Gesundheit! Now go wash your hands before you spread that flu to everyone else

I had a little bird, And its name was Enza. I opened the window And in-flew-enza.

A skipping rhyme about the 1918 H1N1 flu pandemic, the most lethal influenza pandemic that killed more people than all the casualties from the then-recent World War I put together (estimates range from 20 to 100 million people). This virus was a result of an avian flu virus making the jump successfully into humans.

Influenza is a viral infection that generally affects the upper respiratory tract; that is to say, the mouth, nose and throat. Symptoms often last a week or so, and range from a sudden high fever, coughing, headache, muscle and joint pain, severe fatigue, to sore throat and runny nose. Although the virus can be transmitted at all times, it is typically a seasonal infection that peaks during winter in temperate countries, presumably because more people are packed closer together in winter; the influenza virus is also able to survive for longer outside the body in cold weather. Influenza is passed from person to person via aerosolized droplets i.e. by sneezing and coughing, and contact with contaminated surfaces. It is also able to infect people of all ages; however, the most vulnerable are the very young, the very old, and those with suppressed immune systems. Special care should be taken in these cases, as severe illness or death may result. ImageIn the United States, seasonal influenza epidemics have caused the deaths of more than 30,000 people yearly, and the hospitalization of more than 100,000. More virulent strains may claim the lives of 10,000 – 15,000 more people each year. Influenza pandemics are caused by strains that are so virulent that in the 1918 flu pandemic, more than 2.5% of those that fell ill died, compared to a case fatality rate of less than 0.05% for the more typical virus strain; these pandemic strains are also able to spread rapidly even in the summer, during what is supposedly their “off” season.

There are three types of influenza virus (A, B & C), but the one that we are most concerned about is the influenza A virus. When we’re talking about H1N1, H2N3, and H7N9, we are talking about the influenza A virus – an RNA virus of the orthomyxoviridae (influenza virus) family that is able to infect birds, pigs, and humans, amongst other animals. Variants of the virus that are endemic in birds are called avian influenza; variants that are endemic in pigs are called swine influenza.

In the naming of the subtypes of influenza A virus, ‘H’ stands for hemagglutinin, and ‘N’ for neuraminidase, both of which are antigens embedded on the lipid envelope surface of influenza A virus particles. HA is a protein that mediates binding of the virion to, and entry of the viral genome into, the host cell, while NA is involved in the release of new influenza virions from infected cells. There are 17a different known hemagglutinin (HA) antigens, and 11 different known neuraminidase (NA) antigens; therefore, there are 187 possible different combinations of HA and NA antigens that can theoretically be expressed on the surface of an influenza A virus particle. The genome of the influenza A virus is segmented; that is to say, the genome is broken up into different segments, and each segment codes for different parts of the viral particle.

Influenza A virus schematic

Influenza A virus schematic; M2 Ion channel is important for viral replication by controlling pH; RNP stands for ribonucleic protein and holds the RNA genome. Illustration by CDC.

Several small details are all that differentiate avian flu from human flu; for example, avian flu HA binds to alpha 2–3 sialic acid receptors on the avian cell surface, while human flu HA binds to alpha 2–6 sialic acid receptors on the human cell surface. Unfortunately, swine flu viruses have the ability to bind both types of sialic acid receptors on swine cell surfaces – this makes them dangerous because virulent avian flu viruses could jump into pigs, undergo reassortment and gain the ability to bind to alpha 2-6 sialic acid receptors, then jump into humans and consequently cause a pandemic. This sudden change in the genetic makeup of the influenza virus is known as antigenic shift.

The best way to prevent being infected by the influenza virus is, of course, by getting the flu vaccine. Typically available as a seasonal trivalent vaccine (that means that it is protective against three viruses, usually two influenza A viruses and one influenza B virus), the seasonal flu vaccine is recommended for people at high risk of getting flu, particularly during its peak season in the winter months. It is also only provides protection for one season (one year) because the surface protein antigens on the influenza viruses mutate over time such that the antibodies put out by our immune system against one year’s vaccine will no longer recognize next year’s viral antigens. In fact, the genes for an influenza virus evolve at a rate which is approximately a million times faster than that of animal (including human) genes. This gradual mutation of antigens is known as antigenic drift.

