J. Biomedical Science and Engineering, 2010, 3, 1-12
doi:10.4236/jbise.2010.31001 Published Online December 2009 (http://www.SciRP.org/journal/jbise/
Published Online December 2010 in SciRes. http://www.scirp.org/journal/jbise
The interaction between the 2009 H1N1 influenza A
hemagglutinin and neuraminidase: mutations, co-mutations,
and the NA stalk motifs
Wei Hu
Department of Computer Science, Houghton College, Houghton, NY, USA.
Email: wei.hu@houghton.edu
Received 29 October 2009; revised 6 November 2009; accepted 9 November 2009.
As the world is closely watching the current 2009
H1N1 pandemic unfold, there is a great interest and
need in understanding its origin, genetic structures,
virulence, and pathogenicity. The two surface proteins,
hemagglutinin (HA) and neuraminidase (NA), of the
influenza virus have been the focus of most flu re-
search due to their crucial biological functions. In our
previous study on 2009 H1N1, three aspects of NA
were investigated: the mutations and co-mutations, the
stalk motifs, and the phylogenetic analysis. In this
study, we turned our attention to HA and the interac-
tion between HA and NA. The 118 mutations of 2009
H1N1 HA were found and mapped to the 3D homology
model of H1, and the mutations on the five epitope
regions on H1 were identified. This information is es-
sential for developing new drugs and vaccine. The dis-
tinct response patterns of HA to the changes of NA
stalk motifs were discovered, illustrating the functional
dependence between HA and NA. With help from our
previous results, two co-mutation networks were un-
covered, one in HA and one in NA, where each muta-
tion in one network co-mutates with the mutations in
the other network across the two proteins HA and NA.
These two networks residing in HA and NA separately
may provide a functional linkage between the muta-
tions that can impact the drug binding sites in NA and
those that can affect the host immune response or vac-
cine efficacy in HA. Our findings demonstrated the
value of conducting timely analysis on the 2009 H1N1
virus and of the integrated approach to studying both
surface proteins HA and NA together to reveal their
interdependence, which could not be accomplished by
studying them individually.
Keywords: Co-Mutations; Entropy; Epitope; H1N1;
Hemagglutinin; Influenza; Mutation; Mutual
Information; Neuraminidase; Phylogenetic Analysis;
Stalk Motif; Swine Flu
Influenza viruses caused several pandemics in history
such as the Spanish flu (H1N1, 1918), the Asian flu
(H2N2, 1958), and the Hong Kong flu (H3N2, 1968),
where the H1N1 virus has the longest recorded history
of human infection. In March and April 2009, a new A
(H1N1) influenza virus first emerged in Mexico and the
United States. Antigenically the new virus is similar to
North American swine A (H1N1) viruses but distinct
from seasonal human A (H1N1). This virus consisting of
gene segments in swine or humans has acquired the ca-
pacity to spread quickly by human-to-human transmis-
sion across the globe and therefore has attracted interna-
tional attention. On June 11, 2009, the World Health
Organization (WHO) declared the H1N1 virus a pan-
The influenza A viral genome is composed of 8 genes
encoding 11 proteins, including two surface glycopro-
teins, hemagglutinin (HA) and neuraminidase (NA). The
main influenza antigens targeted by the human immune
system are these two proteins, and influenza A subtypes
are classified by the antigenic distinctions of the HA and
NA proteins. There are 16 subtypes of HA and 9 sub-
types of NA. HA mediates virus binding to sialic acid
receptor on a host cell surface to initiate infection, and
NA cleaves the binding to promote release of viral
progeny. Otherwise, the viral progeny particles will re-
main aggregated at the cell surface. HA is also the main
target of the host immune system. Once in a host cell,
the HA protein comes under selective pressure for
change to evade the host immune response. HA and NA
have been of great interest in flu research due to their
pivotal role in viral infection and replication.
The HA is a cylindrically shaped homotrimer mole-
cule composed of three identical HA polypeptides,
which are cleaved by protease into two subunits HA1
and HA2 during virus maturation. The globular region of
the molecule is based mainly on the HA1 residues, and
2 W. Hu / J. Biomedical Science and Engineering 3 (2010) 1-12
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the stem contains some residues of HA1 and all of HA2.
The enzymatic domain of NA is held away from the vi-
rus surface by a long, thin stalk of variable length. The
replication efficiency of viruses in eggs and mice corre-
lates the NA stalk length [1]. NA with a short stalk was
found to be inefficient in virion progeny since an active
site located too close to the viral envelop could not ac-
cess its substrate correctly [2]. The percentage of viruses
with a short NA stalk has increased steadily in recent
years [3].
