DOI:10.1111/irv.12219
www.influenzajournal.com
Original Article
Genetic characterization of seasonal influenza A (H3N2)
viruses in Ontario during 2010–2011 influenza season:
high prevalence of mutations at antigenic sites
AliReza Eshaghi,a Venkata R. Duvvuri,a,b,c Aimin Li,a Samir N. Patel,a,d Nathalie Bastien,e Yan Li,e Donald
E. Low,a,b,f Jonathan B. Gubbaya,b,d,f
a
Ontario Agency for Health Protection and Promotion, Toronto, ON, Canada. bMount Sinai Hospital, Toronto, ON, Canada. cCentre for Disease
Modelling, York University, Toronto, ON, Canada. dUniversity of Toronto, Toronto, ON, Canada. eNational Microbiology Laboratory, Public Health
Agency of Canada, Winnipeg, MB, Canada. fThe Hospital for Sick Children, Toronto, ON, Canada.
Correspondence: Jonathan B. Gubbay, Ontario Agency for Health Protection and Promotion, 81 Resources Road, Toronto, ON, Canada M9P 3T1.
E-mail: jonathan.gubbay@oahpp.ca
Accepted 26 October 2013. Published Online 6 December 2013.
The direct effect of antigenic site mutations in
influenza viruses on antigenic drift and vaccine effectiveness is
poorly understood.
Background
To investigate the genetic and antigenic characteristics
of human influenza A (H3N2) viruses circulating in Ontario during
the early 2010–2011 winter season.
Objective
We sequenced the hemagglutinin (HA) and
neuraminidase (NA) genes from 41 A(H3N2) viruses detected in
nasopharyngeal specimens. Strain typing was performed by
hemagglutination inhibition (HI) assay. Molecular and phylogenetic
tree analyses were conducted.
Study design
HA and NA genes showed high similarity to the 2010–2011
vaccine strain, A/Perth/16/2009 (H3N2)-like virus (977–985% and
987–995% amino acid (AA) identity, respectively). Compared to
A/Perth/16/2009 strain, HA gene mutations were documented at 28
different AA positions across all five H3 antigenic sites, with a range
Results
of 5–11 mutations in individual viruses. Thirty-six (88%) viruses
had 8 AA substitutions in common; none of these had reduced HI
titer. Among Ontario isolates, 11 antigenic site AAs were positively
selected with an increase in glycosylation sites.
Conclusion The presence of antigenic site mutations with high
frequency among 2010–2011 influenza H3N2 isolates confirms
ongoing adaptive H3N2 evolution. These may represent early
phylogenetic changes that could cause antigenic drift with further
mutations. Clinical relevance of antigenic site mutations not causing
drift in HI assays is unknown and requires further investigation. In
addition, viral sequencing information will assist with vaccine strain
planning and may facilitate early detection of vaccine escape.
Keywords Antigenic site mutations, genetic and antigenic characterization, phylogenetic analysis, positive selection analysis, seasonal
influenza A (H3N2) virus.
Please cite this paper as: Eshaghi et al. (2014) Genetic characterization of seasonal influenza A (H3N2) viruses in Ontario during 2010–2011 influenza season:
high prevalence of mutations at antigenic sites. Influenza and Other Respiratory Viruses 8(2), 250–256.
Introduction
Influenza viruses are considered one of the most common
causes of respiratory infection among humans.1,2 Although
all age groups are infected by influenza viruses, most of the
influenza-related hospitalizations occur in young children
(<5 years of age) and in the elderly (>65 years of age), and
most deaths are reported in the elderly.3 Subtypes of
influenza A viruses (IAV) are distinguished based on the
unique antigenic properties of the two surface glycoproteins,
hemagglutinin (HA) and neuraminidase (NA).4
Hemagglutinin is known to be a major target region of
neutralizing antibodies which inhibit binding with sialic acid
receptors effectively.5 Mutations in the HA antigenic sites,
250
designated A, B, C, D, and E in IAV of H3N2 subtype, may
result in strains which can escape recognition by pre-existing
neutralizing antibodies.7–9 Gradual accumulation of mutations at these sites is noted to be an integral component of
evolutionary dynamics and impacts viral survival and fitness.
