Human Influenza


(Credit: CDC)
Generic Influenza Virus


(Credit: FluView)
Week of Nov. 29


What causes influenza?

Influenza pandemics have been recognized for several centuries.  Initially bacteria were cited as the causal agent: in 1892 a bacterium identified during an influenza pandemic was wrongly believed to be causing the disease and named Haemophilus influenzae.  We now know that, while bacteria can co-infect influenza patient, producing pneumonia and related illness, influenza is caused by a virus.  This virus was isolated in ferrets and identified in 1933, three years after the first electron microscope was developed.

The influenza virus is an Orthomyxovirus.  (This name derives from the Greek word 'myxa' = mucus.)  Its genome is made of RNA, not of DNA; only viruses can have RNA genomes.

Morphology:  Influenza virus particles are highly pleiomorphic (variable), mostly spherical/ovoid with a ~100 nm (0.000003937 inches) diameter, but many forms occur, including long filamentous particles.

RNA virus1RNA virus2
Image credits: CDC

Unlike bacteria, viruses are too small to be stopped by filters.  However, unlike DNA, RNA is very labile and does not survive for long at ambient temperature.  In labs RNA is stored at -100oF in order to preserve it.

Influenza Types and Host Range:

  • Influenza A viruses infect birds and a wide variety of mammals, including man, horses, pigs and ferrets. This type is the main human pathogen, associated with epidemics and pandemics.
  • Influenza B viruses infect mammals only and cause disease, but generally not as severe as A types.
  • Influenza C viruses also infect mammals only, but rarely cause disease. They are genetically and morphologically distinct from A and B types.

Commonly Circulating Seasonal Influenza Types and Subtypes (Human):

Strains of Influenza Type A and Type B circulate every season around the world.  Type A strains are further grouped in subtypes; subtype H1N1 and H3N2 are usually present in the population.  This year a new strain of subtype H1N1 virus, first appeared in Mexico in mid-February, is causing a world-wide pandemic.  Different names have been used to identify this virus (popularly, "the swine flu"): pandemic H1N1, 2009 H1N1, Swine-Origin Influenza Virus (S-OIV) or Ca/04/09 (from the strain isolated in California in April '09 and adopted as reference strain by the World Health Organization).

Past Influenza Season

What is an Influenza A Subtype?

Influenza A viruses have a segmented genome comprised by 8 RNA segments encoding a total of 10 proteins (10 genes).  Due to their position, surface proteins Hemagglutinin (HA) and Neuraminidase (NA) interact with host cells.  Also due to their position, they generate an immune response in the host and determine the "shape" of new antibodies that protect the host from repeated infection.  Thus, they are key to vaccine production.

There are 16 hemagglutinin subtypes (H1 to H16) and 9 neuraminidase subtypes (N1 to N9), based on serological classification (= using antibodies). When infected, the human body reacts to each of these subtypes producing antibodies with a specific shape, which can only bind to that particular viral subtype.


Emergence of New Strains and Subtypes

These different serological subtypes undergo constant mutations (antigenic drift) and produce new strains.

There is a second mechanism that leads to more dramatic changes and the appearance of completely new genomes in influenza viruses, antigenic shift.

Possible mechanisms of antigenic shift:

  • As the influenza virus genome is segmented, it is possible for two influenza strains to exchange their genes upon co-infection of a single host.  This process, known as genetic reassortment, is believed to have been the cause of the 1957 ("Asian", H2N2) and 1968 ("Hong Kong", H3N2) pandemics. 
  • A non-human influenza strain acquires the ability to infect humans.  The 1918 ("Spanish") pandemic arose when an avian H1N1 strain mutated to enable its rapid and efficient transfer from human-to-human.

The Influenza Virus Cycle

  • Wild birds are flu virus reservoir (airways + intestines).  They are usually healthy carriers and, thus, a perennial reservoir.  Also, they can be migratory and effective world-wide spreading agents.
  • They infect domestic bird (respiratory illness)
  • Domestic birds infect pigs in the same farm.  Also humans can infect pigs. (Animal-to-human passage, or vice versa, is called a zoonosis)
  • The genes from avian, swine and human viruses can re-combine in the pig, producing a new virus.  If the new virus can bind to human cells and replicate within them, it can be passed back to humans. 
  • "Humanization" of an avian or swine strain is a rare event.  It can lead to a pandemic because the virus is completely new (no previous immunological protection).

Image source: CDC

The Current H1N1 Pandemic

Hemagglutinin and neuraminidase are both very important for effective viral infection.  When the Eurasian swine NA (not observed for almost 20 years) came together with the North-American swine HA (present in pigs for more than 10 years in the so-called "triple re-assortant" virus), a new human virus was created.

The mixing vessel for the current reassortment could have been a swine or a human host but remains unknown.

Pig Liking Kid(maybe it was this kid....)

It has been known since 1935, only two years after the influenza virus identification, that human-swine exchange is possible.  If influenza strains routinely contain genes of swine-origin, why is the current pandemic more virulent?  Why is it particularly dangerous for the young?

Influenza Deaths

The answers to these questions are not fully known.  Several genes may play a role in the clinical outcome of a 2009 H1N1 infection.  We do know that, fortunately, this strain does not contain the lethal mutation present in the HA protein of the deadly H5N1 avian influenza.  Overall mortality directly caused by the pandemic H1N1 is below 1%, probably because many cases are not reported.  (Human mortality caused by the avian influenza is presently around 60%; luckily humans are infected at extremely low rate by this avian virus.)

