, whereas geographic distances within the flyways have little effect on H5N1 transmission.

(Continue . . . )

 

For more on the recent emergence and spread of the H5N8 virus, and how it compares to the sudden expansion of H5N1 in the middle of the last decade, you may wish to revisit:

H5N8: A Case Of Deja Flu?

 

PNAS: A Vaccine Evading Variant Poliovirus

Photo Credit WHO

 

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For those born after 1960, it is probably difficult to understand the kind of fear that Polio generated in the United States and around the world during the 1950s.  While only one infection in a hundred resulted in paralysis or death, polio was extremely infectious, and the United States routinely saw between 18,000 and 25,000 paralytic cases each year – mostly among young children.

 

Hospital wards were filled with paralyzed children trapped in iron lungs (a grim technology many younger adults have no memory of), which were used to keep them alive. The following short film clip may be hard for some to look at, but is a reminder of how things were . . . not so very long ago.

 

 

 

In 1954  the first major field trials of the Salk vaccine took place, and the following year – after review of the data - a national vaccination campaign was launched. By 1957, after two years of vaccination - the number of new polio cases in the United States dropped to under 6,000, and by 1964 that number had dropped to just 121 cases.

 

There was suddenly tremendous optimism that modern science had within its power to eliminate even the worst childhood scourges, and indeed over the next decade tremendous progress was made against the lesser threats of measles, mumps, pertussis and chickenpox.

 

But, as we’ve seen with the recent resurgence of measles, mumps, and pertussis – and the steady decline in the effectiveness of once powerful antibiotics – mankind’s victories over diseases are sometimes fleeting.

 

Polio – which just a few short years ago seemed on the verge of global eradication – has also made a comeback.  So much so that last May we saw the WHO Declare Polio Spread A Public Health Emergency Of International Concern. 

 

As a result, new, strict polio vaccination requirements are being implemented for those countries with `active polio’.

 

In 2010 there was a particularly severe outbreak of polio in the Republic Of Congo (ROC), primarily in and around the port city of Pointe Noire (see WHO GAR update).  This outbreak was unusual in several respects:

• The median age of victims was 20 (not under 5 as is normally the case)
• The fatality rate – normally in the single digits – was 47%
• Cases occurred among previously vaccinated adults

 

Yesterday, the journal PNAS published a study by an international group of researchers (including such familiar names as Christian Drosten  and Marion Koopmans) that examined this particular strain of polio, and found genetic changes in it that allowed it to evade the protective effects of the inactivated polio vaccine.

 

Robustness against serum neutralization of a poliovirus type 1 from a lethal epidemic of poliomyelitis in the Republic of Congo in 2010

Jan Felix Drexler, Gilda Grard, Alexander N. Lukashev, Liubov I. Kozlovskaya, Sindy Böttcher, Gökhan Uslu, Johan Reimerink, Anatoly P. Gmyl, Raphaël Taty-Taty, Sonia Etenna Lekana-Douki, Dieudonné Nkoghe, Anna M. Eis-Hübinger, Sabine Diedrich, Marion Koopmans, Eric M. Leroy, and Christian Drosten

Significance

In 2010, a large outbreak of poliomyelitis involving 445 laboratory-confirmed cases occurred in the Republic of Congo. The 47% case-fatality rate was unusually high. Outbreak severity was attributed to low immunization coverage but vaccine-mediated immunity against the outbreak virus was never investigated. We isolated the poliovirus type 1 responsible for the outbreak and located its evolutionary origins to Southeast Asia. Fatal cases showed evidence for previous vaccination against polioviruses and the outbreak virus was refractive against neutralization by monoclonal and vaccine-derived antibodies. This pointed to immune escape contributing to the severity of the outbreak. Sustained vaccination regimens in polio-free regions, together with clinical and environmental poliovirus surveillance will be necessary to combat antigenetically variant polioviruses in the poliomyelitis eradication endgame.

 

While people who had previously received the weaker inactivated poliovirus vaccine (IPV) were more vulnerable to this variant poliovirus, those who had recently received the live-attenuated Oral Polio Vaccine (OPV) were still protected. 

 

This discovery – of essentially a `mutated’ strain of polio – shows that the poliovirus can evolve over time.  While this particular variant appears to have been stamped out, the authors worry that more variants could appear in the future, complicating attempts to eradicate this virus.

 

In the battle against infectious diseases we’ve seen many wonderful advances made over the past century: Vaccines, antibiotics, even monoclonal antibodies. But no matter how sophisticated our response, the old adage – that nature always bats last – carries with it more than just a grain truth.  

 

A reminder that a loss of focus, or a break in vigilance, and even once defeated enemies can come back to bite us.

PNAS: Genetic Marker & Cytokine Levels Linked To Severity Of Human H7N9 Infection

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Influenza is a highly variable viral infection that can produce a wide spectrum of illness, ranging from mild or even asymptomatic presentation, to severe and/or life threatening. 

 

While we think of a patient’s age and/or co-morbidities (COPD, Asthma, pregnancy, etc. ) as being predictive of a greater chance of complications, with the 2009 Swine Flu of 2009 (H1N1) and with several strains of avian flu (H5N1, H7N9), we’ve seen young, otherwise healthy adults quickly overwhelmed by their infections.

