Genotyping HIV-1 non-B subtypes in Ireland: comparison of env and pol methods

Abstract number: 1134_01_275

Goins L., Coughlan S., Fitzpatrick F., Bergin C., Mulcahy F., Sheehan G., Hall W.W.

Characterisation of HIV-1 subtypes provides important epidemiological information and also has a potential impact on diagnosis, and therapy. The dominant HIV-1 strain in Ireland is subtype B, however other strains have also been identified. Most subtyping in our institution is performed using pol nucleotide sequence analysis.

Aims:  

To establish methods for amplification and subtyping of HIV-1 env (V3 region) gene and to compare pol and env genotypes in non subtype B HIV-1 samples.

Methods:  

HIV-1 viral pol sequences of stored samples were obtained and an approximate subtype assigned using the online HIV-1 Genotyping Tool (http://www.ncbi.nlm.nih.gov/projects/genotyping/formpage.cgi). 25 samples (viral loads 440–500,000 copies/ml) containing non subtype B viral pol regions were chosen for further analysis. Viral RNA from the env region of each sample was amplified and nucleotide sequences generated. The env and pol sequences were inputted into the above online genotyping tool, sequences were aligned using ClustalW and a neighbor-joining phylogenetic tree was created. (Joe Feldstein, http://evolution.genetics.washington.edu/phylip.html).

Results:  

15 subtype categories were defined by pol genotyping. When compared to env genotyping, four samples (16%) had the same, fourteen (56%) similar and seven (28%) samples possessed divergent env and pol genotypes.

Conclusion:  

We have developed a feasible method for obtaining env V3 region sequence and subtype data. Only 16% of samples tested possessed truly the ‘same’ subtype. Overall, data presented in this study illustrates that subtyping based on simply the pol or env region may overlook interesting nuances of subtype variation and recombination and therefore efficient and effective methods for rapid subtyping of both regions, must continue to be developed. Larger studies may provide a clearer picture of the similarity between pol and env region genotypes. Such data could prove to be a helpful tool for more thorough and comprehensive analyses of patient subtype distributions.