Skip to main content

Comparative codon usage analysis of HIV-1 and HIV-2 genomes

Background

Compared to HIV-1, HIV-2 infection is associated with slower disease progression and transmission, longer latency period and low or undetectable plasmatic viral levels. In an attempt to understand underlying reasons for the varying pathogenicity between HIV-1 and HIV-2 at the molecular level, we analyzed the differences in codon usage pattern of all nine coding genes.

Materials and methods

Thirty five full length HIV-2 genome sequences deposited during the period 1986-2008 were downloaded from LANL. The effective number of codons (NC), GC, GC3s and Relative Synonymous Codon Usage data corresponding to each gene were calculated using Codon W and Correspondence analysis (CA).

Results

The NC for all the nine genes ranged from 43 – 55.2, indicating that the genes of HIV-2 are also poorly biased, as has been reported earlier for HIV-1, resulting in low levels of expression of these proteins in general. The NC value of the tat gene of HIV-2 was higher than that HIV-1. The CA of all nine genes revealed that the factors influencing the expression of different genes were not the same.

Conclusion

The codon usage pattern of HIV-2 is distinctly different from that of HIV-1, and appears to be majorly shaped by the genomic composition rather than translational selection. The high Nc value of tat is suggestive of a lower level of expression of the protein in HIV-2 as compared to HIV-1, implying that this could be one of the viral factors responsible for lower levels of HIV-2 replication and delayed disease progression.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to LE Hanna.

Rights and permissions

Open Access  This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.

The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.

To view a copy of this licence, visit https://creativecommons.org/licenses/by/4.0/.

The Creative Commons Public Domain Dedication waiver (https://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Vidyavijayan, K., Hassan, S., Precilla, L. et al. Comparative codon usage analysis of HIV-1 and HIV-2 genomes. BMC Infect Dis 14 (Suppl 3), E2 (2014). https://doi.org/10.1186/1471-2334-14-S3-E2

Download citation

  • Published:

  • DOI: https://doi.org/10.1186/1471-2334-14-S3-E2

Keywords