 

For a number of years researchers have been looking for a hematological or genetic marker that would help predict which patients would be most likely to experience severe influenza, and which were more likely to recover without incident.

 

Increasingly, scientists have been zeroing in on the Interferon-induced transmembrane protein 3 (IFITM3) protein,  whose levels are controlled by the IFITM3 gene

 

In late 2009, in The Best Defense, we looked at research from Harvard Medical School and the Howard Hughes Medical Institute, that  identified the IFITM3 protein as capable of inhibiting the replication of influenza, and other viruses, such as West Nile and Dengue.

 

We revisited the IFITM3 story again in early 2012, in Luck Of The Draw, when we looked at research from the Wellcome Trust Sanger Institute, that found that people who carried a particular variant of the IFITM3 gene - (SNP rs12252-C) -  were more likely to be hospitalized with severe influenza.

 

Earlier this year Nature Communications carried a study (Interferon-induced transmembrane protein-3 genetic variant rs12252-C is associated with severe influenza in Chinese individuals) that found that this SNP rs12252-C allele – while relatively rare in Caucasians, is much more common in Han Chinese.  The abstract makes for fascinating reading (excerpts follow):

 

Here we report that the CC genotype is found in 69% of Chinese patients with severe pandemic influenza A H1N1/09 virus infection compared with 25% in those with mild infection. Specifically, the CC genotype was estimated to confer a sixfold greater risk for severe infection than the CT and TT genotypes. More importantly, because the risk genotype occurs with such a high frequency, its effect translates to a large population-attributable risk of 54.3% for severe infection in the Chinese population studied compared with 5.4% in Northern Europeans. Interferon-induced transmembrane protein-3 genetic variants could, therefore, have a strong effect of the epidemiology of influenza in China and in people of Chinese descent.

 

All of which serves as prelude to a study that appeared yesterday in PNAS, that finds this IFITM3 CC gene variant (aka C/C Genotype) is linked to hypercytokinemia (aka a `Cytokine Storm’), and a severe outcome, in H7N9 infections. 

 

Briefly, Cytokines are a category of signaling molecules that are used extensively in cellular communication. They are often released by immune cells that have encountered a pathogen, and are designed to alert and activate other immune cells to join in the fight against the invading pathogen.

 

This  `Cytokine Storm' has been described as a positive feedback loop, where immune cells - encountering a pathogen - secrete  signaling cytokines which call more immune cells to the site of infection - which in turn secrete more cytokines - which call even more immune cells to join in the fight . . .

 

This cascade of immune cells rushing to the infection can, in rare instances, literally kill the patient. Their lungs can fill with fluid (which makes a terrific medium for a bacterial co-infection), and cells in the lungs (Type 1 & Type II Pneumocytes) can sustain severe damage.

 

The lead author is Laureate Professor Peter C. Doherty (who shared the 1996 Nobel Prize for medicine for his work in immunology), who divides his time between St Jude Children’s Research Hospital in Memphis and the Department of Microbiology and Immunology at the University of Melbourne.

 

 

Early hypercytokinemia is associated with interferon-induced transmembrane protein-3 dysfunction and predictive of fatal H7N9 infection

Zhongfang Wang, Anli Zhang, Yanmin Wan, Xinian Liu, Chao Qiu, Xiuhong Xi, Yanqin Ren, Jing Wang, Yuan Dong, Meijuan Bao, Liangzhu Li, Mingzhe Zhou, Songhua Yuan, Jun Sun, Zhaoqin Zhu, Liang Chen, Qingsheng Li, Zhiyong Zhang, Xiaoyan Zhang, Shuihua Lu, Peter C. Doherty, Katherine Kedzierska, and Jianqing Xu

PNAS 2013 ; published ahead of print December 23, 2013, doi:10.1073/pnas.1321748111

Significance

A unique avian-origin H7N9 influenza virus caused 134 human infections with 44 deaths. The host factors contributing to moderate vs. severe disease are not clear. Here, we show that H7N9 severity was associated with a higher level of cytokines/chemokines. We demonstrate that the cytokines in the infected lung were 100- to 1,000-fold higher than those in the plasma. Furthermore, we found that the IFN-induced transmembrane protein-3 (IFITM3) C/C genotype was associated with severe clinical outcome, as reflected by reduced time in seeking medical aid; more rapid progression to acute respiratory distress syndrome; and higher viral load, cytokine/chemokine levels, and mortality rate. Overall, our data suggest that the IFITM3 genotype is a primary driver of the observed differences in clinical outcome after H7N9 infection.

 

The entire study is available to download, and is well worth doing so.

 

It is important to note that while the variant C/C genotype was over represented among seriously ill patients (compared to its prevalence in the local population), and the C/C genotype was also linked to more rapid disease progression than with the others, that severe disease was also seen with the T/C and the T/T WT genotypes.

 

So it doesn’t mean that if you have one of the other genotypes, you are guaranteed an easy time of it.  But your odds of a bad outcome apparently go up with the C/C genotype.

 

The authors suggest that rs12252 sequencing along with the monitoring of plasma cytokines could help predict which patients would be most at risk of developing a severe, or even life-threatening, infection.

