Resistance is Futile
Of all the things that convince me about the future, nothing
is so stark, so definite, so telling, and so real than the human hubris. No
don’t get me wrong; we live in an environment of self-proclaimed wizards, the
same snake-oilmen, quasi-intellectuals who can charm the socks off of anyone. We
are the experts that hail from the top of Mount Sinai and yet in that very
expertise of existence there is this gnawing, irritating human trait called
humanism, or more aptly describes as arrogance, the one that is seduced by the
vapors of grandeur, by the deluding sense of perfection, by the lofty sense of
perfect knowledge. Oh but I digress into the jungle of human existence.
We exist on this planet with billions of other species. And
to be certain there are estimates derived from fossilized records that over a
billion species have perished between life and now and that three species go
extinct every hour. We are one of those species too but with a short lifespan
overall thus far as we hasten towards self-annihilation. True we are the ones
gifted with the bipedal motion, the extensions of arms and the dexterity of
hands that has culminated in populating this planet with monoliths as high as
the Stone Henge, Empire State Building, Khobar Towers and the like and made
cities where once water and swamp reigned. Yes we are the quintessence of dust
as Shakespeare called us, not because we are great or majestic, but because we
have the power of reason and that sprinkle of pixie dust called hubris.
"Look deep into nature, and then you will understand everything better." ~Albert Einstein
And then this:
We must rid mankind of all maladies!
Really?
I mean have we thought this one through at all. Have we
reasoned? Have we spent an evening thinking about the entire collective life on
this planet as a whole? Have we?
Tuberculosis
Take for example the TB conundrum. We started out with this
scourge and found some medicines to combat it. And we were successful. A
tincture of Streptomycin and the scourge was no more. Where previously sanatoriums
had been constructed to isolate the infected and infirmed till their self-healing
or death, now the magic of an injection arrested the continuum of that horrid
vigil.
Soon better drugs reigned, like Ethambutol or EMB, Isoniazid
or INH and Rifampin or RMP. Each garnered a better share of the TB bug. We all
celebrated the onslaught against this vile bacterium that had cost so many
lives and we had won. The flag of security had been flown atop the TB
gravesite.
But then came the discovery of these clever critters finding
little loopholes and infecting humans again. Mathematical Modeling revealed a
stark but deafening verdict. TB was undergoing mutations and becoming resistant
to our glorified, impenetrable lines of defenses. And that Mathematical Model
was verified in real life!
“The rationale for using multiple drugs to treat TB is
based on simple probability. The frequency of spontaneous mutations that confer
resistance to an individual drug are well known: 1 in 107 for EMB, 1 in 108 for
STM and INH, and 1 in 1010 for RMP.”
And not only that, but these little bacterial buggers were
becoming more aggressive and thus more deadly in their behavior. What once was
a relatively long survival, albeit in the sanatorium, to complete riddance of
the TB bacterium now killed humans with impunity within a short span of days.
A study in Los Angeles found that about 6% of cases of
MDR-TB were clustered. Multi-drug resistant tuberculosis (MDR-TB) is defined as
TB that is resistant at least to INH and RMP. Isolates that are multi-resistant
to any other combination of anti-TB drugs but not to INH and RMP are not
classed as MDR-TB. Yet the MDR bug had climbed its way into the inner sanctums
of inner city!
“There is currently an epidemic of XDR-TB South Africa.
The outbreak was first reported as a cluster of 53 patients in a rural hospital
in KwaZulu-Natal
of whom 52 died. What was particularly worrying was that the mean survival from
sputum specimen collection to death was only 16 days and that the majority of
patients had never previously received treatment for tuberculosis.”
To be accurate about the Mathematical Model here is a short
excerpt to understand the conundrum better:
“A patient with extensive pulmonary TB has approximately
1012 bacteria in his body, and therefore will probably be harboring
approximately 105 EMB-resistant bacteria, 104 STM-resistant bacteria, 104
INH-resistant bacteria and 10² RMP-resistant bacteria. Resistance mutations
appear spontaneously and independently, so the chances of him harboring a
bacterium that is spontaneously resistant to both INH and RMP is 1 in 108 x 1
in 1010 = 1 in 1018, and the chances of him harboring a bacterium that is
spontaneously resistant to all four drugs is 1 in 1033. This is, of course, an
oversimplification, but it is a useful way of explaining combination therapy.”
So a new barrage of drugs are being crafted and drafted in
the battle to circumvent this new abrogation in the paradigm of human thought;
that we have control.
Hepatitis B Virus
Just so we don’t get too comfortable with the thought that
this is only a single bug. Heck we can smash it in no time. Let me take you
into the machinery of the HBV also known as the Hepatitis B Virus.
The gene that encodes the HBV polymerase overlaps with the gene that encodes the viral envelope, and so mutations in the overlapping reading frame can change both proteins.
The HBV is composed of 3400 base pairs and five genes. Each
has a specific purpose.
The hepatitis B virus (HBV) is a DNA virus that replicates
its genome via an RNA intermediate using reverse transcription. What is
interesting is that for its replicative maneuvers, it converts itself into
these CCCDNAs or Covalently Closed Circular DNA that is tightly wound together
DNA machinery and is impervious to the drugs targeted against the HBV.