This evolutionary mechanism, known as antigenic drift, is
the basis for frequent updating of the composition of
seasonal influenza vaccines.6 Antigenic drift variants of H3
viruses occur often, and these tend to replace older ones.7
The higher rate of amino acid (AA) substitutions (00097 per
site per year) of H3 HA when compared to H1 HA (00058
per year per site) supports their higher evolutionary rates.8
Previous studies proposed that an antigenic drift variant of
epidemiological importance usually requires simultaneous
ª 2013 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use,
distribution and reproduction in any medium, provided the original work is properly cited.
Seasonal influenza A (H3N2) antigenic site mutations
accumulation of at least four AAs across two or more
antigenic sites of A to E.9–11 The current study reports the
HA genetic and antigenic relatedness between H3N2 viruses
circulating during August 2010 to January 2011 in Ontario
and A/Perth/16/2009(H3N2)-like virus (A/Perth/16/2009),
which was recommended as the H3N2 component of the
2010–2011. Further, we extended this study to understand
the mutational trends at antigenic sites of global IAV (H3N2)
isolates from 2010–2011, which were grouped by continent.
Methods
Specimen collection, RT-PCR and sequencing
Forty-one H3N2-positive samples were included in this
study, which consisted of all early season samples and a
random selection from later in the season. Real-time reverse
transcription PCR (rRT-PCR) for influenza A and B was
performed as an initial screen on samples from hospital
(admitted patients only) and outbreak settings. Samples from
ambulatory patients (office settings and emergency patients
not admitted) underwent viral culture for respiratory viruses
using rhesus monkey kidney cells [(RMK) (Diagnostic
Hybrids, Inc., Athens, OH, USA)]. Following total nucleic
acid extraction, overlapping primers were used to amplify
four and three fragments encompassing the coding region of
HA and neuraminidase (NA) gene, respectively12; amplicons
subsequently underwent Sanger sequencing.
Genetic characterization and phylogenetic analysis
HA1 sequence assembly was carried out using Vector NTI
ContigExpress (Life TechnologiesTM, Carlsbad, CA, USA).
BioEdit was used for raw sequence curation and for multiple
alignments of protein and nucleotide sequences.
A HA1 phylogenetic tree of Ontario’s strains and a
selection of global sequences were generated with Molecular
Evolutionary Genetic Analysis (MEGA 4.0) using the neighborjoining method algorithm.13 Evolutionary distance was
computed using the maximum composite likelihood
method. Statistical significance of the tree topology was
tested by bootstrap analysis of 1000 pseudoreplicate datasets.13 The tree was visualized using DENDROSCOPE version
2.2.1.14
Estimation of positive selection
To assess whether Ontario HA1 of H3N2 virus underwent
positive selection when compared to MDCK-grown A/
Perth/16/2009 (GenBank accession # GQ293081.1), we
assessed the site-specific dN/dS and likelihood-ratio tests
(LRT) using phylogenetic analysis using maximum likelihood (PAML 4.4 version).15 Bayes empirical Bayes (BEB)
approach (implemented in CODEML) was used to calculate the posterior probabilities, ‘pp’ (taking sampling
errors into account) of the inferred positively selected
sites (PSS). Sites with high pp coming from the class with
dN/dS> 1 (P > 95%) are inferred to be under positive
selection.
Antigenic characterization
A representative subset of Ontario’s isolates was submitted to
Canada’s National Microbiology Laboratory for strain characterization by hemagglutination inhibition (HI) assay. This
was performed using 4 hemagglutination units of virus, 05%
v/v turkey red blood cells and post-infection ferret antisera
against A/Perth/16/2009. HI titers were defined as the
reciprocal of the highest dilution of serum that completely
inhibited hemagglutination of 05% v/v turkey red blood
cells; an eightfold reduction in titer compared to the
reference strain was considered significant.21
Prediction of glycosylation sites
Potential N-linked glycosylation sites were predicted using
NetNGlyc 1.0 Server.16 A threshold value of >05 average
potential predicts glycosylation sites.
Structural modeling
Three-dimensional structures of the HA proteins of representative Ontario isolates were compared with A/Perth/16/
2009 and constructed using related crystal structures (A/
Aichi/2/1968; Protein Data Bank accession number 3HMG)
using PYMOL.17
Sequence data collection and usage
In addition to 41 HA sequences obtained from Ontario’s
isolates, the analysis was performed with an enhanced
dataset. A total of 1072 HA protein sequences of H3N2
(August 2010–January 2011) viruses of different circulating
strains from Africa (73), Asia (372), Europe (133), Oceania
(85), South America (60) North America (349; Canada
excluded), and Canada (67; Ontario excluded) were downloaded from the GISAID (the Global Initiative on Sharing All
Influenza Data) database.
