EID Journal: The Rapidly Expanding Range Of HPAI Viruses

# 9971

 

What a difference a year makes.

 

In January of 2014 a new, HPAI H5N8 virus (which had only rarely been sighted in China before) turned up in a big way in South Korea’s poultry and wild bird population, and proceeded to infect dozens of farms, resulting in the culling of millions of birds.  

 

The virus briefly appeared in Southern Japan (see Japan: Detection Of H5 Avian Flu At Poultry Farm) in April of last year, but was pretty much considered an `Asian’ problem – and one that was far less well distributed across the landscape than was H5N1.

But early last November the world awoke to find HPAI H5N8 had made its way to western Europe, when a farm in Germany reported the virus (see Germany Reports H5N8 Outbreak in Turkeys), followed 10 days later  by reports from the Netherlands (see Netherlands: `Severe’ HPAI Outbreak In Poultry), and again from Japan (see Japan: H5N8 In Migratory Bird Droppings).

H5N8 Branching Out To Europe & Japan

 

Suddenly H5N8 was on the move, in a manner which we hadn’t seen since the great H5N1 diaspora of 2006 – when that virus spread out of Asia and into Europe, Africa, and the Middle East.

 

Soon the UK, Italy, China and Russia would be added to the list of nations where H5N8 was showing up, as would Taiwan towards the end of the year. 

But the biggest surprise came when HPAI H5 virus literally crossed oceans and turned up – first in Canada’s Pacific Northwest (see Fraser Valley B.C. Culling Poultry After Detecting H5 Avian Flu) in early December – and then began spreading across the western United States (see EID Journal: Novel Eurasian HPAI A H5 Viruses in Wild Birds – Washington, USA).

.

And somewhat ominously, as H5N8 has arrived in Taiwan, Canada, and the United States, it  reassorted with local avian flu viruses and produced unique reassortant viruses (H5N2 and H5N1 in North America, H5N2, H5N3 in Taiwan).

How viruses shuffle their genes (reassort)

 

Of these, H5N2 appears to be spreading the fastest, and causing the most damage to the poultry industry.  But the possibility of seeing additional reassortments emerge is real, and their behavior – and their pathogenicity in birds and humans – is quite frankly, impossible to predict.

Yesterday the EID Journal published a dispatch on the recent arrival of these HPAI H5 viruses, their evolution to date, and how their propensity for viral reassortment may lead to the creation of additional subtypes in the future.  I’ve only posted some excerpts, follow the link to read it in its entirety.

 

Dispatch

Rapidly Expanding Range of Highly Pathogenic Avian Influenza Viruses

Jeffrey S. Hall , Robert J. Dusek, and Erica Spackman

Author affiliations: US Geological Survey National Wildlife Health Center, Madison, Wisconsin, USA (J.S. Hall, R.J. Dusek); US Department of Agriculture, Athens, Georgia, USA (E. Spackman)

Abstract

The movement of highly pathogenic avian influenza (H5N8) virus across Eurasia and into North America and the virus’ propensity to reassort with co-circulating low pathogenicity viruses raise concerns among poultry producers, wildlife biologists, aviculturists, and public health personnel worldwide. Surveillance, modeling, and experimental research will provide the knowledge required for intelligent policy and management decisions.

The recent introduction of highly pathogenic avian influenza (HPAI) subtype H5N8 virus into Europe and North America poses major risks to poultry industries, zoologic collections, and wildlife populations; thus, this introduction warrants continued and heightened vigilance.

First discovered in early 2014 in poultry and wild birds in South Korea, HPAI H5N8 virus apparently arose in China from reassortment events between HPAI subtype H5N1 virus (clade 2.3.4.4) and several low pathogenicity viruses (LPAIVs) (1–3). The H5N8 virus was subsequently detected in waterfowl in Russia in September 2014, and since then, H5N8 virus and reassortants have been detected in poultry and wild birds in Europe (Netherlands, Germany, Italy, the United Kingdom, Hungary, and Sweden), Taiwan, Japan, Canada (British Columbia), and the western and central United States (Washington, Oregon, California, Idaho, Utah, Minnesota, Missouri, Arkansas, Kansas, Wyoming, and Montana).

Wild waterfowl are a primary natural host for LPAIVs, and infection rates in these populations peak at autumn migratory staging locations, where large numbers of immunologically naive juvenile birds congregate (4). The HPAI H5N8 virus has apparently adapted to wild waterfowl hosts: few or no clinical signs or adverse effects are apparent in these hosts when infected with the virus. Thus, it seems probable that the virus was disseminated out of Russia into Europe, East Asia, and North America by migrating waterfowl during autumn 2014 (5).

