Structural differences among hemagglutinins of influenza A virus subtypes are reflected in their antigenic architecture: analysis of H9 escape mutants

We used a panel of monoclonal antibodies to H9 hemagglutinin to select 18 escape mutants of mouse-adapted influenza A/Swine/Hong Kong/9/98 (H9N2) virus. Cross-reactions of the mutants with the antibodies and the sequencing of hemagglutinin genes revealed two minimally overlapping epitopes. We mapped the amino acid changes to two areas of the recently reported three-dimensional structure of A/Swine/Hong Kong/9/98 hemagglutinin. The grouping of the antigenically relevant amino acid positions in H9 hemagglutinin differs from the pattern observed in H3 and H5 hemagglutinins. Several positions in site B of H3 hemagglutinin are distributed in two sites of H9 hemagglutinin. Unlike any subtype analyzed so far, H9 hemagglutinin does not contain an antigenic site corresponding to site A in H3 hemagglutinin. Positions 145 and 193 (H3 numbering), which in H3 hemagglutinin belong to sites A and B, respectively, are within one site in H9 hemagglutinin. This finding is consistent with the peculiarity of the three-dimensional structure of the H9 molecule, that is, the absence from H9 hemagglutinin of the lateral loop that forms site A in H3 and the equivalent site in H5 hemagglutinins. The escape mutants analyzed displayed phenotypic variations, including decreased virulence for mice and changes in affinity for sialyl substrates. Our results demonstrate a correlation between intersubtype differences in three-dimensional structure and variations among subtypes in the distribution of antigenic areas. Our findings also suggest that covariation and pleiotropic effects of antibody-selected mutations may be important in the evolution of H9 influenza virus, a possible causative agent of a future pandemic.     

Conservation and variation in the hemagglutinins of Hong Kong subtype influenza viruses during antigenic drift.

The nucleotide sequence was determined for the hemagglutinin gene of the Hong Kong subtype influenza strain A/Bangkok/1/79. The amino acid sequence predicted from these data shows a total of 36 amino acid changes as compared with hemagglutinin for a 1968 Hong Kong strain, 11 more than had occurred in a 1975 strain. The distribution of these changes confirmed that there are conserved and highly variable regions in hemagglutinin as the viral gene evolves during antigenic drift in the Hong Kong subtype. Of the four variable regions found in this study, only two have been seen previously. Correlation of highly variable areas in the hemagglutinins of Hong Kong subtype field strains with sites of amino acid changes in antigenically distinct influenza variants enabled us to predict likely antigenic regions of the protein. The results support and extend similar predictions made recently, based on the three-dimensional arrangement of hemagglutinin from a 1968 influenza strain.     

The Wilhelmine E. Key 1999 Invitational lecture. Predicting the evolution of human influenza A

We studied the evolution of the HA1 domain of the H3 hemagglutinin gene from human influenza virus type A. The phylogeny of these genes showed a single dominant lineage persisting over time. We tested the hypothesis that the progenitors of this single evolutionarily successful lineage were viruses carrying mutations at codons at which prior mutations had helped the virus to avoid human immune surveillance. We found evidence that eighteen hemagglutinin codons appeared to have been under positive selection to change the amino acid they encoded in the past. Retrospective tests show that viral lineages undergoing the greatest number of mutations in the positively selected codons were the progenitors of future H3 lineages in nine of eleven recent influenza seasons. Codons under positive selection were associated with antibody combining sites A or B or the sialic acid receptor binding site. However, not all codons in these sites had predictive value. Monitoring new H3 isolates for additional changes in positively selected codons might help identify the most fit extant viral strains that arise during antigenic drift.     

Molecular evolution of influenza A (H3N2) viruses circulated in Fujian Province, China during the 1996–2004 period

We studied the genetic and epidemic characteristics of influenza A (H3N2) viruses circulated in human in Fujian Province, south of China from 1996 to 2004. Phylogenetic analysis was carried out for genes encoding hemagglutinin1 (HA1) of influenza A virus (14 new and 11 previously reported reference se-quences). Our studies revealed that in the 8 flu seasons, the mutations of HA1 genes occurred from time to time, which were responsible for about four times of antigenic drift of influenza H3N2 viruses in Fujian, China. The data demonstrated that amino acid changes were limited to some key codons at or near antibody binding sites A through E on the HA1 molecule. The changes at the antibody binding site B or A or sialic acid receptor binding site 226 were critical for antigenic drift. But the antigenic sites might change and the key codons for antigenic drift might change as influenza viruses evolve. It seems important to monitor new H3 isolates for mutations in the positively selected codons of HA1 gene in south of Asia.     

