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Commentary · Volume 2, Issue 4, 3 October 2015 · Open Access

Intra-Host Bayesian Phylogeography Linking Viral Evolution and Pathogenesis Comes to an Age

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Affiliations & Notes ⌄
  1. 1Department of Pathology, Immunology, and Laboratory Medicine
  2. 2Emerging Pathogens Institute, University of Florida,, Gainesville, FL 32610, USA
Article Info ⌄
Journal:
Hosts and Viruses
Published:
3 October 2015
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From the article

  • Intra-Host Bayesian Phylogeography Linking Viral Evolution and Pathogenesis Comes to an Age.
  • Infection of a single host can be viewed similarly as an epidemic spread on a microscale, creating a unique opportunity for the application of phylogeography at the intra-host level, which has until recently been limited by dataset quality and the lack of a rigorous statistical framework.
  • Therefore, incorporation of spatial and temporal information – i.e. tissue/cell of origin and sampling time of viral sequences – into the evolutionary analysis is crucial for understanding how viral population dynamics are ultimately linked to disease.
  • The intra-host evolutionary and population dynamics of human immunodeficiency virus type 1: a phylogenetic perspective.

Selected from the article's own text.

Abstract

Bayesian phylogeographic analysis has recently been at the forefront of understanding epidemiological processes through the reconstruction of evolutionary history and spatial dissemination of pathogens. Infection of a single host can be viewed similarly as an epidemic spread on a microscale, creating a unique opportunity for the application of phylogeography at the intra-host level, which has until recently been limited by dataset quality and the lack of a rigorous statistical framework. As recently described in studies using the SIV-macaque model of neuroAIDS, the incorporation of
spatial, temporal, and demographic inference into intra-host evolutionary analysis using Bayesian phylogeography allows for inference of pathogen migration between infected tissues and cell types, provides valuable insight into immunopathological processes, and ultimately paves the way for a better understanding of the interplay between viral evolution and pathogenesis.

ACKNOWLEDGEMENTS

BDR and MS were supported by National Institutes of Health funding grants R01 NS063897-01A2.

Figures

Figure 1
Figure 1.

Schematic representation of the intra-host phylogeography framework.

References

  1. Bielejec, F., Rambaut, A., Suchard, M.A., Lemey, P. (2011). SPREAD: Spatial Phylogenetic Reconstruction of Evolutionary Dynamics. Bioinformatics 27. 2910-12. http://dx.doi.org/10.1093/bioinformatics/btr481[CrossRef]
  2. Burdo, T.H., Lackner, A., Williams, K.C. (2013). Monocyte/macrophages and their role in HIV neuropathogenesis. Immunology Reviews 254, 102-13. http://dx.doi.org/10.1111/imr.12068[CrossRef]
  3. Burdo, T.H., Soulas, C., Orzechowski, K,. Button, J., Krishnan, A., Sugimoto, C., Alvarez, X., Kuroda, M.J., Williams, K.C. (2010) Increased monocyte turnover from bone marrow correlates with severity of SIV encephalitis and CD163 levels in plasma. PLoS Pathogens 6, e1000842. http://dx.doi.org/10.1371/journal.ppat.1000842[CrossRef]
  4. Coombs RW, Speck CE, Hughes JP, Lee, W. Sampoleo, R., Ross, S.O., Dragavon, J., Peterson, G., Hooton, T.M., Collier, A.C., Corey, L., Koutsky, L., Krieger, J.N. (1998). Association between culturable human immunodeficiency virus type 1 (HIV-1) in semen and HIV-1 RNA levels in semen and blood: evidence for compartmentalization of HIV-1 between semen and blood. Journal of Infectious Diseases 177, 320-30. http://dx.doi.org/10.1086/514213[CrossRef]
  5. Drummond, A.J., Ho, S.Y., Phillips, M.J. Rambaut, A. (2006). Relaxed phylogenetics and dating with confidence. PLoS Biology 4, e88. http://dx.doi.org/10.1371/journal.pbio.0040088[CrossRef]
  6. Faria, N.R. Suchard, M.A., Rambaut, A., Lemey, P. (2011). Toward a quantitative understanding of viral phylogeography. Current Opinions in Virology 1, 423-9. http://dx.doi.org/10.1016/j.coviro.2011.10.003[CrossRef]
  7. Gray, R.R., Salemi, M., Lowe, A., Nakamura, K.J., Decker, W.D., Sinkala, M., Mulligan, C.J., Thea, D.M., Kuhn, L., Aldrovandi, G., Goodenow, M.M. (2011). Multiple independent lineages of HIV-1 persist in breast milk and plasma. AIDS 25, 143- 52. http://dx.doi.org/10.1097/QAD.0b013e328340fdaf[CrossRef]
  8. Gray, R.R., Salemi, M., Klenerman, P., Pybus, O.G. (2012a). A new evolutionary model for hepatitis C virus chronic infection. PLoS Pathogens 8, e1002656. http://dx.doi.org/10.1371/journal.ppat.1002656[CrossRef]
  9. Gray, R.R., Strickland, S.L., Veras, N.M.C., Goodenow, M.M., Pybus, O.G., S. Lemon, M., Fried, M.W., Nelson, D.R., Salemi, M. (2012b). Unexpected Maintenance of Hepatitis C Viral Diversity Following Liver Transplantation. Journal of Virology 86, 8432-9. http://dx.doi.org/10.1128/JVI.00749-12[CrossRef]
  10. Haeckel, E. (1876). The History of Creation: Or the Development of the Earth and Its Inhabitants by the Action of Natural Causes. London: King.
  11. Korber, B.T., Kunstman, K.J., Patterson, B.K., Furtado, M., McEvilly, M.M., Levy, R., Wolinsky, S.M. (1994). Genetic differences between blood- and brain-derived viral sequences from human immunodeficiency virus type 1-infected patients: evidence of conserved elements in the V3 region of the envelope protein of brain-derived sequences. Journal of Virology 68, 7467-81.
  12. Lemey, P., Rambaut, A., Drummond, A.J., Suchard, M.A. (2009). Bayesian phylogeography finds its roots. PLoS Computational Biology 5, e1000520. http://dx.doi.org/10.1371/journal.pcbi.1000520[CrossRef]
  13. Lemey, P., Rambaut, A., Welch, J.J., Suchard, M.A. (2010). Phylogeography takes a relaxed random walk in continuous space and time. Molecular Biology & Evolution 27, 1877-85. http://dx.doi.org/10.1093/molbev/msq067[CrossRef]
  14. Minin, V.N., Bloomquist, E.K., Suchard, M.A. (2008). Smooth Skyride through a rough Skyline: Bayesian coalescent-based inference of population dynamics. Molecular Biology & Evolution 25. 1458-71. http://dx.doi.org/10.1093/molbev/msn090[CrossRef]
  15. Salemi, M. (2013). The intra-host evolutionary and population dynamics of human immunodeficiency virus type 1: a phylogenetic perspective. Infectious Disease Reports 5, s1e3. http://dx.doi.org/10.4081/idr.2013.s1.e3[CrossRef]
  16. Strickland, S.L., Rife, B.D., Lamers, S.L., Nolan, D.J., Veras, N.M., Prosperi, M.C., Burdo, T.H., Autissier, P., Nowlin, B., Goodenow, M.M., Suchard, M.A., Williams, K.C., Salemi, M. (2014). Spatiotemporal dynamics of simian immunodeficiency virus brain infection in CD8+ lymphocyte-depleted rhesus macaques with neuroAIDS. Journal of General Virology 95, 2784-95. http://dx.doi.org/10.1099/vir.0.070318-0[CrossRef]

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