There is a balanced interplay between HA and NA;
one serves as receptor binder and one as receptor de-
stroyer, to facilitate efficient virus replication in host
cells [4]. Influenza viruses can overcome host restriction
and become adapted to a new host by making changes in
HA or/and NA [5], i.e., concomitant changes in HA and
NA are required for influenza viruses to survive in host
cells. The deficiency in NA activity conferred by the
shortened protein stalk could be compensated by modu-
lating the receptor binding affinity of HA to restore the
functional balance between HA and NA [4]. In [6] a spe-
cial stalk motif, commonly found in H5N1 in the past,
was discovered in the 2009 H1N1 strains for the first
time. This finding is significant given the fact that the
viruses with this motif tend to have high virulence [3].
One of the goals of this study was to investigate the im-
pact of the NA motifs on HA in the 2009 H1N1 strains.
As the 2009 H1N1 virus continues to transmit effec-
tively from human to human, the occurrence of drug-
resistant viruses is expected. One recent study [7]
showed that the novel mutations of the 2009 H1N1 virus
NA are located at sites that do not interfere with the ac-
tive site so the currently used three drugs oseltamivir
(Tamiflu®), zanamivir (Relenza®), and peramivir re-
main effective. Another study [6] identified two net-
works of co-mutations of 2009 H1N1 NA that may af-
fect the active site from a greater distance.
As the principal antigen on the virus surface, HA is
the main viral target for the human immune system,
which can neutralize the virus through blocking viral
binding to the receptors on host cells. An epitope is a
region on the surface of an antigen, such as the HA in
this study, capable of eliciting an immune response. An-
tigenic variation of HA is one mechanism employed by
the flu virus to escape the response of the host immune
system. One report found that one single amino acid
substitution in 1918 H1N1 HA changes receptor binding
specificity [8]. Influenza HA evolution is typically a
combination of functional constraint and positive selec-
tion in epitope regions. As such, the identification of
epitope regions on HA is important for both drug and
vaccine development. Epitope mapping using mono-
clonal antibodies and the availability of the 3-dimen-
sional structure have identified five antigenic sites in the
HA of H3 subtype [9,10]. Corresponding antigenic sites
have subsequently been mapped to H1 and H2 subtypes
[11,12]. With new technology as the one employed in
[9,10], a recent refinement of the definition of H1 epi-
topes was conducted in [13]. One of the tasks of our
study was to map the sequence mutations of the 2009
H1N1 HA relative to the five epitope regions of H1. We
were also interested in finding the co-mutations in HA
and co-mutations between HA and NA of 2009 H1N1.
2.1. Sequence Data
Published HA sequences of 3936 influenza A virus from
2005 to 2009, H1 sequences of 1900 from 1918 to 2008,
and H1 sequences of 508 in 2009 were downloaded from
the Influenza Virus Resource (http://www.ncbi/nlm.nih-
giv/genomes/FLU/FLU.html) of the National Center for
Biotechnology Information (NCBI) on Oct. 13, 2009.
We were mainly interested in the sequences in 2009, but
also needed the sequences in several years before 2009
to provide comparison in the study. All the sequences
used in the study were aligned with MAFFT [14].
2.2. Entropy and Mutual Information
In information theory [15], entropy is a measure of dis-
order or randomness associated with a random variable.
be a discrete random variable that has a set of
possible values with probabilities
where . The entropy H
{,, ,...}
aaa a
Px ap
pp 3
{,, ,...}
p p
() log
xp p
The mutual information of two random variables is a
quantity that measures the mutual dependence of the two
variables or the average amount of information that
conveys about , which can be defined as
(, )()()(, )
xyHx Hy Hxy
where ()xis the entropy of
, and
(, )xy is the
joint entropy of
and. if and only if y(, )Ixy0
and are independent random variables. y
In current study, each of the n columns in a multiple
sequence alignment of a set of HA sequences of N resi-
dues is considered as a discrete random variable i
i N) that takes on one of the 20 (n=20) amino acid
types with some probability. ()
has its minimum
value 0 if all the residues at position i are the same, and
achieves its maximum if all the 20 amino acid types ap-
pear with equal probability at position i, which can be
verified by the Lagrange multiplier technique. A position
of high entropy means that the amino acids are often
varied at this position. While
x measures the ge-
netic diversity at position i in our current study,
measures the correlation between residue sub-
Ix y
W. Hu / J. Biomedical Science and Engineering 3 (2010) 1-12
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Figure 1. These five plots show the entropy distribution of HA residues in H1N1 from 2005
to 2009.
stitutions at positions i and j. A brief overview of the
extensive applications of entropy and mutual informa-
tion in sequence analysis, in particular the flu virus se-
quences, can be found in [6].
