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.

Gay men, sex and AIDS.

This is a dialogue-form essay I wrote for a Coursera.org course on AIDS a couple of months ago, sort of in reply to a friend. As part of the assignment, I asked around for common (or not so common) myths about AIDS, and got a reply from a friend who was indignant about why gay men were banned from donating blood. So this was the essay I ended up writing. The requirement was that the essay should debunk the myth, in script form. Of course, I took liberties with imagining my friend’s replies XD I’ve removed the references that referred to the course lectures, but rest assured that the statements are legitimate. So if you see a number reference but no reference link below the essay, it means I was referring to a course lecture.

L: I don’t understand why gay men aren’t allowed to donate blood just because they are more likely to contract AIDS? Is it even true that they are more likely to contract AIDS? (When pressed) I’m not quite sure about how people contract AIDS, though.

L: I mean, seriously – isn’t that some kind of discrimination or something?

Me: Well, firstly, you say that you don’t know how HIV/AIDS is transmitted, right?

L: Yeeeeeah. And what’s the difference between HIV and AIDS?

Me: Hmm. HIV stands for Human Immunodeficiency Virus, which is what causes AIDS, or Acquired Immunodeficiency Syndrome – kind of like how the influenza virus causes the flu. One is the germ, and the other is the illness.

L: It’s a little confusing, but I think I get it. Why don’t they call it the same thing though?

Me: It’s a history thing[1]. Well, basically HIV is transmitted via body fluids – mostly blood, semen and vaginal fluids. 37% of men who have sex with men (MSM) have had anal sex [2], and the figure jumps to 42-44% when younger MSM are surveyed [2, 3]. One of the things about anal sex is that first, the inner lining of the anus is more delicate than the vagina, and therefore tears more easily; hence it’s easier for HIV to enter the bottom’s bloodstream from the top’s semen [5]. Second, the anus lacks the mucus produced by the vagina, which provides a small amount of protection from HIV transmission [4]. The virus can also move from the blood, if any, in the bottom’s anus to the exposed parts of the top’s penis [5], particularly if the top is uncircumsized [5, 6]. In developed countries like ours, unprotected anal sex is 17.5 times as likely to allow for HIV to be transmitted compared to vaginal sex, on a per-act basis [4]. And the crux is, only one in six MSM use condoms consistently when participating in anal sex [7, 8]. So in gay men, there is a higher chance that they will have contracted AIDS. And since one of the ways that HIV is transmitted is via blood, that’s why they’re not allowed to donate blood. However, it is true that 36% of younger women have also had anal sex [3], so the risk is equally relevant to them. The wording on blood donation forms should probably be changed to reflect that. Actually, there’s lots of things we can do about this issue, but people who have anal sex do tend to be more likely to contract AIDS.

L: Huh.

[2] http://onlinelibrary.wiley.com/doi/10.1111/j.1743-6109.2011.02438.x/abstract

[3] http://www.cdc.gov/nchs/data/nhsr/nhsr036.pdf

[4] http://ije.oxfordjournals.org/content/39/4/1048.long

[6] http://www.ncbi.nlm.nih.gov/pubmed/20139750

[7] http://www.aidsmap.com/Consistent-condom-use-in-anal-sex-stops-70-of-HIV-infections-study-finds-but-intermittent-use-has-no-effect/page/2586976/#item2586982

[8] http://www.retroconference.org/2013b/Abstracts/45832.htm

HIV (what a nasty little bug)

Hi guys! Sorry I went on unannounced hiatus for a while – hope you haven’t been too lonely!

Anyway, here’s a really detailed and fascinating video of the Human Immunodeficiency Virus (HIV), showing its structure and genetic make-up.

This video by Christopher Harkins won the VIDEO first prize in the autopack Visualization Challenge 2012.

HIV, the virus that causes acquired immunodeficiency syndrome (AIDS), is spread through body fluids such as blood, semen, and vaginal fluids, and can also be present in minute amounts in breast milk, saliva, and tears; however, it is only able to infect someone when there is a break in the barrier provided by our skin or the mucosal layers of our digestive and respiratory tracts.

HIV is a lentivirus, which means that it is able to stay dormant for a long time in the body without any apparent symptoms. It’s also able to mutate rapidly, so much so that it has proven exceedingly difficult to pin it down with a single, workable vaccine, or even a single, workable anti-viral treatment; HIV-1, the predominant form of HIV, has been divided into at least four subgroups, which is then split into further subtypes, based on how virulent the form is.

There are two advances in HIV research that have led to cautious optimism amongst researchers, however – first, that sufficiently rapid treatment with anti-viral drugs may halt HIV in its tracks; the most newsworthy item regarding the baby who was functionally cured of HIV has also been backed up by a small study of 70 people, 14 of whom were also functionally cured of HIV. Second, that a chemical called mellitin found in bee venom, when loaded onto specifically designed nanoparticles, is able to poke holes in the external membrane of HIV, thus disrupting its structure and destroying it. This bypasses the problem of the rapidity of HIV mutation entirely, and should also be applicable for all the different types of HIV.

