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The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin.

Thyagarajan B, Bloom JD - Elife (2014)

Bottom Line: We used deep mutational scanning to examine the extent to which a high inherent mutational tolerance contributes to this antigenic evolvability.These data enable us to infer the preference for each amino acid at each site in hemagglutinin.These inferences are consistent with existing knowledge about the protein's structure and function, and can be used to create a model that describes hemagglutinin's evolution far better than existing phylogenetic models.

View Article: PubMed Central - PubMed

Affiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.

ABSTRACT
Influenza is notable for its evolutionary capacity to escape immunity targeting the viral hemagglutinin. We used deep mutational scanning to examine the extent to which a high inherent mutational tolerance contributes to this antigenic evolvability. We created mutant viruses that incorporate most of the ≈10(4) amino-acid mutations to hemagglutinin from A/WSN/1933 (H1N1) influenza. After passaging these viruses in tissue culture to select for functional variants, we used deep sequencing to quantify mutation frequencies before and after selection. These data enable us to infer the preference for each amino acid at each site in hemagglutinin. These inferences are consistent with existing knowledge about the protein's structure and function, and can be used to create a model that describes hemagglutinin's evolution far better than existing phylogenetic models. We show that hemagglutinin has a high inherent tolerance for mutations at antigenic sites, suggesting that this is one factor contributing to influenza's antigenic evolution.

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Properties of the HA codon-mutant library as assessed by Sanger sequencing of 34 individual clones drawn roughly evenly from the three experimental replicates.(A) There are an average of 2.1 codon mutations per clone, with the number per clone following a roughly Poisson distribution. (B) The codon mutations involve a mix of one-, two-, and three-nucleotide mutations. (C) The nucleotide composition of the mutant codons is roughly uniform. (D) The mutations are distributed uniformly along HA's primary sequence. (E) There is no tendency for mutations to cluster in primary sequence. Shown is distribution of observed pairwise distances between mutations in multiply mutated clones vs the expected distribution when the mutations are placed independently in the clones. All plots show results only for substitution mutations; insertion/deletion mutations are not shown. However, only two insertion/deletion mutations (0.06 per clone) were identified. The data and computer code used to generate this figure are at https://github.com/jbloom/SangerMutantLibraryAnalysis/tree/v0.2.DOI:http://dx.doi.org/10.7554/eLife.03300.004
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fig2: Properties of the HA codon-mutant library as assessed by Sanger sequencing of 34 individual clones drawn roughly evenly from the three experimental replicates.(A) There are an average of 2.1 codon mutations per clone, with the number per clone following a roughly Poisson distribution. (B) The codon mutations involve a mix of one-, two-, and three-nucleotide mutations. (C) The nucleotide composition of the mutant codons is roughly uniform. (D) The mutations are distributed uniformly along HA's primary sequence. (E) There is no tendency for mutations to cluster in primary sequence. Shown is distribution of observed pairwise distances between mutations in multiply mutated clones vs the expected distribution when the mutations are placed independently in the clones. All plots show results only for substitution mutations; insertion/deletion mutations are not shown. However, only two insertion/deletion mutations (0.06 per clone) were identified. The data and computer code used to generate this figure are at https://github.com/jbloom/SangerMutantLibraryAnalysis/tree/v0.2.DOI:http://dx.doi.org/10.7554/eLife.03300.004

Mentions: Sanger sequencing of 34 individual clones indicated that the libraries contained an average of slightly over two codon mutations per gene, with a very low rate of insertions and deletions (less than 0.1 per gene). The number of mutations per clone was distributed around this average in an approximately Poisson fashion (Figure 2). The mutations consisted of a mix of one-, two-, and three-nucleotide codon changes, and were roughly uniform in their nucleotide composition and location in the gene (Figure 2).10.7554/eLife.03300.004Figure 2.Properties of the HA codon-mutant library as assessed by Sanger sequencing of 34 individual clones drawn roughly evenly from the three experimental replicates.


The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin.