The HPAI H5N8 virus has encountered, interacted with, and reassorted with co-circulating LPAIVs in migratory and overwintering waterfowl populations, creating new HPAI viruses (HPAIVs). In Taiwan, new Eurasian lineage reassortant HPAIVs (i.e., H5N2 and H5N3 subtypes) and the parental H5N8 subtype virus have been detected in poultry and wild birds (6). In North America, HPAI H5N8 virus continues to circulate among waterfowl and commercial and backyard poultry flocks. In addition, new HPAIV reassortants (i.e., H5N2 and H5N1 subtypes) that are combinations of HPAI H5N8 virus and genetic elements from Eurasian and North American viruses are also circulating in these populations (7,8) (Figure).

<SNIP>

As HPAIVs continue spreading and evolving, the questions posed here, along with many more questions, will need to be answered to understand the risks to agriculture, zoologic collections, wildlife, and, potentially, human populations. As other researchers have recently pointed out, robust, targeted surveillance programs among wild birds (11) and poultry, modeling of the movements of HPAIV-infected wild birds, and experimental research studies will provide the knowledge required for intelligent policy and management decisions regarding agriculture, wildlife, and public health.

(Continue . . .)

 

While we can’t know what new reassortments may appear next fall or winter in North America, the idea that somehow we in North America are somehow insulated from the Asian and Eurasian avian flu strains by oceans and distance seems pretty well demolished.

 

For more on how these viruses may be able to cross oceans and continents, you may wish to revisit:

USGS: Alaska - A Hotspot For Eurasian Avian Flu Introductions

Erasmus Study On Role Of Migratory Birds In Spread Of Avian Flu

PNAS: H5N1 Propagation Via Migratory Birds

EID Journal: A Proposed Strategy For Wild Bird Avian Influenza Surveillance

PLoS One: North Atlantic Flyways Provide Opportunities For Spread Of Avian Influenza Viruses

EID Journal: Rapid Emergence Of Novel HPAI H5 Subtypes

How viruses shuffle their genes (reassort)

 

# 9912

 

After more than 17 years of relative stability (1996-2013) - during which time we only had one major HPAI H5 avian virus (H5N1) to concern ourselves with - we’ve seen a sudden and unprecedented expansion of highly pathogenic H5 avian subtypes around the globe.

The first minor crack in H5’s veneer appeared in 2008, when two mallard ducks in Eastern China tested positive for a new subtype H5N5 (see Novel H5N5 Avian Influenza Detected In China).

 

The account of its discovery appeared in the 2011 EID Journal Dispatch called Novel Reassortant Highly Pathogenic Avian Influenza (H5N5) Viruses in Domestic Ducks, China, where they identified the likely parental viruses (H5N1 and H6N5) both circulating in local domestic ducks.

While never a huge `player’ in the avian flu world, H5N5 demonstrated that H5N1 could reassort into a novel subtype, and suggested that domestic ducks could serve as `mixing’ vessels for creating new subtypes of influenza viruses. 

In an instance of particularly good timing – in the middle of March of 2013, just two weeks before we learned of the emergence of H7N9 in China – the EID Journal published a research Article on Predicting Hotspots for Influenza Virus Reassortment. 

 

While the northern plains of India, the western Korean Peninsula and southwestern Japan were mentioned, their two biggest hotspots were Eastern China, and the Nile Valley of Egypt – both regions that have produced either new subtypes, or new clades (see Emergence Of A Novel Cluster of H5N1 Clade 2.2.1.2), of HPAI H5 viruses over the past two years.

 

 

In January of 2014, an emerging HPAI H5N8 appeared in South Korea, and rapidly spread through that nation’s poultry and wild bird population.  It showed up in Japan in April, and was subsequently reported in China.  

 

During the winter of 2014-15, H5N8 migrated to Russia, Western Europe, and even North America – and along the way spawned additional reassortants (H5N2, H5N3, H5N1) when it mixed with local avian flu subtypes.  Thus far, none of these H5N8 derived viruses have proven pathogenic in humans.

During the Spring of 2014 another HPAI H5 appeared in Southeast Asia; H5N6.   Unlike the H5N8 virus (and its descendents), H5N6 has caused serious (even fatal) human illness (see China Reports 3rd H5N6 Case (Fatal) – Yunnan Province).

 

Suddenly we’ve gone from one HPAI H5 virus of concern, to a half dozen.  And as these viruses spread, and mingle with other viruses, more novel subtypes may yet emerge.   And as the following dispatch from the EID Journal points out, their future behavior may be unpredictable.

 

 

Dispatch

Rapid Emergence of Highly Pathogenic Avian Influenza Subtypes from a Subtype H5N1 Hemagglutinin Variant

Erik de Vries , Hongbo Guo¹, Meiling Dai¹, Peter J.M. Rottier, Frank J.M. van Kuppeveld, and Cornelis A.M. de Haan  Abstract

In 2014, novel highly pathogenic avian influenza A H5N2, H5N5, H5N6, and H5N8 viruses caused outbreaks in Asia, Europe, and North America. The H5 genes of these viruses form a monophyletic group that evolved from a clade 2.3.4 H5N1 variant. This rapid emergence of new H5Nx combinations is unprecedented in the H5N1 evolutionary history.

