Rhiza Labs FluTracker Forum

Pandemic H1N1 evolution scenario:
Multiple non-competing variants?

As pandemic H1N1 fall wave evolves, questions arise on possible 1918 pandemic parallels. Differently from 1957 an 1968 pandemics, 1918 pandemic, has all 8 mRNA segments markedly different from recent seasonal influenza. The same is truth about the 2009 pandemic H1N1 genome.

Among possible parallels the 1918 pandemics singular timing is the major source of concern.
The 1918 pandemic presented 3 sucessive waves over a 9 months period. Other pandemics show different interplays with influenza seasonality, spanning longer periods (2-5 years). It has been proposed that 1918 pandemic would require the presence of non-competitive virus variants to cope with that pattern.

We examine in this thread some potentialities of a similar scenario for the 2009 pandemic H1N1, conjecturing it could evolve toward a number of non competitive fit variants sharing rather similar HA and NA, and therefore, roughly equivalent vis a vis the human adaptive immune response. That is the reason why vaccines use HA an NA segments only.

The crucial point is that they are non competing variants. Of course a fit improvement would make the variant “more competitive”, in the sense that it becomes potentially harmful. However, as far as our immunological system is concerned, genetic changes on other segments such as PB2 or NS would be barely distinguishable. This feature gives a “free pass” of the new variants, which can further reassort and/or recombine at will with the remaining pandemic H1N1 variants (under evolutionary pressure). Multiple variants can coalesce into a fewer number non competitive clades with different fits, which can potentially produce close spaced pandemic waves.

The same is not true with seasonal influenza, since the host herd (their “habitat”, so to speak) already possess an acquired immune response. Viruses don’t need to fight each other. The outspacing of competitive viruses is performed mainly by the host immunity to the old strain. It is an irony: our own immunologic fittnes paves the way to pandemic H1N1 introduction and hability to dominate the scene!

The concept of pandemic multiple fit variants was introduced by Taubenberger and Morens, as a crucial component of the epidemiologic scenario of “3 pandemic waves of 1918–1919, which occurred in the spring-summer, summer-fall, and winter (of the Northern Hemisphere), respectively” (1).

As a guideline, an attached graphic allows comparison between the dynamics of 4 precedent influenza pandemics:

Mortality Distributions and Timing of Waves of Previous Influenza Pandemics.
Time scales different to each graphic. Vertical stripes are winter influenza seasons. Vertical scales are also adapded to each pandemic. Mortality percentage on peak tops.


A number of H1N1 co-circulant variants scenarios are reviewed below:

HA
Co circulation of at least 2 H1N1 variants with slightly differents HA was conceived as a possible explanation of 1918 pandemics singular timing of 3 sucessive waves over a 9 months period (1).

A brief reminder of pandemic development:
“In the 1918–1919 pandemic, a first or spring wave began in March 1918 and spread unevenly through the United States, Europe, and possibly Asia over the next 6 months (Figure 1). Illness rates were high, but death rates in most locales were not appreciably above normal. A second or fall wave spread globally from September to November 1918 and was highly fatal. In many nations, a third wave occurred in early 1919.”

The 1918 timing shows specific hallmarks and attempted explanations:
“But 3 extensive pandemic waves of influenza within 1 year, occurring in rapid succession, with only the briefest of quiescent intervals between them, was unprecedented. The occurrence, and to some extent the severity, of recurrent annual outbreaks, are driven by viral antigenic drift, with an antigenic variant virus emerging to become dominant approximately every 2 to 3 years. … … The timing and spacing of influenza epidemics in interpandemic years have been subjects of speculation for decades. Factors believed to be responsible include partial herd immunity … … most favorable circumstances, which include lower environmental temperatures and human nasal temperatures … optimal humidity, increased crowding indoors, and imperfect ventilation due to closed windows and suboptimal airflow.”

“However, such factors cannot explain the 3 pandemic waves of 1918–1919, which occurred in the spring- summer, summer-fall, and winter (of the Northern Hemisphere), respectively. The first 2 waves occurred at a time of year normally unfavorable to influenza virus spread. The second wave caused simultaneous outbreaks in the Northern and Southern Hemispheres from September to November. Furthermore, the interwave periods were so brief as to be almost undetectable in some locales. Reconciling epidemiologically the steep drop in cases in the first and second waves with the sharp rises in cases of the second and third waves is difficult. Assuming even transient postinfection immunity, how could susceptible persons be too few to sustain transmission at 1 point, and yet enough to start a new explosive pandemic wave a few weeks later? Could the virus have mutated profoundly and almost simultaneously around the world, in the short periods between the successive waves? Acquiring viral drift sufficient to produce new influenza strains capable of escaping population immunity is believed to take years of global circulation, not weeks of local circulation. And having occurred, such mutated viruses normally take months to spread around the world.”.