To decide which influenza viruses to include in each year’s trivalent vaccine, scientists study influenza viruses in the wild to determine which are the most predominant, or most likely to become predominant, in the following year; these viruses are then cultivated, then inactivated or attenuated, and included in the following year’s influenza vaccine. There are three types of inactivated vaccines (with decreasing risk of the virus regaining virulence if the inactivation is carried out improperly): whole virus vaccines, split virus vaccines, and subunit vaccines. Whole and split virus vaccines have names that are mostly self-explanatory, while subunit vaccines make use of only certain antigens from the influenza virus; in this case, primarily HA and NA. Live, attenuated influenza vaccines, on the other hand, are weaker and avirulent strains of the live influenza virus. Live, attenuated vaccines are the most effective, but they are also the ones that are most likely to revert to the virulent strain of influenza.

Influenza viruses that are suspected to be able to cause pandemics are used to create monovalent influenza vaccines; this is primarily to allow for control of manufacture, transport, and administration of the vaccine, so as to reduce the risk of the virus regaining its virulence and spreading throughout the population.

Deaths from pandemics were caused by both the virus (and the immune system’s reaction to the virus) as well as secondary infections that turned lethal when the infected person’s immune system was too busy fighting off the virus. When antibiotics were discovered, the mortality rate of pandemic influenza viruses fell as secondary bacterial pneumonia could now be treated effectively. Antivirals such as Tamiflu, a neuraminidase inhibitor, are a recent development, but they have been shown to be effective against influenza in the most recent 2009 H1N1 influenza pandemic, causing the case fatality rate to fall further to 0.03% – very close to the case fatality rate for seasonal influenza.


J. K. Taubenberger and D. M. Morens 1918 Influenza: the Mother of All Pandemics

Note a: An 18th hemagglutinin antigen was found recently in bats


Ow, my liver! (or, Why hepatitis is a real pain in the stomach)

Hepatitis, which has the defining feature of liver inflammation, can be due to a variety of reasons, including consuming excessive amounts of alcohol and/or other toxins, bacteria, and viruses. One of the most important viruses in hepatitis is the hepatitis B virus (HBV). Image

Hepatitis B is endemic in many parts of the world, including sub-Saharan Africa, East Asia, and eastern and central Europe. Transmitted by body fluids and blood, HBV causes liver inflammation, vomiting, fatigue, fever, and jaundice; in less than 1% of cases, HBV causes fulminant hepatitis, which has a high mortality rate. Approximately 5%, or 350 million, are chronic carriers who go on to develop cirrhosis of the liver, and liver cancer. In endemic areas, transmission of HBV most frequently occurs from mother to her unborn child; this is known as vertical transmission. In non-endemic areas, HBV is transmitted from person to person most frequently by unprotected sex or needle sharing; this is known as horizontal transmission. The infection early on in life occurring from vertical transmission is correlated with a higher chance of chronic infection, possibly because the baby’s immune system gets used to the HBV antigen, and does not recognize it as a foreign protein; thus the immune system is unable to clear the virus from the body.

Hepatitis B virus schematic

Schematic of HBV; HbsAg is Hepatitis B surface antigen; HbcAg is Hepatitis B core antigen; notice the partially double-stranded DNA genome.

HBV is a hepadnavirus, with a partial double-stranded DNA genome and a viral envelope. It is also one of the smallest animal viruses, measuring just 42nm across. To infect us, the HBV binds to the surface of a hepatocyte (liver cell), and enters the cell. It then moves to the cell nucleus, and delivers the partial double-stranded genome into the nucleus. In the nucleus, the genome is completed so as to become fully double-stranded, and thus the complete genome can now serve as the template for the four viral RNAs that will eventually produce more copies of HBV viral particles and its genome. After more copies have been produced, the various parts that make up a HBV virion self-assemble, forming many more virions, and exit the cell to infect more hepatocytes.