Life Cycle within a human body
So while
all viral particles floating around in the blood stream may be rid by the
directed therapy, the CCCDNAs residing in the liver tissue by the billions
laugh it off in comfort saying “We’ll get you in the end.” The CCCDNA survive
to form a large reservoir for replication, reactivation and their own survival
in the human body when the selective pressures of therapy are presented.
Hepatitis B Virus
It is important to note that the signs and symptoms from the
HBV infection come not from the viral replication but from the Immune response
initiated by the body to kill the virus itself. The genetic mutations occur at a glacial pace based on linear time. The rate is 1 nulceotide mutation per year (Mutation Rate = 5*10^-5).
The selection pressures allow the virus to mutate and create
quasispecies to live within the liver: It is the constant destruction of the
liver cells and the immune response mediated that determines the clinical
behavior. “Mathematical modeling showed that the half-life of hepatocytes
varies from 30 to 100 days, depending on individuals' immune response.”
The composition of the viral quasispecies evolves over time
depending on the selective pressure including, vaccination and antiviral
therapy and the host immune response. Escape mutants may then spread in the
liver and become the dominant species depending on their fitness (i.e., their
capacity to replicate and dominate wild-type strain in the presence of
antiviral pressure) and the replication space available for their dissemination
in the liver.
PCR Genotyping
The issues of genotyping plague a well-balanced assessment
of the HBV quasispecies because of the many pitfalls in the process itself. Yet
these are the known methods of determination at present and we have to make the
most from them. The dilemma of study is compounded by the dilemma of the
limitations of knowledge. Genotyping of the whole virus is tedious but remains the gold standard today. Yet studies continue to use partial genome analysis for reportage that hurts validity and confounds the truth in literature. Besides a single SNP or dual SNP cannot be ascertained by whole genome testing. It has to be done on a SNP by SNP basis with specific endonucleases... so there, now you have the most of it, if not all!
PCR Genotyping Methodology
“(Genotyping relies on either DNA sequencing or
hybridization. Sequencing-based methods include standard population-based
polymerase chain reaction (PCR), cloning of PCR products, and restriction
fragment-length polymorphism analyses. Direct PCR-based DNA sequencing can
detect a particular mutant only if it is present ≥20% of the total quasi
species pool.61 Cloning can overcome this problem, but analysis of large
numbers of clones is required. Viral mutants that constitute as little as 5% of
the total population can be detected by restriction fragment-length
polymorphism analyses, but separate sets of endonuclease reactions must be
designed specifically for each (and known) mutant of interest. These methods
are labor intensive, require highly skilled personnel, and are not suitable for
high-throughput screening.)”
The virus exhibits the following drug resistant mutations
referenced below in the Addendum: primary resistance mutations (rtM204I),
secondary resistance mutations
(rtL180M with rtM204V) and compensatory mutations (rtV173L)
So after the facts and the implied human hubris, we are left
with a rather sobering thought; species are coevolving and each species finds a
niche to survive and progress. It is after all in the Darwin’s dictate that,
“Survival of the Fittest.” Choosing to ignore such an important message based
on aggregated evolutionary evidence is the hallmark of a callous disrespectful
self-indulgent human mind. Say it ain’t so!
"All, everything that I understand, I understand only because I love." ~Leo Tolstoy
References:
David HL (November 1970). "Probability
Distribution of Drug-Resistant Mutants in Unselected Populations of
Mycobacterium tuberculosis". Applied Microbiology 20 (5):
810–14.
Sarah McGregor. "New TB
strain could fuel South Africa AIDS toll". Reuters. Retrieved
2006-09-17
http://www.ihlpress.com/pdf%20files/hepdart09_presentations/emergence_prevention_vr/2_locarniniHepDart%20FINAL_SLocarnini_031209_REVISED.pdf
http://www.natap.org/2009/HBV/111109_01.htm
Addendum: (On HBV Drug Resistance)
The available agents currently in use against the HBV:
Interferon alfa-2b INTRON® A Merck/Schering 1991
Lamivudine EPIVIR-HBV® GlaxoSmithKline 1998
Adefovir dipivoxil HEPSERA ™ Gilead Sciences 2002
Entecavir BARACLUDE ™ Bristol-Myers Squibb 2005
Peginterferon alfa-2a PEGASYS® Genentech/Roche 2005
Telbivudine TYZEKA ™ Idenix/Novartis 2006
Tenofovir VIREAD ™ Gilead Sciences 2008
The viral mutations causing resistance over time to
antiviral agents:
Interferon alfa-2a
(Intron A) Interferon 1991 None
Lamivudine
(Epivir-HBV) Nucleoside reverse
transcriptase inhibitor 1998 14 - 32% at Year 1; 60 - 70% at year 5
Adefovir (Hepsera) Nucleoside reverse
transcriptase inhibitor 2002 0% at year 1; 29% at year 5
Entecavir (Baraclude) Nucleoside reverse transcriptase
inhibitor 2005
1.2% in treatment naïve at year 6; 57% in
lamivudine resistant at year 6
Peginterferon alfa-2a (Pegasys) Interferon 2005 None
Telbivudine (Tyzeka) Nucleoside reverse transcriptase
inhibitor
2006 25% in HBeAg positive at year 2; 11% in HBeAg negative at year 2
Tenofovir (Viread) Nucleoside Reverse transcriptase
inhibitor 2006
0% at year 2; adefovir resistant HBV should be treated
with tenofovir and another HBV antiviral
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