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The "Flu"

Influenza is a viral infection of the lungs characterized by fever, cough, and severe muscle aches. In the elderly and infirm, it is a major cause of disability and death (often as a result of secondary infection of the lungs by bacteria). Even in the young and healthy, influenza produces a prostrating disease of a few days duration and one not soon forgotten.

Influenza is not Influenza was responsible for the most devastating plague in human history — the "Spanish" flu that swept around the world in 1918 killing 675,000 people in the U.S. and an estimated 20–50 million people worldwide. (A disease that attacks a large fraction of the population in every region of the world is called a pandemic.) (It is uncertain where the flu first appeared, but it certainly wasn't in Spain.)

No one at the time even knew what disease agent was causing the pandemic. Not until 1930 (in pigs) and 1933 (in humans) was it established that influenza is caused by a virus.

This electron micrograph (courtesy of Dr. K. G. Murti) shows several influenza virus particles (at a magnification of about 265,000x). The surface projections are molecules of hemagglutinin and neuraminidase (see below).

There are three types of influenza:

The Influenza A Virus

The influenza A virion is Each of the 8 RNA molecules is associated with

The Genes of Influenza A

The 8 RNA molecules (the number in brackets is the designated segment number):

The Disease

The influenza virus invades cells of the respiratory passages.

The result is a viral pneumonia. It usually does not kill the patient (the 1918 pandemic was an exception; some victims died within hours) but does expose the lungs to infection by various bacterial invaders that can be lethal. Before the discovery of the flu virus, the bacterium Hemophilus influenzae was so often associated with the disease that it gave it its name.

Pandemics and Antigenic Shift

Three pandemics of influenza have swept the world since the "Spanish" flu of 1918.

(The pandemic of 1957 probably made more people sick than the one of 1918. But the availability of antibiotics to treat the secondary infections that are the usual cause of death resulted in a much lower death rate.)

The hemagglutinin of the 1918 flu virus was H1, its neuraminidase was N1, so it is designated as an H1N1 "subtype". Here are some others.

Some strains of influenza A
1918H1N1pandemic of "Spanish" flu
1957A/Singapore/57H2N2pandemic of "Asian" flu
1968A/Aichi/68H3N2pandemic of "Hong Kong" flu
1976A/New Jersey/76H1N1swine flu in recruits
1977A/USSR/77H1N1"Russian" flu
2009A/California/09H1N1pandemic of "swine" flu [now designated A(H1N1)pdm09]

Until 2009, these data suggest that flu pandemics occur when the virus acquires a new hemagglutinin and/or neuraminidase. For this reason, when an H1N1 virus appeared in a few recruits at Fort Dix in New Jersey in 1976, it triggered a massive immunization program (which turned out not to be needed). However, an H1N1 virus appeared the following year (perhaps escaped from a laboratory) causing the "Russian" flu. We now know that this virus was a direct descendant of the 1918 flu. While accumulating mutations that made it less dangerous, it had been infecting humans until it was replaced by the H2N2 "Asian" flu of 1957. Because most people born before the Asian flu pandemic of 1957 had been exposed to the H1N1 viruses circulating before, the Russian flu primarily affected children and young adults. For the same reason, this pattern was also seen in the 2009-10 pandemic of "swine" flu.

Where do the new H or N molecules come from?

Birds appear to be the source. Both the H2 that appeared in 1957 and the H3 that appeared in 1968 came from influenza viruses circulating in birds.

The encoding of H and N by separate RNA molecules probably facilitates the reassortment of these genes in animals simultaneously infected by two different subtypes. For example, H3N1 virus has been recovered from pigs simultaneously infected with swine flu virus (H1N1) and the Hong King virus (H3N2). Probably reassortment can also occur in humans with dual infections.

Epidemics and Antigenic Drift

No antigenic shifts occurred between 1957 ("Asian") and 1968 ("Hong Kong"). So what accounts for the epidemics of 1962 and 1964?