A highly pathogenic avian influenza (HPAI) A(H5N1) virus (A/goose/Guangdong/1/1996) was first detected in China in 1996. Multiple clades, defined by phylogenetic characterization of the H5 hemagglutinin (HA) (1), have evolved and spread across Asia, Africa, and Europe, causing enormous losses to the poultry industry. A total of 694 human infections (death rate 58%) were recorded during 2003–2014 (2).

During the evolution of HPAI H5N1 viruses, reassortment events involving the 6 internal gene segments have often been detected (reviewed in [3]), but novel subtypes (i.e., combinations of HPAI H5 with other N subtypes) have rarely been isolated. In 2014, a novel highly virulent reassortant HPAI H5N6 virus (4) caused multiple outbreaks in Southeast Asia and 1 lethal human infection, which led the Food and Agricultural Organization of the United Nations to issue a warning (5). Outbreaks of novel HPAI H5N8 virus in South Korea (6,7), China (8), and Japan raised further concern, and in November 2014, this subtype emerged outside Eastern Asia, causing outbreaks in poultry farms in Germany, the Netherlands, the United Kingdom, Canada, and the United States.

<SNIP>

Conclusion

(Excerpt)

In this study, we exclusively focused on the unique occurrence of new HA–NA combinations. Recent publications have already described the reassortment events of the internal gene segments of several of the viruses mentioned above (6–8,11–14). In contrast to novel HA–NA combinations, novel constellations of internal gene segments are far from unique and have frequently been observed for HPAI H5N1 viruses (3). Our analysis indicates that new HPAI viruses have emerged that carry H5 proteins capable of matching with multiple NA subtypes. Whether the formation of new HA–NA combinations confers a selective advantage that contributed to the emergence of these novel subtypes is not known and requires elaborate research. However, the balance between HA (receptor binding) and NA (receptor cleavage) protein activities is known to be critical to cell entry and host tropism and may be an important factor that lead to the emergence of new HA–NA combinations. In contrast to HPAI H5N1, the novel clade 2.3.4.4 viruses, excluding H5N6 viruses, have not caused human infections. However, it is unknown to what extent the repeated acquisition of a new NA proteins could enhance the rate of evolution of the HA protein. Obviously such changes could further affect host and tissue specificity, potentially having serious consequences. Therefore, surveillance is required to monitor further spread, evolution, and potential changes in host range.

 

Given the recent emergence of H5N8, H5N6, H5N3 in Asia and novel reassortants of H5N2 and H5N1 in North America, and it comes as little surprise that the World Health Organization recently released a pointed warning that H5 Is Currently The Most Obvious Avian Flu Threat.

 

CIDRAP: FAO Reports Mutations In H5N1 Virus From Egyptian Poultry

 

# 9543

 

Last night CIDRAP published a piece by News Editor Robert Roos which looks at genetic characterizations of H5N1 viruses sampled from Egyptian poultry recently. According to the FAO, this analysis showed signs of several troubling `mammalian adaptations’, although two isolates taken from humans recently reportedly showed no major genetic changes.

First some excerpts from  Robert’s detailed report (but you’ll want to read the whole thing), then I’ll be back with a little more.

 

FAO notes mutations in H5N1 samples from Egypt's poultry

Robert Roos | News Editor | CIDRAP News

Jan 07, 2015

Amid a flurry of human H5N1 influenza cases in Egypt, scientists have found H5N1 viruses in Egyptian poultry that have two mutations that are usually associated with adaptation to mammals, a United Nations Food and Agriculture Organization (FAO) official reported today.

Juan Lubroth, DVM, PhD, the FAO's chief veterinary officer, told CIDRAP News that the mutations were identified through genetic sequencing of 52 recent isolates from poultry. But he also said a recent analysis of viruses from two human patients in Egypt showed no major genetic changes.

Egypt has had a surge of human H5N1 cases over about the past 7 weeks, after reporting very few during the preceding 2 years. According to media reports based on health ministry statements, the country had 29 cases with 11 deaths in 2014, most of them in November and December. All or nearly all of the patients had contact with poultry, and no signs of human-to-human transmission have been reported, but the cases have prompted some speculation about whether the virus has changed in some way.

In addition, Egypt has had a big increase in reported poultry outbreaks of H5N1 recently, according to the FAO. A graph supplied by Lubroth showed about 70 outbreaks in November (2014) and close to 180 outbreaks in December, compared with fewer than 10 in each of those months in 2013.

(Continue . . . )

 

The evolutionary path that would take an avian influenza virus – like H5N1 – to the point where it was well-enough adapted to mammals to pose a pandemic threat isn’t well mapped. There are a lot of interactive `moving parts’ inside a virus, and how evolutionary changes (via accrued amino acid substitutions) affect the virus’s behavior are only partially understood.

