Subtype Classification by Polymerase and Gag Genes of HIV-1 Iranian Sequences Registered in the NCBI GenBank

Author(s): Behzad Dehghani, Zahra Hasanshahi, Tayebeh Hashempour*, Parvin Afsar Kazerooni*

Journal Name: Current Proteomics

Volume 18 , Issue 2 , 2021

Become EABM
Become Reviewer
Call for Editor

Graphical Abstract:


Background: The rate of Human Immunodeficiency Virus type 1 (HIV-1) infection in Iran has increased dramatically in the last few years.

Objective: The aim of this study was to investigate the HIV subtype amongst all Iranian HIV sequences, using 8 websites.

Methods: In this study, 637 sequences of polymerase, and gag genes of HIV-1 were obtained from NCBI. HIV-1 subtyping was done, using 8 reliable software.

Results: The final results of the 8 online tools indicated that the majority of sequences were HIV-1 subtype CRF35 AD. However, it appeared that in some genes, a few programs could not determine specific subtypes and in some cases they described different subtypes.

Conclusion: Considering the CRF35 AD diagram, it was clear that integrase was not an appropriate region to define this subtype. Also the full length of gag gene should be used for subtyping. For CRF1, AE envelop gene is a reliable region to define this subtype. Stanford software was used to determine the drug resistance prevalence and in 5.7% of the sequences, drug resistance mutations were found.

Keywords: HIV, subtyping, bioinformatics, Iran, CRF35 AD, drug resistance.

