Avian Flu - H5N1/H5N2/H5N8 - Pacific Northwest

Emergence of Highly Pathenogenic Flu in the Pacific Northwest (H5N1, H5N2 and H5N8)

Northern Pintail, British Columbia

A Highly Pathenogenic Strain of Avian Flu (WHO), H5N1, has appeared in Whatcom County, Washington, in the Pacific Northwest, according to a report filed by Dr John Clifford, United States Department of Agriculture with the World Organisation for Animal Health (OIE). The report was filed 1/20/2015 for an event starting on 12/29/2014.  The incident involved a Green-winged Teal:Anatidae (Anas carolinensis).

The H5N1 strain's Eurasian lineage genes ( (PB2, H5, NP, MP) are over 99% identical to a gyrfalcon H5N8 strain found in Whatcom County.  It's North American lineage gene PB1 is 98% identical to a Northern Pintail H5N2 strain also found in Whatcom County, while other North American lineage genes (PA, N1, NS) are of low pathenogenicity (LPA I), according to the report filed with the OIE. This strain is a novel strain, and is different than strains appearing in Asia.

Discussion by Recombinomics  raises "the possibility of multiple constellations with the H5N2 sero-type"

The Pacific Northwest has experienced H5N2 and H5N8 strains during this fall and winter season in bird populations, as indicated by the US Department of Agriculture.

Mallard, British Columbia

Birds affected by avian flu this fall/winter 2014/5 season have included:

H5N1:  Green-winged Teal, Whatcom County, Washington.

H5N2:  Northern Pintail (Whatcom County, Washington), Broiler, Table Egg Layer, Turkey, chickens (Southern British Columbia), ducks and geese (Clallam County, Washington), mallard (Fern Ridge, Oregon), falcons (Canyon County, Idaho), turkeys, chicken, guinea fowl, water fowl (Benton County, Washington) .

H5N8: guinea fowl, chickens, ducks, geese (Winston, Douglas County, Oregon) , Wild Ducks (Idaho), grylfalcons, American Wigeon. guinea fowl, chickens, ducks and geese (Whatcom County, Washington)

The distribution of H5N2 and H5N8 in the Pacific Northwest shows an interesting pattern. Whatcom County, adjacent to the border between Washington State and British Columbia (Sumas-Lynden border crossing) offers an opportunity for mixing of the various avian flu types, given migratory paths and poultry stocks in the area. Other areas of concentration include Benton County, Washington, near Hanford, Washington as well as areas in Oregon and Idaho.

Avian Flu has a considerable impact on bird populations.  There have been limited cases of H5N1 in the human population, although one did occur in 2014 resulting from a flight from Beijing to Vancouver Canada and on to Edmonton.

Avian influenza is a disease naturally occurring in wild aquatic birds which can infect domestic poultry and other bird and animal species.  It is very difficult for humans to become infected by avian influenza, although there have been some limited human cases.  H5N1 is sustained in the avian (bird) population but not is not currently sustained in the human population.

There has been one human death from H5N1 in North America.  On December 27, 2013, a woman travelling from Beijing, China, to Vancouver, B.C. and then onto Edmonton, Alberta, Canada, became ill on the Beijing to Vancouver leg of the flight. She was admitted on January 1, 2014 to an Edmonton hospital and died two days later.

The Centers for Disease Control and Prevention (CDC) is the lead U.S. Agency for the management of health issues and has information on Avian Flu.

Recombinations and reassortments of influenza viruses provide potential opportunity for the development of new strains or of human to human transmission.  The occurrence of  H5N1, H5N2 and H5N8 in the Pacific Northwest in the fall-winter 2014-5 season raise interesting questions as to the development of the one H5N1 case identified this season and as to whether there is any relationship with the H5N1 death which occurred in the prior (2013-2014) fall-winter season.

It is interesting to consider various factors which may account for the development of highly pathenogenic avian influenza in the Pacific Northwest.  These considerations may involve the locations in which the birds were found, migratory patterns, climate change, environmental factors, and the availability of reservoirs and vectors in which the virus can mix, spread and potentially become sustained in various host or intermediate host various populations.