Missense mutations in the hemagglutinin (H) gene.

Flu infections create a strong antibody response. After a pandemic or major epidemic, most people will be immune to the virus strain that caused it. The flu virus has two options:

The gradual accumulation of new epitopes on the H (and N) molecules of flu viruses is called antigenic drift. Spontaneous mutations in the H (or N) gene give their owners a selective advantage as the host population becomes increasingly immune to the earlier strains.

Flu Vaccines

Although a case of the flu elicits a strong immune response against the strain that caused it, the speed with which new strains arise by antigenic drift soon leaves one susceptible to a new infection. Immunization with flu vaccines has proved moderately helpful in reducing the size and severity of new epidemics.

Some vaccines incorporate inactivated virus particles; others use the purified hemagglutinin and neuraminidase. Both types incorporate antigens from the three major strains in circulation, currently:

Because of antigenic drift, the strains used must be changed periodically as new strains emerge that are no longer controlled by people's residual immunity.

The process:

The whole process can take up to six months. A promising way to speed things up is described below.

Strains used in vaccines for the flu seasons shown.
SeasonH1N1H3N2Type B
86–87A/Chile/83*A/Mississippi/85B/Ann Arbor/86
* As the 86–87 season got underway, it was found that A/Chile/83 no longer gave protection so A/Taiwan/86 was offered as a second shot late in that season.
87–88A/Taiwan/86A/Leningrad/86B/Ann Arbor/86
00–01A/New Caledonia/99A/Panama/99B/Yamanashi/98
01–02A/New Caledonia/99A/Panama/99B/Victoria/00 or similar
02–03A/New Caledonia/99A/Moscow/99B/Hong Kong/2001
03–04A/New Caledonia/99A/Moscow/99B/Hong Kong/2001
04–05A/New Caledonia/99A/Fujian/2002B/Shanghai/2002
05–06A/New Caledonia/99A/California/2004B/Shanghai/2002
06–07A/New Caledonia/99A/Wisconsin/2005B/Malaysia/2004
07–08A/Solomon Islands/06A/Wisconsin/2005B/Malaysia/2004
Because of antigenic drift, A/Wisconsin/2005 provided only limited protection against the H3N2 virus that circulated in the 07-08 season.
The B/Malasia component of the vaccine provided no protection at all. So all three components of the 08–09 vaccine were changed as shown on the next line.
Because the 2009–2010 pandemic of the newly-emerged "swine flu" virus drove the "seasonal" H1N1 viruses (e.g., A/Brisbane/2007) to near extinction,
the "swine flu" H1N1 – now called A(H1N1)pdm09 – replaced the "seasonal" H1N1 in the 10–11 vaccine.
11–12All three components were unchanged from the previous year
Several vaccines for the 2017-18 season will be quadrivalent; that is, contain a fourth component B/Phuket/2013.


On 17 June 2003, the U. S. Food and Drug Administration (FDA) approved FluMist® – a live-virus vaccine that is given as a spray up the nose.

The viruses have been weakened so that they do not cause illness, but are able to replicate in the relatively cool tissues of the nasopharynx where they can induce an immune response. Presumably this is tilted towards IgA production, a better defense against infection by inhaled viruses than blood-borne IgG antibodies. In any case, FluMist® induces a more rapid response than inactivated vaccine and there is some evidence that it provides better protection against antigenic drift as well.

Four strains of flu (H1N1, H3N2, and two strains of B) are included. As new strains appear, they can be substituted.

This new vaccine (technically known as LAIV "Live Attenuated Influenza Vaccine") was only approved for children older than 24 months and adults younger than 50. People with immunodeficiency (e.g., AIDS) should also be cautious about taking it.

Update: For as yet unknown reasons, the nasal spray did not work during the 2015–2016 season, and it was not recommended for the following season.