The authors also suggest that given the high frequency of the C/C genotype in China, it may be worth considering preferentially targeting that cohort for (routine,or presumably pandemic) influenza immunization. They caution, however, that `a thorough assessment of the relative risk of vaccination, as well as its protective efficacy in the C/C group, needs to be determined first.’

 

These findings may mean that anti-inflammatory drugs, or other therapies that can reign in a runaway immune response (see Study: Calming The Cytokine Storm), may prove effective in treating severe influenza.

 

And returning briefly to the Nature Communications study on the incidence of the CC genotype in Han Chinese, mentioned above, the authors compare the incidence of this genetic variant between Asian and Caucasian populations and write:

 

It is intriguing that the CC genotype⁴ is rare in Northern Europeans and common in Asian populations. As many other viral infections are restricted by IFITM3 in vitro, including severe acute respiratory syndrome (SARS) coronavirus, Dengue virus and West Nile virus^{1, 7} the high population allele frequencies may have been influenced by complex virus exposures.

<SNIP>

In conclusion, our data clearly extend the earlier observation in a European cohort that the IFTM3-rs12252CC genotype is significantly associated with influenza severity. The association is primarily with severity of disease rather than susceptibility to infection, although larger studies are required to prove this specific association. IFITM3 may have an important role in virus replication and dissemination following the initial infection. The much higher level of the CC genotype in the Han Chinese population compared with Caucasians may place the Chinese at a higher risk for developing severe illness upon influenza infection. It is not known whether those who are more severely infected with influenza virus are more likely to spread the infection. If this is the case, the high frequency of the C allele in Asian populations may influence the epidemiology of influenza.

 

Which may mean that the high morbidity and mortality rates we’ve seen with the H7N9 virus in China might be moderated somewhat, should the virus spread to populations where this genetic variant is less common.

 

Or not, as we are still in early days in understanding  how pandemic viruses behave across a diverse population.

 

A final thought, in 2006 we saw a Lancet study called Estimation of potential global pandemic influenza mortality on the basis of vital registry data from the 1918—20 pandemic: a quantitative analysis that found as much as a 30-fold difference in population mortality as the Spanish Flu traversed the globe.  While good records were not always kept, anecdotal reports suggest that China and India were hit many times harder than Northern Europe, or North America.

 

While a large number of variables (economic, climatic, population density, access to healthcare, diet) might well account for this, a genetic propensity towards more severe infection might have been a factor as well.

 

Questions that we’ll hopefully have much better answers for after the next severe pandemic has passed, and has been thoroughly analyzed. 

PNAS: MERS Pneumonia In A Macaque Model

Photo Credit Wikipedia

 

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Two weeks ago, in Nature: Animal Testing Of Drug Combo Shows Potential For Treating MERS, we looked at the the potential role of Interferon-α2b & ribavirin in the treatment of MERS-CoV infection, based on a NIAID led study conducted on rhesus macaques. At the time I cautioned that, while encouraging, the following caveats should be kept in mind:

 

• First, the macaque model is not a perfect substitute for humans, as they tend not to be as severely impacted by the MERS virus. 
• Second, treatment was initiated 8 hours post infection, which is an earlier pharmacological intervention than most humans could hope to see. 
• And third, most severe human infections have been seen in people with co-morbidities like COPD, cancer, diabetes, asthma . . . variables this study does not attempt to replicate.

 

These same group of researchers are back with a another study - published yesterday in the journal  PNAS - that looks at the pathogenesis of MERS-CoV in rhesus macaques.  Once again, caveats 1 and 3 need to be considered.

 

The study is called:

 

Middle East respiratory syndrome coronavirus (MERS-CoV) causes transient lower respiratory tract infection in rhesus macaques

Emmie de Wit^a, Angela L. Rasmussen^b, Darryl Falzarano^a, Trenton Bushmaker^a, Friederike Feldmann^c, Douglas L. Brining^c, Elizabeth R. Fischer^d, Cynthia Martellaro^a, Atsushi Okumura^b, Jean Chang^b, Dana Scott^c, Arndt G. Benecke^b,^e, Michael G. Katze^b, Heinz Feldmann^a,^f,¹, and Vincent J. Munster^a,¹

Significance

The Middle East respiratory syndrome coronavirus (MERS-CoV) is the latest emerged coronavirus causing severe respiratory disease with a high case fatality rate in humans. To better understand the disease caused by MERS-CoV, we developed a rhesus macaque model. Infection of rhesus macaques with MERS-CoV resulted in the rapid development of a transient pneumonia, with MERS-CoV replication largely restricted to the lower respiratory tract. This affinity of MERS-CoV for the lungs partly explains the severity of the disease observed in humans. The MERS-CoV rhesus macaque model will be instrumental in developing and testing vaccine and treatment options for an emerging viral pathogen with pandemic potential.