2.3. Mutual Information Evaluation
In order to assess the significance of our mutual infor-
mation values of residue pairs of HA, it is necessary to
show that these values are significantly higher than those
based on random sequences. For each residue position of
HA, we randomly permuted the amino acids from dif-
ferent sequences at that position and calculated the mu-
tual information of these random sequences. This pro-
cedure was repeated 1000 times. The P value was calcu-
lated as the percentage of the mutual information values
of the permuted sequences that were higher than those of
the sequences of HA.
2.4. Random Forest Clustering
Random Forest, proposed by Leo Breiman in 1999 [16],
is an ensemble classifier based on many decision trees.
The structure of a single tree could be easily altered by a
small perturbation of data. Random Forest overcomes
this problem by averaging across different decision trees.
For many data sets, Random Forest produces a highly
accurate classifier for supervised learning, comparable to
Support Vector Machine, the state of the art ma-
chine-learning algorithm. It computes proximities be-
tween cases and this technique can be extended to unla-
beled data, leading to unsupervised clustering.
4 W. Hu / J. Biomedical Science and Engineering 3 (2010) 1-12
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Table 1. Amino acids on epitopes A, B, C, D, and E of H1 (A/California/04/2009 numbering) from [13].
tope Amino acids
Number of
A 118,120,121,122,126,127,128,129,132,133,134,135,137,139,140,141,142,143,146,147,149,165,252,253 24
B 124,125,152,153,154,155,156,157,160,162,183,184,185,186,187,189,190,191,193,194,195,196 22
C 34,35,36,37,38,40,41,43,44,45,269,270,271,272,273,274,276,277,278,283,288,292,295,297,298,302,303,
D 170,171,172,173,174,176,179,198,200,202,204,205,206,207,208,209,210,211,212,213,214,215,216,222,2
E 47,48,50,51,53,54,56,57,58,66,68,69,70,71,72,73,74,75,78,79,80,82,83,84,85,86,102,257,258,259,260,26
Table 2. 2009 H1N1 HA mutations on the five epitopes.
Epitope Mutation Residues Number of Mutations
A 126, 127, 128, 129,132,134,137,140,141,165, 252 11
B 152, 154,155,156, 183,184,185,189,193,194,195 11
C 35, 44, 269, 271,272,273,276,277,297,307 10
D 95, 167, 169, 204,206,207, 208, 210,215,223,226,244 12
E 50, 53, 56, 68, 70, 71, 72, 73, 82, 83, 84, 85, 257,259,260 15
To view the clusters formed by Random Forest, mul-
tidimensional scaling [17] was utilized to project high-
dimensional data down into a low-dimensional space
while preserving the distances between them. First the
proximities between cases i and j form a symmetric and
positive definite matrix {prox(i,j)}. Then a second posi-
tive definite and symmetric matrix {cv(i,j)} is con-
structed using the entries of {prox(i,j)}. Random Forest
extracts a few largest eigenvalues of the cv matrix and
their corresponding eigenvectors. The values of
() ()eivi are referred to as the ith scaling coordinate,
where and are the ith eigenvalue and ei-
genvector of matrix cv. In this study, the first and second
scaling coordinates were utilized to visualize the data.
()ei ()vi
2.5. Important Sites in HA and NA
The NA active site is a shallow pocket constructed from
conserved residues, some of which contact the substrate
directly and participate in catalysis, while others provide
a structural framework [18]. According to the numbering
in [7], these residues of N1 are 118, 119, 151, 152, 156,
179, 180, 223, 225, 228, 247, 277, 278, 293, 295, 368,
and 402. The antigenic sites of N1 are residues 83 – 143,
156 – 190, 252 – 303, 330, 332, 340 –345, 368, 370,387
– 395, 431 – 435, 448 – 468.
The HA active site located in a cleft is composed of
the residues 91, 150, 152, 180, 187, 191, and 192. The
active site cleft of HA is formed by its right edge
(131_GVTAA) and left edge (221_RGQAGR) [19]. The
human immune system responds primarily to the five
epitope regions, A, B, C, D, and E, of the HA protein in
H1N1. Table 1 presents the 160 amino acids on the five
eiptope regions of HA in H1N1 as discovered in [13].
