Evolutionary Principles in Viral Epitopes - Mathematical Methods and Models in Biomedicine - page 68

HBV, the only member of the hepadnaviridae family that infects humans, is a
small, enveloped virus with a partially double-stranded circular DNA genome of
3.2 kbp. HBV has a high prevalence—with about three hundred fifty million carriers
of HBV world-wide [ 58 ]. The HBV genome contains the following four protein-
coding open reading frames: (a) The preCore/Core reading frame encodes for the
capsid protein (Core) and for the HBeAg protein whose function is not fully clear.
HBeAg is known to be secreted and is thought to have a role in the regulation of
the immune response [ 11 , 12 , 18 , 42 , 43 ]. (b) In the same transcript (called pgRNA),
which also acts as a template for the virus replication, there is the open reading
frame for Polymerase, which has a reverse transcriptase activity [ 10 , 16 ]. (c) The
preS S open reading frame encodes for Surface proteins: large, middle and small

intermembrane proteins located on the ER membrane. The large Surface protein is
probably the protein that interacts with the receptor on the hepatocyte membrane
and has a role in the release of the virus from the cell [ 10 , 16 ]. (d) The fourth
open reading frame encodes for the X protein which thought to have transcription
regulation activity by some studies [ 22 , 37 ]. It is also proposed to have a cytosolic
function as a regulator of proteasome cleavage of some proteins [ 49 ]. The entire
Surface gene, the C-terminus of preCore/Core and the N-terminus of X overlap
with Polymerase [ 17 ].
X can accumulate 10,000-50,000 copies per cell in WHV-hepadnavirus that
infects woodchucks [ 14 ]. We assume that the protein copy number in HBV is not
very different. Surface is a structural protein. It also exists in multiple copies per
virion. By the same logic, the virus should attempt to hide it. Thus, simply based
on the copy number, it is expected that X, Core and Surface should be subject to a
more stringent pressure than Polymerase.
We first tested for a general decrease in the epitope density in HBV. We used
the SIR score to evaluate the epitope density in each protein compared to the
score of the same protein in non-human orthologues. The SIR baselines defined
by random viruses can bias the result, since different proteins have different amino
acid compositions. While the basic characters of a protein are conserved during
evolution, the immunological characters are species-specific. Non-human hosts have
different MHC and TAP molecules (although they share a similar proteasome)
[ 9 , 31 , 40 , 51 ]. Thus, if a specific evolutionary pressure induces epitope removal
in HBV, its SIR score should be lower than the ones of non-human hepadnaviruses.
The average HBV SIR score as well as the scores of the HBV Surface, Core and
X proteins are indeed significantly lower than in other hepadnaviruses (T test, p

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5e 3, Fig. 9 ) (note that X is expressed exclusively in mammalian hepadnaviruses).

In Polymerase, however, the SIR score of the HBV protein is similar to or even
higher than in the non-human hepadnavirus protein (T test, p

−

3).Thus,
evolutionary pressure seems to affect the epitope number in Core, Surface and X,
but not in Polymerase. The high epitope density in Polymerase can either be due to a
high fitness cost of mutations or the weak immune pressure induced by Polymerase,
as shall be further discussed.
Since the above SIR score is averaged over the 33 most frequent HLA alleles,
we further tested the SIR score of HBV for each allele separately and compared it

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