 

On a `macro level’, we know that avian viruses bind preferentially to the type of receptor cells (α-2,3) found in the gastrointestinal tract of birds, and that mammalian-adapted viruses would have to evolve to bind preferentially to α-2,6 receptor cells – they type found in the upper respiratory tract of mammals.

We also believe that an adapted virus would have to thrive and replicate in the slightly cooler environment found in their upper respiratory tracts (birds run `hotter’  than mammals by several degrees).

 

While both are viewed as important, it is likely that there are other – perhaps subtle – changes that must occur before an avian virus can effectively jump to a mammalian host.  Robert’s article cites the following changes:

 

Genetic sequencing of 52 isolates revealed that the hemagglutinin (H5) genes in the virus continue to evolve but that all the isolates belong to clade 2.2.1, the same as seen in previous years. However, the scientists also identified two "fixed mutations": a "combination of [delta]129 and I151T," and a "T156A causing a loss of glycosylation at receptor binding site."

"Both mutations enhance alpha 2-6 receptor binding (which is associated with mammalian adaptation)," the statement said. It added that the virus is nonetheless still regarded as an avian one.

However, the FAO also reported the emergence in 2014 of a new H5N1 cluster with three other mutations—D54N, R189K, and R474K. It said this cluster also remains within clade 2.2.1, but the significance of the mutations needs to be assessed.

 

Although we talk about the H5N1 virus as if it were a single entity, the virus has evolved into numerous clades, and sub-clades, around the globe – with a range of  variants within each.  As a result, the H5N1 virus circulating in Egypt is not the same H5N1 virus circulating in Cambodia. 

 

H5N1 alone has produced more than 20 clades and sub-clades over the years (not all continue to circulate).

Diversity of circulating H5N1 Clades – Credit WHO

 

While these evolutionary variations mostly come about slowly due to antigenic drift, more abrupt changes can come through antigenic `shift’ – or reassortment.  With the recent expansion of the constellation of HPAI H5 viruses expanding around the globe (including H5N1, H5N8, H5N6, H5N2, H5N3), the opportunities for reassortment only increase.

 

Although concerning, we’ve seen similar pronouncements regarding `mammalian adaptations’  detected in H7N9, H9N2, and even H5N1 virus in recent years (see Study: H5 Clade 2.3.4.6 Receptor Binding & Nature Comms: Host Adaptation Of Avian Influenza Viruses), and yet none of these viruses has managed to make the leap to mammals.

 

Some scientists suspect there may be some kind of `species barrier’ that will prevent any of these avian viruses from ever making the jump, pointing out that only H1, H2, and H3 influenza viruses have (at least, in the 120 year history we know about) caused significant human illness (see  Are Influenza Pandemic Viruses Members Of An Exclusive Club?).

 

Other scientists point out that 120 years of influenza observation is hardly enough to base any solid conclusions.  That nature is full of surprises.

 

So we watch these viruses circulate in the wild, watching for changes both in their genetics and in their behavior, in the hopes that we might get some early warning of a pandemic.  Time enough to make a vaccine, or with a lot of luck, time enough to contain an outbreak.

 

The biggest problem being - that when you don’t know exactly what any novel pandemic virus will look like - you never really know how close – or how far away -  you are to seeing one emerge.

Study: Ebola Virus Is Rapidly Evolving

Credit CDC PHIL

 

# 9015

 

One of the concerns we have when any zoonotic virus spills over into the human population is that over time, as it passes from one person to the next, it could pick up host adaptations – mutations – that could make the virus a greater threat over time.

 

In the laboratory, researchers will often conduct serial passage experiments (see Serial Passage Of H5N2 In Mice) to observe these evolutionary changes, and try to figure out what they mean.

 

Often, these genetic changes are of little or no effect, and can sometimes even be detrimental to the `biological fitness’ of the virus. Those that favor replication in the new found host, however, tend to carry on to produce more progeny, advancing their new lineage forward,  drowning out the earlier `wild type’ virus in the host.

 

A recent concern has been that Ebola - which up until now has never really spread in kind of long chains of human cases that we are seeing now – could better adapt to human physiology over time.

 

Today we’ve a study appearing in the Journal Science where scientists sequenced 99 Ebola viruses taken from 78 people from Sierra Leone during the month of June, and found that the virus is showing a marked propensity to accumulate `interhost and intrahost genetic variation’ as it passages through the population.

 

First a bit from the study, then I’ll be back with more.

