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Co-evolution networks of HIV/HCV are modular with direct association to structure and function

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  • Ahmed Abdul Quadeer
  • David Morales-Jimenez
  • Matthew R McKay

Abstract

Mutational correlation patterns found in population-level sequence data for the Human Immunodeficiency Virus (HIV) and the Hepatitis C Virus (HCV) have been demonstrated to be informative of viral fitness. Such patterns can be seen as footprints of the intrinsic functional constraints placed on viral evolution under diverse selective pressures. Here, considering multiple HIV and HCV proteins, we demonstrate that these mutational correlations encode a modular co-evolutionary structure that is tightly linked to the structural and functional properties of the respective proteins. Specifically, by introducing a robust statistical method based on sparse principal component analysis, we identify near-disjoint sets of collectively-correlated residues (sectors) having mostly a one-to-one association to largely distinct structural or functional domains. This suggests that the distinct phenotypic properties of HIV/HCV proteins often give rise to quasi-independent modes of evolution, with each mode involving a sparse and localized network of mutational interactions. Moreover, individual inferred sectors of HIV are shown to carry immunological significance, providing insight for guiding targeted vaccine strategies.Author summary: HIV and HCV cause devastating infectious diseases for which no functional vaccine exists. A key problem is that while individual mutations in viral epitopes under immune pressure may substantially compromise viral fitness, immune escape is typically facilitated by other “compensatory” mutations that restore fitness. These compensatory pathways are complicated and remain poorly understood. They do, however, leave co-evolutionary markers which may be inferred from measured sequence data. Here, by introducing a new robust statistical method, we demonstrated that the compensatory networks employed by both viruses exhibit a remarkably simple decomposition involving small and near-distinct groups of protein residues, with most groups having a clear association to biological function or structure. This provides insights that can be harnessed for the purpose of vaccine design.

Suggested Citation

  • Ahmed Abdul Quadeer & David Morales-Jimenez & Matthew R McKay, 2018. "Co-evolution networks of HIV/HCV are modular with direct association to structure and function," PLOS Computational Biology, Public Library of Science, vol. 14(9), pages 1-29, September.
  • Handle: RePEc:plo:pcbi00:1006409
    DOI: 10.1371/journal.pcbi.1006409
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    References listed on IDEAS

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    4. Marko Novinec & Matevž Korenč & Amedeo Caflisch & Rama Ranganathan & Brigita Lenarčič & Antonio Baici, 2014. "A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods," Nature Communications, Nature, vol. 5(1), pages 1-10, May.
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    Cited by:

    1. Hang Zhang & Ahmed Abdul Quadeer & Matthew R. McKay, 2023. "Direct-acting antiviral resistance of Hepatitis C virus is promoted by epistasis," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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