Link to the Abstract(Pubmed)

Bibliography ------

 Aissani, B., Shrestha, S., Wiener, H. W., Tang, J., Kaslow, R. A., & Wilson, C. M. (2014). Mitochondrial DNA variation and virologic and immunological HIV outcomes in African Americans. AIDS, 28(13), 1871- 1878.10.1097/QAD.0000000000000371.  Link to the abstract(PubMed): https://www.ncbi.nlm.nih.gov/pubmed/24932613  PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5004594/  Publisher Full Text (HTML): http://journals.lww.com/aidsonline/pages/articleviewer.aspx? year=2014&issue=08240&article=00003&type=abstract  Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5004594/pdf/nihms- 811646.pdf  Rights and availability: o The authors reserve copyright o Open Access article o Free  Publisher: HH Public Access o Open Access organization  Availability: Online Only  Did LMU pay a fee for this article: No  This article is related to the research project because of the profuse amount of data that influences divergence outcomes in respect to mitochondria.

 English, S., Katzourakis, A., Bonsall, D., Flanagan, P., Duda, A., Fidler, S., … Frater, J. (2011). Phylogenetic analysis consistent with a clinical history of sexual transmission of HIV-1 from a single donor reveals transmission of highly distinct variants. Retrovirology, 8, 54. http://doi.org/10.1186/1742-4690-8-54  Link to the abstract(PubMed): https://www.ncbi.nlm.nih.gov/pubmed/21736738  Link to full text (PubMedCentral): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161944/  Link to full text (Publisher’s site): http://retrovirology.biomedcentral.com/articles/10.1186/1742-4690-8- 54  Link to PDF: http://download.springer.com/static/pdf/917/art%253A10.1186%252F1742-4690-8-54.pdf? originUrl=http%3A%2F%2Fretrovirology.biomedcentral.com%2Farticle%2F10.1186%2F1742-4690-8- 54&token2=exp=1475017816~acl=%2Fstatic%2Fpdf%2F917%2Fart%25253A10.1186%25252F1742-4690- 8-54.pdf*~hmac=07b573bf4ef4005c3619fe03cf83330dd818c690b49c991853835224112d74e8  Rights and availability: o The authors reserve copyright (on PDF) o Open Access article o Free  Publisher: BioMed Central o Open Access organization  Availability: o Online only  Did LMU pay a fee for this article: Yes; but the article is >6 months old.  This article is related to the research project because it orients and presents the same parameters of the project in the same way as the Markham paper. The divergence relationships are clearly noted and support the same relationship of CD4-T decline and divergence.  Ward, A. B., & Wilson, I. A. (2015). Insights into the trimeric HIV-1 envelope glycoprotein structure. Trends in biochemical sciences, 40(2), 101-107. https://dx.doi.org/10.1016%2Fj.tibs.2014.12.006  Link to the abstract (PubMed): https://www.ncbi.nlm.nih.gov/pubmed/25600289  Link to Full Text PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310573/  Link to Full Text Publisher’s site: http://www.sciencedirect.com/science/article/pii/S0968000414002333  Publisher Full Text (PDF): http://ac.els-cdn.com/S0968000414002333/1-s2.0-S0968000414002333- main.pdf?_tid=a208bc40-89c8-11e6-80cd- 00000aacb361&acdnat=1475540728_b4571047e41c0aa6efe64a64f0c8c9ef  Rights and availability: o Copyright © 2015 Elsevier Ltd. All rights reserved. o Not Open Access o Article is available 6 months after publication  Publisher: Trends in biochemical sciences o Journal  Availability: print and online  Did LMU pay a fee: yes; LMU subscribes to this journal, but since this review paper is >6 months old, we could have gotten access anyway.  This review paper is useful to the research because they collect multiple accounts of the env gene and its relative changes in respect to divergence.

 Zhao, J., Nie, J., Jiao, Y., Li, L., Zhang, T., Liu, Q., ... & Wang, Y. (2016). Effect of the maturation of neutralizing antibodies on human immunodeficiency virus (HIV) envelope evolution in HIV-infected subjects.Infection, Genetics and Evolution, 38, 82-89. https://dx.doi.org/10.1016/j.meegid.2015.12.012  Link to the abstract (PubMed): https://www.ncbi.nlm.nih.gov/pubmed/26706846  Link to Full Text PubMed Central: N/A  Link to Full Text Publisher’s site: http://www.sciencedirect.com/science/article/pii/S1567134815300770  Publisher Full Text (PDF): http://ac.els-cdn.com/S1567134815300770/1-s2.0-S1567134815300770- main.pdf?_tid=35d29058-89c5-11e6-ab03- 00000aab0f26&acdnat=1475539258_cbf2fc106472909cdfee3e78309116d6  Rights and availability: o The 2015 Elsevier B.V. All rights reserved o Not Open Access o Article is available 6 months after publication  Publisher: Infection, Genetics and Evolution o Journal  Availability: print and online  Did LMU pay a fee for this article: yes; LMU subscribes to this journal, but since the article is >6 months old, we could have gotten access anyway.  This article is relevant because it is detail-oriented regarding the envelope protein structure and its changes with respect to mutations and divergence.