HA and NA study sequences have been submitted to
GenBank under accession numbers JQ658888 to JQ658927
and JQ658928 to JQ658967, respectively.
Ethics Statement
This study was exempt from The University of Toronto’s
Health Sciences Research Ethics Board review as it involved
deidentified respiratory tract samples that were tested as
part of a clinical virology service provided by Public Health
Ontario Laboratories. All test-positive samples and a
proportion of test-negative samples are stored for possible
further laboratory-based surveillance work. Samples and
isolates included in this study were analyzed as part of the
routine respiratory viral molecular surveillance program
that supports Ontario’s Ministry of Health and Long-Term
Care.
ª 2013 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.
251
Eshaghi et al.
Results
Sequence and phylogenetic analysis
Complete HA and NA sequences of the 41 Ontario H3N2
samples were analyzed and compared against vaccine strains
and were shown to be most closely related to the 2010–2011
seasonal vaccine H3N2 strain, A/Perth/16/2009, with 978–
990% and 980–987% identity at the nucleotide level,
respectively. Identity at the AA level was 977–985% and
987–995%, respectively.
Comparative analysis with A/Perth/16/2009 revealed a
mean of 87 (range 5–11) mutations across all antigenic sites.
Thirty-six (88%) Ontario isolates had eight AA antigenic site
substitutions in common. These included K144N at antigenic
site A, D53N and E280A at site C, T212A, S214I, and I230V
at site D, and K62E and Y94H at site E. In addition, 15 (37%)
Ontario isolates had a unique substitution of isoleucine by
methionine at residue 140 in antigenic site A, not observed
among other Canadian or global isolates. Several other
mutations at antigenic sites were observed among Ontario’s
strains such as T48A, E50K/G, N312S, and A304T (site C);
S146G and M168I (site A); R208K V213A, I242K (site D);
I260M, R261Q, Q75H, and K92R (site E); and S199A, F159Y,
and I192T (site B). Mutations outside of antigenic sites also
documented were as follows: T10P, P162S, R220K, N225D,
D291E, and V323I. AA residues at the HA receptor binding
sites remained conserved among all isolates except two, A/
Ontario/C728447/2011 and A/Ontario/C76206/2011, harboring N133D and N225D, respectively (Figure S1). When the
HA of Ontario’s isolates was compared to A/Victoria/361/
2011, the 2012–2013 vaccine strain (GISAID isolate id #
EPI_ISL_101506), they showed an identity of 978–99% and
972–987% at the nucleotide and AA levels, respectively.
The HA phylogenetic tree showed that 38 (93%) isolates
fell within the recently emerged Victoria/208/2009 clade, and
the remaining 3 (7%) belong to the Perth/16/2009 clade
(Figure 1). Four recognizable genetic groups were identified
among Ontario’s strains that were placed within the Victoria/
208/2009 clade due to the presence of specific non-synonymous substitutions: I. N312S (three isolates, 7%), II. I192T
(10 isolates, 24%), III. S199A (seven isolates, 17%), IV. I140V
(15 isolates, 37%). Three of these genetic groups (II, III, and
IV; 86% of Ontario isolates) were clustered with the newly
emerged subclade, A/Hong Kong/2121/2010, defined by
D53N, Y94H, I230V, and E280A within the Victoria/208/
2009 clade.18 The HA protein structure of a representative
Ontario isolate demonstrates conformational changes in
antigenic sites as a result of the point mutations detected
(Figure 2 and Figure S2).
The NA gene phylogenetic tree showed the same distribution pattern as HA. Compared with the NA gene of A/
Perth/16/2009, 38 (92%) of Ontario’s isolates carried the
substitution of serine (S) by asparagine (N) at position 367
252
(S367N), lysine (K) by threonine (T) at position 369
(K369T), and isoleucine (I) by leucine (L) at position 464
(I464L). Less frequent non-synonymous mutations that
include E41N, M34V I62M, D127N, T138A, I176V, R210K,
I307M, L338F, N342D, I381M, N402D, K415R, and R430S
were observed among 2–4% of isolates. No mutations were
observed at any of eight catalytic residues, which contact the
NA inhibitor, oseltamivir, directly or among the 11 framework residues responsible for stabilizing the active binding
site.19,20
Glycosylation patterns
The nine putative N-glycosylation sites (Asn-Xaa-Ser/Thr)
predicted at AA positions 8, 22, 38, 63, 126, 133, 165, 246,
and 285 in A/Perth/16/2009 were identified in all of Ontario’s
2010–2011 isolates. In addition, 38 (93%) isolates were
shown to possess an additional glycosylation site (NNS) due
to a K144N substitution. This K144N substitution was also
observed among 722% of global isolates [range 42% to 97%
of global isolates (Table S2)].