Dehghani, B.; Dehghani, A.; Sarvari, J. Knowledge and awareness regarding hepatitis B, hepatitis C, and human immunodeficiency viruses among college students: A report from Iran. Int. Q. Community Health Educ., 2020, 41(1), 15-23.
Ghassabi, F. Bacterial etiology and antibiotic resistance pattern of septicemia in HIV and non-HIV patients admitted to tertiary care hospitals, Shiraz, South of Iran. Cellular mol. Boil. (Noisy-le-Grand, France), 2017, 63(9), 115-121.
Ghassabi, F.; Malekzadegan, Y.; Sedigh Ebrahim-Saraie, H.; Heidari, H.; Sabet, M.; Bagheri, A.; Bagheri, N.; Raeisi Shahraki, H.; Hasanabadi, A.; Motamedifar, M. Gonorrhea and syphilis co-infection and related risk factors in HIV patients from Shiraz, South of Iran. Caspian J. Intern. Med., 2018, 9(4), 397-402.
[PMID: 30510656]
Lloyd, S.B.; Kent, S.J.; Winnall, W.R. The high cost of fidelity. AIDS Res. Hum. Retroviruses, 2014, 30(1), 8-16.
[] [PMID: 24180375]
Klimas, N.; Koneru, A.O.B.; Fletcher, M.A. Overview of HIV. Psychosom. Med., 2008, 70(5), 523-530.
[] [PMID: 18541903]
Roques, P.; Robertson, D.L.; Souquière, S.; Damond, F.; Ayouba, A.; Farfara, I.; Depienne, C.; Nerrienet, E.; Dormont, D.; Brun-Vézinet, F.; Simon, F.; Mauclère, P. Phylogenetic analysis of 49 newly derived HIV-1 group O strains: high viral diversity but no group M-like subtype structure. Virology, 2002, 302(2), 259-273.
[] [PMID: 12441070]
Lin, Y-T.; Lan, Y.C.; Chen, Y.J.; Huang, Y.H.; Lee, C.M.; Liu, T.T.; Wong, W.W.; Yang, J.Y.; Wang, C.T.; Chen, Y.M. Molecular epidemiology of HIV-1 infection and full-length genomic analysis of circulating recombinant form 07_BC strains from injection drug users in Taiwan. J. Infect. Dis., 2007, 195(9), 1283-1293.
[] [PMID: 17396997]
Kemal, K.S.; Anastos, K.; Weiser, B.; Ramirez, C.M.; Shi, Q.; Burger, H. Molecular epidemiology of HIV type 1 subtypes in Rwanda. AIDS Res. Hum. Retroviruses, 2013, 29(6), 957-962.
[] [PMID: 23458210]
Hanna, L.E.; Neogi, U.; Ranga, U.; Swaminathan, S.; Prasad, V.R. Phylogenetic characterization of six full-length HIV-1 subtype C molecular clones from three patients: identification of rare subtype C strains containing two NF-κB motifs in the long terminal repeat. AIDS Res. Hum. Retroviruses, 2014, 30(6), 586-591.
[] [PMID: 24387762]
Buonaguro, L.; Tornesello, M.L.; Buonaguro, F.M. Human immunodeficiency virus type 1 subtype distribution in the worldwide epidemic: pathogenetic and therapeutic implications. J. Virol., 2007, 81(19), 10209-10219.
[] [PMID: 17634242]
Odaibo, G.N.; Olaleye, D.O.; Heyndrickx, L.; Vereecken, K.; Houwer, K.; Jassens, W. Mother-to-child transmission of different HIV-1 subtypes among ARV Naïve infected pregnant women in Nigeria. Rev. Inst. Med. Trop. São Paulo, 2006, 48(2), 77-80.
[] [PMID: 16699628]
Abecasis, A.B.; Wensing, A.M.; Paraskevis, D.; Vercauteren, J.; Theys, K.; Van de Vijver, D.A.; Albert, J.; Asjö, B.; Balotta, C.; Beshkov, D.; Camacho, R.J.; Clotet, B.; De Gascun, C.; Griskevicius, A.; Grossman, Z.; Hamouda, O.; Horban, A.; Kolupajeva, T.; Korn, K.; Kostrikis, L.G.; Kücherer, C.; Liitsola, K.; Linka, M.; Nielsen, C.; Otelea, D.; Paredes, R.; Poljak, M.; Puchhammer-Stöckl, E.; Schmit, J.C.; Sönnerborg, A.; Stanekova, D.; Stanojevic, M.; Struck, D.; Boucher, C.A.; Vandamme, A.M. HIV-1 subtype distribution and its demographic determinants in newly diagnosed patients in Europe suggest highly compartmentalized epidemics. Retrovirology, 2013, 10(1), 7.