HBV is unusual; it is a pararetrovirus – that is to say, it is one of the few known non-retroviruses that use reverse transcription in its replication. Reverse transcription is noteworthy because it reverses the usual flow of information from DNA to RNA, and instead goes from RNA to DNA. However, HBV is not a retrovirus because it has an RNA intermediate instead of a DNA intermediate, meaning that the genetic information flow in HBV replication goes from DNA à RNA à DNA, instead of RNA à DNA à RNA, as in retroviruses.

In the process of replication, HBV produces a large amount of excess viral particles, so much so that one of the first instances that viral particles were detected was from the blood serum of HBV infected people; they are non-infectious because they do not have a genome. These genome-less viral particles are known as virus-like particles (VLPs), and have become important in vaccine creation because of they are very immunogenic, while at the same time being non-infectious. HBV VLPs are commonly spherical or filamentous, compared to the spherical HBV virion.

HBV has four serotypes, and eight genotypes. Different serotypes produce different antibody reactions from our adaptive immune system; however, the genotype of a HBV virion has no relation with which serotype is presented on its surface. Genotypes are correlated with the geographical distribution of HBV, with some genotypes being more predominant in some regions; we are also able to trace the evolution of HBV through its genotypes.

Although HBV does cause cell damage upon infection, a lot of damage is done by the reaction of our immune system to infection. After being activated by antiviral cytokines, white blood cells, particularly virus-specific cytotoxic T cells, set about destroying infected hepatocytes, thus causing liver inflammation, and other liver-related symptoms, such as jaundice and liver cancer. When T cells die as a result of responding to the infection, more antiviral cytokines are produced. The higher the level of antiviral cytokines, the stronger the signal to recruit more T cells, resulting in more hepatocytes destroyed, and more severe liver inflammation.

Treatment primarily deals with interfering with DNA synthesis via nucleoside and nucleotide analogues, thus interrupting HBV replication. Unfortunately, there is no drug available that will help infected persons clear HBV from their bodies faster.

The first vaccines were essentially injections of HBsAg (HBV surface antigen) that would induce the production of antibodies to counteract HBsAg, and consequently HBV virions themselves. They were initially purified from the blood of people already infected with HBV; all viruses were destroyed, leaving behind the HBsAg. This was withdrawn over fears of HIV contamination, as the people most likely to have HBV were also at high risk for HIV. Recombinant vaccines were then developed, where the gene for HBsAg was transfected into yeast, thus producing HBsAg without the risk of contamination from other pathogens. Because HBsAg is able to self-assemble into VLPs, these vaccines are also considered the first VLP vaccines. This is also one of the first vaccines against cancer, due to the link between chronic HBV carriers and liver cancer.


WHO | Media Center | Hepatitis B

WHO | Global Alert and Response | Hepatitis B

D. Grimm, R. Thimme, and H. E. Blum. HBV life cycle and novel drug targets Hepatol Int. 2011 June; 5(2): 644–653. doi:  10.1007/s12072-011-9261-3

A. J. Cann. Principles of Molecular Virology, 4th Edition. Elsevier 2005

Dengue virus; coming soon to a mosquito near you!

Dengue is endemic today in over 100 countries in Asia, the Pacific, the Americas and Africa, affecting mostly urban and sub-urban tropical and sub-tropical areas. DengueIt typically causes a flu-like illness known as dengue fever; the “dengue triad” of symptoms is a fever, a headache, and a rash. It also causes severe joint and muscle pain – thus it has also been called “bonebreak fever”. The more severe version is known as dengue haemorrhagic fever (DHF) and dengue shock syndrome (DSS), where patients experience blood loss and shock. There are four fivea serotypes of the dengue virus in humans – DENV-1, DENV-2, DENV-3, and DENV-4; each of them with different viral protein antigens on the surface of the virus.

The transmission of the dengue virus involves both its human host and the Aedes aegypti mosquito vector; when a female mosquito sucks blood from a dengue-infected person, the virus goes along. The virus then infects the mosquito, eventually reaching its salivary glands. Then just before the infected mosquito sucks blood from another person, it injects its anesthetic saliva into the person, thus passing the virus to the second person. And the cycle repeats.