Published Online August 28 2014

Science DOI: 10.1126/science.1259657

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

Stephen K. Gire¹,²,*, Augustine Goba³,*,†, Kristian G. Andersen¹,²,*,†, Rachel S. G. Sealfon²,⁴,*, Daniel J. Park²,*, Lansana Kanneh³, Simbirie Jalloh³, Mambu Momoh³,⁵, Mohamed Fullah³,⁵,‡, Gytis Dudas⁶, Shirlee Wohl¹,²,⁷, Lina M. Moses⁸, Nathan L. Yozwiak¹,², Sarah Winnicki¹,², Christian B. Matranga², Christine M. Malboeuf², James Qu², Adrianne D. Gladden², Stephen F. Schaffner¹,², Xiao Yang², Pan-Pan Jiang¹,², Mahan Nekoui¹,², Andres Colubri¹, Moinya Ruth Coomber³, Mbalu Fonnie³,‡, Alex Moigboi³,‡, Michael Gbakie³, Fatima K. Kamara³, Veronica Tucker³, Edwin Konuwa³, Sidiki Saffa³, Josephine Sellu³, Abdul Azziz Jalloh³, Alice Kovoma³,‡, James Koninga³, Ibrahim Mustapha³, Kandeh Kargbo³, Momoh Foday³, Mohamed Yillah³, Franklyn Kanneh³, Willie Robert³, James L. B. Massally³, Sinéad B. Chapman², James Bochicchio², Cheryl Murphy², Chad Nusbaum², Sarah Young², Bruce W. Birren², Donald S. Grant³, John S. Scheiffelin⁸, Eric S. Lander²,⁷,⁹, Christian Happi¹⁰, Sahr M. Gevao¹¹, Andreas Gnirke²,§, Andrew Rambaut⁶,¹²,¹³,§, Robert F. Garry⁸,§, S. Humarr Khan³,‡§, Pardis C. Sabeti¹,²,†§

 

In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2,000x coverage. We observed a rapid accumulation of interhost and intrahost genetic variation, allowing us to characterize patterns of viral transmission over the initial weeks of the epidemic. This West African variant likely diverged from Middle African lineages ~2004, crossed from Guinea to Sierra Leone in May 2014, and has exhibited sustained human-to-human transmission subsequently, with no evidence of additional zoonotic sources. Since many of the mutations alter protein sequences and other biologically meaningful targets, they should be monitored for impact on diagnostics, vaccines, and therapies critical to outbreak response.

• In Depth Infectious Disease Genomes reveal start of Ebola outbreak

  • Gretchen Vogel
  Science 29 August 2014: 989-990.
  • Summary
  • Full Text
  • Full Text (PDF)

These researchers found that the virus had evolved into three distinct lineages in Sierra Leone during the month of June (one of which appears to have died out), along with accumulating scores of amino acid changes to its genome.

 

It should be noted that while scientists have the ability to sequence and compare these variant viruses, they don’t necessarily know what these individual mutations (or their aggregate) means to the virus, or how it might change its behavior. 

 

Based on the location of some these changes, there are concerns that the PCR primers currently used to detect it patients may need adjusting, and that some of the antiviral drugs being developed could be impacted as well. 

 

And while it is theoretically possible that changes to the genome could affect the transmissibility of the virus, we haven’t seen any evidence of that happening.

 

Unknown at this time are what genetic changes might be occurring in the virus in Liberia and Guinea, or even Nigeria. The bottom line, however, is that the longer this virus circulates in humans, the better chance it has of producing a mutation we really don’t want to see.

 

For some more coverage on this report, NPR’s Goats & Soda Blog has:

 

Ebola Is Rapidly Mutating As It Spreads Across West Africa

by Michaeleen Doucleff

 

 

This from Scientific American:

 

Patient Zero Believed to be Sole Source of Ebola Outbreak

By pinpointing the virus’s source, a new report validates steps health care workers are taking to battle the disease

Aug 28, 2014 |By Dina Fine Maron

And this from Nature News. 

 

Ebola virus mutating rapidly as it spreads

Outbreak likely originated with a single animal-to-human transmission.

Eurosurveillance: Genetic Tuning Of Avian H7N9 During Interspecies Transmission

 

# 8788

 

 

This week’s Eurosurveillance bonanza of avian flu transmission & evolution papers has more than enough good stuff to keep us busy reading for hours. All of these papers are of great interest, but one in particularly grabbed my attention, mainly due to the potential impact of its findings.

A study that looks at the continual evolution of the H7N9 virus in Mainland China.

 

To recap: in February of last year a new and dangerous avian influenza virus (H7N9)  jumped to humans in Eastern China, although we did not learn about it until the end of March (see More Details Emerge On Shanghai H7N9 Case). Unlike many of the other avian influenza viruses we’ve seen - this virus produced no visible signs of illness in poultry - making it particularly difficult to detect and control.

Benign in poultry, but not in humans, H7N9 often produces a severe form of pneumonia.  One that has killed roughly 30% of those known to have been infected.

 

The only saving grace has been this virus has not yet achieved the ability to transmit efficiently from one human to another. The vast majority of human cases appear to be the result of direct exposure to infected birds or to their environment.