Marilyn Dunstan Photography
Mallard Duck Flying
Ducks

Centers for Disease Control & Prevention:
CDC
CDC-Avian Flu
Human Infection with Avian Influenza A (H5N1) Virus


World Health Organization:
WHO
WHO-Avian Flu

World Organisation for Animal Health (OIE)
Gyrfalcon H5N8
Northern Pintail H5N2

US Department of Agriculture (USDA-Avian Flu)

Flu.gov
Flu
H5N1

Recombinomics:
Fujian H5N1 Reassortment in Washington
Fujian H5N2 Clade 2.3.4.4 in North America
Fujian H5N8 Clade 2.3.4.4 spread in 2014

BBC News:
First N America H5N1 Bird Flu Death Confirmed in Canada

Wikipedia:
Green-Winged Teal
Northern Pintail
Influenza Virus Subtype H5N1
Influenza Virus Subtype H5N2
Influenza Virus Subtype H5N8

Ebola

Raudfjorden Beach, Svalbard, Norway

The Ebola outbreak has proven to a challenge for worldwide heatlh leaders.  The CDC has information about Ebola on its website, as does the World Health Organization (WHO).  The CDC information is delineated into a number of topical areas of interest to subject audiences.  I'm interested in the etiology of Ebola, its transmission, and issues surrounding its current outbreak.

My interest in Ebola began during my actuarial career, reading the "Hot Zone" , a 1994 non-fiction book about incidents involving viral hemorrhagic fevers, including ebolaviruses and marbug viruses. The memory of the book stayed with me since I was reading it while sailing down the west coast of Vancouver Island in 15 foot swells in a sailing vessel.  I can recall eating copious amounts of ginger cookies to ward off seasickness as I read of hemorrhagic fevers killing off people very quickly, in a very bloody and gory fashion, as all the while I was lurching back and forth in the sea and swell on the Pacific Ocean.  The ginger cookies did their job and the memory is etched in my experience, gone but not forgotten, as Ebola emerges again, this time, expressed  in the news of an outbreak.

These hemorrhagic diseases killed off people before they had a chance to spread extensively, and, were confined to certain areas in Africa and mostly away from major population centers.

According to the CDC, the virus can be spread through direct contact with blood and body fluids of a person infected with Ebola, with objects such as syringes infected with Ebola and infected fruit bats or primates.  The question remains as to factors impacting the geographical distribution of Ebola, how it independently arises, factors of etiology and its potential spread elsewhere.

The recent upswing in the Ebola virus prompted me to question its etiology, transmission and other issues.  For example, because of the increase in number of cases, I wondered if the virus had recombined with another virus to increase its transmission and decrease its mortality, or if there were other factors.   In this blog article I consider a number of issues, and raise some questions relating to the virus.


Etiology

• Does Ebola predate the AIDs/SIV/HIV viruses and does it provide some idea of the origin of these viruses? The CDC expresses that it does not know the origin of the original host of the Ebola Virus;  It is interesting to study the context of the Ebola virus regarding its emergence out of the Kinshasha Highway  across the Congo into Uganda as discussed in "The Hot Zone".  Did the virus have origins in bat habitats such as caves, rock, lava tubes, environments exposed to varying bacteria and archaea?
• The Ebola virus is a negative sense RNA virus. The production of proteins from a negative sense RNA virus require first the production of Messenger RNA (mRNA) and then proteins from mRNA. Ebola does not have reverse transcriptase, which would ordinarily be needed to enable insertion of its genetic contents into the DNA.   Is its 'purpose' then to directly produce mRNA (messenger RNA), and why? Research has shown that the filoviruses behind Ebola are very old and that there is direct insertion of genetic content with indications of evolutionary divergence a long time ago.  - The Lin Edwards article, "Ebola and Marburg viruses may be much older than thought" discusses this subject.
• Does the Ebola virus relate to issues concerning New World Monkeys and Old World Monkeys and the divergence of the two species?  If so, would this tend to indicate the same type of environmental conditions that may have existed at the time of that divergence?
• What is the distribution of the virus?  Does the virus act with regards to specific populations, affecting certain populations in a negative or positive way, and leaving others untouched.  What factors in these populations would account for the outbreak?  Are other populations at risk?