Awesome, isn’t it?

Ever wondered how each cell in your body has the same genes as each other?

Remember in my last post I mentioned that our DNA is like a language that allows us to form words?

Well, just like how individual words don’t make sense unless put into context (can you imagine trying to make sense of the word ‘the’ if there was no context?), we have to think of DNA in terms of genes to give it context.

Genes are units of heredity, made up of DNA codons – this means that the traits that your parents have passed down to you, like blonde hair, brown eyes, your height and whether you have dangly earlobes – are all handed down via genes. This also means you can have lots of different combinations of genes (also known as genotypes), which, when expressed, means lots of different kinds of people (also known as phenotypes) – kind of like how you can make almost any kind of sculpture you want with LEGOs.

Notice how I said “almost any kind”? That’s because genes are linked together on structures known as chromosomes. Chromosomes help keep genes neat and tidy in your cells, so that they don’t float around and get in the way of proteins that are trying to do their work, and most importantly, so that all 2 m (about 6 ft) of your DNA can fit into each of your cells, which are only about 10 µm in width – about 200000 times smaller.

Two sets of chromosomes; a chromatid vs a chromosome

Genes that are stored on the same chromosome are said to be linked, and the closer they are to each other on the chromosome, the more closely they are linked. Because genes are stored on chromosomes in a fixed order, linked genes tend to be inherited together, kind of like how if you tried to tear out a picture of Iron Man from a magazine, you would also be tearing out the article on the Hobbit that was behind it. This decreases the number of possible combinations of genes, because it places restrictions on how the genes can be re-arranged, but the number of combinations is still a pretty big number.

linked genes

In fact, because genes are almost always found in the same locations – meaning that gene is always found at location on chromosome a – scientists have come up with a system of naming the locations of genes, also known as a locus. (Hey look, I said ‘almost’ again. I won’t be covering why here though, because that would make this blog post too long. Look out for a post on genetic mutation for an explanation on that.)

Here’s where it gets a teensiest bit confusing – genes also come in different flavours, called alleles, and different flavours of genes share the same locus – kind of like how you can use differently-coloured LEGO bricks for the house you are building out of LEGO pieces.

For instance, the reason why people have A, B, AB and O blood types is because there are three different ‘colours/flavours’ of the gene that determines blood type in humans. These three alleles are called IA, IB, and IO. All humans (and many other organisms) are diploid, meaning that they have two sets of chromosomes – one from their mother, and one from their father. Depending on their parents, people may inherit IAIA, IAIO, IBIB, IBIO, IOIO or IAIB. (Remember – combinations of genes are known as genotypes!) IA and IB are co-dominant to each other, and both are dominant to IO. This means that the people with that carry the combinations of IAIA and IAIO will have blood type A; likewise for people with blood type B, and IBIB and IBIO. Only people with IOIO combination will have blood type O; on the other hand, because of co-dominance, people with the IAIB combination will have blood type AB. Differing blood types is a kind of phenotype, so we can say that some people have a phenotype of type A blood, while other people have a phenotype of type AB blood.

Blood types A, B, AB and O; methods of inheritance

Because there are at least 20,000 genes, and if each gene has at least two different alleles, the chances that someone shares a genetic profile with you (unless you have an identical twin) is 1 in 10 to the power of several thousands. Yes, that is a rather mind-boggling set of zeros. However, our technology thus far only allows us to narrow the chance that the DNA of two people (who both don’t have identical twins) will match down to 1 in 100 billion.

But if everyone starts out with two sets of chromosomes (one from each parent) – how did our parents each give us only one set?

Parental inheritance gone wrong

Because, aside from regular cells, there is a special subset of cells known as gametes – or more simply, sex cells. (Geddit? Sex cells? Hurhur.)

Anyway, these gametes carry only one set of chromosomes instead of the usual two, by a process known as meiosis.

First, we have a regular old stem cell with two sets of chromosomes.


Via meiosis, the two sets of chromosomes are first duplicated, resulting in four sets of chromosomes (1). Then the cell splits into two, and then into two again, resulting in four different daughter cells; the four sets of chromosomes are dragged apart, so that each cell only ends up with one set of chromosomes. (2) These, then, are four different gametes, or sex cells.

When two gametes combine, the resulting cell that then forms has two sets of chromosomes, and eventually grows up to become another person; inside this person, more sex cells are being produced, which will potentially combine with other sex cells to produce more people, and so on and so forth.

What does all this have to do with why our cells all have (almost) the same DNA, you ask? Because ordinary cells go through a similar process called mitosis, where the two sets of chromosomes are again duplicated, resulting in two copies of two sets of chromosomes. The cell splits into only two daughter cells this time, and each daughter cell has two sets of chromosomes. Both sets of chromosomes are mostly identical copies of one another, so each daughter cell has (almost) the same DNA as its parent, as well as its sister cell. (Oh hey, again with the ‘almost’ and ‘mostly’. Just look out for the post on genetic mutation.)