[] [PMID: 23317093]
Kuiken, C.; Thakallapalli, R.; Esklid, A.; de Ronde, A. Genetic analysis reveals epidemiologic patterns in the spread of human immunodeficiency virus. Am. J. Epidemiol., 2000, 152(9), 814-822.
[] [PMID: 11085392]
Kijak, G.H.; Tovanabutra, S.; Rerks-Ngarm, S.; Nitayaphan, S.; Eamsila, C.; Kunasol, P.; Khamboonruang, C.; Thongcharoen, P.; Namwat, C.; Premsri, N.; Benenson, M.; Morgan, P.; Bose, M.; Sanders-Buell, E.; Paris, R.; Robb, M.L.; Birx, D.L.; De Souza, M.S.; McCutchan, F.E.; Michael, N.L.; Kim, J.H. Molecular evolution of the HIV-1 Thai epidemic between the time of RV144 immunogen selection to the execution of the vaccine efficacy trial. J. Virol., 2013, 87(13), 7265-7281.
[] [PMID: 23576510]
Organization, W.H. WHO, UNODC. UNAIDS technical guide for countries to set targets for universal access to HIV prevention, treatment and care for injecting drug users-2012 revision. 2012.
Dehghani, A.; Dehghani, P.; Dehghani, B. hiv/aids knowledge and attitude among high school students in Shiraz, Iran in 2015. J. Midwifery Reproduct. Health, 2017, 5(2), 897-903.
Baesi, K.; Moallemi, S.; Farrokhi, M.; Alinaghi, S.A.; Truong, H.M. Subtype classification of Iranian HIV-1 sequences registered in the HIV databases, 2006-2013. PLoS One, 2014, 9(9), e105098.
[] [PMID: 25188443]
Keyvani, H. Immunoinformatics study of gp120 of human immunodeficiency virus type 1 subtype CRF35_AD isolated from Iranian patients. Arch. Clin. Infect. Dis., 2016, 11(4)
Hamkar, R.; Mohraz, M.; Lorestani, S.; Aghakhani, A.; Truong, H.M.; McFarland, W.; Banifazl, M.; Eslamifar, A.; Foroughi, M.; Pakfetrat, A.; Ramezani, A. Assessing subtype and drug-resistance-associated mutations among antiretroviral-treated HIV-infected patients. AIDS, 2010, 24(Suppl. 2), S85-S91.
[] [PMID: 20610954]
Dehghani, B.; Hasanshahi, Z.; Hashempour, T. HIV Capsid and protease, new targets of Melittin. Int. J. Pept. Res. Ther., 2020, 26, 2057-2065.
Dehghani, B. The possible regions to design Human Papilloma Viruses vaccine in Iranian L1 protein. Biologia, 2020, 75(5), 749-759.
Hashempour, T. Evaluating drug resistant mutations to HCV NS3 protease inhibitors in iranian Naïve patients. Int. J. Pept. Res. Ther., 2020, 26, 1699-1710.
Musavi, Z. Antibody development to HCV alternate reading frame protein in liver transplant candidate and its computational analysis. Curr. Proteomics, 2020, 17(2), 154-170.
Dehghani, B.; Hashempour, T.; Hasanshahi, Z. Interaction of human herpesvirus 8 viral interleukin-6 with human interleukin-6 receptor using in silico approach: the potential role in HHV-8 pathogenesis. Curr. Proteomics, 2020, 17(2), 107-116.
Dehghani, B. Bioinformatics analysis of domain 1 of HCV-core protein: Iran. Int. J. Pept. Res. Ther., 2020, 26(1), 303-320.
Dehghani, B.; Hashempour, T.; Hasanshahi, Z. Using immunoinformatics and structural approaches to design a novel HHV8 vaccine. Int. J. Pept. Res. Ther., 2020, 26, 321-331.
Dehghani, B. Functional and structural characterization of Ebola virus glycoprotein (1976-2015)—an in silico study. Int. J. Biomath., 2017, 10(08), 1750108.
Moattari, A.; Dehghani, B.; Khodadad, N.; Tavakoli, F. In silico functional and structural characterization of H1N1 influenza a viruses hemagglutinin, 2010-2013, Shiraz, Iran. Acta Biotheor., 2015, 63(2), 183-202.
[] [PMID: 25963671]