Transmission

• Did the Ebola virus recombine with another virus (for example the Corona Mers Virus  , Seasonal Flu Virus or enteroviruses) to allow it to decrease its mortality rate and increase its transmission?  Is it continuing to do so and would further recombination with the current seasonal flu change it further along these lines? 
• A subject of interest to is transmission of Ebola from the natural host to a target population.  Is Ebola being expressed, sustained within the target population or being sequestered?  Does this imply sequestration in a host for transmission or expression later under circumstances that may enable it to be used as a regulatory operator or a mediator of group identity or expression of  immunity systems?  Is it developing a symbiotic relationship with the host or another virus in a toxin/anti-toxin sort of manner (discussed by my blog article on Dr Luis Villarreal and his work on group identity systems)? How does this concept explain the existence of this virus in a reservoir species?
• What is the risk for the spread of Ebola?  To what extent is the risk environmental and to what extent can it be transmitted from person to person? 
• Is Ebola being transmitted in a less than lethal form under our eyes without our knowledge?
• Can Ebola be spread by more species of animals than listed under the CDC website?  
• How might Ebola change to become more transmissible to a greater variety of populations impacted by different environmental factors?  How would this risk change if the Ebola virus were to combine with the seasonal flu in a variety of different ways?

Geological Factors

• What factors in Africa are most significant in the etiology of Ebola?  Heat, humidity, coeexistence with and diversity of animal species, alkaline environments, carbon dioxide sequestration and outgassing (e.g. Lake Nyos), the Archaean basement substrate of the West African bedrock, granite, uranium, endospores such as bacillus anthracis, and  natural nuclear fission reactors from underground uranium (Gabon)? 
• What is the impact of the African mining fields?  Iron, gold, lead, silver, arsenic, mercury , uranium and nickel are among products of mining.  Nickel has a positive feedback impact on inflammatory markers. 
• How do endospores such as bacillus anthracis  fit into the story of Ebola, set in the mining context of West Africa, with its iron, gold, silver, arsenic, uranium, nickel and mercury, and the expression of inflammatory markers and feedback indicators?
• Are these various environmental issues constrained to Africa or are they present in other environments, and where do other similar environmental conditions exist?  Do these conditions have to exist in the same place or can an individual experience them by exposure to a variety of locations? For example, Archaean basement layers of rock exist in the Arctic, in Svalbard, which I visited in 2005. How would exposure to Archaea and other factors present in West Africa differ from the situation in Svalbard where it is much colder! Where else can we find archaea and chiral substances?
• How do increases in solar radiation  and changes in the Earth's magnetic field impact the expression of Ebola in Africa? To what extent would these factors affect the expression of Ebola in other areas of the planet?

Environment and Physiology

•  Does the emergence of a disease that promotes bleeding have significance as it relates to climate change or other planetary or environmental factors?    Is some environmental change occurring that would result in blood clotting more easily, something that would need to be countered by less viscous blood and changes in the coagulation cascade?
• How might the environmental factors in Africa affect blood coagulation?  Through mitochondrial regulation as it is impacted by environment, haplogroups and uncoupling in oxidative phosphorylation?  Through the impacts of oxygen reactive species?  Through solar radiation, geomagnetic storms and cycles?  Through the Warburg effect  (which replaces aerobic respiration with glycolysis)? Through arsenic mining?  Through positive feedback mechanisms involving hypoxemia  and inflammatory responses?  
• Is it possible that the Archaean basement layer of rock in West Africa impacts the blood coagulation cascade  and the blood vasculature through chirality?  Would concepts of fractal dimension  and tortuosity explain concepts of blood coagulation and vascular inflammation and other disorders, including stroke and cancers, including those of the blood and lymphatic systems?  
• What impact does the water people drink (and breathe through water vapor) impact people, including the impact on group identity systems and physiological parameters?
• Does the outgassing  of carbon dioxide  as a result of global warming, the release of iron from iron sequestered in the rock, and the release of endospores from sequestration, explain any of the natural events happening today, as regards vascular and coagulation issues?
• Is it possible that Ebola, as a disorder that promotes bleeding, developed as a feedback mechanism to counter the impact of increased blood coagulation due to the environmental impacts raised above? 
•  Bleeding may increase as blood coagulation factors are used up; does Ebola act to promote such bleeding to counter increases in clotting factors secondary to these environmental issues?  Is it possible that Ebola thus impacts the regulatory mechanisms of the coagulation cascade?