3.1. Unusually High Entropy Activities of HA in
2009 H1N1
HA is the primary target for neutralizing antibodies, and
the gradual accumulation of substitutions at the antibody
sites of HA is the main cause for flu virus to resist hu-
man immunity. As entropy measures the disorder of
amino acid frequency at each residue of HA, we sought
to compare the entropy activities of 2009 H1N1 HA with
those in the previous years. Due to the rapid spread of
the 2009 H1N1 A virus around the world, unusual en-
tropy patterns of its sequences are anticipated. The se-
quence variation within the 2009 H1N1 strains as re-
flected by its entropy distribution along with other H1N1
HA sequences from 2005 to 2008 are illustrated in Fig-
ure 1, where the high entropy activities of 2009 H1N1
HA were observed, especially in the HA1 domain, indi-
cating the 2009 H1N1 strains are under high immune
3.2. Mutations of HA in 2009 H1N1
To find the sequence variation of HA in 2009 H1N1,
three strains (A/California/04/2009(H1N1), A/South
Carolina/1/1918(H1N1), and A/Mississippi/UR06-0537/
2007(H1N1)) were aligned with MAFFT [14] and the
resulting multi-sequence alignment was visualized in
Jalview [20] (Figure 1). There were 118 mutations, 59
of which (50%) were mutations on the five epitopes,
implying that HA in particular has a high amino acid
substitution rate in its epitope regions. More precisely,
11 mutations were on epitope A, 11 mutations on B, 10
mutations on C, 12 mutations on D, and 15 mutations on
E. The detailed distribution of these mutations on the
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Table 3. Comparison of amino acid residues of 2009 H1N1 HA near the receptor-binding sites. The numbers in paren-
thesis indicate the entropy of the amino acids of HA at that position.
Residues/Amino Acids
Right edge 131 132 133 134 135
A/California/04/2009 G (0.0) V (0.06)T (0.36)A (0.04)A (0.36)
A/Mississippi/UR06-0537/2007 G V S A S
A/South Carolina/1/1918 G V T A A
Left edge 221 222 223 224 225 226
A/California/04/2009 R (0.0) D (0.22)Q (0.05)E (0.01)G (0.0) R (0.0)
A/Mississippi/UR06-0537/2007 R D Q E G R
A/South Carolina/1/1918 R D Q A G R
Receptor binding 91 150 152 180 187 191 192
A/California/04/2009 Y (0.0) W (0.0)V (0.37)H (0.0)D (0.18)L (0.03) Y (0.0)
A/Mississippi/UR06-0537/2007 Y W T H D L Y
A/South Carolina/1/1918 Y W T H D L Y
Figure 2. Three sequence alignment using MAFFT and visualized by Jalview: the top sequence is A/California/04/
2009(H1N1), the middle one is A/Mississippi/UR06-0537/2007(H1N1), and the bottom one is A/South Caro-
five epitopes is in Table 2. Epitopes A and B are the
dominant ones as they have the highest mutation rate
among the five, suggesting that A and B are under the
most pressure from the immune system. The information
about the dominant epitopes can be used to calculate the
Pepitope, a specific measure of antigenic distance be-
tween two strains of influenza to estimate the vaccine
efficacy [21]. We first displayed the five epitope regions
of 2009 H1N1 HA in the homology 3D model built in
[13] in Figure 3 and then mapped these 118 mutations of
2009 H1N1 HA to this 3D model (Figure 4).
To learn the sequence variation at or around the active
site of 2009 H1N1 HA, we built Table 3 to show that the
amino acids at these sites were highly conserved, which
was in agreement with the previous findings in [22].
There were three residues, 133 and 135 on the left edge
and 152 on the active site, that had high entropy and
amino acid substitution. In [19] residue 152 was found to
allow the substitution for a hydrophobic residue based
on an investigation of 191 different sequences of 15
subtypes of HAs, a discovery illustrated in our analysis
as well (Table 3).
A recent study [23] indicated that substitutions F71S,
T128S, E302K, M314L in HA1 of 2009 H1N1 are es-
sential for the interaction between swine and humans;
and residues 94, 196 and 274 are predicted to be “hot
spots” for mutations that may increase infectivity of the
virus (Figure 2). It also found that the highly conserved
6 W. Hu / J. Biomedical Science and Engineering 3 (2010) 1-12
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Figure 3. Left plot and right plot display two views of the five epitope regions of H1: A is in
yellow, B in blue, C in green, D in grey, and E in pink. The five regions are all shown on one
HA monomer within the HA trimer structure (PDB code: 1RU7).