Antigenic analysis
Eighteen representative H3N2 isolates were submitted for HI
assay; all were antigenically related to the A/Perth/16/2009.
Only one strain, A/Ontario/U10611/2010, showed eightfold
reduction in HI titer (HI titer 80) when compared with A/
Perth/16/2009 (HI titer 640). This strain exhibited four
mutations at antigenic sites A (AA 144), D (AA 212 and 214),
and E (AA 62). Three additional HA mutations, D291,
K468T, and D489N, were exclusive to this isolate; there were
no significant neuraminidase mutations.
The remaining 17 isolates were antigenically similar to A/
Perth/16/2009. Eleven percent and 17% of isolates exhibited
non-significant fourfold and twofold reductions, respectively.
Three of the 10 isolates with a mutation (I192T) at antigenic
site B were tested by HI; all showed non-significant twofold
to fourfold HI titer reductions. The remaining seven I192T
isolates were not of adequate HI titer to characterize. No
correlation was observed between the presence of 10AA
mutations across four antigenic sites (A, C, D and E) and HI
titers (Table 1).
Evidence for positive selection
The average dN/dS ranged from 0149 to 0340 among all
codon substitution models (Table S1). Both the M8 and M2a
models suggested the presence of PSS with a proportion
ranging from 40% (p1 = 0040 with x2 = 6144) to 33%
(p2 = 0033 with x2 = 6839). A total of eleven PSS, 53, 62,
94, 140, 144, 192, 199, 212, 214, 230, and 280, were observed
with posterior probability >50% (Table S1). All 11 mutations
were observed across the four HA antigenic sites, of which
seven substitutions (K144N in site A; D53N and E280A in site
C; T212A and S214I in site D; K62E and Y94H in site E) were
ª 2013 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.
Seasonal influenza A (H3N2) antigenic site mutations
A
B
Figure 1. Phylogenetic relationship of full-length HA (A) and NA (B) sequences of influenza A(H3N2) virus isolates identified in Ontario during 2010–
2011 influenza season. Multiple sequences alignment and phylogenetic trees were constructed using Clustal W and neighbor-joining algorithm running
within MEGA 5.05 software. Tree topology was supported by bootstrap analysis with 1000 pseudo-replicate datasets. Bootstrap values >70% are included
for key nodes. The scale bar represents the number of nucleotide substitutions per site between close relatives. Viruses characterized in the present study
are marked with a filled diamond. Reference strains are in bold face. Vaccine strains for 2009–2012 (A/Perth/16/2009) and 2012–2013 (A/Victoria/361/
2011-like virus) are bolded and italicized. Signature AA changes in HA tree are annotated at the nodes of each cluster.
observed among 85–100% of Ontario isolates and substitution I140M in 37% of the Ontario isolates (Figure S1).
Mutational patterns in global isolates
Ontario’s isolates showed higher mutational frequency at
positions I140M (present in 15/41, 37%) and I192T (present
in 10/41, 24%) when compared with global isolates; these
mutations were only present in 11 (096%) and 37 (32%)
global isolates analyzed, respectively. Five (positions 144,
280, 212, 214, and 62) of 11 positively selected sites were
conserved in the isolates from the Americas (North and
South America). The only substitution conserved among all
global isolates irrespective of their origin was S214I (Table
S2).
ª 2013 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.
253
Eshaghi et al.