In silico analysis of genes nucleoprotein, neuraminidase and hemagglutinin: a comparative study on different strains of influenza A (Bird flu) virus sub-type H5N1

The avian influenza (bird flu) is an infectious disease of birds, ranging from a mild to a severe form of illness. Influenza viruses pose significant challenges to both human and animal health. The proteins, nucleoprotein (NP), neuraminidase (NA) and hemagglutinin (HA) of influenza A virus (Bird flu virus) sub-type A/Hatay/2004/(H5N1) from chicken were selected for this study. Our in silico analysis predicted that HA of influenza A virus is highly sensitive to mutations and hence it is significant for its pathogenic nature. None of the mutations was detected as an important change except in NA where K332R was at a PKC phosphorylation site. Analysis of the sequence comparison showed that the maximum number of mutations were observed in HA. These mutations are significant as they are involved in change in polarity or hydrophobicity as well as in propensity of each amino acid residue to stabilize the secondary structure. The program MAPMUTATION can be used to monitor the mutations, and predict the trend of mutations.     

Analysis of the evolution and variation of the human influenza A virus nucleoprotein gene from 1933 to 1990.

This study examined the evolution and variation of the human influenza virus nucleoprotein gene from the earliest isolates to the present. Phylogenetic reconstruction of the most parsimonious evolutionary path connecting 49 nucleoprotein sequences yielded a single lineage. The average calculated rate of mutation was 3.6 nucleotide substitutions per year (2.3 x 10(-3) substitutions per site per year). Thirty-two percent of these mutations resulted in amino acid substitutions, and the remainder were silent mutations. Analysis of virus isolates from China and elsewhere showed no significant differences in their rate of evolution, genetic diversity, or mean survival time. The nearly constant rate of change was maintained through the two antigenic shifts, and there were no obvious changes in the number or types of mutations associated with the changes in the surface proteins. A detailed comparison of the changes that have occurred on the main evolutionary path with those that have occurred on the side branches of the phylogenetic tree was made. This showed that while 35% of the mutations on the side branches resulted in amino acid changes, only 21% of those on the main path affected the protein sequence. These results suggest that although the rate of change of the human influenza virus nucleoprotein is much higher than that previously described for avian influenza viruses, there are measurable constraints on the evolution of the surviving virus lineage. Comparison of the nucleoproteins of virus isolates adapted to chicken embryos with the nucleoproteins of those grown only in MDCK cells revealed no consistent differences between the virus pairs. Thus, although the nucleoprotein is known to be critical for host specificity, its adaptation to growth in eggs apparently involves no immediate selective pressures, such as are found with hemagglutinin.     

Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties

Background

The influenza A(H1N1)2009 virus has been the dominant type of influenza A virus in Finland during the 2009–2010 and 2010–2011 epidemic seasons. We analyzed the antigenic characteristics of several influenza A(H1N1)2009 viruses isolated during the two influenza seasons by analyzing the amino acid sequences of the hemagglutinin (HA), modeling the amino acid changes in the HA structure and measuring antibody responses induced by natural infection or influenza vaccination.

Methods/Results

Based on the HA sequences of influenza A(H1N1)2009 viruses we selected 13 different strains for antigenic characterization. The analysis included the vaccine virus, A/California/07/2009 and multiple California-like isolates from 2009–2010 and 2010–2011 epidemic seasons. These viruses had two to five amino acid changes in their HA1 molecule. The mutation(s) were located in antigenic sites Sa, Ca1, Ca2 and Cb region. Analysis of the antibody levels by hemagglutination inhibition test (HI) indicated that vaccinated individuals and people who had experienced a natural influenza A(H1N1)2009 virus infection showed good immune responses against the vaccine virus and most of the wild-type viruses. However, one to two amino acid changes in the antigenic site Sa dramatically affected the ability of antibodies to recognize these viruses. In contrast, the tested viruses were indistinguishable in regard to antibody recognition by the sera from elderly individuals who had been exposed to the Spanish influenza or its descendant viruses during the early 20^th century.

Conclusions

According to our results, one to two amino acid changes (N125D and/or N156K) in the major antigenic sites of the hemagglutinin of influenza A(H1N1)2009 virus may lead to significant reduction in the ability of patient and vaccine sera to recognize A(H1N1)2009 viruses.     