Figure 4. Left and right plots display two views of the 118 mutations of HA in 2009 H1N1: all
the mutations are in red except those that are on the five epitope regions are in their own color
as in Figure 3.
region 286–326 of HA1 is a strong determinant for re-
ceptor specificity. As 2009 H1N1 transmits from human
to human, additional HA1 sequence variation will likely
occur to favor the human interaction.
One of the advantages of using entropy over multi-
sequence alignment is that entropy is able to measure
sequence variation before a mutation actually occurs.
Having knowledge of the potential mutation sites may
help us take actions preventatively. Residues 35,
203,310,321, and 416 were not mutations yet, but they
had high entropy. Furthermore, residues 35 and 310 were
on epitope C, demonstrating their importance. Among
the top 103 high entropy sites in 2009 H1N1 HA in Fig-
ure 5, there were 91 sites in HA1 domain, 82 of which
(90%) were on the five epitope regions, illustrating the
high mutational propensity to escape human immune
response in these regions.
The five epitopes in the HA1 domain were covered
with high entropy sites and there were more of these
sites in the HA1 domain than in the HA2 domain (Fig-
ure 5). In general, the HA1 polypeptide containing the
receptor-binding sites and major epitopes is the anti-
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Figure 5. Two plots show the top 103 residues of highest entropy in HA of 2009 H1N1. Residues that had one dif-
ferent amino acid than the two reference strains in Figure 2 were marked with one asterisk, and those that had two
different amino acids were marked with two asterisks. A corresponding letter of A, B, C, D, and E was appended to a
residue if it was on one of the five epitope regions.
genically variable region of HA, whereas HA2 is a rela-
tively conserved part of HA. This difference is due to
their functions in the HA molecule. HA1 is responsible
for the immune response of the host, while HA2 anchors
the whole structure in the virus membrane.
3.3. Co-mutations of HA in 2009 H1N1
Inter-residue interactions in proteins are commonly re-
flected by mutations at one site that compensate for mu-
tations at another site. Simultaneous mutations at anti-
genic sites collectively enhance antigenic drift in addi-
tion to the single mutations. To find the co-mutation
pairs, we calculated the mutual information of each pos-
sible residue pairs from 548 residues of HA in 2009
H1N1. The 40 top pairs (0.026%) in HA were selected
out of 149878 pairs, and all of them had a P value of
zero. Four networks of co-mutations were identified.
The first one was composed of residues 269, 276, and
309, which were all on epitope C. The second one had
residues 34, 167, 195, and 268. The third one had resi-
dues 129, 210, and 238. All these three networks had one
interesting feature, namely, that each one residue in the
network co-mutated with all the others in the network.
The fourth one had residues 297, 56, 178, 303, and 509,
where residue 297 co-mutated with all the others and
residues 56, 178, 303, and 509 co-mutated with each
other. In the above four co-mutation networks, there
were several antigenic sites: 34, 56, 129, 167, 195, 210,
269, 276, 297, 303, and 309, indicating a selective ad-
vantage for novel amino acid sequences among the anti-
genic regions. As in the single mutation case, most
co-mutation pairs in Table 4 were in the HA1 domain.
3.4. Interaction between HA and NA in 2009
HA and NA depend on each other for efficient virus exit
from and entry into cells, since there must be a balance
between HA activity (binding to sialic acid) and NA ac-
tivity (removing sialic acid). Such balance could be im-
paired under various circumstances such as transmission
to a new host, reassortment, or therapeutic intervention.
A previous report [24] found that a non-optimal combi-
nation of HA and NA in a reassortant may be overcome
by specific mutations in HA.
In [6], we categorized the NA stalk motifs in H1N1
and H5N1 in 2007, 2008, and 2009. To continue our
studies on NA stalk motifs, we aimed to investigate the
impact of the length of the NA stalk motifs on HA. To
this end, the pairs of HA and NA sequences from the
same patient in 2009 were collected and each pair of HA
and NA sequences were concatenated to form a single
sequence of length 1017, where the HA sequences had a
length of 548 and the NA sequences had a length of 469.