 

In that first wave about 130 human cases emerged, tapering off only after aggressive controls on live bird markets were imposed in April and May of 2013 (see The Lancet: Poultry Market Closure Effect On H7N9 Transmission). After a quiescent summer, colder fall and winter temperatures brought with it a resurgence in the number of human cases, with the second wave roughly double the size of the first (cite).

Two Waves of H7N9  - Credit Hong Kong’s CHP

 

A month ago, 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.

As we’ve discussed before, the genetic contributions from the avian H9N2 virus appear to be significant. 

 

Of the three avian flu viruses we are currently watching with the most concern – H5N1, H7N9, 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

 

It turns out the relatively benign and ubiquitous H9N2 is actually a fairly promiscuous virus, as bits and pieces of it keep turning up in new reassortant viruses.  See PNAS: Reassortment Of H1N1 And H9N2 Avian viruses & PNAS: Reassortment Potential Of Avian H9N2 for some earlier looks at H9N2’s active social life.

 

Today, in research from a group of scientists working for China’s National and Provincial CDCs, we learn that the genetic diversity of the H7N9 virus is even greater than previously described, and that continual reassortment with the H9N2 virus, along with passage through a variety of host species, appears to be influencing its ongoing evolution.

 

A process the authors call `genetic tuning’.

 

Non-scientists will likely find this article tough sledding (parts certainly were for me), as it is more than a little technical.  It is, however, a fascinating paper. 

 

With apologies in advance to any real scientists who may be reading this - come back after the link and abstract - and I’ll do my best to hack through some of the tall grass and go over a few of the highlights.

 

 

          Eurosurveillance, Volume 19, Issue 25, 26 June 2014

Research articles

Genetic tuning of the novel avian influenza A(H7N9) virus during interspecies transmission, China, 2013

D Wang^1,2, L Yang^1,2, R Gao¹, X Zhang³, Y Tan⁴, A Wu⁵, W Zhu¹, J Zhou¹, S Zou¹, Xiyan Li¹, Y Sun⁶, Y Zhang⁷, Y Liu⁸, T Liu⁹, Y Xiong¹⁰, J Xu¹¹, L Chen¹², Y Weng¹³, X Qi¹⁴, J Guo¹, Xiaodan Li¹, J Dong¹, W Huang¹, Y Zhang¹, L Dong¹, X Zhao¹, L Liu¹, J Lu¹, Y Lan¹, H Wei¹, L Xin¹, Y Chen¹, C Xu¹, T Chen¹, Y Zhu¹, T Jiang⁵, Z Feng¹⁵, W Yang¹⁵, Y Wang¹⁵, H Zhu¹⁶, Y Guan¹⁶, G F Gao¹⁵, D Li¹, J Han¹, S Wang¹, G Wu¹, Y Shu ()¹

Date of submission: 28 July 2013

---

A novel avian influenza A(H7N9) virus causing human infection emerged in February 2013 in China. To elucidate the mechanism of interspecies transmission, we compared the signature amino acids of avian influenza A(H7N9) viruses from human and non-human hosts and analysed the reassortants of 146 influenza A(H7N9) viruses with full genome sequences.

We propose a genetic tuning procedure with continuous amino acid substitutions and reassorting that mediates host adaptation and interspecies transmission.

When the early influenza A(H7N9) virus, containing ancestor haemagglutinin (HA) and neuraminidase (NA) genes similar to A/Shanghai/05 virus, circulated in waterfowl and transmitted to terrestrial poultry, it acquired an NA stalk deletion at amino acid positions 69 to 73. Then, receptor binding preference was tuned to increase the affinity to human-like receptors through HA G186V and Q226L mutations in terrestrial poultry. Additional mammalian adaptations such as PB2 E627K were selected in humans.

The continual reassortation between H7N9 and H9N2 viruses resulted in multiple genotypes for further host adaptation. When we analysed a potential association of mutations and reassortants with clinical outcome, only the PB2 E627K mutation slightly increased the case fatality rate. Genetic tuning may create opportunities for further adaptation of influenza A(H7N9) and its potential to cause a pandemic.

 

 

What these researchers did was to collect specimens (as well as clinical and epidemiological information) from human H7N9 cases, along with avian and environmental samples from areas where human cases were identified. 

 

From this they assembled 173 influenza A(H7N9) viruses (103 human and 70 non-human) and analyzed them to try to determine how (and from where) they had evolved.

 

Remarkably, out of 146 H7N9 viruses with full genome sequences, they detected at least 26 seperate genotypes, mostly from the first wave in 2013. Of those 26, twenty were only detected once or twice, suggesting they were transient, and perhaps not as `biologically fit’ as some of the other genotypes.