Abstract

(Excerpt)

Upon a combination of intratracheal, ocular, oral, and intranasal inoculation with 7 × 10⁶ 50% tissue culture infectious dose of the MERS-CoV isolate HCoV-EMC/2012, rhesus macaques developed a transient lower respiratory tract infection. Clinical signs, virus shedding, virus replication in respiratory tissues, gene expression, and cytokine and chemokine profiles peaked early in infection and decreased over time. MERS-CoV caused a multifocal, mild to marked interstitial pneumonia, with virus replication occurring mainly in alveolar pneumocytes. This tropism of MERS-CoV for the lower respiratory tract may explain the severity of the disease observed in humans and the, up to now, limited human-to-human transmission.

 

In simple language, once infected, macaques developed mild to moderate, albeit short-lived pneumonia, with infection and viral replication most prominently seen in the lower lung tissue. This tropism (affinity) of the virus for the lower respiratory tract in macaques does match what we’ve seen in severe human cases, but in macaques the severity and duration of MERS infection was limited.

 

We lack a fully predictive animal model for human medical research. Mice, guinea pigs, and ferrets are often employed because of their small size, low cost, and ease of use.  Rhesus macaques, on the other hand, are more difficult to obtain and to work with, but are viewed as being a closer human analog. 

 

Still, results with these animals must be accepted with a certain degree of caution. The old saying in biomedical research is that `Mice lie, and monkeys exaggerate.’

 

We’ve seen mild MERS infections in humans, primarily in younger patients and those without co-morbidities, and so it may well be that the young, healthy macaques used in this study are mirroring that cohort.

 

What this study does tell us is that this virus prefers the lower respiratory tract (in macaques), and that that may help explain both its severity in humans, and its limited human-to-human transmission to date. 

 

For more on this story, Robert Roos of CIDRAP NEWS wrote an excellent overview last night.

 

Macaque study: MERS-CoV settles deep in lungs

Robert Roos | News Editor | CIDRAP News

Sep 23, 2013

Researchers say the macaque model will be useful in developing and testing vaccines and treatments for MERS.

If rhesus macaques are good stand-ins for humans in studying Middle East respiratory syndrome coronavirus (MERS-CoV), the virus prefers the environment deep in the lungs, a finding that may help explain some features of the disease in humans, according to new research.

The scientists say that in macaques, the virus mainly affects the lower respiratory tract, which may help explain why the human disease is often severe but does not spread very easily from person to person.

(Continue . . .)

PNAS: Abundant Antibiotic Resistance Genes In Chinese Swine Farms

Inoculated MacConkey agar culture plate cultivated colonial growth of Gram-negative, small rod-shaped and facultatively anaerobic Klebsiella pneumoniae bacteria. – CDC PHIL.

UPDATE:  I’m happy to report that Maryn McKenna has posted on this story as well, and includes comments from one of the authors. 

By all means read:

Antibiotic-Resistant Bacteria Surround Big Swine Farms — In China As Well As The US

• By Maryn McKenna 02.12.13  12:15 PM

 

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We’ve discussed the emergence of antibiotic resistant bacteria often in this blog (see here, here, and here for a few examples), and it has been a mainstay of Maryn McKenna’s always excellent Superbug Blog.

 

The reckless and unrestricted use of antibiotics threatens to render our antibiotic arsenal useless, and many warn that in a few years we could be thrown back into a `pre-antibiotic era’, where even simple infections are once again deadly.

 

Today, a study appears in PNAS that illustrates just how damaging the unrestricted use of antibiotic used in agriculture can be, with an examination of the staggering number of antibiotic resistant genes (ARGs) found in swine manure in three locations in China.

 

First, the press release from the Michigan State University, then a link to the PNAS article, followed by comments from Professor Peter Collignon, an infectious diseases expert from the  Australian National University.

Published: Feb. 11, 2013

Unchecked antibiotic use in animals may affect global human health

Contact(s): Layne Cameron , James Tiedje

The increasing production and use of antibiotics, about half of which is used in animal production, is mirrored by the growing number of antibiotic resistance genes, or ARGs, effectively reducing antibiotics’ ability to fend off diseases – in animals and humans.

 

A study in the current issue of the Proceedings of the National Academy of Sciences shows that China – the world’s largest producer and consumer of antibiotics – and many other countries don’t monitor the powerful medicine’s usage or impact on the environment.

 

On Chinese commercial pig farms, researchers found 149 unique ARGs, some at levels 192 to 28,000 times higher than the control samples, said James Tiedje, Michigan State University Distinguished Professor of microbiology and molecular genetics and of plant, soil and microbial sciences, and one of the co-authors.

 

“Our research took place in China, but it reflects what’s happening in many places around the world,” said Tiedje, part of the research team led by Yong-Guan Zhu of the Chinese Academy of Sciences. “The World Organization for Animal Health and the U.S. Food and Drug Administration have been advocating for improved regulation of veterinary antibiotic use because those genes don’t stay local.”

 

Antibiotics in China are weakly regulated, and the country uses four times more antibiotics for veterinary use than in the United States. Since the medicine is poorly absorbed by animals, much of it ends up in manure – an estimated 700 million tons annually from China alone. This is traditionally spread as fertilizer, sold as compost or ends up downstream in rivers or groundwater, taking ARGs with them. Along with hitching rides in fertilizer, ARGs also are spread via international trade, immigration and recreational travel.

(Continue . . . )

 

 

The Abstract from PNAS (the entire article is available).