Detection

• Could an easy detection test be done for Ebola using, for example, saliva? This might prove less expensive and easier to measure for initial testing prior to full blood workups if it was sufficiently sensitive and specific.
• Could the d-dimer test and PPT tests be used as early indicators of Ebola.
• Can a series of early indicators, including markers of respiratory and coagulation system function and exposure to certain environmental factors, be developed to ascertain risk patterns for specific populations?  
• Where might the solution to Ebola be found?  Only time will tell.  Are lamprey VLR's a potential solution for isolating, detecting, and finding a cure for Ebola, considering their ability to detect bacillus anthracis and their affinity for carbohydrate glycoproteins?  Considering the age of the filoviruses and the characteristics of Ebola itself, is this a potential area to investigate?

Summary

Does the emergence of Ebola reflect the re-emergence of ancient historical patterns?  Have these patterns been carried by reservoir species from the depths of time to the particular victims of Ebola? Will Ebola adapt and spread elsewhere or re-emerge in other parts of the planet, independently?

Are the issues happening in West Africa an early indicator ('Canary in a Coal Mine')  of planetary changes?  These changes include changes in Earth's magnetic field, climate change, global warming and solar radiation, and downstream effects including release of sequestered minerals and gases such as carbon dioxide and methane from rock and oceans.  These are all areas of concern.  Historical examples of changes in Earth's magnetic field are shown over longer periods of time and more recent geologic time periods in this Wikipedia article on the Earth's Magnetic Field.

Finally, I am reminded of the childhood game, "Animal, vegetable or mineral" and associations with the "Tree of Life" (and probably, by extension, "The Tree of Good and Evil").  Ebola is a disease with a past, reflecting deep phylogeny and the rivers of time as embedded in the history of our rocks.

Sources:

marilyndunstan.blogspot.com
Evolution of Adaptive Immunity

Wikipedia:
Ebola virus disease
"The Hot Zone"
Kinshasha Highway
Archaea
Sense (molecular biology)
Messenger RNA
Reverse Transcriptase
Filoviridae
New World Monkey
Lake Nyos
Endospore
Bacillus Anthracis
Natural nuclear fission reactor
Nickel
Chirality
Sunlight
Earth's Magnetic Field
Oxidative Phosphorylation
Reactive Oxygen Species
Geomagnetic Storm
Warburg Effect
Glycolysis
Coagulation Cascade
Fractal Dimension
Tortuosity
Outgassing
Carbon Sequestion
Animal Sentinel
Earth's Magnetic Field-Geomagnetic Polarity
Earth's Magnetic Field-Brunhes Geomagnetism
Earth's Magnetic Field

World Health Organization:
Ebola Virus Disease

CDC:
CDC
Ebola (Ebola Virus Disease
2014 Ebola Outbreak in West Africa (Outbreak Distribution Map)

Phys Org: 
Ebola and Marburg Viruses May be Much Older Than Thought

JoVE Visualize: Anthrax lethal toxin inhibits translation of hypoxia inducible factor 1? and causes decreased tolerance to hypoxic stress

Geology and Mineral Resources of West Africa - The Archaean Basement

National Academy of Sciences: High-affinity lamprey VLRA and VLRB monoclonal antibodies

Berkeley Lab: Structure of the Ebola Virus Glycoprotein Bound to an Antibody from a Human Survivor

NASA Science News - Earth's Inconsistent Magnetic Field

Evolution of Adaptive Immunity

Two Trees (creative digital image)

I attended a "Weiser Endowed Lecture in Immunology" featuring Dr Max Cooper of the Emory University School of Medicine, speaking on "Evolution of adaptive immunity" at the University of Washington in 2012.  Dr Cooper's work is foundational in this subject area.