 

Based on their observations, the authors propose that `a genetic tuning procedure with continuous amino acid substitutions and reassortations, mediates the host adaptation and interspecies transmission of H7N9 viruses (Figure 4)’.

 

Essentially, they describe two processes that they believe  facilitate the evolution and adaptation of the virus.  Processes that may be `tuning’ the virus in the direction of  a `human-adapted’ pathogen.

 

The first is ongoing reassortment with H9N2 viruses.  

 

Reassortment occurs when two different influenza viruses infect the same host simultaneously.  In `close quarters’ they can swap out gene segments, and if they hit the right combination, generate a successful hybrid virus. 

 

Reassortment also produces the biggest, and most abrupt changes in the virus, and is believed the mechanism behind the emergence of many pandemic viruses.  You can view a short (3 minute) video from NIAID on reassortment here.

 

Based on 26 distinct genotypes described in this paper, the reassortment of H7N9 appears to be a vigorous, and ongoing, process. The greatest concentration of genotypes was found in the Yangtze river delta (see map below), suggesting this may be the region where the virus first emerged.

 

The second evolutionary path occurs as these reassortant viruses passage through different species and pick up specific amino acid changes.

 

When a virus infects a cell, it immediately sets upon making thousands of copies of itself in order to spread the infection throughout the host. Single-stranded RNA influenza viruses are notoriously sloppy replicators, so invariably, some of these viral copies will carry small transcription errors (in the form of amino acid substitutions).

 

Most of these `variants’  will prove either neutral or perhaps even detrimental to the survival and propagation of the virus, but occasionally a helpful change occurs (positive selection) that increases the `biological fitness’ of the virus  – at least for the current host species. 

 

Viral progeny that are the best suited for their host usually win the replication wars, and soon outnumber and overrun less `fit’ variants. As a result, a better `adapted’ virus can emerge.  And if those adaptations help it jump to another host species, it is a viral win-win.

 

The authors point out that the `mixed bird’ environment of live markets may have helped H7N9’s evolution along, as it was able to spread stealthily, and without interruption, among a variety of species – picking up useful adaptations along the way.

 

As an example, avian flu viruses bind preferentially to the α2-3 receptor cells found in the gastrointestinal tract of birds.  But the H7N9 virus also binds (albeit, not as robustly) to human α2-6 human receptor cells, which are found in mammalian tracheas and upper airways (see Nature: Receptor Binding Of H7N9).

. 

 

The authors speculate H7N9’s partial affinity to α2-6 receptor cells may have been picked up when it passaged through quail or pigeons, which are known to carry both types of cells.

 

And even once it infects man, the H7N9 virus continues to adapt and evolve, with the PB2 E627K mutation detected in a large number of human isolates.  E627K and/or D701N mutations in the PB2 protein are considered critical for mammalian adaptation of avian influenza viruses, as they allow the virus to replicate efficiently in the lower temperatures found in the upper airway.

 

As H7N9 reassorts and passages through different species – a process the authors call `genetic tuning’ - it continues to evolve, and reinvent itself.  Meaning that the virus we get next fall , winter, or spring may not act like the virus we saw during the first two waves. 

 

Obviously, I’ve just covered some of the highlights, and then, only with the broadest of strokes.  I’m certain many of my readers will want to read the entire paper.  But to close, I’ll let the authors speak to the significance of their findings.

 

Genetic tuning not only mediated species switching, but may also allow the virus to adapt so that it infects humans more easily and transmits among people more efficiently. Recently, Malaysia reported its first human case of influenza A(H7N9), imported from Guangdong province, China [28]. Rapid transportation and frequent travelling have made it possible to transfer the virus from China to other regions.

Overall, due to the genetic tuning procedure, the potential pandemic risk posed by the novel avian influenza A(H7N9) viruses is greater than that of any other known avian influenza viruses. A response to this threat requires the combined effort of different sectors related to human health, poultry and wild birds, as well as vigilance and co-operation of the world.

mBio: Spread, Circulation, and Evolution of MERS-CoV

Distribution of MERS-CoV clades in time and space. - mBio

 

# 8313

 

Although MERS has receded from the headlines over the past couple of months, it continues to circulate in the Middle East, and occasionally jump to humans.   Exactly how it circulates, and how it jumps to humans, isn’t known – although recent research has pointed a finger at both camels and bats as being possible reservoir hosts for the virus.

 

Today, the open access journal mBio carries a review of what is known about the Middle East Respiratory Syndrome Coronavirus (MERS-CoV), with an emphasis on the evolutionary changes observed in the virus over time. 

 

As the number of genetic sequences on deposit has increased, so have the number of MERS variants. None, however, have shown the kind of persistence one would associate with efficient human-to-human transmission.

 

The primary assumption is that the virus is maintained in an (as yet, unidentified) animal reservoir, and that intermittent spillovers from animal hosts to humans has resulted in localized clusters. But thus far, none of these outbreaks has demonstrated a basic reproductive number (R0) high enough (>1.0) to sustain an outbreak (see The Lancet: Transmissibility Of MERS-CoV for additional background).