van Harmelen, J.; Wood, R.; Lambrick, M.; Rybicki, E.P.; Williamson, A.L.; Williamson, C. An association between HIV-1 subtypes and mode of transmission in Cape Town, South Africa. AIDS, 1997, 11(1), 81-87.
[] [PMID: 9110079]
Iordanskiy, S.; Waltke, M.; Feng, Y.; Wood, C. Subtype-associated differences in HIV-1 reverse transcription affect the viral replication. Retrovirology, 2010, 7(1), 85.
[] [PMID: 20939905]
Kaleebu, P.; Ross, A.; Morgan, D.; Yirrell, D.; Oram, J.; Rutebemberwa, A.; Lyagoba, F.; Hamilton, L.; Biryahwaho, B.; Whitworth, J. Relationship between HIV-1 Env subtypes A and D and disease progression in a rural Ugandan cohort. AIDS, 2001, 15(3), 293-299.
[] [PMID: 11273208]
Vasan, A.; Renjifo, B.; Hertzmark, E.; Chaplin, B.; Msamanga, G.; Essex, M.; Fawzi, W.; Hunter, D. Different rates of disease progression of HIV type 1 infection in Tanzania based on infecting subtype. Clin. Infect. Dis., 2006, 42(6), 843-852.
[] [PMID: 16477563]
Kiwanuka, N.; Laeyendecker, O.; Robb, M.; Kigozi, G.; Arroyo, M.; McCutchan, F.; Eller, L.A.; Eller, M.; Makumbi, F.; Birx, D.; Wabwire-Mangen, F.; Serwadda, D.; Sewankambo, N.K.; Quinn, T.C.; Wawer, M.; Gray, R. Effect of Human Immunodeficiency Virus Type 1 (HIV-1) subtype on disease progression in persons from Rakai, Uganda, with incident HIV-1 infection. J. Infect. Dis., 2008, 197(5), 707-713.
[] [PMID: 18266607]
Sacktor, N.; Nakasujja, N.; Skolasky, R.L.; Rezapour, M.; Robertson, K.; Musisi, S.; Katabira, E.; Ronald, A.; Clifford, D.B.; Laeyendecker, O.; Quinn, T.C. HIV subtype D is associated with dementia, compared with subtype A, in immunosuppressed individuals at risk of cognitive impairment in Kampala, Uganda. Clin. Infect. Dis., 2009, 49(5), 780-786.
[] [PMID: 19622045]
Geretti, A.M.; Harrison, L.; Green, H.; Sabin, C.; Hill, T.; Fearnhill, E.; Pillay, D.; Dunn, D. UK collaborative group on HIV drug resistance. Effect of HIV-1 subtype on virologic and immunologic response to starting highly active antiretroviral therapy. Clin. Infect. Dis., 2009, 48(9), 1296-1305.
[] [PMID: 19331585]
Lee, C.K.; Lee, H.K.; Loh, T.P.; Sethi, S.K.; Koay, E.S.; Tang, J.W. An in-house HIV genotyping assay for the detection of drug resistance mutations in Southeast Asian patients infected with HIV-1. J. Med. Virol., 2012, 84(3), 394-401.
[] [PMID: 22246824]
Kiertiburanakul, S.; Chaiwarith, R.; Sirivichayakul, S.; Ditangco, R.; Jiamsakul, A.; Li, P.C.; Kantipong, P.; Lee, C.; Ratanasuwan, W.; Kamarulzaman, A.; Sohn, A.H.; Sungkanuparph, S. TREAT Asia studies to evaluate resistance surveillance and monitoring studies. Comparisons of primary HIV-1 drug resistance between recent and chronic HIV-1 infection within a sub-regional cohort of Asian patients. PLoS One, 2013, 8(6), e62057.
[] [PMID: 23826076]
Yilmaz, G.; Midilli, K.; Türkoğlu, S.; Bayraktaroğlu, Z.; Kuşkucu, A.M.; Ozkan, E.; Atasever, L.; Calangu, S.; Altaş, K. Genetic subtypes of Human Immunodeficiency Virus type 1 (HIV-1) in Istanbul, Turkey. Int. J. Infect. Dis., 2006, 10(4), 286-290.
[] [PMID: 16516519]
Alexander, C.S.; Montessori, V.; Wynhoven, B.; Dong, W.; Chan, K.; O’Shaughnessy, M.V.; Mo, T.; Piaseczny, M.; Montaner, J.S.; Harrigan, P.R. Prevalence and response to antiretroviral therapy of non-B subtypes of HIV in antiretroviral-naive individuals in British Columbia. Antivir. Ther. (Lond.), 2002, 7(1), 31-35.
[PMID: 12008785]
Delatorre, E.O.; Bello, G. Phylodynamics of HIV-1 subtype C epidemic in east Africa. PLoS One, 2012, 7(7), e41904.
