Abstract
The generation of genetic diversity is a fundamental characteristic of HIV-1 replication, allowing the virus to successfully evade the immune response and antiviral therapies. Although mutations are the first step towards diversity, mixing of the mutations through the process of recombination increases the variation and allows for the faster establishment of advantageous strains within the viral population. Therefore, studying recombination of HIV-1 provides insights into not only the mechanisms of HIV-1 replication but also into the potential for spread of antiviral drug resistance mutations within and across viral subtypes. This chapter describes, in detail, a highly sensitive recombination assay designed to measure the frequency of recombination between two viruses. This assay allows us to investigate the requirements, mechanisms, and final products of recombination. Additionally, software-based phylogenetic tools are described in this chapter, which allow for the identification of specific recombination events within patient samples or viral progeny from the recombination assay.
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Acknowledgments
We thank Dr. Jianbo Chen for reading of this chapter; Drs. Vinay K. Pathak, Jianbo Chen, and Olga Nikolaitchik for intellectual input and discussions.
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© 2008 Humana Press, a part of Springer Science+Business Media, LLC
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Moore, M.D., Chin, M.P.S., Hu, WS. (2008). HIV-1 Recombination: An Experimental Assay and a Phylogenetic Approach. In: Prasad, V.R., Kalpana, G.V. (eds) HIV Protocols. Methods In Molecular Biology™, vol 485. Humana Press. https://doi.org/10.1007/978-1-59745-170-3_7
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DOI: https://doi.org/10.1007/978-1-59745-170-3_7
Publisher Name: Humana Press
Print ISBN: 978-1-58829-859-1
Online ISBN: 978-1-59745-170-3
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