Hemagglutinin mutations related to antigenic variation in H1 swine influenza viruses.

The hemagglutinin (HA) of a recent swine influenza virus, A/Sw/IN/1726/88 (H1N1), was shown previously to have four antigenic sites, as determined from analysis of monoclonal antibody (MAb)-selected escape mutants. To define the HA mutations related to these antigenic sites, we cloned and sequenced the HA genes amplified by polymerase chain reaction of parent virus and MAb-selected escape mutants. The genetic data indicated the presence of four amino acid changes. After alignment with the three-dimensional structure of H3 HA, three changes were located on the distal tip of the HA, and the fourth was located within the loop on the HA. We then compared our antigenic sites, as defined by the changed amino acids, with the well-defined sites on the H1 HA of A/PR/8/34. The four amino acid residues corresponded with three antigenic sites on the HA of A/PR/8/34. This finding, in conjunction with our previous antigenic data, indicated that two of the four antigenic sites were overlapping. In addition, our previous studies indicated that one MAb-selected mutant and a recent, naturally occurring swine isolate reacted similarly with the MAb panel. However, their amino acid changes were different and also distant on the primary sequence but close topographically. This finding indicates that changes outside the antigenic site may also affect the site. A comparison of the HA amino acid sequences of early and recent swine isolates showed striking conservation of genetic sequences as well as of the antigenic sites. Thus, swine influenza viruses evolve more slowly than human viruses, possibly because they are not subjected to the same degree of immune selection.     

2009年中国流行的甲型流感病毒（H1N1）血凝素特征分析

目的研究甲型流感病毒（H1N1）暴发流行以来中国各地甲型流感病毒血凝素（HA）的特征。方法搜索甲型流感病毒（H1N1）暴发流行以来中国各地报道的血凝素（HA）的氨基酸序列,比较当年不同时期血凝素（HA）的氨基酸序列的变化,并比较2009年报道的血凝素（HA）的氨基酸序列和2008年、2007年报道的血凝素（HA）的氨基酸序列作比较,以分析和前2年血凝素（HA）氨基酸序列相比所发生的变化。结果2009年中国各地甲型流感病毒（H1N1）的血凝素（HA）的氨基酸序列（人源）的同源性为99%-100%,但和2008年以及2007年的同源性非常低,分别为70%-77%和71%-90%。结论2009年暴发流行的甲型流感病毒（H1N1）的血凝素氨基酸序列较往年发生了很大程度的变异,这可能是今年甲型流感病毒（H1N1）暴发流行的主要原因。     

Clonal Interference in the Evolution of Influenza

The seasonal influenza A virus undergoes rapid evolution to escape human immune response. Adaptive changes occur primarily in antigenic epitopes, the antibody-binding domains of the viral hemagglutinin. This process involves recurrent selective sweeps, in which clusters of simultaneous nucleotide fixations in the hemagglutinin coding sequence are observed about every 4 years. Here, we show that influenza A (H3N2) evolves by strong clonal interference. This mode of evolution is a red queen race between viral strains with different beneficial mutations. Clonal interference explains and quantifies the observed sweep pattern: we find an average of at least one strongly beneficial amino acid substitution per year, and a given selective sweep has three to four driving mutations on average. The inference of selection and clonal interference is based on frequency time series of single-nucleotide polymorphisms, which are obtained from a sample of influenza genome sequences over 39 years. Our results imply that mode and speed of influenza evolution are governed not only by positive selection within, but also by background selection outside antigenic epitopes: immune adaptation and conservation of other viral functions interfere with each other. Hence, adapting viral proteins are predicted to be particularly brittle. We conclude that a quantitative understanding of influenza’s evolutionary and epidemiological dynamics must be based on all genomic domains and functions coupled by clonal interference.     

The nature of amino acid substitution in antigenic drift of hemagglutinin N3 and neuraminidase N2 from the influenza virus

The nature of amino acid replacements in 16 drift variants of hemagglutinin H3 subtype and 5 drift variants of neuraminidase N2 subtype of the influenza A virus were studied. The dependences of relative replacement frequencies and relative quantities of frequent replacements upon differences of properties of substituted residues are plotted. In contrast to most of the known proteins, amino acid replacements in hemagglutinin and neuraminidase depend weakly on the physico-chemical parameters of amino acids. For the antigenic determinants studied the replacement frequencies were compared to those calculated according to two models: one for conservative replacements and the other for accidental mutation of the genetic code. The differences in the nature of amino acid replacements are found in four antigenic determinants of hemagglutinin. The replacements in experimentally selected proteins are shown to go beyond limitations of natural variants. The explanations of the reasons of low epidemicity of some strains and ineffective attempt to imitate the natural antigenic drift of viruses by using experimental selection are proposed. The causes of time-limited circulation of H3N2 influenza virus subtype are discussed.     

