Subtypes and phylogenetic analysis of human immunodeficiency virus-1 in Jayapura

Main Article Content

Mirna Widiyanti
Tri Wibawa
Holy Arif Wibowo

Abstract

BACKGROUND Human immunodeficiency virus (HIV) is a retrovirus that infects human immune system. HIV is genetically differentiated into HIV-1 and HIV-2. HIV- 1 is classified into 3 groups : M,N and O. M Group is divided into 9 subtypes, namely : A, B, C, D, F, G, H, J and K. HIV subtype mapping would become a good reference to study the epidemiology of HIV-1. HIV phylogenetic analysis required to understand virus origin, geographical distribution and tracking parameter of HIV transmission process in sample area. The objective of this study was to determine HIV-1 subtype distribution and the relationship between HIV-1 subtypes from with genBank HIV isolate based on envelope gene fragment. METHODS A cross setional design was conducted involving 36 subjects in Jayapura between January to March 2013. Blood samples were taken and analyzed using reverse transcription polymerase chain reaction (RT-PCR), nested PCR and confirmed with sequencing. Phylogenetic analysis performed along 400 bp of envelope gene fragment. The data were analyzed with Bioedit ver.7 and MEGA 5.1. software. RESULT Two types of HIV-1 subtype were found in Jayapura Regency. CRF01_AE was confirmed in 31 patients (86.1%) and subtype B in 5 patients (13.9%). Phylogenetic analysis showed phylogenetic relationship between CRF01_AE from jayapura with subtype from Singapore and Thailand, while subtype B from Jayapura were closely related with subtype from United States and United Kingdom CONCLUSION This study reflect the independent introduction of multiple HIV-1 strains into Papua, with the rapid spread in the majority of infected patients tested of single strain of HIV-1 (CRF01_AE).

Article Details

How to Cite
Widiyanti, M., Wibawa, T., & Wibowo, H. A. (2014). Subtypes and phylogenetic analysis of human immunodeficiency virus-1 in Jayapura. Universa Medicina, 33(1), 49–57. https://doi.org/10.18051/UnivMed.2014.v33.49-57
Section
Review Article

References

Grant I, Sacktor N, McArthur J. HIV

neurocognitive disorders. In: Gendelman HE,

Grant I, Everall I, Lipton SA, Swindells S,

editors. The neurology of AIDS. 2nd ed. London:

Oxford University Press;2005.p.357-70.

Buonaguro L, Tornesello ML, Buonaguro FM.

Human immunodeficiency virus type 1 subtype

distribution in the worldwide epidemic:

pathogenetic and therapeutic implications. J

Virol 2007;81:10209-19.

World Health Organization United Nations

AIDS. HIV prevalence map: a global view of

HIV infection;2010. Available at: http://www.

unaids.org. Accessed February 25, 2014.

Abecasis AB, Annemarie MW, Dimitri P, Jurgen

V. HIV-1 subtype distribution and its

demographic determinants in newly diagnosed

patients in Europe suggest highly

compartementalized epidemic. Retrovirology

;10:1-13.

Yebra G, Mulder, Holguin A. Description of HIV-

group M molecular epidemiology and drug

resistance prevalence in Equatorial Guinea from

migrants in Spain. Plos One 2013;8:e64293.

Djoko DF, Rimoin AW, Vidal N, Tamoufe U,

Wolfe ND, Butel C, et al. High HIV-1 type 1

group M Pol diversity and low rate of

antiretroviral resistance mutations among the

Uniformed Services in Kinshasa Democratic

Republic of the Congo. AIDS Res Hum

Retroviruses 2011;27:323-9.

Chaplin B, Elisen G, Idoko J, Onwujekwa D.

Impact of HIV type-1 subtype on drug resistance

mutation in Nigeria patients failing first-line

theraphy. AIDS Res Hum Retroviruses 2011;27:

-80.

Buonaguro L, Tagliamonte M, Tornesello ML,

Buonaguro FM. Genetic and phylogenetic

evolution of HIV-1 in a low subtype

heterogenecity epidemic: the Italian example.

Retrovirology 2007;4:341-9.

Los Alamos National Laboratory. HIV

circulating recombinant forms (CRFs); 2012.

Available at: http://www.hiv.lanl.gov/content/

sequence/HIV/CRFs/CRFs.html. Accessed July

, 2012.

Boonchawalit B, Jullaksorn D, Uttiyong J,

Yowang A. Molecular evolution of HIV-1

CRF01_AE env in Thai patients. Plos One 2011;

:1-11.

Srisuphanut M, Sukeepaisarnchaeron W,

Kucherer C, Pauli G. Epidemiology of HIV-1

subtypes in infected patients from Northeastern

Thailand. Southeast Asian J Tropmed Public

Health 2004;35:641-6.

Direktorat Jenderal Pemberantasan Penyakit

Menular dan Penyehatan Lingkungan. Statistik

kasus HIV/AIDS di Indonesia. Jakarta:

Kementerian Kesehatan RI.;2013.

Dinas Kesehatan Provinsi Papua. Statistik kasus

HIV/AIDS di Papua. Jayapura: Bidang

Pemberantasan Penyakit Menular; 2012.

Wibowo HA, Setyawaty V, Salwati E.

Epidemiologi molekuler genotipe HIV-1 pada

ODHA di Jawa Timur dan DKI Jakarta. Buletin

Penelitian Kesehatan 2011;39:1-9.

Santoro MM, Perno CF. HIV-1 genetic variability

and clinical implication. ISRN Microbiology

Article ID 481314, 20 pages. doi.org/10.

/2013/481314.

Zhang H, Hoffman F, He J, He X, Kankasa C,

West JT, et al. Characterization of HIV-1 subtype

C envelope glycoproteins from perinatally

infected childrens with different courses of

disease. Retrovirology 2006;3:1-15.

Foley B. Donegan E, Silitonga N, Wignall F,

Busch M, Delwart E. Importation of multiple

HIV type 1 strains into West Papua Indonesia

(Irian Jaya). AIDS Res Hum Retroviruses 2001;

:1655-9.

Gifford RJ. Oliveira T, Rambat A, Pybus OG,

Dunn D, Vandamme AM, et al. Phylogenetic

surveillance of viral genetic diversity and the

envolving molecular epidemiology of HIV type

J Virol 2007;81:13050-6.

Michu E. A short to phylogeny reconstruction.

Plant Soil Environ 2007;53:442-6.

Harrison CJ, Langdale JA. Techniques for

molecular analysis: a step by step guide to

phylogeny reconstruction. Plant J 2006;45:561-