Although the present pandemic is clearly less severe, and although it is of swine-origin, the 2009 H1N1 virus appears to have some common characteristics with the deadly avian-derived 1918 H1N1 virus that caused the so-called "Spanish Flu".  In both cases, the HA protein, again, plays a major role in infection.  The part of the molecule responsible for high pathogenicity is, however, not the same that plays a role in avian influenza deaths.

Host Specificity and Pathogenicity

The HA "Cleavage site" is involved in avian influenza's virulence, while different mutations in the HA "Receptor binding site" are the likely cause of the above-average pathogenicity of the 2009 H1N1 and the 1918 H1N1 viruses.  The shape of the binding site determines host-specificity; this site anchors the virus to the host cell, the first step in the infection process.

Lessons Learned from the Influenza Pandemic of 1918

The influenza pandemic of 1918-1919 killed more people than WWI, 20-to-50 million people. It is the most devastating epidemic in recorded world history. More people died of influenza in a single year than in four-years of the Black Death Bubonic Plague from 1347 to 1351. Known as "Spanish Flu" or "La Grippe" the influenza of 1918-1919 was a global disaster. In the U.S., about 500,000 to 675,000 died. (  [About 36,000 people die every year in the U.S. from all seasonal flu-related causes (CDC)].

flu death

  • Influenza death-vs-age charts are usually U-shaped curves (very young and very old die); the 1918 flu had a W shape with high death rate among 15-34 year olds. (Similar to current pandemic.)
  • Mortality rate high (2.5%) compared to 0.1% for modern epidemics. 

Conventional flu viruses replicate mainly in the upper respiratory tract: the mouth, nose and throat. The 1918 virus replicates in the upper respiratory tract, but also in the lungs, causing primary pneumonia among its victims.  Autopsies of 1918 flu victims often revealed fluid-filled lungs severely damaged by hemorrhaging due to a massive immunoresponse, stronger in young adults.  The ability of the virus to take over the lungs was thought to be associated with the pathogen's high level of virulence, but the genes that conferred that ability were unknown.  In 1997 72-year old pathologist Johan Hultin traveled to Brevig Mission in Alaska and was able to recover samples of the Spanish flu virus preserved in the lungs of victims buried in permafrost.  All genes could be sequenced.  In 2005 the 1918 virus was reconstructed in a lab and it was revealed that it originated in birds and mutated to infect people.  This incredible feat shed some light on the differences in the binding sites of different influenza strains.

HA Binding Sites, Host Cell Receptors and Pathogenicity

Influenza viruses bind via their surface HA (hemagglutinin) to receptors consisting of sialic acid in alpha 2,3 or alpha 2,6 linkage with galactose on the host cell surface. Sialic acid in 2,6 linkages is characteristic of human cells while 2,3 linkages are characteristic of avian cells.  This difference results in a different shape of the receptors on cells of the upper respiratory tract: human receptors are wide, while avian receptors are narrow.  Both types of receptors are present in pigs, which explains why these animals can act as a mixing vessel for the viruses.  When mutations alter the width of the HA binding site, host-specificity may change, leading to the infection of a different species.  This is what happened in the case of the Spanish Flu virus and it may be true, although to a lesser extent, also in the case of the current 2009 pandemic.  No direct evidence at the molecular level has been provided yet in support of this model, but experimental data demonstrate that also the 2009 H1N1 virus can reach the lower respiratory tract and enter the lungs.  The ability to attack human lung cells, where receptors are narrow-shaped, suggests the presence of an altered binding site in the viral HA.

How can we fight back?

I) Vaccines

  • Every year vaccine recommendations are issued for each of the two hemispheres, as "flu season" progresses from one to the other.  World-wide surveillance of the movements of influenza strains is very important.
  • This year two types of vaccines are available, one for the seasonal influenza (a trivalent vaccine produced using three different types/subtypes) and one (monovalent) for the pandemic H1N1

II) Anti-viral Drugs

     At the present moment two types of antiviral drugs are known (commercial names are in parentheses):

  • Drugs such as Oseltamivir (Tamiflu, liquid) and Zanamivir (Relenza, by inhaler ) block the NA protein
  • Drugs such as Amantadine (Symmetrel, tablets, syrup etc.) and Rimantadine (Flumadine) block the M2 protein

Drug-resistance is becoming an increasing problem for all influenza A subtypes.  The 2009 Pandemic H1N1 is intrinsically resistant to amantadine and oseltamivir-resistance has been detected in a few strains.

III) Improved Diagnostics

Under development:

  • Faster tests providing multiple answers and resulting in quick, appropriate drug selection
  • Portable instruments for diagnostics on location, allowing rapid outbreak confinement

On February 17, President Obama signed the American Recovery and Reinvestment Act (ARRA) into law. On September 1, an ARRA grant was sub-contracted to this lab at Brandeis for the development of a new assay able to distinguish between seasonal and pandemic influenza and to identify drug-resistance.


Dr. Cristina Hartshorn

Useful Resources:

  • WHO (World Health Organization)
  • FDA (U.S. Food and Drug Administration; U.S. Department of Health and Human Services)
  • CDC (Centers for Disease Control and Prevention)
  • CIDRAP (Center for Infectious Disease Research & Policy, University of Minnesota)
  • NIAID (National Institute of Allergy and Infectious Diseases, NIH)