[] [PMID: 22848653]
Tatt, I.D.; Barlow, K.L.; Nicoll, A.; Clewley, J.P. The public health significance of HIV-1 subtypes. AIDS, 2001, 15(Suppl. 5), S59-S71.
[] [PMID: 11816176]
Khoja, S.; Ojwang, P.; Khan, S.; Okinda, N.; Harania, R.; Ali, S. Genetic analysis of HIV-1 subtypes in Nairobi, Kenya. PLoS One, 2008, 3(9), e3191.
[] [PMID: 18784834]
Siemieniuk, R.A.; Beckthold, B.; Gill, M.J. Increasing HIV subtype diversity and its clinical implications in a sentinel North American population. Can. J. Infect. Dis. Med. Microbiol., 2013, 24(2), 69-73.
[] [PMID: 24421804]
Rolland, M.; Modjarrad, K. Multiple co-circulating HIV-1 subtypes in the Middle East and North Africa. AIDS, 2015, 29(11), 1417-1419.
[] [PMID: 26091303]
Baesi, K. Phylogeny and drug resistance of HIV PR gene among HIV patients receiving RT inhibitors in Iran. Asian Pac. J. Trop. Biomed., 2016, 6(5), 451-454.
Baesi, K. Drug resistance profile and subtyping of HIV-1 RT gene in Iranian patients under treatment. Iranian J. Biotechnol., 2012, 10(1), 1-7.
Naderi, H.R.; Tagliamonte, M.; Tornesello, M.L.; Ciccozzi, M.; Rezza, G.; Farid, R.; Buonaguro, F.M.; Buonaguro, L. Molecular and phylogenetic analysis of HIV-1 variants circulating among injecting drug users in Mashhad-Iran. Infect. Agent. Cancer, 2006, 1(1), 4.
[] [PMID: 17150133]
Sarrami-Forooshani, R.; Das, S.R.; Sabahi, F.; Adeli, A.; Esmaeili, R.; Wahren, B.; Mohraz, M.; Haji-Abdolbaghi, M.; Rasoolinejad, M.; Jameel, S.; Mahboudi, F. Molecular analysis and phylogenetic characterization of HIV in Iran. J. Med. Virol., 2006, 78(7), 853-863.
[] [PMID: 16721846]
Tagliamonte, M.; Naderi, H.R.; Tornesello, M.L.; Farid, R.; Buonaguro, F.M.; Buonaguro, L. HIV type 1 subtype A epidemic in Injecting Drug User (IDU) communities in Iran. AIDS Res. Hum. Retroviruses, 2007, 23(12), 1569-1574.
[] [PMID: 18160015]
Eybpoosh, S. Spatio-temporal dynamics of HIV-I subtype B and circulating recombinant form 01_AE clades in Iran: a phylogeographic approach. Iran. Red Crescent Med. J., 2017, 19(2), e34609.
Eybpoosh, S.; Bahrampour, A.; Karamouzian, M.; Azadmanesh, K.; Jahanbakhsh, F.; Mostafavi, E.; Zolala, F.; Haghdoost, A.A. Spatio-temporal history of HIV-1 CRF35_AD in Afghanistan and Iran. PLoS One, 2016, 11(6), e0156499.
[] [PMID: 27280293]
Mousavi, S.M.; Hamkar, R.; Gouya, M.M.; Safaie, A.; Zahraei, S.M.; Yazdani, Z.; Asbaghi Namini, S.; Bertagnolio, S.; Sutherland, D.; Sandstrom, P.; Brooks, J. Surveillance of HIV drug resistance transmission in Iran: experience gained from a pilot study. Arch. Virol., 2010, 155(3), 329-334.
[] [PMID: 20052598]
Jahanbakhsh, F.; Hattori, J.; Matsuda, M.; Ibe, S.; Monavari, S.H.; Memarnejadian, A.; Aghasadeghi, M.R.; Mostafavi, E.; Mohraz, M.; Jabbari, H.; Kamali, K.; Keyvani, H.; Azadmanesh, K.; Sugiura, W. Prevalence of transmitted HIV drug resistance in Iran between 2010 and 2011. PLoS One, 2013, 8(4), e61864.
[] [PMID: 23626742]
Farrokhi, M.; Moallemi, S.; Baesi, K.; Ahsani-Nasab, S.; Gholami, M.; Sadeghi, L.; Mohraz, M. HIV drug resistance and phylogeny profile in naive and antiretroviral-experienced patients in Tehran, Iran. Intervirology, 2016, 59(3), 131-136.
[] [PMID: 27974715]

Rights & PermissionsPrintExport Cite as

Article Details

Year: 2021
Published on: 10 May, 2020
Page: [153 - 161]
Pages: 9
DOI: 10.2174/1570164617999200510233018
Price: $25

Article Metrics

PDF: 101