Although A. aegypti is primarily found in tropical and sub-tropical areas, secondary Aedes vectors are able to survive in colder climates like those of the United States and Europe. As a consequence, the dengue virus is quickly gaining a foothold in these regions. 

Dengue virus schematic

Dengue virus; Illustration by David S. Goodsell and the RCSB PDB.

The dengue virus is a single-stranded RNA flavivirus.The dengue virus envelope protein, found on the surface of the virus, attaches to the surface of our cells, and causes our cells to take in the virus. It would be useful to block this action in treating dengue; unfortunately, the precise way the envelope protein is binding to the surface of our cells is still not known, so we are unable to develop any drugs in this direction.

Flaviviruses like dengue are also able to block our immune system from responding during infection by inhibiting signaling within the response of our innate immune system, leading to a slower clearance of the virus from our bodies.

Because there is currently no drug or vaccine available for dengue, doctors can only offer symptomatic relief to patients. One of the main problems with developing a vaccine for dengue is because of its four five serotypes. Our immune system fights off viral infections by producing antibodies in response to viral antigens; because the immune system retains these antibodies, there is long-term protection against the serotype we were originally infected with. However, cross-protection between serotypes is only transient, depending on antibody levels, which decrease with time. When antibody levels are high, antibodies against one serotype can cross-protect against other serotypes; when antibody levels are low, the effects of the antibodies are negligible. However, when antibody levels are in the mid-range, antibody-dependent enhancement kicks in, and then people who have initially been infected with one dengue virus serotype have a higher chance of developing DHF or DSS if infected with another serotype. Thus any vaccine developed has to protect against all fourb serotypes simultaneously so as to minimize the chance of DHF or DSS developing in people who have been given a vaccine protecting against one serotype but not another. These types of vaccines are known as tetravalent vaccines, because they counter all four serotypes at the same time. At this point in time, the most promising vaccine is being developed by Sanofi Pasteur, which is currently in Phase III of clinical trials.

Vaccines against dengue virus currently under development

Developer Status
Sanofi Pasteur Live attenuated chimeric tetravalent vaccine, phase 3 clinical trials
Inviragen Live attentuated tetravalent vaccine, phase 2 clinical trials
Butantan Live attenuated tetravalent vaccine, phase 2 clinical trials
Merck Subunit protein tetravalent vaccine, phase 1 clinical trials
Glaxosmithkline Purified inactivated tetravalent vaccine, phase 1 clinical trials
Naval Medical Research Center Plasmid DNA vaccine, phase 1 clinical trials

The best way to prevent infection by the dengue virus is to stop its vectors – namely, the Aedes mosquitos; the easiest way to do this is by reducing the number of places where it can lay its eggs, by clearing any standing water.




WHO | Dengue Control

R. Perera and R. J. Kuhn. Structural Proteomics of Dengue Virus Curr Opin Microbiol. 2008 August; 11(4): 369–377. doi:  10.1016/j.mib.2008.06.004

Michael S.Diamond. Mechanisms of Evasion of the Type I Interferon Antiviral Response by Flaviviruses Journal of Interferon & Cytokine Research. September 2009, 29(9): 521-530. doi:10.1089/jir.2009.0069.

B. Adams, E. C. Holmes, C. Zhang, M. P. Mammen, Jr, S. Nimmannitya, S. Kalayanarooj, and M. Boots.Cross-protective immunity can account for the alternating epidemic pattern of dengue virus serotypes circulating in Bangkok Proc Natl Acad Sci U S A. 2006 September 19; 103(38): 14234–14239. doi:  10.1073/pnas.0602768103



Footnote a: In October 2013, scientists announced the discovery of a fifth dengue serotype, found in the blood of a dengue patient from Malaysia.

Footnote b: As there has only been one case of the fifth serotype being found in humans, it is likely that primates other than humans still remain as the hosts for the fifth serotype – meaning that the infection of the patient in Malaysia with the fifth serotype was accidental. However, if more cases are found, we will have to factor this fifth serotype into our vaccines.