Subscribe to our Newsletter and get informed about new publication regulary and special discounts for subscribers!

ILNS > ILNS Volume 7 > Identifying Overlapping Phylogenetic and...
< Back to Volume

Identifying Overlapping Phylogenetic and Geographic Roots of HIV – 1 Evolution through Computational Analyses

Full Text PDF


HIV-1 or Human Immuno Deficiency Virus-1 is the main causative agent of Acquired Immuno Deficiency Syndrome (AIDS). Human host infected with HIV - 1 extensively harbours many viral variants but very little is known about the difference in pattern[17] of evolution of phylogenetic lineages of HIV-1 non recombinant, normal inter subtype recombinant and main two specific recombinant forms of HIV-1 i.e., Circulating Recombinant Forms (CRFs) and Unique Recombinant Forms (URFs). This study is mainly concerned with study of the difference in evolutionary lineages of non-recombinant and recombinant sequences of HIV-1 genome sequences and identification of geographically rich areas which has reported high degree of HIV-1 occurrence and variety. Total 1550 HIV-1 genome sequences were obtained from HIV Los Alamos Database. The sequences were aligned using MAFFT (Multiple Alignment using Fast Fourier Transform) web server tool. Alignment was carried out using 10 different set of alignment parameter values. After alignment the aligned file was used for constructing N-J phylogenetic tree using Clustal X2 tool. Phylogenetic analysis was performed keeping in mind the category to which the sequence belongs. Upon analysis it was observed that the clade containing the probable ancestor belongs remained constant in all cases of different alignment values. Non recombinant isolates, inter subtype recombinants, CRFs, URFs all followed different patterns of evolution. Non recombinant sequences were found geographically specific and subtype specific to some extent whereas, normal recombinants were subtype specific and less geographically specific. CRFs showed variation among the pattern of their evolution. At some instances the sequences occurred as sister taxa of non-recombinant or normal inter subtype recombinant sequences, while at some instances as sister taxa of other CRFs where they were geographically specific. Three CRFs existed as completely diverged sequences. URFs were four in number; two of them were Indian isolates of while other two were Japanese isolates. URFs were found to be totally geographically specific. Geography wise high rate of variation was observed in India and Japan as these two countries had sequences belonging to all of the above categories. Cameroon and South Africa have very large number isolates and a considerable amount of genetic variation among isolates but they lack URFs.


International Letters of Natural Sciences (Volume 7)
P. K. Singh et al., "Identifying Overlapping Phylogenetic and Geographic Roots of HIV – 1 Evolution through Computational Analyses", International Letters of Natural Sciences, Vol. 7, pp. 23-29, 2014
Online since:
December 2013

Huson D. H., Bryant D., Mol Biol Evol. 23(2) (2006) 254-67.

T. L. Goldberg, Preventive Veterinary Medicine 61 (2003) 59-70.

Ling Su, et al, Journal of Virology (2000) 11367-11376.

Larkin M. A., et al, Bioinformatics 23 (2007) 2947-2948.

Kristen Chalmet, et al, BMC Infectious Diseases 10 (2010) 262.

Gaschen B., Kuiken C., Korber B., Foley B., Bioinformatics 17(5) (2001) 415-8.

Katoh Standley, Molecular Biology and Evolution 30 (2013) 772-780.

http: /www. hiv. lanl. gov/content/sequence/HIV/REVIEWS/HXB2. html.

Sonia Resik, et al, Aids Research And Human Retroviruses 23(3) (2007) 347-356.

H. R. Naderi, et al, Infectious Agents and Cancer 1 (2006) 4.

Sabri Saeed Sanabani, et al, Virology Journal 2009, doi: 10. 1186/1743-422X-6-78.

English, et al. Retrovirology 8 (2011) 54.

Dong-Hun Lee1, Yeup Yoon, Chan-Hee Lee1, The Journal of Microbiology (2003) 232-238.

N. Pierre Roque, et al, AIDS 18 (2004) 1371-1381.

Liam J. Revell, Luke J. Harmon, David C. Collar, Journal: Systematic Biology - SYST BIOL 57(4) (2008) 591.

Gouy M., Guindon S., Gascuel O., Molecular Biology and Evolution 27(2) (2010) 221-224.

Philippe Lemey, et al, PLoS Computational Biology 3(2) (2007) e29.

Saitou N., Nei M., Mol Biol Evol. 4(4) (1987) 406-25.

W. M. Fitch, Phil. Trans. R. Soc. Land. B 349 (1995) 93-102.

Perrière G., Gouy M., Biochimie 78 (1996) 364-369. ( Received 02 December 2013; accepted 07 December 2013 ).

Show More Hide
Cited By:
This article has no citations.