Figure 2. Effect of hemagglutinin protein antigenic site mutations on protein structure. An Ontario representative isolate detected during the 2010–11
influenza season is compared to the A/Perth/16/2009(H3N2)-like virus. Three-dimensional models of the H3 HA molecules of A/Ontario/C706264/2010
(H3N2) (I and III) and A/Perth/16/2009(H3N2) were constructed based on the HA crystal structure of A/Aichi/2/1968 (Protein Data Bank code: 2HMG). The
isoleucine at position 192 in antigenic site B, which has not mutated from the wild type in this isolate, is shown in red. Mutations in antigenic sites A
(K144N, I140M; cyan), C (D53N, E280A; orange), D (T212A, S214T; yellow), and E (K62E, Y94H; green) are also shown. The structures are presented
using PYMOL. For sequence alignment of A/Ontario/C706264/2010(H3N2) to A/Perth/16/2009(H3N2), see Figure S2.
Table 1. Hemagglutination inhibition antibody titers and antigenic site mutations in influenza A(H3N2) isolates observed in Ontario, Canada,
between November 2010 and February 2011
Mutations occurred at antigenic sites (positively selected sites)
HI assay titers
Ontario isolates
Specimen
RA#
Sp/
RA#
A/Ontario/C575591/10
A/Ontario/C627683/10
A/Ontario/U10611/10
A/Ontario/C543493/10
A/Ontario/C1995/10
A/Ontario/C575478/10
A/Ontario/C582096/10
A/Ontario/P21548/10
A/Ontario/C706264/10
A/Ontario/C582093/10
A/Ontario/C720531/10
A/Ontario/C537546/10
A/Ontario/C526567/10
A/Ontario/C653602/11
A/Ontario/R3296/11
A/Ontario/C76206/11
A/Ontario/C582144/10
640
320
80
320
80
320
320
320
640
640
640
640
320
640
320
320
320
320
640
640
320
160
320
320
320
640
320
320
320
160
1280
1280
1280
320
2
1/2
1/8
1
1/2
1
1
1
1
2
2
2
2
1/2
1/2
1/4
1
Site A
Site B
140
144
192
–
–
–
–
–
M
M
M
M
–
M
M
M
–
–
–
M
–
–
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
–
–
–
–
–
–
–
–
–
–
–
–
–
T
T
T
–
Site C
Site D
Site E
199
53
280
212
214
230
62
94
260
261
No. of
mutations
–
–
–
–
–
–
–
–
–
A
–
–
–
–
–
–
A
–
–
–
N
N
N
N
N
N
N
N
N
N
N
N
N
N
–
A
–
A
A
A
A
A
A
A
A
A
A
A
A
A
A
–
–
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
–
–
–
V
V
V
V
V
V
V
V
V
V
V
V
V
V
–
–
E
E
E
E
E
E
E
E
E
E
E
E
E
E
E
–
–
–
H
H
H
H
H
H
H
H
H
H
H
H
H
H
M
M
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
Q
Q
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
3
4
4
8
8
9
9
9
9
9
9
9
9
9
9
9
10
RA#, Reference antigen: A/Perth/16/09; Sp/RA#, Specimen/Reference antigen ratio.
Discussion
In this study, we have characterized seasonal clusters of
Influenza A(H3N2) circulating during the 2010–2011 winter
season in Ontario. Nucleotide analysis of the complete
254
coding region of these isolates showed close similarity to the
vaccine strain, A/Perth/16/2009. HA nucleotide identity was
higher than the NA identity when compared with A/Perth/
16/2009. However, HA had a lower AA identity with the A/
Perth/16/2009. This implies that nucleotide mutations in HA
ª 2013 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.
Seasonal influenza A (H3N2) antigenic site mutations
are more likely to be non-synonymous than those occurring
in NA, in keeping with the propensity of this protein to
evolve at a higher rate.8 Mutations were documented at 28
different AA positions within H3 antigenic sites. Five to 11
antigenic site AA mutations were observed in individual
isolates (Figure S1).