Prediction of mutations in H5N1 hemagglutinins from influenza A virus

In this study, we determine the mutation relation among 333 H5N1 hemagglutinins of influenza A viruses according to their amino acid and RNA codon sequences. Then, we calculate seven probabilistic numbers, which have been developed by us since 1999, for each amino acid in these hemagglutinins. With the seven numeric numbers as independents and the probability of occurrence of mutation at each hemagglutinin position as dependent, we use the logistic regression to model 967 missense point mutations from 333 hemagglutinins to get the population estimates. Thereafter, we predict the future mutation positions in H5N1 hemagglutinin. Finally, we use the translation probabilities between RNA codons and mutated amino acids to predict the would-be-mutated amino acids in H5N1 hemagglutinin.     

Complete structure of A/duck/Ukraine/63 influenza hemagglutinin gene: animal virus as progenitor of human H3 Hong Kong 1968 influenza hemagglutinin

We have explored the possibility that an animal viral reservoir contained a direct ancestor gene for the H3 hemagglutinin type present in influenza A viruses in humans since 1968. For this purpose, the duck/Ukraine/1/63 hemagglutinin gene was cloned and sequenced. From the comparison of its complete primary structure with that of several human H3 hemagglutinins as well as those of an H2 and an H7 hemagglutinin, we conclude that the duck/Ukraine/63 hemagglutinin sequence fully corroborates its previous identification by immunological and other methods as belonging to the H3 subtype. Moreover, the duck/Ukraine/63 amino acid sequence is more closely related structurally and presumably antigenically to the human Aichi/68 hemagglutinin, which formed the beginning of the H3N2 pandemic in humans, than to that of Victoria/75, which has undergone an additional 7 year drift period in humans. This observation could best be explained by a common ancestor hemagglutinin gene for duck/Ukraine/63 and human Aichi/68. On the basis of silent, accumulated base changes, we estimate that the strain carrying this postulated common progenitor hemagglutinin gene was circulating in the period 1949–1953 in the animal reservoir. This relatively recent divergence, as well as the closer kinship between the duck/Ukraine/63 and the human Aichi/68 hemagglutinin, as compared with the later Victoria/75, strongly suggests that the influenza A virus of the H3N2 subtype circulating in the human population since 1968 has derived its hemagglutinin gene from a strain in the animal reservoir. Undoubtedly, this occurred by reassortment between previously present human H2N2 virus and this animal strain. These results provide support at the molecular level for the general idea that the wide variety of influenza viruses known to be present in animals can serve as a gene reservoir for human influenza A viruses.     

2009−2015年中国甲型H1N1流感病毒血凝素基因进化分析

【目的】为了解中国地区2009?2015年甲型H1N1流感病毒流行态势,分析血凝素(Hemagglutinin,HA)基因的变异情况及其遗传进化特征。【方法】汇集国家流感中心2009?2015年流感周报的流感流行数据,分析甲型H1N1流感的流行病学特征;从全球共享禽流感数据倡议组织数据库及美国国家生物技术中心数据库下载甲型H1N1流感病毒HA基因序列,采用生物学软件进行系统进化和遗传特性的分析。【结果】2009?2015年全国共发生4次甲型H1N1流感的流行高峰。2009?2015年毒株与参考毒株A/California/07/2009(H1N1)的HA基因同源性逐年降低。遗传进化分析显示同一年份的毒株在系统进化树上基本呈现集中分布,2011年的毒株独立形成2个分支。分子特征表现为HA基因的4个抗原决定簇氨基酸位点均有变异,其中Ca区的203位、Sa区的163位和Sb区的185位氨基酸位点逐渐替换为新的氨基酸。除2010年与2012年,其他年份的毒株通过不同模型均得到正向压力选择HA氨基酸位点240。【结论】甲型H1N1流感在中国地区成为主要流行的亚型之一。HA基因与其编码的氨基酸逐年变异,未来进一步的流感监测能力还需加强。     

Accumulation of amino acid substitutions promotes irreversible structural changes in the hemagglutinin of human influenza AH3 virus during evolution

