Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin.


Abstract

Influenza genes evolve mostly via point mutations, and so knowing the effect of every amino-acid mutation provides information about evolutionary paths available to the virus. We and others have combined high-throughput mutagenesis with deep sequencing to estimate the effects of large numbers of mutations to influenza genes. However, these measurements have suffered from substantial experimental noise due to a variety of technical problems, the most prominent of which is bottlenecking during the generation of mutant viruses from plasmids. Here we describe advances that ameliorate these problems, enabling us to measure with greatly improved accuracy and reproducibility the effects of all amino-acid mutations to an H1 influenza hemagglutinin on viral replication in cell culture. The largest improvements come from using a helper virus to reduce bottlenecks when generating viruses from plasmids. Our measurements confirm at much higher resolution the results of previous studies suggesting that antigenic sites on the globular head of hemagglutinin are highly tolerant of mutations. We also show that other regions of hemagglutinin-including the stalk epitopes targeted by broadly neutralizing antibodies-have a much lower inherent capacity to tolerate point mutations. The ability to accurately measure the effects of all influenza mutations should enhance efforts to understand and predict viral evolution.

Submission Details

ID: EepmqWV43

Submitter: Shu-Ching Ou

Submission Date: July 23, 2018, 4:22 p.m.

Version: 1

Publication Details
Doud MB;Bloom JD,Viruses (2016) Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin. PMID:27271655
Additional Information

Study Summary

Number of data points 11280
Proteins Hemagglutinin
Unique complexes 10717
Assays/Quantities/Protocols Experimental Assay: Generation of Mutant HA Virus Libraries
Libraries Overall Merged Site-Specific Amino-Acid Preferences

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
5VLI 2017-09-27 1.8 Computationally designed inhibitor peptide HB1.6928.2.3 in complex with influenza hemagglutinin (A/PuertoRico/8/1934)
6ONA 2019-05-01 1.95 Crystal structure of Influenza hemagglutinin from strain A/Hickox/JY2/1940
1RVX 2004-03-30 2.2 1934 H1 Hemagglutinin in complex with LSTA
1RVZ 2004-03-30 2.25 1934 H1 Hemagglutinin in complex with LSTC
5W5S 2017-10-04 2.28 Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141019 (P5)
1RU7 2004-03-30 2.3 1934 Human H1 Hemagglutinin
5W5U 2017-10-04 2.46 Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141037 (P4)
5W6T 2017-10-04 2.59 Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP151070 (P7)
1RUY 2004-03-30 2.7 1930 Swine H1 Hemagglutinin
5W6R 2017-10-04 2.73 Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141099 (P6)
5W6U 2017-10-04 2.88 Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP121068 (P2)
5W6I 2017-10-04 3.1 Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141046 (P3)

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
90.3 Hemagglutinin A4K143 HEMA_I54A2
90.1 Hemagglutinin A4GCH5 HEMA_I83A1
90.3 Hemagglutinin P18875 HEMA_I79A4
90.3 Hemagglutinin A4GCJ7 HEMA_I80AA
90.5 Hemagglutinin A4GBX7 HEMA_I77AA
90.6 Hemagglutinin P18876 HEMA_I54A0
90.8 Hemagglutinin A4U7A6 HEMA_I51A0
90.8 Hemagglutinin P03453 HEMA_I77AB
91.2 Hemagglutinin P03454 HEMA_I33A0
91.3 Hemagglutinin Q0HD60 HEMA_I40A0
93.3 Hemagglutinin A4U6V2 HEMA_I45A0
93.3 Hemagglutinin A4GCK8 HEMA_I43A0
95.8 Hemagglutinin A4GCL9 HEMA_I35A3
96.3 Hemagglutinin A4GCI6 HEMA_I36A0
100.0 Hemagglutinin P03452 HEMA_I34A1