A conceptual question is rised:
"Were the 3 Waves in 1918–1919 Caused by the Same Virus? If So, How and Why?"

The multiple fits hypothesis is proposed as an explanation of this sucecessive waves pattern:
“…. at least 2 H1N1 receptor-binding variants co-circulated in 1918: 1 with high-affinity binding to the human receptor and 1 with mixed-affinity binding to both avian and human receptors.” (1).

The authors refer to a number of HA SNP differences among the 5 available 1918 isolates sequences. As explained earlier by the autors,
“The switch from this avian receptor configuration requires of the virus only 1 amino acid change (30), and the HAs of all 5 sequenced 1918 viruses have this change, which suggests that it could be a critical step in human host adaptation. A second change that greatly augments virus binding to the human receptor may also occur, but only 3 of 5 1918 HA sequences have it .”

Note: The subject is discussed on the thread “Is the virus peaking?” Page 4:
http://fluboard.rhizalabs.com/forum/viewtopic.php?f=5&t=1308&start=20
also discussed on: http://fluboard.rhizalabs.com/forum/viewtopic.php?f=26&t=1053


PB2
Clearly the genetic optimization of Polimerase Basic PB2 carries the key genetic signatures to optimized viral fitness specific to the human host. The PB2 E627K acquisition modulates the replication temperature in human nose in a cold weather is a classical influenza pandemic acquisition. As a matter of fact, “In both the reassortment events that generated the 1957 and 1968 pandemic viruses, the PB2 gene segment was acquired from a human virus”(2),(3).
Recent PB2 E627K detections in Netherlands is disussed on topic “[i]E627K In The Netherlands[/i]”:
http://fluboard.rhizalabs.com/forum/viewtopic.php?f=26&t=1561
A “H1N1 PB2 E627K short review”, is presented on the thread “Sequence Updates” (Oct 06, 2009 8:34 pm Post).
http://fluboard.rhizalabs.com/forum/viewtopic.php?f=26&t=1053

NS
Another strong candidate to strongly modulate H1N1 fitness in the human host is the Non Structural NS gene. It encodes the NS1 protein, responsible for the crucial interferon antagonist function. As pointed out By Wendy Barclay, “It is possible that avian virus NS1 genes do not function in this role efficiently in the mammalian host, perhaps due to inherent differences in innate immunity between birds and mammals.”(3).

In 2009 H1N1 Swine Origin Influenza, H1N1, some degree of mammalian adaptation is already accomplished. H1N1 NS gene can be traced to North American Classical Swine lineages. Mammalian adaptation certainly occurred along decades on swine hosts. However, swine is not just any mammalian! Swine are somewat more robust than humans, as far as influenza is concerned. Evolution pressure being smaller, swine influenza can preserve some older “avian-like” genetic properties. Therefore, H1N1 NS gene is also expected to evolve toward human host interferon antagonist optimization. I will show on the next post a comparison between NS1 gene of 1918 1solate, Pandemic H1N1 and seasonal H1N1.

It is worth to make a short reminder of the interferon role in host innate immune system: “When a virus enters a cell (left), the infection is sensed and the cell responds by producing IFNs. These cytokines bind to specific receptors on the cell surface, causing the production of hundreds of proteins encoded by interferon-stimulated genes, or ISGs. These proteins have anti-viral activity, and can stop a viral infection.” (4).

However, “The fact that viruses routinely and frequently cause disease shows that our defense mechanisms are imperfect. This is in large part due to the fact that nearly every viral genome encodes one or more countermeasures to modulate host defenses. Influenza virus is no exception. One of the viral proteins, called NS1, is particularly adept at impairing the synthesis of interferons (IFN) by cells”(5), (6).

Therefore, I believe H1N1 NS gene should be actively monitored, since minute modification in this gene can strongly modulate pathogenic levels via interferon antagonist.

(1) 1918 Influenza: the Mother of All Pandemics,
Jeffery K. Taubenberger and David M. Morens, Emerging Infectious Diseases, Vol. 12, No. 1, January 2006

(2) Characterization of the 1918 influenza virus polymerase genes
Jeffery K. Taubenberger, Ann H. Reid, Raina M. Lourens, Ruixue Wang, Guozhong Jin & Thomas G. Fanning
Nature - Vol 437, 6 October 2005.