In order to clarify the effect of an accumulation of amino acid substitutions on the hemadsorption character of the influenza AH3 virus hemagglutinin (HA) protein, we introduced single-point amino acid changes into the HA1 domain of the HA proteins of influenza viruses isolated in 1968 (A/Aichi/2/68) and 1997 (A/Sydney/5/97) by using PCR-based random mutation or site-directed mutagenesis. These substitutions were classified as positive or negative according to their effects on the hemadsorption activity. The rate of positive substitutions was about 50% for both strains. Of 44 amino acid changes that were identical in the two strains with regard to both the substituted amino acids and their positions in the HA1 domain, 22% of the changes that were positive in A/Aichi/2/68 were negative in A/Sydney/5/97 and 27% of the changes that were negative in A/Aichi/2/68 were positive in A/Sydney/5/97. A similar discordance rate was also seen for the antigenic sites. These results suggest that the accumulation of amino acid substitutions in the HA protein during evolution promoted irreversible structural changes and therefore that antigenic changes in the H3HA protein may not be limited.     

Bioinformatics models for predicting antigenic variants of influenza A/H3N2 virus

MOTIVATION: Continual and accumulated mutations in hemagglutinin (HA) protein of influenza A virus generate novel antigenic strains that cause annual epidemics. RESULTS: We propose a model by incorporating scoring and regression methods to predict antigenic variants. Based on collected sequences of influenza A/H3N2 viruses isolated between 1971 and 2002, our model can be used to accurately predict the antigenic variants in 1999-2004 (agreement rate = 91.67%). Twenty amino acid positions identified in our model contribute significantly to antigenic difference and are potential immunodominant positions.     

Adaptation of a duck influenza A virus in quail

Quail are thought to serve as intermediate hosts of influenza A viruses between aquatic birds and terrestrial birds, such as chickens, due to their high susceptibility to aquatic-bird viruses, which then adapt to replicate efficiently in their new hosts. However, does replication of aquatic-bird influenza viruses in quail similarly result in their efficient replication in humans? Using sialic acid-galactose linkage-specific lectins, we found both avian (sialic acid-α2-3-galactose [Siaα2-3Gal] linkages on sialyloligosaccharides)- and human (Siaα2-6Gal)-type receptors on the tracheal cells of quail, consistent with previous reports. We also passaged a duck H3N2 virus in quail 19 times. Sequence analysis revealed that eight mutations accumulated in hemagglutinin (HA) during these passages. Interestingly, many of the altered HA amino acids found in the adapted virus are present in human seasonal viruses, but not in duck viruses. We also found that stepwise stalk deletion of neuraminidase occurred during passages, resulting in reduced neuraminidase function. Despite some hemagglutinin mutations near the receptor binding pocket, appreciable changes in receptor specificity were not detected. However, reverse-genetics-generated viruses that possessed the hemagglutinin and neuraminidase of the quail-passaged virus replicated significantly better than the virus possessing the parent HA and neuraminidase in normal human bronchial epithelial cells, whereas no significant difference in replication between the two viruses was observed in duck cells. Further, the quail-passaged but not the original duck virus replicated in human bronchial epithelial cells. These data indicate that quail can serve as intermediate hosts for aquatic-bird influenza viruses to be transmitted to humans.     

Positive selection on the H3 hemagglutinin gene of human influenza virus A.

The hemagglutinin (HA) gene of influenza viruses encodes the major surface antigen against which neutralizing antibodies are produced during infection or vaccination. We examined temporal variation in the HA1 domain of HA genes of human influenza A (H3N2) viruses in order to identify positively selected codons. Positive selection is defined for our purposes as a significant excess of nonsilent over silent nucleotide substitutions. If past mutations at positively selected codons conferred a selective advantage on the virus, then additional changes at these positions may predict which emerging strains will predominate and cause epidemics. We previously reported that a 38% excess of mutations occurred on the tip or terminal branches of the phylogenetic tree of 254 HA genes of influenza A (H3N2) viruses. Possible explanations for this excess include processes other than viral evolution during replication in human hosts. Of particular concern are mutations that occur during adaptation of viruses for growth in embryonated chicken eggs in the laboratory. Because the present study includes 357 HA sequences (a 40% increase), we were able to separately analyze those mutations assigned to internal branches. This allowed us to determine whether mutations on terminal and internal branches exhibit different patterns of selection at the level of individual codons. Additional improvements over our previous analysis include correction for a skew in the distribution of amino acid replacements across codons and analysis of a population of phylogenetic trees rather than a single tree. The latter improvement allowed us to ascertain whether minor variation in tree structure had a significant effect on our estimate of the codons under positive selection. This method also estimates that 75.6% of the nonsilent mutations are deleterious and have been removed by selection prior to sampling. Using the larger data set and the modified methods, we confirmed a large (40%) excess of changes on the terminal branches. We also found an excess of changes on branches leading to egg-grown isolates. Furthermore, 9 of the 18 amino acid codons, identified as being under positive selection to change when we used only mutations assigned to internal branches, were not under positive selection on the terminal branches. Thus, although there is overlap between the selected codons on terminal and internal branches, the codons under positive selection on the terminal branches differ from those on the internal branches. We also observed that there is an excess of positively selected codons associated with the receptor-binding site and with the antibody-combining sites. This association may explain why the positively selected codons are restricted in their distribution along the sequence. Our results suggest that future studies of positive selection should focus on changes assigned to the internal branches, as certain of these changes may have predictive value for identifying future successful epidemic variants.     