So that’s why you can take the cheek cells of a person, test the DNA inside them, and say to that person, “There is, like, a one in 100 billion chance (barring laboratory errors) that the DNA in your cheek cells matches the DNA found in the blood on the knife. Man, you are soooo guilty.” (P.S. Ask me about human chimeras sometime.)

In summary,

Genes – how traits are inherited by the next generation – e.g. hair colour, eye colour, whether you’re balding or not; made up of DNA

Alleles – different flavours of genes; e.g. blonde hair, black hair, brown hair, red hair. Not blue or green hair, though, sadly enough

Chromosomes – an organization of genes, like a chapter in a book (if the book is an instruction manual on how to build a human)

Locus – where genes are found on a chromosome

Linked genes – genes that are generally found on the same chromosome (or the same chapter, if you prefer), and are hence usually inherited (or handed down) together

Chromatid – the really, really singular version of ‘chromosome’

Genotype – the combination of genes in anybody; can be thought of as a kind of DNA profile

Phenotype – the person that results when the combination of genes is expressed altogether; two people may have different genotypes but share a phenotype, e.g. John may have genotype IBIB and Beth may have genotype IBIO but they both have phenotype blood type B

Diploid – having two sets of chromosomes (Also, haploid – having one set of chromosomes)

Meiosis – a cell-splitting procedure by which a cell goes from having two pairs of two sets of chromosomes (2×2 = 4) to dividing into four cells with one set of chromosomes each; used for producing sex cells (hurhur)

Mitosis – a cell-splitting  procedure by which a cell goes from having two pairs of two sets of chromosomes to dividing into two cells with two sets of chromosomes each; regular old cell division; also, kind of why you can match a person to the DNA left behind at a crime scene

DNA = You (Or, How to assemble a human)

Many of you may know that DNA is the code that is stored in tightly-wrapped bundles in our cells; you may also know that our genes are what is being coded for by our DNA; you may even know that genes are important to us because they determine how we are made. But do you know how to get from DNA to you?


If your body was a program, DNA would be kind of like computer code; to figure out the program, first you need to know how the coding language works. Scientists have figured this out a long time ago; the DNA code is very simple, and only made up of four letters (called bases) – A for Adenosine, T for Thymine, G for Guanine and C for Cytosine. Each ‘word’ in DNA, also known as a codon, is made up of three letters; for example, you could have TAC, ATC, ACT or ATT. These all make itty-bitty pieces of your body’s cells, which will eventually end up as you.

However, your cells can’t read DNA directly; what they can read is a similar language called RNA (ribonucleic acid). RNA is made up of four letters too – A, G, C and instead of T, RNA has U for Uracil. This process of converting DNA to RNA is called transcription, and is carried out by a protein called RNA polymerase. The DNA words above would then be read as UAC, AUC, ACU or AUU. Or would they?

One thing about the bases A, T, G and C is that they bind with one another to form two different sets of base pairs – A always binds to T or vice versa, and G always binds to C or vice versa. (In the case of RNA, just substitute U for T and you won’t go wrong!)


When DNA is converted into RNA, RNA polymerase makes use of this base pairing to carry out its transcription work – in other words, G in DNA is transcribed into C in RNA, and vice versa; T in DNA is transcribed into A in RNA, but A in DNA is transcribed into U in RNA. (See – just substitute U for T in RNA!) So the DNA words transcribed into RNA would be AUG, UAG, UGA or UAA. Easy, isn’t it?

So now we have:

DNA -> complementary RNA -> ??? -> you!

What’s next?

After transcribing DNA into RNA, we need to translate RNA into amino acids, which can then be assembled into proteins; in order to do so, we need the help of a protein molecule known as a ribosome.

If we think of RNA as kind of like an IKEA instruction manual, the ribosome then acts a little like a very meticulous person putting together a piece of IKEA furniture. It reads the RNA code, and makes sure that each amino acid that corresponds to each RNA codon is present. The ribosome then assembles a protein molecule out of the amino acids according to the RNA code, but unlike some people who put together IKEA furniture in any old order, the ribosome puts the protein together in a sequential manner, reading off one codon after another.

RIbosomes, tRNA, mRNA, and amino acids

A special molecule (also made up of RNA) called transfer RNA brings different amino acids to the ribosome, kind of like a friend or a trained monkey bringing different parts of the IKEA furniture to the very meticulous person.

Because both tRNA and the RNA code (also known as memory RNA, or mRNA) are both made up of RNA, they are able to form complementary base pairings with each other. So like the trained monkey being able to match the shape of a screw in the IKEA manual to an actual screw, a tRNA is able to match the RNA codon to the amino acid it has bound to, and hands it to the ribosome, which attaches the new amino acid to the previous amino acid.

The beginning of a protein

Proteins are made up of long sequences of amino acids, folded into different configurations. (For more information, I will soon release a post on protein folding. Soon.) Different sequences of amino acids yield different proteins; different proteins then come together with lipids and carbohydrates to make cells. Many cells are put together, and thus make up organs, which when assembled together in the proper fashion, become you. And me.

DNA->complementary RNA->proteins->cells->you!

Et voila, one human, fresh off the assembly line.