 

Diverse and abundant antibiotic resistance genes in Chinese swine farms

Yong-Guan Zhu, Timothy A. Johnson, Jian-Qiang Su, Min Qiao,  Guang-Xia Guo, Robert D. Stedtfeld, Syed A. Hashsham, and James M. Tiedje

Abstract

Antibiotic resistance genes (ARGs) are emerging contaminants posing a potential worldwide human health risk. Intensive animal husbandry is believed to be a major contributor to the increased environmental burden of ARGs. Despite the volume of antibiotics used in China, little information is available regarding the corresponding ARGs associated with animal farms.

 

We assessed type and concentrations of ARGs at three stages of manure processing to land disposal at three large-scale (10,000 animals per year) commercial swine farms in China. In-feed or therapeutic antibiotics used on these farms include all major classes of antibiotics except vancomycins. High-capacity quantitative PCR arrays detected 149 unique resistance genes among all of the farm samples, the top 63 ARGs being enriched 192-fold (median) up to 28,000-fold (maximum) compared with their respective antibiotic-free manure or soil controls.

 

Antibiotics and heavy metals used as feed supplements were elevated in the manures, suggesting the potential for coselection of resistance traits. The potential for horizontal transfer of ARGs because of transposon-specific ARGs is implicated by the enrichment of transposases—the top six alleles being enriched 189-fold (median) up to 90,000-fold in manure—as well as the high correlation (r² = 0.96) between ARG and transposase abundance. In addition, abundance of ARGs correlated directly with antibiotic and metal concentrations, indicating their importance in selection of resistance genes.

 

Diverse, abundant, and potentially mobile ARGs in farm samples suggest that unmonitored use of antibiotics and metals is causing the emergence and release of ARGs to the environment.

 

 

And lastly, a radio interview with Professor Peter Collignon, on  Australia’s ABC Radio Network, where he states that this study provided, `bigger and larger numbers than even I would have expected and it just shows how we really have to take better stock of what we do.’

Follow the link for the transcript and audio file.

Rampant antibiotic use in China may impact Australian food

Simon Lauder reported this story on Tuesday, February 12, 2013 08:15:18

 

 

While I dabble in the issues of antibiotic resistance, undoubtedly the best coverage has come from flublogia’s favorite `scary disease girl’ Maryn McKenna editor of the Superbug blog.

 

If you’ve not already read Maryn’s eye-opening 2nd book, Superbug: The Fatal Menace of MRSA, I would urge you to do so.

Superbug (MRSA) Book

PNAS: Virulence & Transmissibility Of H1N2 Influenza Virus In Ferrets

 

 

 

# 6547

 

Timing is, as they say, everything.

 

And coming on the heels the announcement 10 days ago of three human infections with a swine-origin H1N2 influenza (see Minnesota Reports Swine H1N2v Flu), a study that appears today in PNAS is certainly well timed.

 

The study, conducted at Chungbuk National University South Korea examined viruses circulating in Korean swine (H1N2 & H3N2), and found - for the most part - they were not particularly pathogenic in ferrets.

 

The exception was a triple reassortant H1N2 virus dubbed Sw/1204, that had picked up two notable mutations, and it not only transmitted efficiently, it also caused severe (even fatal) disease in the test animals.

 

The study, is called:

 

Virulence and transmissibility of H1N2 influenza virus in ferrets imply the continuing threat of triple-reassortant swine viruses

Philippe Noriel Q. Pascua, Min-Suk Song, Jun Han Lee, Yun Hee Baek, Hyeok-il Kwon, Su-Jin Park, Eun Hye Choi, Gyo-Jin Lim, Ok-Jun Lee, Si-Wook Kim, Chul-Joong Kim, Moon Hee Sung, Myung Hee Kim, Sun-Woo Yoon, Elena A. Govorkova, Richard J. Webby, Robert G. Webster, and Young-Ki Choi

 

Ed Yong, writing for Nature has the details  on this paper:

 

Need for flu surveillance reiterated

Study of Korean pigs finds virus with pandemic potential.

Ed Yong 10 September 2012

 

 

One to the two mutations discussed in this paper is hemagglutinin (HA) (Asp-225-Gly) – also known as D225G – which is something we’ve looked at a number of times in the past.

 

This mutation involves a single amino acid change in the HA gene at position 225 (H3 numbering) from aspartic acid (D) or Asp to glycine (G), and was first linked to more severe pandemic flu by Norwegian Scientists in 2009.

 

The evidence for the D222G/N  amino acid substitution driving increased virulence, and deep lung infection, has been mixed, however. A few earlier blogs include:

 

Eurosurveillance: Debating The D222G/N Mutation In H1N1

Study: Receptor Binding Changes With H1N1 D222G Mutation

WER Review: D222G Mutation In H1N1

 

The second mutation, called NA-315 (serine to asparagine the in neuraminidase) isn’t as well studied, but is believed to assist the virus in breaking out of infected cells after replicating.

 

As Ed Yong mentions in his article - viruses often have multiple amino acid changes – and we are really just beginning to understand the ramifications of these different genetic combinations. 

 

Whether this particular virus ever ends up posing a public health threat is impossible to say, but it does illustrate these swine reassortant viruses aren’t always mild in mammals.