It is interesting that immunity systems follow a phylogenetic pathway much as the phylogeny of species themselves do. The evolutionary pathway of jawless vertebrates (of whom hagfish and lampreys are surviving members), possess differences in comparison to the common evolutionary pathway followed by other vertebrates.

Lampreys and hagfish do not possess a thymus , nor do they possess a spleen.    Lampreys and hagfish do not possess Major Histocompatibility Complex (MHC) 1 or 2, T-cell receptors or recombination activating genes (RAG 1 and 2) which play an active role in the recombination of T-cell and immunoglobulin  receptors. Lampreys and hagfish posses hematopoietic tissue, the former in the intestine and the latter in the portal vein.  With these changes, the lampreys and hagfish diverged off the common immune system evolutionary pathway prior to the development of certain MHC class immunity in other species.  This is an important benchmark due to the major role that the MHC class plays in vertebrates.  It is a vital aspect which makes the concept of a separate phylogenetic pathway earmarked for the immune system so interesting.  If lampreys do not possess a thymus, then what substitutes in its place?

Lampreys and hagfish utilize a system of leucine-rich repeats )(LRR's) to mediate immune system responses using Variable Lymphocyte Receptor (VLRs), (VLRA's, VLRB's and VLRC's).  The interesting aspect of the jawless vertebrate immune system function is comparing its action in structure and function to the immune systems we are familiar with.  VLRB's have structures similar to toll like receptors (proteins that play a key role in the innate immune system), while their functions are similar to those of antibodies,  and they possess humoral characteristics (using macromolecules in extracellular fluids in immunity systems). They act using discrete populations of lymphocytes (types of white blood cells) .

VLRBs act as an adaptive immune system and can differentiate foreign from self in recognizing lymphocytes.

Lampreys posses a diverse variety of leucine-rich repeats which code for germline and mature genes. They possess a specificity for carbohydrate and protein receptors on bacterial and mammalian cells. They bind antigens with high avidity and affinity, describing the binding capacity of multiple versus single interactions of antibodies with antigenic epitopes.

 In "Evolutionary implications of a third lymphocyte lineage in lamprey", the authors find a thymoid source for VLRA and VLRC assembly in the lamprey gill tips, while VLRB assembly occurs in hematopoietic typhosole and kidney tissues.  VLRC appeared more numerous than VLRA, and predominated in the skin.  They conclude that a similar body plan of two T-cell type lymphocytes in a thymoid type structure and one B-cell type lymphocyte in the blood and kidneys shows some similarity in basic structure to the immune system for jawed vertebrate, while achieving adaptive immunity through different means.

Monclonal VLRB antibodies  from immunized lamprey larvae can recognize plasma cells from myeloma patients.  VLR4, a monoclonal VLRB specific for BclA, the bacillus collagen-like protein, has shown to be specific for B. Anthracis spores.  Information on B. Anthracis can be obtained from the US Centers for Disease Control (CDC) CDC - Anthrax and the World Health Organization (WHO) WHO - Anthrax.

Research indicates a number of applications where VLR's can recognize certain immumogens  An immunogen is any antigen that is capable of inducing humoral and/or cell-mediated immune response rather than immunological tolerance.  These applications include diagnosis, research and bioterrorism investigations.

PANSPERMIA and EVOLUTION

Mars Spirit Lander and Bonneville Crater in Color

 Image Credit: NASA/JPL-Caltech/Univ. of Arizona 

Panspermia  is a concept which portrays how life might be distributed throughout the universe.  These means include a wide variety of astronomical or celestrial objects  including meteors, comets, asteroids, and factors such as the solar wind.  The theory of panspermia, however does not really address how life began in the first place.