There were 144 such sequences assembled and then di-
vided into three categories. The first category (n=88) had
full-length stalk motifs, the second (n=39) had partially
deleted stalk motifs, and the third (n=17) had deleted
stalk motifs. It turned out that the HA sequences in the
first category had high entropy in both the HA1 and
HA2 domains. The HA sequences in the second category
had high entropy only in the HA1 domain, and the HA
sequences in the third category had high entropy only in
the HA2 domain (Figure 6). These three distinct entropy
responses from HA to the changes of NA motifs pro-
8 W. Hu / J. Biomedical Science and Engineering 3 (2010) 1-12
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Table 4. Top 40 pairs of co-mutations in HA of 2009 H1N1. All have a P value of zero. A corresponding letter of A, B, C, D, and E
was appended to a residue if it was on one of the five epitope regions.
(34-C,167-D) (34-C,195-B) (34-C,268) (44-C,449) (46,248) (56-E,297-C) (68-E,156-B) (71-E,132-A)
(71-E,287) (81,277-C) (84-E,182) (95-D,165-A)(127-A,189-B)(129-A,210-D)(129-A,238) (132-A,287)
(134-A,492) (145,207-D) (145,307-C) (155-B,259-E)(167-D,195-B)(167-D,268) (167-D,471) (178,294)
(178,297-C) (178,509) (195-B,268) (195-B,372) (195-B,471) (167-D,471) (207-D,307-C) (207-D,401)
(210-D,238) (268,372) (269-C,276-C) (269-C,309-C)(276-C,309-C)(294,297-C) (297-C,509) (307-C,401)
Table 5. Top 53 pairs of co-mutations in between HA and NA of 2009 H1N1. All have a P value of zero.
(46,13) (248,13) (320,13) (226,15) (269,16) (276,16) (309,16) (226,19) (55,21) (403,23)
(95,34) (165,34) (55,42) (373,47) (240,48) (55,59) (314,75) (44,173) (155,189) (259,189)
(44,220) (314,232) (271,234) (46,241) (248,241) (44,257) (56,263) (178,263) (297,263) (509,263)
(151,264) (46,257) (256,269) (56,288) (178,288) (297,288) (509,288) (507,289) (56,321) (178,321)
(297,321) (509,321) (154,336) (275,341) (472,341) (154,382) (55,385) (509,389) (209,427) (207,432)
(307,432) (401,432) (249,453)
vided another support of the notion that HA and NA
need to maintain a functional balance.
In addition to the study of the impact of the NA stalk
motifs on HA, we also discovered co-mutation pairs, one
mutation in HA and one in NA, that correlated each
other across the two proteins. We calculated the mutual
information of each possible residue pairs from 1017
residues of HA and NA (as a single sequence) in 2009
H1N1. The top 57 pairs (0.011%) were selected out of
516636 pairs in the sequences of HA and NA, and they
all had a P value of zero. Discarding the pairs in HA or
NA, and retaining only those with one residue in HA and
one residue in NA resulted in 53 pairs (Table 5). Among
the pairs found, there were two co-mutation networks,
one in HA consisting of residues 56, 178, 297, and 509
and one in NA consisting of residues 263, 288, and 321,
where each residue in the network co-mutated with all
residues in the other network.
NA residues 263 and 321 were a part of a co-mutation
network in NA consisting of residues 149, 263, 321, and
389 discovered in [6], which had a property that each of
the residues in this network co-mutated with all the other
three. NA residues 263 and 288 were also antigenic sites
in NA. NA residue 288 was located in a cluster of muta-
tion sites consisting of residues 285, 286, 287, 288, and
289 in NA. The fact that NA residue 288 was part of a
NA network of residues 263, 288, and 321 that
co-mutated with a HA network of residues 56, 178, 297,
and 509 suggested there might be a link between the
mutation cluster in NA near residue 288 and the co-mu-
tation network of residues 149, 263, 321, and 389 found
in [6]. This conclusion could not be inferred if we were
only using the information from NA along to study NA.
3.5. Phylogenetic Analysis of HA in 2009 H1N1
The HA and NA genes of 2009 H1N1 are in the classical
swine lineage and the Eurasian swine genetic lineage
respectively [25]. In [6], it was shown that the eight rep-
resentatives of the novel NA sequences in 2009 H1N1
were diverse enough to cover the major branches of the
phylogenetic tree of past NA strains. With more HA se-
quences available to date than in May or June 2009, we
constructed the phylogenetic tree of the representative
HA sequences from 1918 to 2009 with the neighbor-
joining method using MEGA 4 software [26]. Seven HA
sequences in 2009 were selected using cd-hit with iden-
tity removed at 98.5% from all the HA sequences in
2009. HA sequences of 29 were selected using cd-hit
with identity removed at 98% from all the HA sequences
in the years prior to 2009. In contrast to the diversity of
NA sequences in 2009 H1N1 [6], the seven representa-
tive HA sequences were mainly clustered together in the
phylogenetic tree in Figure 7, which implied that the HA
sequences had remained the same diversity as they were
on 16 May 2009 when a similar phylogenetic tree was
constructed from a collection of HA sequences in [25].