 

New strains of influenza come about from reassortment; the swapping of genetic material between two different flu strains in a common host. We tend to focus on swine, simply because they are highly susceptible to a variety of influenza viruses, and have a history of producing reassorted viruses.  

 

 

The pandemic virus that emerged in the spring of 2009 was the end product of several influenza strains that had kicked around the world’s swine population for many years, trading bits of genetic material back and forth, until they produced a version capable of jumping to humans.

 

But any host (human, swine, avian, or other mammal) could produce a reassorted virus.

 

For more on the flu risks from swine reassortments, I continue to heartily recommend Helen Branswell’s terrific piece in SciAm  from late 2010 called Flu Factories.

Flu Factories

The next pandemic virus may be circulating on U.S. pig farms, but health officials are struggling to see past the front gate

By Helen Branswell  | December 27, 2010 |

 

And for some of my earlier looks at swine influenza, you may wish to revisit:

 

H3N2v: When Pigs Flu

You Say You Want An Evolution?

The (Swine) Influenza Reassortment Puzzle

PNAS: A Hypothesis On The Effects Of La Niña On Influenza Reassortment

 

 

# 6078

 

 

 

We have an interesting hypothesis being offered today by a pair of well-respected researchers (Jeffrey Shaman of Columbia University's Mailman School of Public Health and Marc Lipsitch of the Harvard School of Public Health), who note that the weather patterns prior to the pandemics of 1918, 1957, 1968 and 2009 all showed the Pacific ocean to be in a La Niña cycle.

 

We know, of course, that correlation doesn’t necessarily imply causation, but an apparent association between two events can often provide a useful starting point for further scientific investigation.

 

And that’s what these researchers are calling for.

 

Whether this correlation is casual, or is simply coincidental, is for now unknown.  

 

For those unfamiliar with the basics of El Niño and La Niña, a very brief overview:

 

The Pacific Ocean cycles between an El Niño pattern (warmer) and a La Niña (colder) than normal water temperatures in the Equatorial Pacific Ocean.

 

These water temperature cycles can have major effects on climate and weather far removed from the Pacific. During La Niña years, for example, the Atlantic Hurricane season is usually more active.

 

 

La Niña (December 2000)

El Niño (December 1997)

Sea surface temperature anomalies (°C)

Photo Credit- NOAA 

 

La Niña's occur every 2 to 7 years, and over the past 62 years 14 have been observed. During that time, we saw 3 pandemics (1957, 1968, 2009).

 

Graph Credit- Wikipedia

 

 

We’ve  the Press Release from Columbia University's Mailman School of Public Health, but after a quick visit to the PNAS journal website I wasn’t able to locate the article online. I imagine it will be online shortly.

 

Does the La Niña weather pattern lead to flu pandemics?

 

Public release date: 16-Jan-2012

 

Worldwide pandemics of influenza caused widespread death and illness in 1918, 1957, 1968 and 2009. A new study examining weather patterns around the time of these pandemics finds that each of them was preceded by La Niña conditions in the equatorial Pacific. The study's authors--Jeffrey Shaman of Columbia University's Mailman School of Public Health and Marc Lipsitch of the Harvard School of Public Health—note that the La Niña pattern is known to alter the migratory patterns of birds, which are thought to be a primary reservoir of human influenza. The scientists theorize that altered migration patterns promote the development of dangerous new strains of influenza.

 

The study findings are currently published online in PNAS.

 

To examine the relationship between weather patterns and influenza pandemics, the researchers studied records of ocean temperatures in the equatorial Pacific in the fall and winter before the four most recent flu pandemics emerged. They found that all four pandemics were preceded by below-normal sea surface temperatures—consistent with the La Niña phase of the El Niño-Southern Oscillation. This La Niña pattern develops in the tropical Pacific Ocean every two and seven years approximately.

 

The authors cite other research showing that the La Niña pattern alters the migration, stopover time, fitness and interspecies mixing of migratory birds. These conditions could favor the kind of gene swapping—or genetic reassortment—that creates novel and therefore potentially more variations of the influenza virus.

 

"We know that pandemics arise from dramatic changes in the influenza genome. Our hypothesis is that La Niña sets the stage for these changes by reshuffling the mixing patterns of migratory birds, which are a major reservoir for influenza," says Jeffrey Shaman, PhD, Mailman School assistant professor of Environmental Health Sciences and co-author of the study.

 

Changes in migration not only alter the pattern of contact among bird species, they could also change the ways that birds come into contact with domestic animals like pigs. Gene-swapping between avian and pig influenza viruses was a factor in the 2009 swine flu pandemic.

 

 

For the record, the Pacific is currently in a La Niña cycle, and the forecast is for it to remain so well into the Northern Hemisphere spring of 2012.

 

 

This is an interesting hypothesis, and should promote some fascinating avenues of investigation.

The Birth Of The Flus

 

 

# 5963

 

 

Southeast Asia has long been considered `the cradle of influenza’, an area of the world where influenza viruses circulate year round, more than a billion people live in close proximity, and where humans and farm animals often come into close contact with one another.

 

An ideal breeding ground, and launching pad, for flu pandemics. 