Co-circulation of variants distinguished by specific AA
substitutions was seen among Ontario’s H3N2 strain. Phylogenetic trees of the HA and NA genes show that Ontario’s
2010–11 isolates fell into two distinct genetic clades represented by A/Perth/16/2009 and A/Victoria/208/2009, with the
majority (93%) belonging to Victoria 208 clade. Several
phylogenetic subgroups within the A/Victoria/208/2009 clade
were identified, with the majority (86%) of Ontario’s isolates
falling within the newly emerged subclade, A/Hong Kong/
2121/2010. Due to the emergence of the Victoria 208 clade of
A/Perth/16/2009 strain, WHO recommended a change to the
H3N2 strain component of the 2012–2013 influenza vaccine,
to A/Victoria/361/2011-like virus.21
Evolutionary analysis of the HA of Ontario’s 2010–2011
H3N2 isolates revealed strong evolutionary selection pressure
(dN/dS = 68), resulting in 11 PSS compared to A/Perth/16/
2009 (Table S1). Three of the PSSs (53, 144, and 192) were
reported as frequently changeable sites in H3N2 HA evolution and also observed in previously reported vaccine escape
mutants.22,23 The mutation at AA 192 was observed among
Canadian isolates (including Ontario isolates), but not other
global isolates. AA 192 is located within the 190 helix, which
contains receptor binding sites (RBS). It has been shown that
certain AA alterations within the receptor binding regions
can alter sialic acid receptor binding specificity. Although
one study documented a shift in sialic acid receptor binding
specificity from a-2,3 to a-2,6 glycans following a T192I
change in H5N1, another publication did not show any
change in receptor specificity as a result of generation of a
I192T mutation on a wild-type H5N1 background.24, 25 This
mutation has not been evaluated in the setting of a human
H3N2 background.
All of Ontario’s 2010–2011 isolates possessed the same
nine glycosylation sites identified in A/Perth/16/2009. Thirtyeight (93%) of Ontario’s viruses were shown to possess an
additional glycosylation site (NNS) due to a K144N substitution, which also resulted in an AA change in antigenic site
A. This mutation was also common among global isolates
(Table S2). A position 144 N-glycosylation site has previously
been observed as an infrequent mutation in H3N2 evolution
and reported to be involved in masking the key site for
antigenic change in A/Fujian/411/02-like strains from the
2002–2003 influenza season.26 However, this mutation was
not responsible for the antigenic drift from A/Moscow/10/99
to A/Fujian/411/02.11 We did not observe the N144D
mutation in the Ontario H3N2 isolates, whereas it was
present in European and African H3N2 isolates (2010–2011),
documented in 13% and 35% of respective strains. AA
substitutions, particularly in antigenic site A (140–146), were
reported as a typical signature for antigenically distant
viruses of epidemic significance.5
A substitution from isoleucine to methionine at position
140 was observed in 37% of Ontario’s 2010–2011 isolates,
but was only found in 096% of other global 2010 to 2011
isolates. I140M was previously detected in six A/Brisbane/10/
2007-like H3N2 isolates collected in the USA in 2008
(accession no: ADY05342, ACD69148) and 2009
(ACT67814, ACT67819, ADK94334, and ADM26784). Substitutions D53N (in antigenic site C) and I140M (in antigenic
site A) were found to decrease affinity of H3N2-specific
antibodies based on microneutralization (MN) assay with A/
Perth/16/2009 (H3N2) antiserum; however, their impact on
immune recognition is not known.27
Despite the presence of up to 11 mutations at four
antigenic sites, considerable evidence for antigenic drift was
not observed based on the data obtained by HI assay. This is
in contrast to the previously held idea that four mutations
across two or more antigenic sites would predict a propensity
for antigenic drift.28 Only one strain in our 2010–2011
collection has shown evidence of drift in the HI assay
(eightfold difference with A/Perth/16/2009). Genome
sequence and phylogenetic analysis of this isolate revealed
highest homology to isolates from Central America. This was
consistent with the patient history of recent travel to
Honduras shortly before sampling (Figure 1). Interestingly,
this isolate only has four substitutions at site A (144), site D
(212, 214), and site E (62). Our findings emphasize the poor
correlation between antigenic profile and AA substitutions in
the HA protein of influenza viruses, as has been previously
observed.29 During winter of 2010–2011, the emergence of
>4 substitutions in three different H3 antigenic sites was
observed in Quebec, Canada, suggesting antigenic drift.
However, HI and MN results showed reduced titer in only
one strain (eightfold difference in titers), while 19 others
remained antigenically similar to A/Perth/16/2009, but
exhibited titer differences (twofold to fourfold), below the
standard definition of antigenic drift.28 Of interest, all three
isolates carrying I192T HA mutation and of adequate HA
titer for strain typing had a mild twofold to fourfold HI titer
reduction. In addition, a five province Canadian study of
influenza vaccine effectiveness in ambulatory patients found
similar H3N2 HA mutations at antigenic sites without any
changes in HA titers, along with a low vaccine effectiveness of
39% in an interim analysis during the early part of the 2012–
13 influenza season.30
The majority of the antigenic site mutations identified in
this study appear at the surface structures of antigenic sites
that are accessible to antibodies and resulted in conformational changes (Figure 2). Such structural changes at antigenic sites (epitopes) could possibly facilitative escape from
ª 2013 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.