(3) Influenza virus : cell interactions,
Wendy Barclay
Emergence of New Epidemic Viruses through Host Switching
September 6-8, 2005

(4) Viral evasion of innate host defenses ,
Vincent Racaniello Ph.D.* - Virology blog, 12 June 2009
http://www.virology.ws/2009/06/12/viral-evasion-innate-host-defenses/
* Professor of Microbiology at Columbia University Medical Center

(5)How influenza virus inhibits early antiviral responses
Vincent Racaniello Ph.D. Virology blog, 4 June 2009
http://www.virology.ws/2009/06/04/how-influenza-virus-inhibits-early-antiviral-responses/

(4) The NS1 Protein of the 1918 Pandemic Influenza Virus Blocks Host Interferon and Lipid Metabolism Pathways.
by: Rosalind Billharz, Hui Zeng, Sean C. Proll, Marcus J. Korth, Sharon Lederer, Randy Albrecht, Alan G. Goodman, Elizabeth Rosenzweig, Terrence M. Tumpey, Adolfo García-Sastre, Michael G. Katze
Journal of virology (12 August 2009)

Thanks, Neuromedia, for this post. While I don't understand every single word at this moment, the references in the post make it possible for me to do some homework.

several sorts of immunity.
Local, ell based immunity does recognize all the genes,proteins


what flu was around in 2007 ? Was it H3N8 from the
1889 pandemic or H1N1 from 1900

we usually have H3N2 seasons or H1N1 seasons, rarely both.
So they "compete".

Shortterm they should compete even with flu-B or other viruses
by fever-->macrophages, interferon

_________________
no patents on genes, publish the GISAID sequences !

that explains things - nice article Neuro - big thanks (did you write that?)

a few questions

how is this different from a "mutant swarm?"

what about co-infections?

would interferon be effective if/when NS mutation occurs?

I understand that “mutant swarm" refers to the error-prone virus replication. Viral replication on patient cells has a “mutation generator”, which makes slightly imperfect copies. This imperfect replication is part of the virus infection “strategy”, since it allows potential infection of different tissues. As far as I understand this mechanism is partially responsible to the wide variety of influenza aggression and sequels. The overall virus identity is preserved on the virus “consensus”. When the patient virus is “amplified” (lab multiplied) on a PCR test, the final result is likely to miss details of this local variety.

Viral prone error replication is linked to the rather new “quasispecies” concept, and I don’t know to what extent it is well accepted by the research and medical community. The idea was first proposed in the paper:
Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population
http://jvi.asm.org/cgi/content/full/80/17/8653
The whole “quasispecies" concept is presented on a pedagogic text:
The quasispecies concept
http://www.virology.ws/2009/05/11/the-quasispecies-concept/

Co-infection by different influenza strains is an evolutionary opportunity to influenza viruses, since they can exchange genetic material which, a potential source of evolutionary opportunity.

NS mutation modifies “anti-interferon” virus mechanisms. Pandemic H1N1 NS1 sequence shows a number of local differences as compared with both 1918 NS sequence AND a 2008 seasonal H1N1. There is a potential to further pandemic H1N1 NS1 “improvement”.

The discussion covered HA and NA as the main antigenic influenza virus perceived by the human host immunologic system.
This approach is not meat to exaust all the remainig possibilities, and a sketchy picture of the remaining immunity recognition is welcome!


I’m unable to answer right now, perhaps by lack of specific influenza erudiction. I’ll try to drill further.

They certainly did compete! However, this competition cannot be framed by classical competition standards, such as lions and zebras in an African savanna. Viruses do not compete as conventional “predators”. Competition mathematical models (such as the Lotka-Volterra predator-prey coupled equations) cannot be directly applied to viruses, since the ever changing host immune system is part of viruses "habitat".

There was an alternating pattern between seasonal H3N2 and H1N1. This interesting pattern was observed during “normal” (steady state) influenza seasons, which are governed by the season zeitgeber (*) (literally, “time generator”), to use an expression borrowed from chronobiology.

I’m not sure I understand the point. If possible, expand reasoning.

(*)zeitgeber (literally, “time generator”), in the context of chronobiology (which keeps the original german name) is a time-synchronizing variable. Day & night cycle is the most obvious zeitgeber. Moon phase driven reproductive and hunt cycles is another known example. The 4 seasons constitute a quite clear zeitgeber of plant life and agriculture. Last but not least, influenza seasonality is indirectly driven by the solar year.