R0 (pronounced R-nought) or Basic Reproductive Number.

Essentially, the number of new cases in a susceptible population likely to arise from a single infection. With an R0 below 1.0, a virus (as an outbreak) begins to sputter and dies out. Above 1.0, and an outbreak can have `legs’.

 

The authors do offer an alternative explanation, however, writing:

 

An alternative hypothesis is that the virus has now infected a sufficient number of humans to account for the observed distribution and diversity of the virus but the infection is asymptomatic in many individuals. A recent serosurvey of 363 individuals in the Saudi Arabia failed, however, to find MERS-CoV-seropositive individuals (13).

 

First a link to the study, and  some excerpts, after which I’ll have a bit more.

 

Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus

Matthew Cotten^a, Simon J. Watson^a, Alimuddin I. Zumla^b,c,d, Hatem Q. Makhdoom^e, Anne L. Palser^a, Swee Hoe Ong^a, Abdullah A. Al Rabeeah^b, Rafat F. Alhakeem^b, Abdullah Assiri^b, Jaffar A. Al-Tawfiq^f, Ali Albarrak^g, Mazin Barry^h, Atef Shibl^h, Fahad A. Alrabiahⁱ, Sami Hajjarⁱ, Hanan H. Balkhy^j, Hesham Flemban^k, Andrew Rambaut^l,m, Paul Kellam^a,c,d, Ziad A. Memish^b,n

ABSTRACT

The Middle East respiratory syndrome coronavirus (MERS-CoV) was first documented in the Kingdom of Saudi Arabia (KSA) in 2012 and, to date, has been identified in 180 cases with 43% mortality. In this study, we have determined the MERS-CoV evolutionary rate, documented genetic variants of the virus and their distribution throughout the Arabian peninsula, and identified the genome positions under positive selection, important features for monitoring adaptation of MERS-CoV to human transmission and for identifying the source of infections.

Respiratory samples from confirmed KSA MERS cases from May to September 2013 were subjected to whole-genome deep sequencing, and 32 complete or partial sequences (20 were ≥99% complete, 7 were 50 to 94% complete, and 5 were 27 to 50% complete) were obtained, bringing the total available MERS-CoV genomic sequences to 65. An evolutionary rate of 1.12 × 10⁻³ substitutions per site per year (95% credible interval [95% CI], 8.76 × 10⁻⁴; 1.37 × 10⁻³) was estimated, bringing the time to most recent common ancestor to March 2012 (95% CI, December 2011; June 2012).

Only one MERS-CoV codon, spike 1020, located in a domain required for cell entry, is under strong positive selection.

Four KSA MERS-CoV phylogenetic clades were found, with 3 clades apparently no longer contributing to current cases. The size of the population infected with MERS-CoV showed a gradual increase to June 2013, followed by a decline, possibly due to increased surveillance and infection control measures combined with a basic reproduction number (R₀) for the virus that is less than 1

<SNIP>

IMPORTANCE

MERS-CoV adaptation toward higher rates of sustained human-to-human transmission appears not to have occurred yet. While MERS-CoV transmission currently appears weak, careful monitoring of changes in MERS-CoV genomes and of the MERS epidemic should be maintained. The observation of phylogenetically related MERS-CoV in geographically diverse locations must be taken into account in efforts to identify the animal source and transmission of the virus.

<SNIP>

DISCUSSION

In conclusion, the rapid identification and isolation of cases, combined with an R₀ of less than 1, may control the human-to-human transmission as long as the virus transmission properties remain the same. Full control of the MERS epidemic requires identification of the source of infections to prevent the initiation of the observed human-to-human transmission chains.

(Continue . . . )

 

The conclusion is simply an academic’s way of saying, so far, we’ve been lucky with this virus.

It didn’t come fully transmissible `out of the box’, and it still requires some evolutionary tweaking before it can spark a greater epidemic threat. 

 

But each human infection is another opportunity for MERS-CoV to `figure us out’, and the big challenge right now is to find the reservoir host of the virus (camels, bats, baboons, rodents, etc. . . ) in order to stop these spillovers before the virus learns to adapt to us.

 

I’ll leave it to Dr. Vincent Racaniello or Dr. Ian Mackay to parse and interpret the more technical aspects of this study, as a lot of it is truly above my pay grade. 

 

In the meantime, for some additional background on MERS, check out some of Ian’s recent  blogs on the topic:

 

Middle East respiratory syndrome coronavirus (MERS-CoV): summing up 100 weeks

Monkey magic: Vero cells make more MERS-CoV RNA than any other animal's...

MERS-CoV antibodies in dromedary camels from Dubai, UAE, as far back as 2005...

A date with Middle East respiratory syndrome coronavirus (MERS-CoV)..