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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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Related in: MedlinePlus

The per-codon read depth as a function of primary sequence.This plot is typical of the samples. The read depth varied fairly consistently as a function of primary sequence, presumably due to biases in the positions at which the HA gene tended to fragment. This plot is the file replicate_3/DNA/replicate_3_DNA_codondepth.pdf described at http://jbloom.github.io/mapmuts/example_WSN_HA_2014Analysis.html.DOI:http://dx.doi.org/10.7554/eLife.03300.008
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fig3s3: The per-codon read depth as a function of primary sequence.This plot is typical of the samples. The read depth varied fairly consistently as a function of primary sequence, presumably due to biases in the positions at which the HA gene tended to fragment. This plot is the file replicate_3/DNA/replicate_3_DNA_codondepth.pdf described at http://jbloom.github.io/mapmuts/example_WSN_HA_2014Analysis.html.DOI:http://dx.doi.org/10.7554/eLife.03300.008

Mentions: In order to reduce the sequencing error rate, the HA molecules were fragmented to roughly 50 nucleotide fragments using Illumina's transposon-based Nextera kit, and then sequenced with overlapping paired-end reads (Figure 3—figure supplement 1). We only called codon identities for which both paired reads concur—this strategy substantially increases the sequencing fidelity, since it is rare for the same sequencing error to occur in both reads. For each sample, we obtained in excess of 107 overlapping paired-end reads that could be aligned to HA (Figure 3—figure supplement 2). As shown in Figure 3—figure supplement 3, the read depth varied somewhat along the primary sequence, presumably due to known weak biases in the insertion sites for the Nextera transposon (Adey et al., 2010). However, these biases were fairly mild, and so we obtained well over 2 × 105 unique paired reads for nearly all HA codons.


The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin.

Thyagarajan B, Bloom JD - Elife (2014)

The per-codon read depth as a function of primary sequence.This plot is typical of the samples. The read depth varied fairly consistently as a function of primary sequence, presumably due to biases in the positions at which the HA gene tended to fragment. This plot is the file replicate_3/DNA/replicate_3_DNA_codondepth.pdf described at http://jbloom.github.io/mapmuts/example_WSN_HA_2014Analysis.html.DOI:http://dx.doi.org/10.7554/eLife.03300.008
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3s3: The per-codon read depth as a function of primary sequence.This plot is typical of the samples. The read depth varied fairly consistently as a function of primary sequence, presumably due to biases in the positions at which the HA gene tended to fragment. This plot is the file replicate_3/DNA/replicate_3_DNA_codondepth.pdf described at http://jbloom.github.io/mapmuts/example_WSN_HA_2014Analysis.html.DOI:http://dx.doi.org/10.7554/eLife.03300.008
Mentions: In order to reduce the sequencing error rate, the HA molecules were fragmented to roughly 50 nucleotide fragments using Illumina's transposon-based Nextera kit, and then sequenced with overlapping paired-end reads (Figure 3—figure supplement 1). We only called codon identities for which both paired reads concur—this strategy substantially increases the sequencing fidelity, since it is rare for the same sequencing error to occur in both reads. For each sample, we obtained in excess of 107 overlapping paired-end reads that could be aligned to HA (Figure 3—figure supplement 2). As shown in Figure 3—figure supplement 3, the read depth varied somewhat along the primary sequence, presumably due to known weak biases in the insertion sites for the Nextera transposon (Adey et al., 2010). However, these biases were fairly mild, and so we obtained well over 2 × 105 unique paired reads for nearly all HA codons.

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