Thanks again neuro - great info

a few more questions:

who's checking for these variants - how often are they checking?

what would most likely cause increased virulence - variant non-competive strains, co-existing, or mutant swarm - does it matter?

are their different treatment recommendations for these diference viruses?
(did you see the article Tex posted about the interferon?)

can co-existing be non-competative varaints?

any evidence of E627K or NS variant in North America?

H1N1 NS1: 2008 seasonal x 2009 S-OIV x 1918 pandemic


Picture below: amino acid NS1 gene comparison between a 2008 seasonal H1N1, 2009 S-OIV and 1918 pandemic sequences.
The reference sequence (in black) is the S-OIV NS1. The sequence is aligned with both the H1N1 seasonal (blue) and (reconstructed) 1918 NS1 gene. For clarity, regions of identity not displayed, so that only mismatches are visible.

/gene="NS1"

There are a number of polymorphisms common to 2008 seasonal H1N1 AND Brevig Mission/1/18 and NOT by pandemic H1N1. Since these polymorphisms are present in two entirely independent sequences, both well adapted to human host, it is likely that some of them could be acquired by pandemic H1N1, either by antigenic drift or by recombination with the remaining seasonal H1N1 (genetic hitchhiking).

Sequences sources:
Influenza A virus (A/District of Columbia/WRAMC-1154048/2008(H1N1))
http://www.ncbi.nlm.nih.gov/nuccore/CY038774?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum

Influenza A virus (A/California/07/2009(H1N1))
http://www.ncbi.nlm.nih.gov/nuccore/FJ969528?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum

Influenza A virus (A/Brevig Mission/1/1918(H1N1))
http://www.ncbi.nlm.nih.gov/nuccore/13173347

Influenza evolutionary dynamics


Viral ecology: The source/sink dynamics model
In the case of the better-sampled A/H3N2 subtype, the pattern exposed by our
coalescent-based analysis is of an annual series of peaks in genetic
diversity interspersed by strong genetic bottlenecks at the end of most
influenza seasons.(1)

Northern and Southern Hemispheres seasonal cycles:Seasonal H3N2 + H1N1 genetic dynamics:
"genomic evolution of influenza A virus is characterized
by a complex interplay between frequent reassortment and periodic selective sweeps."


source:
(1) The genomic and epidemiological dynamics of human influenza A virus
Andrew Rambaut, Oliver G. Pybus, Martha I. Nelson3, Cecile Viboud, Jeffery K. Taubenberger & Edward C. Holmes
Nature, Vol 453|29 May 2008

ABSTRACT
The evolutionary interaction between influenza A virus and the human immune system, manifest as ‘antigenic drift’ of the
viral haemagglutinin, is one of the best described patterns in molecular evolution. However, little is known about the
genome-scale evolutionary dynamics of this pathogen. Similarly, how genomic processes relate to global influenza
epidemiology, in which the A/H3N2 and A/H1N1 subtypes co-circulate, is poorly understood. Here through an analysis of
1,302 complete viral genomes sampled from temperate populations in both hemispheres, we show that the genomic
evolution of influenza A virus is characterized by a complex interplay between frequent reassortment and periodic selective
sweeps. The A/H3N2 and A/H1N1 subtypes exhibit different evolutionary dynamics, with diverse lineages circulating in
A/H1N1, indicative of weaker antigenic drift. These results suggest a sink–source model of viral ecology in which new
lineages are seeded from a persistent influenza reservoir, which we hypothesize to be located in the tropics,
to sink populations in temperate regions.

South Hemisphere: the first Pandemic wave

The winter South Hemisphere pandemic wave shows a timing comparable to the regular seasonal peak.
That is not always the rule for pandemic waves, but this is the first South hemisphere pandemic wave.

Although it is a pandemic wave, source/sink model could also apply to this particular wave on a limited extent : pandemic H1N1 acquires additional genetic material from source reservoir.

Note that the influenza strains involved on the South hemisphere winter are, of course, different from last winter seasonal.

(a) As a reference, 2008-09 last US winter peak, delayed 1/2 year or 26 weeks.
(b) Australian 2009 pandemic wave, Queensland State. (week 26 aligned with US week 1)
(c) Brazilian H1N1 pandemic wave, aligned by the week with the Australian wave.
(d) Brazilian H1N1 pandemic wave, percentage subtyping.

--->Seasonal A is gradually outspaced by Pandemic S-OIV H1N1