Evolution of the H3 influenza virus hemagglutinin from human and nonhuman hosts.

The nucleotide and amino acid sequences of 40 influenza virus hemagglutinin genes of the H3 serotype from mammalian and avian species and 9 genes of the H4 serotype were compared, and their evolutionary relationships were evaluated. From these relationships, the differences in the mutational characteristics of the viral hemagglutinin in different hosts were examined and the RNA sequence changes that occurred during the generation of the progenitor of the 1968 human pandemic strain were examined. Three major lineages were defined: one containing only equine virus isolates; one containing only avian virus isolates; and one containing avian, swine, and human virus isolates. The human pandemic strain of 1968 was derived from an avian virus most similar to those isolated from ducks in Asia, and the transfer of this virus to humans probably occurred in 1965. Since then, the human viruses have diverged from this progenitor, with the accumulation of approximately 7.9 nucleotide and 3.4 amino acid substitutions per year. Reconstruction of the sequence of the hypothetical ancestral strain at the avian-human transition indicated that only 6 amino acids in the mature hemagglutinin molecule were changed during the transition between an avian virus strain and a human pandemic strain. All of these changes are located in regions of the molecule known to affect receptor binding and antigenicity. Unlike the human H3 influenza virus strains, the equine virus isolates have no close relatives in other species and appear to have diverged from the avian viruses much earlier than did the human virus strains. Mutations were estimated to have accumulated in the equine virus lineage at approximately 3.1 nucleotides and 0.8 amino acids per year. Four swine virus isolates in the analysis each appeared to have been introduced into pigs independently, with two derived from human viruses and two from avian viruses. A comparison of the coding and noncoding mutations in the mammalian and avian lineages showed a significantly lower ratio of coding to total nucleotide changes in the avian viruses. Additionally, the avian virus lineages of both the H3 and H4 serotypes, but not the mammalian virus lineages, showed significantly greater conservation of amino acid sequence in the internal branches of the phylogenetic tree than in the terminal branches. The small number of amino acid differences between the avian viruses and the progenitor of the 1968 pandemic strain and the great phenotypic stability of the avian viruses suggest that strains similar to the progenitor strain will continue to circulate in birds and will be available for reintroduction into humans.     

Gnarled-trunk evolutionary model of influenza A virus hemagglutinin

Human influenza A viruses undergo antigenic changes with gradual accumulation of amino acid substitutions on the hemagglutinin (HA) molecule. A strong antigenic mismatch between vaccine and epidemic strains often requires the replacement of influenza vaccines worldwide. To establish a practical model enabling us to predict the future direction of the influenza virus evolution, relative distances of amino acid sequences among past epidemic strains were analyzed by multidimensional scaling (MDS). We found that human influenza viruses have evolved along a gnarled evolutionary pathway with an approximately constant curvature in the MDS-constructed 3D space. The gnarled pathway indicated that evolution on the trunk favored multiple substitutions at the same amino acid positions on HA. The constant curvature was reasonably explained by assuming that the rate of amino acid substitutions varied from one position to another according to a gamma distribution. Furthermore, we utilized the estimated parameters of the gamma distribution to predict the amino acid substitutions on HA in subsequent years. Retrospective prediction tests for 12 years from 1997 to 2009 showed that 70% of actual amino acid substitutions were correctly predicted, and that 45% of predicted amino acid substitutions have been actually observed. Although it remains unsolved how to predict the exact timing of antigenic changes, the present results suggest that our model may have the potential to recognize emerging epidemic strains.