 

During the 20th century, 2 of the 3 influenza pandemics (1957 Asian Flu, 1968 Hong Kong Flu) originated from this region.

 

But new research on the the spread of influenza A, published yesterday in PNAS, indicates that Southeast Asia isn’t the only birthplace of the flu.

 

The dauntingly titled open access study can be found at:

 

 

Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans

Published online before print November 14, 2011, doi: 10.1073/pnas.1109314108 PNAS November 14, 2011

Justin Bahl, Martha I. Nelson, Kwok H. Chan, Rubing Chen, Dhanasekaran Vijaykrishna, Rebecca A. Halpin, Timothy B. Stockwell, Xudong Lin, David E. Wentworth, Elodie Ghedin, Yi Guan, J. S. Malik Peiris, Steven Riley, Andrew Rambaut, Edward C. Holmes, and Gavin J. D. Smith

 

(EXCERPT)

Although the virus population that migrated between Southeast Asia and Hong Kong persisted through time, this was dependent on virus input from temperate regions and these tropical regions did not maintain a source for annual H3N2 influenza epidemics.

 

We further show that multiple lineages may seed annual influenza epidemics, and that each region may function as a potential source population. We therefore propose that the global persistence of H3N2 influenza A virus is the result of a migrating metapopulation in which multiple different localities may seed seasonal epidemics in temperate regions in a given year.

 

Such complex global migration dynamics may confound control efforts and contribute to the emergence and spread of antigenic variants and drug-resistant viruses.

 

 

The entire study is available online, but for those of us who find the finer details of Bayesian phylogeographic analysis of viral migration above our pay grade, we’ve a press release from Duke University Medical Center that helps summarize this paper.

 

Study finds tropical areas aren't the only source of seasonal flu

DURHAM, N.C. and SINGAPORE – A commonly held theory says that flu virus originates every year in Southeast and Eastern Asia, making this region the source of seasonal flu epidemics in other parts of the world.

 

However, researchers at Duke-NUS Graduate Medical School in Singapore have found that influenza virus in tropical areas isn't the only global source of flu epidemics. The international team of scientists involved in the work found that any one of the urban centers they studied could act as a source for a flu epidemic in any other locality.

 

"We found that these regions are just one node in a network of urban centers connected by air travel, through which flu virus circulates and causes a series of local epidemics that overlap in time," said Gavin Smith, PhD, senior author and Associate Professor in the Program in Emerging Infectious Diseases at Duke-NUS.

 

The study was published the week of Nov. 14 in the online Early Edition of the Proceedings of the National Academy of Sciences.

 

The research team chose to study influenza A because it is much more prevalent than both influenza B and C. Influenza is a significant cause of human illness and death worldwide – the World Health Organization estimates that 250,000 to 500,000 influenza A related deaths occur per year worldwide, and about 49,000 deaths occur in the United States.

 

The team obtained RNA sequences of virus samples from 2003 to 2006 in Australia, Europe, Japan, New York, New Zealand and Southeast Asia, as well as some more recently sequenced viruses from Hong Kong. The virus populations from tropical Southeast Asia and Hong Kong showed relatively low levels of genetic diversity and no seasonal fluctuations in comparison with annual temperate-area epidemics.

 

The analysis used time and space parameters to reveal high rates of viral migration among the urban centers tested. Although the virus population that migrated between Southeast Asia and Hong Kong persisted through time, the pattern of infections also depended on virus input from temperate regions that have distinct seasons. None of the temperate and tropical regions they examined was the source of all of the new flu strains in a given year.

 

The scientists showed that multiple lineages of a virus could seed annual flu epidemics, and that each region could function as a potential source population.

(Continue . . . )

 

 

Six weeks before the 2009 H1N1 pandemic virus emerged in Mexico, I wrote  blog called:

 

Sunday, March 08, 2009

How The Next Pandemic Will Arrive

# 2876

There is a lot we don't currently know about the next pandemic.  We don't know when it will arrive.  We don't know what virus will cause it.  And we don't know how bad it will be.

 

But there is one thing almost certain.

 

It will arrive in most countries by airplane.

The video above, which as been making the rounds for several months, was made by ZHAW (Zürcher Hochschule für Angewandte Wissenschaften) or The Zurich University of Applied Sciences.

(Continue . . .)

 

 

Before the advent and explosion in international air travel, the tropical regions of Southeast Asia probably played a much bigger role in the the creation, incubation, and spread of influenza viruses. 

 

With man’s help, influenza today has become an accomplished world traveler. No longer are we protected by vast oceans and long transit times.

 

New strains and viral reassortments that a few decades ago might have sputtered and died out unnoticed in some remote region of the world, or have been detected and quarantined aboard slow moving ships, can now hop a plane and find new hosts in a matter of hours.

 

Something we saw as recently as the 2009 H1N1 pandemic, which began not in Asia, but in the Americas.

 

Further proof that as the world evolves and become more complex, so does the threat from emerging infectious diseases.

PNAS: Reassortment Potential Of Avian H9N2

 

 

 

# 5675

 

All that is required to spark a pandemic is for a novel influenza virus to emerge that mankind has little or no resistance to, for it to cause significant morbidity and mortality, and for it to adapt to human physiology so that it transmits efficiently.