As man has ventured out into space, with human space travel, or has used unmanned spaceflight, the issue of man (or machine) as a vector or agent of panspermia has become an issue.  This issue parallels the concept of jet travel and airports as a vector in spreading contagion. Migratory birds have been vectors for centuries, landing in Qinghai Lake, China, a saline and alkaline lake and migratory crossroads  or in the Izembek National Wildlife Refuge in Alaska, along the Bering Sea. . Such bird migratory pathways provide fertile ground for recombination and spread of various contagions.

The NASA photo of the Bonneville Crater and Mars Spirit Lander depicts an impact crater on Mars.  Such an impact would have created a large amount of energy upon impact.  Many theories of life involve the discussion of how reorganization and complexity arises as energy is input into a system.  The Miller and Urey experiment in 1953 attempted to address this issue through recreation of a primordial atmosphere laced with water, methane and lightning storms.
 
Henry Eyring, a chemist, discovered Actual Rate Theory or Transition State Theory, which discusses reaction rates of chemicals in the context of potential energy states, complexes activated by chemical reactions, entropy considerations and products formed by the chemical reaction. In considering the input of exogenous energy into a system, this theory would be important in examining the potential reactions that might take place, as the reaction may change the system through transformational change.

In considering the issue of panspermia, therefore, there are a couple of issues; the development of a system and then the spread of that system.  Issues of energy and mixing concern the development or the boot-strapping of a system through transformational change, while panspermia addresses the spread.  Where panspermia occurs through media that spread via impact, the two issues (bootstrapping and spread) tend to co-exist to some extent.

The concept of panspermia requires a vector that is resilient.  It must be able to adapt to environmental factors such as extremes of temperature, must be able to resist impact as well as radiation and other factors such as high levels of salinity.   Such organisms, extremophiles  fit a profile as a candidate for panspermia.

Santa Catalina Mountains seen from Saguaro National Park, Arizona

Recently, I came across an article in Applied and Environmental Microbiology (AEM) on Bacillus Endospores,  written by Patricia Fajardo-Cavazos and Wayne Nicholson, "Bacillus Endospores Isolated from Granite: Close Molecular Relationships to Globally Distributed Bacillus spp. from Endolithic and Extreme Environments".   This article discusses the issue of the diversity of Bacillus spp. populations, and specifically certain endolithic spore populations obtained from near surface granite from the Santa Catalina mountains near Tucson, Arizona.

An endospore is a tough non-reproductive surface that lies dormant for an extended period of time, and can be later revived after many years to a vegetative state.

Anthrax is a bacillus, and may exist in the dormant state as an endospore.  According to a World Health Organization document on studies of anthrax endospores (bacillus anthracis),  "Sporulation requires the presence of free oxygen. In the natural situation, this means the vegetative cycles occur within the low oxygen environment of the infected host and, within the host, the organism is exclusively in the vegetative form. Once outside the host, sporulation commences upon exposure to the air and the spore forms are essentially the exclusive phase in the environment."  Spores are thus spread by release of spores by the dying host into the environment where they are taken up by another animal.

 The focus of the AEM article is on the very issue of panspermia, the issue of transference of microbes through spaceflight, It concerns the measurement of characteristics of various endolithic spore populations obtained through a variety of near surface granites and basalts and even the ultra clean environments of spacecraft assembly facilities.

Blue fluorescence obtained through medium wavelength UV illumination, distinguished certain endospores obtained from near surface granites.  Endospores were grouped into species or strains based on their rRNA  gene sequences. Numbers and diversity of endospores from granite were greater than those obtained from basalts.  This may be due to the lower porosity of basalt versus granite. Limited subsets of Bacillus spp. appeared to occur in certain rock environments that favored them and not other strains. Certain bacillus strains (bacillus subtilis) were used as proxies for bacillus anthracis fluorescence properties in the study.

The issue of panspermia is a very important one, set in the context of space exploration and in consideration of how extraterrestrial impacts may have impacted (and may still be impacting) human life.  The AEM study provides interesting results as to the diversity and characteristics of Bacillus spp. from a variety of environments, including, importantly, granite, set in the context of fluorescence properties.   A bacillus such as anthrax, as studied by the World Health Organization (WHO) or the CDC may provide clues as to how bacillus and endospores fit into our evolutionary framework.