255
Eshaghi et al.
neutralizing antibody. In addition, mutations K62E, Y94H,
and K144N cause alteration in side chain charge. Moreover,
mutations E280A, T212A, and S214I will change the polarity
of these AAs.
In conclusion, the presence of up to 11 positively selected
antigenic site mutations with high frequency among 2010–
2011 influenza season H3N2 isolates confirms the ongoing
adaptive evolution of circulating H3N2 strains. Further work
is needed to better understand the clinical relevance of
mutations at antigenic sites that do not result in drift in HI
assays. In addition, further investigation is needed to better
understand the extent to which viral sequencing should
influence vaccine strain selection, even when there is no
associated drift in HI assays. Relying on detection of
antigenic drift in HI assays before altering candidate vaccine
strains may not be sensitive enough to detect clinically
relevant changes in vaccine effectiveness.
Acknowledgements
We acknowledge the authors, originating and submitting
laboratories of the sequences from GISAID’s EpiFluTM
Database on which this research is based. Authors would
like to thank the associate editor and reviewers for their
insightful comments and suggestions to improve the quality
of this manuscript.
Author contributions
Conceived and designed the study: AE, VRD, JBG. Performed the experiments: AE, AL, NB, YL; Performed
phylogenetic and selection analysis: AE, VRD. Wrote the
paper: AE, VRD, JBG. Contributed reagents ⁄ materials ⁄
analysis tools: SNP, YL, DEL, JBG. All the authors have read
the final version of the paper and approved it.
Competing interests
Dr. Gubbay has received research grants from GlaxoSmithKline Inc. and Hoffman-La Roche Ltd to study antiviral
resistance in influenza; however, these activities are not
relevant to this study. All the other authors declared that they
have no competing interests.
Funding
This study was supported by Public Health Ontario internal
funding and was not supported by any external funding.
References
1 Cox NJ, Subbarao K. Global epidemiology of influenza: past and
present. Annu Rev Med 2000; 51:407–421.
256
2 World Health Organization (WHO). Fact sheet N-211 on Influenza
(Seasonal), April 2009. Available at http://www.who.int/mediacentre/
factsheets/fs211/en/index.html (Accessed 20 September 2012).
3 Lui KJ, Kendal AP. Impact of influenza epidemics on mortality in the
United States from October 1972 to May 1985. Am J Public Health
1987; 77:712–716.
4 Webster RG, Bean WJ, Gorman OT, Chambers TM, Kawaoka Y.
Evolution and ecology of influenza A viruses. Microbiol Rev 1992;
56:152–179.
5 Wiley DC, Wilson IA, Skehel JJ. Structural identification of the
antibody-binding sites of Hong Kong influenza haemagglutinin and
their involvement in antigenic variation. Nature 1981; 289:373–378.
6 Blackburne BP, Hay AJ, Goldstein RA. Changing selective pressure
during antigenic changes in human influenza H3. PLoS Pathog 2008;
4:e1000058.
7 Shih AC, Hsiao TC, Ho MS, Li WH. Simultaneous amino acid
substitutions at antigenic sites drive influenza A hemagglutinin
evolution. Proc Natl Acad Sci 2007; 104:6283–6288.
8 Fitch WM, Leiter JM, Li XQ, Palese P. Positive Darwinian evolution in
human influenza A viruses. Proc Natl Acad Sci USA 1991; 88:4270–
4274.
9 Wilson IA, Cox N. Structural basis of immune recognition of influenza
virus hemagglutinin. Annu Rev Immunol 1990; 8:737–771.
10 Ferguson NM, Galvani AP, Bush RM. Ecological and immunological
determinants of influenza evolution. Nature 2003; 422:428–433.
11 Jin H, Zhou H, Liu H et al. Two residues in the hemagglutinin of A/
Fujian/411/02-like influenza viruses are responsible for antigenic drift
from A/Panama/2007/99. Virology 2005; 336:113–119.
12 Ghedin E, Sengamalay NA, Shumway M et al. Large-scale sequencing
of human influenza reveals the dynamic nature of viral genome
evolution. Nature 2005; 437:1162–1166.
13 Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary
Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007;
24:1596–1599.
