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. 2013 Mar 1;14(3):5013–5024. doi: 10.3390/ijms14035013

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© 2013 by the authors; licensee MDPI, Basel, Switzerland.

This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).

PMC Copyright notice

Recombination analysis of 08BBVCT28ZA IN gene. In 2A & 2B, sequence assignment and bootscanning with REGA was done to determine possible recombination in the integrase gene (bootscanning, window size of 400 and step size 20). 2A shows the sequence as subtype C; 2B shows the bootscanning analysis of the recombination breakpoints with a bootstrap value of more than 70%. The results show that the sequence has a mosaic structure consisting of HIV-1 A1 alternating with a subtype C sequence, suggesting that the virus is a recombinant on the IN gene.