Thyagarajan B, Bloom JD - Elife (2014)

Properties of the HA codon-mutant library as assessed by Sanger sequencing of 34 individual clones drawn roughly evenly from the three experimental replicates.(A) There are an average of 2.1 codon mutations per clone, with the number per clone following a roughly Poisson distribution. (B) The codon mutations involve a mix of one-, two-, and three-nucleotide mutations. (C) The nucleotide composition of the mutant codons is roughly uniform. (D) The mutations are distributed uniformly along HA's primary sequence. (E) There is no tendency for mutations to cluster in primary sequence. Shown is distribution of observed pairwise distances between mutations in multiply mutated clones vs the expected distribution when the mutations are placed independently in the clones. All plots show results only for substitution mutations; insertion/deletion mutations are not shown. However, only two insertion/deletion mutations (0.06 per clone) were identified. The data and computer code used to generate this figure are at https://github.com/jbloom/SangerMutantLibraryAnalysis/tree/v0.2.DOI:http://dx.doi.org/10.7554/eLife.03300.004
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4109307&req=5

fig2: Properties of the HA codon-mutant library as assessed by Sanger sequencing of 34 individual clones drawn roughly evenly from the three experimental replicates.(A) There are an average of 2.1 codon mutations per clone, with the number per clone following a roughly Poisson distribution. (B) The codon mutations involve a mix of one-, two-, and three-nucleotide mutations. (C) The nucleotide composition of the mutant codons is roughly uniform. (D) The mutations are distributed uniformly along HA's primary sequence. (E) There is no tendency for mutations to cluster in primary sequence. Shown is distribution of observed pairwise distances between mutations in multiply mutated clones vs the expected distribution when the mutations are placed independently in the clones. All plots show results only for substitution mutations; insertion/deletion mutations are not shown. However, only two insertion/deletion mutations (0.06 per clone) were identified. The data and computer code used to generate this figure are at https://github.com/jbloom/SangerMutantLibraryAnalysis/tree/v0.2.DOI:http://dx.doi.org/10.7554/eLife.03300.004
Mentions: Sanger sequencing of 34 individual clones indicated that the libraries contained an average of slightly over two codon mutations per gene, with a very low rate of insertions and deletions (less than 0.1 per gene). The number of mutations per clone was distributed around this average in an approximately Poisson fashion (Figure 2). The mutations consisted of a mix of one-, two-, and three-nucleotide codon changes, and were roughly uniform in their nucleotide composition and location in the gene (Figure 2).10.7554/eLife.03300.004Figure 2.Properties of the HA codon-mutant library as assessed by Sanger sequencing of 34 individual clones drawn roughly evenly from the three experimental replicates.

Bottom Line: We used deep mutational scanning to examine the extent to which a high inherent mutational tolerance contributes to this antigenic evolvability.These data enable us to infer the preference for each amino acid at each site in hemagglutinin.These inferences are consistent with existing knowledge about the protein's structure and function, and can be used to create a model that describes hemagglutinin's evolution far better than existing phylogenetic models.

View Article: PubMed Central - PubMed

Affiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.

ABSTRACT
Influenza is notable for its evolutionary capacity to escape immunity targeting the viral hemagglutinin. We used deep mutational scanning to examine the extent to which a high inherent mutational tolerance contributes to this antigenic evolvability. We created mutant viruses that incorporate most of the ≈10(4) amino-acid mutations to hemagglutinin from A/WSN/1933 (H1N1) influenza. After passaging these viruses in tissue culture to select for functional variants, we used deep sequencing to quantify mutation frequencies before and after selection. These data enable us to infer the preference for each amino acid at each site in hemagglutinin. These inferences are consistent with existing knowledge about the protein's structure and function, and can be used to create a model that describes hemagglutinin's evolution far better than existing phylogenetic models. We show that hemagglutinin has a high inherent tolerance for mutations at antigenic sites, suggesting that this is one factor contributing to influenza's antigenic evolution.

Show MeSH
Related in: MedlinePlus