14 Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R.
Dendroscope- An interactive viewer for large phylogenetic trees. BMC
Bioinformatics 2007; 8:460.
15 Yang Z. PAML 4: a program package for phylogenetic analysis by
maximum likelihood. Mol Biol Evol 2007; 24:1586–1591.
16 Gupta R, Jung E, Brunak S. Prediction of N-glycosylation sites in
human proteins. 2005, NetNGlyc 1.0. Available at http://www.cbs.
dtu.dk/services/NetNGlyc (Accessed 26 August 2012).
17 DeLano WL. The PyMOL Molecular Graphics System. 2002, DeLano
Scientific, San Carlos, CA, USA. Available at http://www.pymol.org.
18 European Center for Disease Prevention and Control (ECDC).
Surveillance report, Influenza virus characterization, Summary for
Europe, September 2010.
19 Colman PM, Varghese JN, Laver WG. Structure of the catalytic and
antigenic sites in influenza virus neuraminidase. Nature 1983;
303:41–44.
20 Colman PM, Hoyne PA, Lawrence MC. Sequence and structure
alignment of paramyxovirus hemagglutinin-neuraminidase with influenza virus neuraminidase. J Virol 1993; 67:2972–2980.
21 Ann J, Papenburg J, Bouhy X et al. Molecular and antigenic evolution
of human influenza A/H3N2 viruses in Quebec, Canada, 2009–2011.
J Clin Virol 2012; 53:88–92.
22 World Health Organization. Recommended composition of influenza
virus vaccines for use in the 2012–2013 northern hemisphere
influenza seasons. 23 February 2012 Available at http://www.who.
int/influenza/vaccines/virus/recommendations/2012_13_north/en/
(Accessed 12 March 2013).
23 Nakajima S, Nobusawa E, Nakajima K. Variation in response among
individuals to antigenic sites on the HA protein of human influenza
ª 2013 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.
Seasonal influenza A (H3N2) antigenic site mutations
24
25
26
27
28
29
30
virus may be responsible for the emergence of drift strains in the
human population. Virology 2000; 274:220–230.
Yang ZY, Wei CJ, Kong WP et al. Immunization by avian H5 influenza
hemagglutinin mutants with altered receptor binding specificity.
Science 2007; 317:825–828.
Gao Y, Zhang Y, Shinya K et al. Identification of amino acids in HA
and PB2 critical for the transmission of H5N1 avian influenza viruses in
a mammalian host. PLoS Pathog 2009; 5:e1000709.
Nakajima K, Nobusawa E, Nagy A, Nakajima S. Accumulation of
amino acid substitutions promotes irreversible structural changes in
the hemagglutinin of human influenza AH3 virus during evolution.
J Virol 2005; 79:6472–6477.
Smith DJ, Lapedes AS, de Jong JC et al. Mapping the antigenic and
genetic evolution of influenza virus. Science 2004; 305:371–376.
National Reference Centre of Influenza. Influenza virus surveillance in
Switzerland Season 2011–2012. Laboratory of Virology, University of
Geneva Hospitals. Available at http://virologie.hug-ge.ch/_library/pdf/
Flu2012.pdf (Accessed 15 March 2013).
Bragstad K, Nielsen LP, Fomsgaard A. The evolution of human
influenza A viruses from 1999 to 2006: a complete genome study.
Virol J 2008; 5:40.
Skowronski DM, Janjua NZ, De Serres G et al. A sentinel platform to
evaluate influenza vaccine effectiveness and new variant circulation,
Canada 2010–11 season. Clin Infect Dis 2012; 55:332–342.
Supporting Information
Additional Supporting Information may be found in the
online version of this article:
Figure S1. HA Variability among Ontario’s influenza A
(H3N2) virus during 2010–2011 Influenza season.
Figure S2. Amino acid sequence alignment of A/Ontario/
C706264/2010(H3N2) to MDCK grown A/Perth/16/2009
(Genbank accession # GQ293081.1).
Table S1. Parameter estimates, dN/dS, values of logLikelihood (l), positive selection sites, and Likelihood Ratio
Tests (LRT) in the Hemagglutinin gene analysis of influenza
A H3N2 viruses circulating in Ontario, Canada between
November 2010 and February 2011.
Table S2. Comparative analysis of ON H3N2 HA mutational patterns at antigenic sites with other geographical
regions.
ª 2013 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.
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