On 16 January 2013, the U. S. FDA approved an entirely new type of vaccine. Flublok® is made in cell cultures transformed with recombinant DNA encoding the hemagglutinins of the 3 currently circulating flu strains (H1N1, H3N2, and B). The final concentration of antigens is three times that in the current vaccine. Cultures of insect cells are used so there is no problem with possible egg allergies in those receiving the vaccine.

The production process is much faster than with egg-grown vaccines, so a vaccine against a new flu variant can be ready much sooner (weeks instead of months).

Other weapons against flu

It takes a while for the flu vaccine to build up a protective level of antibodies. What if you neglected to get your flu shot and now an epidemic has arrived?

Amantadine and Rimantadine

These drugs inhibit the M2 matrix protein needed to get viral RNA into the cytosol. They work against A strains only, and resistance to the drugs evolves quickly. By the 2009-2010 flu season, virtually all strains of both H3N2 and H1N1 had developed resistance.

Zanamivir (Relenza®) and Oseltamivir (Tamiflu®)

These drugs block the neuraminidase and thus inhibit the release and spread of fresh virions. Spraying zanamivir into the nose or inhaling it shortens the duration of disease symptoms by one to three days. Unfortunately, by the 2008-2009 flu season, all H1N1 strains circulating in the U.S. had become resistant to Tamiflu.


Antibiotics are of absolutely no value against the flu virus. However, they are often given to patients to combat the secondary bacterial infections that occur and that are usually the main cause of serious illness and death.

Why so few drugs?

The mechanisms by which amantadine and zanamivir work provide a clue.

There are far fewer anti-viral drugs than antibacterial drugs because so much of the virus life cycle is dependent on the machinery of its host. There are many agents that could kill off the virus, but they would kill off host cell as well. So the goal is to find drugs that target molecular machinery unique to the virus. The more we learn about these molecular details, the better the chance for developing a successful new drug.

The "Spanish" Flu

Jeffery Taubenberger and his colleagues have sequenced the genes of the influenza virus that had been recovered from

But even with all of its genes now completely sequenced, why the 1918 strain was so deadly is not fully understood. But deadly it is. They have even been able to replace the 8 genes of a laboratory strain of flu virus with all 8 genes of the 1918 strain (using strict biosafety containment procedures!). The resulting virus kills mice faster than any other human flu virus tested. (Reported in the 7 October 2005 issue of Science.)

The Swine Flu of 2009

A new H1N1 flu began infecting humans in North America in April 2009 and has now spread throughout much of the world. Sequencing its genome revealed a novel virus — now called A(H1N1)pdm09 — that contained genes previously found in four different strains of swine flu:

Why this remarkable assortment of genes has enabled he virus to jump so successfully from pigs to humans remains to be determined.

The amino acid sequence around the critical epitopes of its H1 molecules closely resemble those found in the resurrected 1918 flu virus. This would explain why

"Bird Flu"

Many influenza A viruses are found in birds, both domestic and wild. Most of these cause little or no illness in these hosts. However, some of their genes can enter viruses able to infect domestic animals, as was the case for the PA and PB2 genes of the swine flu of 2009 (above).

On several occasions, bird flu viruses have also infected humans, often with alarmingly-high fatality rates. In 2003, human cases of an H7N7 bird flu virus infection occurred in the Netherlands, and in the same year an H5N1 bird virus caused human cases in large areas of Asia. Most of the human cases seemed to have been acquired from contact with infected birds rather than from human-to-human transmission.

And now in 2013, a new bird flu virus, H7N9, has appeared in humans in China. By the end of the summer of 2013, it had caused 135 observed cases (no one knows yet whether there may also be infected people who are not sick enough to show up at hospitals). 45 of the observed cases were fatal. The victims appear to have been infected through contact with infected poultry with little or no evidence of human-to-human transmission.

As a glance at the tables above will show, humans have had long experience with infections and vaccines by both H1 and H3 flu viruses. But the human population has absolutely no immunity against any H7 viruses. If this virus develops the capability to spread efficiently from human to human, it could lead to another worldwide pandemic.

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11 August 2017