 

The H5N1 virus fulfills these first two criteria, but fails on the third. 

 

For now, anyway.

 

But there are many other influenza viruses circulating in birds, pigs, and other species that have the potential to either mutate - or more likely - reassort (swap gene segments with another flu strain) and adapt to human hosts.

 

Below you’ll find a chart lifted and edited from CIDRAP’s excellent overview Avian Influenza (Bird Flu): Implications for Human Disease  showing non-H5N1 avian flu infections in humans over the past decade.

 

 

Since surveillance is – at best - haphazard (or even non-existent) in many parts of the world, how often these types of novel infections really occur is unknown.  

 

Despite rare known human infections, these viruses need to acquire genetic changes before they could spark a pandemic. Which is why we concern ourselves with their ability to reassort with other – already humanized – flu strains.

 

Reassortment (or Shift), happens when two different influenza viruses co-infect the same host and swap genetic material.

 

 

Influenza A viruses have 8 gene segments (PB2, PB1, PA, HA, NP, NA, M1, M2, NS1, NS2)

.

Which means that any two compatible influenza viruses could conceivably – and under the right conditions – generate 256 different combinations by swapping one or more of their 8 (potentially) interchangeable gene segments.

 

The key words being “under the right conditions”.

 

 

Last February in PNAS: Reassortment Of H1N1 And H9N2 Avian viruses we saw research from Chinese scientists that created – using reverse genetics – 128 reassorted viruses from the avian H9N2 virus and the (formerly pandemic) H1N1 virus.

 

In mouse testing, they found half of the hybrid viruses were biologically `fit’ as far as replication goes, and 8 hybrids were significantly more pathogenic than either of their parental viruses.

 

 

Today, again from PNAS, we have a new study that once again looks at the reassortment potential of the avian H9N2 virus and H1N1.

 

This time, research was done using ferrets, whose respiratory physiology is closer to human than are mice.

 

Compatibility of H9N2 avian influenza surface genes and 2009 pandemic H1N1 internal genes for transmission in the ferret model

J. Brian Kimble, Erin Sorrell,  Hongxia Shao,  Philip L. Martin, and Daniel Roberto Perez

Abstract

In 2009, a novel H1N1 influenza (pH1N1) virus caused the first influenza pandemic in 40 y. The virus was identified as a triple reassortant between avian, swine, and human influenza viruses, highlighting the importance of reassortment in the generation of viruses with pandemic potential.

 

Previously, we showed that a reassortant virus composed of wild-type avian H9N2 surface genes in a seasonal human H3N2 backbone could gain efficient respiratory droplet transmission in the ferret model.

 

Here we determine the ability of the H9N2 surface genes in the context of the internal genes of a pH1N1 virus to efficiently transmit via respiratory droplets in ferrets. We generated reassorted viruses carrying the HA gene alone or in combination with the NA gene of a prototypical H9N2 virus in the background of a pH1N1 virus.

 

Four reassortant viruses were generated, with three of them showing efficient respiratory droplet transmission. Differences in replication efficiency were observed for these viruses; however, the results clearly indicate that H9N2 avian influenza viruses and pH1N1 viruses, both of which have occasionally infected pigs, have the potential to reassort and generate novel viruses with respiratory transmission potential in mammals.

 

The entire study is available online, and open access. 

 

As noted in the abstract above, these authors had previously successfully created laboratory reassortments between seasonal H3N2 and H9N2.  

 

The fact that these hybrid viruses can be created in the laboratory doesn’t automatically mean they would be generated in the field by a co-infected host.

 

Only that it is possible.

 

And with 256 possible combinations, these 4 hybrids might not even represent the most `fit’ reassortments.

 

But research like this continues to show the potential for the H9N2 virus to move towards a more `humanized’ pathogen. And with H1N1 and H9N2 both known to be circulating in pigs in Asia, there are ample opportunities for them to co-infect the same host. 

 

A few notable H9N2 stories from the past include:

• In December 2008 I ran a blog featuring an interview in which world famous Hong Kong virologist Malik Peiris cautioned that the H9N2 virus may be circulating far more commonly than we believe. Revisiting A Malik Peiris Interview On H9N2

• In January of 2010, in H9N2: The Other Bird Flu Threat, I wrote about the World Health Organization  recommending the creation of a candidate vaccine virus for H9N2. According to the latest vaccine update from the WHO, work continues on that candidate vaccine virus.

• And just this past November, in Study: The Continuing Evolution Of Avian H9N2, we looked at computer modeling that suggested that the H9N2 virus moving towards becoming more `human-adapted’.

 

Unlike the H7 and H5 avian flu strains, poultry (and swine) infections by the H9N2 virus are not required to be reported to the OIE.  

 

As we saw in 2009, sometimes a pandemic virus will emerge from an unexpected source, and with a surprising lineage. While the world was waiting for an H5 bird flu to emerge from Asia, we were blindsided by a H1N1 swine flu from North America.

 

All of which highlights the importance of establishing better global surveillance of humans, and farm animals, for the next emerging influenza virus. 

 

Regardless of its strain.