As demonstrated in the study in [6], Random For-
est-based clustering can reveal some subtle features of
sequence clusters that a phylogenetic tree built with the
neighbor-joining method cannot. We attempted to em-
ploy the Random Forest-based clustering technique to
cluster the same sequences used in Figure 7 and the re-
sults are in Figure 8. Due to the space limitation, we
used a number from 1 to 36 to represent a sequence in
Figure 8, where the same number is attached to the start
of the corresponding sequence name in Figure 7. The
numbers 1 to 7 were assigned to the seven representative
HA sequences in 2009 H1N1. In Figure 8, the sequences
numbered 1, 2, 4, 5, 6, and 7 were close in the second
scaling coordinate, and those numbered 1, 4, 5, and 7
were also close in the first scaling coordinate. This de-
tailed clustering information about the seven sequences
W. Hu / J. Biomedical Science and Engineering 3 (2010) 1-12
SciRes Copyright © 2010 JBiSE
Figure 6. Three plots show the three distinct responses from the HA of 2009 H1N1 to the changes of NA
stalk motifs.
provides another view of the current diversity of the HA
sequences in 2009 H1N1 relative to the past HA se-
quences besides the view from the phylogenetic tree in
Figure 7.
In this study, we focused on the single mutations and
co-mutations in HA of 2009 H1N1. There was extensive
research on mutations in H3N2. Studies on H3N2 found
that changes at HA residues 183, 186 and 226 could in-
fluence HA receptor-binding affinity [27], and that resi-
dues 131, 222, 225 and 226 are vital for efficient repli-
cation [28]. In [29] 209 complete genomes of the human
influenza A virus from 1998 to 2004 were sequenced,
and mutations and co-mutations were identified in all the
genes in H3N2. Nucleotide co-occurrence networks
were constructed in [30] using genome sequences of
1032 H3N2 isolates from 1968 to 2006, and another
recent study found co-mutated positions in HA of H3N2
for predicting the antigenic variants using entropy and
mutual information [31].
All the flu drugs currently on the market are NA in-
hibitors; as a result, emergence of resistance mutations
in NA could decrease drug effectiveness. In light of the
steady increasing of NA-inhibitor resistant flu strains
each year, a new study was conducted in [32] to design a
flu drug that can target both HA and NA. For this type of
drug, the mutations in HA as well as those in NA will
have a direct impact on its outcome. When NA activity
is decreased due to NA-inhibitor drug selection, HA
mutations to lower the HA receptor-binding affinity are
frequently observed. Conversely viruses with reduced
HA binding efficiency require less NA activity [5]. Iden-
tifying the co-mutations in HA and NA can benefit the
design and administration of this type of new drugs.
In our study, HA1 and HA2 displayed different entropy
distributions. In general, HA1 had higher entropy than
HA2, implying that HA1 is the main responder to the host
immunity. This fact should not diminish the value of
HA2 being a potential target for vaccine design. The
antibodies recognizing HA1 can neutralize virus infec-
tivity, but do not cross-react to the HAs of other sub-
types of influenza. One report [33] found that antibodies
induced by HA2 are cross-reactive among different sub-
types and may moderate virus infection. This result sup-
ported the notion that identifying the mutations in HA2
are as important as identifying those in HA1, even though
HA1 was the focus of vaccine design in the past.
10 W. Hu / J. Biomedical Science and Engineering 3 (2010) 1-12
SciRes Copyright © 2010 JBiSE
1 H1N1 Washington 01 2009 gi|243031572|g
7 H1N1 St Louis 746 2009 gi|260100660|gb
6 H1N1 St Louis 690 2009 gi|260100658|gb
2 H1N1 PaisVasco RR3427 2009 gi|25459738
5 H1N1 Busan 01 2009 gi|259023925|gb|ACV
32 H1N1 Pennsylvania 16 2007 gi|18807643
31 H1N1 Maldonado FMD1033 2007 gi|183223
4 H1N1 North Carolina 02 2009 gi|2559608
34 H1N1 HongKong 1052 2008 gi|206575146|
25 H1N1 TW 4845 1999 gi|89033083|gb|ABD5
17 H1N2 Stockholm 13 2002 gi|22859335|gb
29 H1N1 New Caledonia V77245 2007 gi|148
30 H1N1 Tehran 30 2006 gi|162956892|gb|A
11 H1N1 human Taiwan 3355 97 gi|14571962
12 H1N1 Switzerland 5389 95 gi|14587045|
33 H1N1 Taiwan VGHYM0725 08 1988 gi|2020
16 H1N1 Fiji 15899 83 gi|11595850|gb|CAC
8 H1N1 Lepine 1948 gi|8096357|gb|BAA9611
9 H1N1 TF 15 1951 gi|8096359|gb|BAA96111
21 H1N1 Fort Worth 50 gi|89114296|gb|ABD
15 H1N1 Rhodes 47 gi|21717604|gb|AAM7668
22 H1N1 Cameron 1946 gi|89903075|gb|ABD7
13 H1N1 Puerto Rico 8 34 Mount Sinai gi|
20 H1N1 Melbourne 35 gi|89148077|gb|ABD6
14 H1N1 Weiss 1943 gi|21717600|gb|AAM766
19 H1N1 Bellamy 1942 gi|89152215|gb|ABD6
23 H1N1 Wilson Smith 33 gi|89782156|gb|A
10 H1N1 South Carolina 1 1918 gi|4325039
18 H1N1 Switzerland 8808 2002 gi|3842252
36 H1N1 Alma Ata 1417 84 gi|385579|gb|AA
3 H1N1 Taiwan T1339 2009 gi|255689237|gb
35 H1N1 Ohio 01 2007 gi|229473302|gb|ACQ
24 H1N1 New Jersey 1976 gi|146759952|gb|
27 H1N1 Philippines 344 2004 gi|11793578
26 H1N1 Iowa CEID23 2005 gi|112456302|gb
28 H1N1 Thailand 271 2005 gi|117935791|g
Figure 7. Phylogenetic tree of the HA protein sequences of the H1 subtype family.
There is a great interest in gaining more understanding
of the 2009 H1N1 virus given the urgency of the current
2009 flu pandemic. In our previous study on 2009 H1N1
[6], three aspects of NA were investigated: the mutations
and co-mutations, the stalk motifs, and the phylogenetic
analysis. In this study, we focused on HA and the inter-
action between HA and NA. The118 mutations of 2009
H1N1 HA were uncovered and mapped to the 3D ho-
mology model of H1, and the mutations on the five epi-
tope regions on H1 were identified. This information is
essential for the development of new drugs and vaccine.
With entropy and mutual information analysis, we were
able to locate several antigenic sites in HA that could
potentially become mutational sites. In addition to the
identification of single mutations and co-mutations in
2009 H1N1 HA, we were also able with help from our
previous results in [6] to find two co-mutation networks,
one in HA and one in NA, where each mutation in one
W. Hu / J. Biomedical Science and Engineering 3 (2010) 1-12
SciRes Copyright © 2010 JBiSE
Figure 8. Random Forest-based clusters of the same HA sequences used in Figure 7. Here a number from 1 to 36
is used to represent a sequence, which is attached to the start of the corresponding sequence name in Figure 7.
network co-mutates with the mutations in the other net-
work across the two proteins HA and NA. These two
networks residing in HA and NA separately may provide
a link between the mutations that can influence the drug
binding sites in NA and those that can affect the host
immune response or vaccine efficacy in HA. The distinct
entropy responses from HA to the changes of NA stalk
motifs were discovered, suggesting the functional de-
pendence between them. Finally, our phylogenetic
analysis indicated that the seven representative se-
quences of HA in 2009 H1N1 were mainly clustered
together in the phylogenetic tree made of past represen-
tative HA sequences, quite contrary to the NA case [6].
The phylogenetic tree in Figure 7 was similar in struc-
ture to the phylogenetic tree constructed from a collec-
tion of HA sequences of 2009 H1N1 on 16 May 2009 in
[25], which implied that the diversity of 2009 H1N1 HA
sequences remained relatively the same. This view is
also supported by the clusters of the same HA sequences
created with the Random Forest-based clustering tech-
nique (Figure 8). Taken together, our results highlighted
the importance of conducting timely analysis on the
2009 H1N1 virus and of the integrated approach to
studying both surface proteins HA and NA together to
reveal their interdependence, which could not be accom-
plished by studying them individually.
We thank Houghton College for its financial support.
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