Multiple Enhancer Motifs in HIV Type 1 Strains from Ethiopia

Johansson, Bo; Sherefa, Kimdar; Sönnerborg, Anders

doi:10.1089/aid.1995.11.761

Cited by 27 publications

(12 citation statements)

References 10 publications

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“…Primer N417R was specifically designed to exploit the features conserved within and flanking the NF-B motif. While most subtype C viruses contain three NF-B sites in their LTRs (17,20,21,32), a number of them have been reported to possess an additional fourth motif that resembles an NF-B site (18,31,46). Although the functional significance of these additional NF-B sites is not clear, their presence in the subtype C LTR is believed to enhance the transactivation property of the viral promoter (31,43,44).…”

Section: Discussionmentioning

confidence: 99%

Identification of Subtype C Human Immunodeficiency Virus Type 1 by Subtype-Specific PCR and Its Use in the Characterization of Viruses Circulating in the Southern Parts of India

Siddappa

Dash

Mahadevan³

et al. 2004

J Clin Microbiol

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Human immunodeficiency virus type 1 (HIV-1) subtype C viruses are associated with nearly half of worldwide HIV-1 infections and are most predominant in India and the southern and eastern parts of Africa. Earlier reports from India identified the preponderance of subtype C and a small proportion of subtype A viruses. Subsequent reports identifying multiple subtypes suggest new introductions and/or their detection due to extended screening. The southern parts of India constitute emerging areas of the epidemic, but it is not known whether HIV-1 infection in these areas is associated with subtype C viruses or is due to the potential new introduction of non-subtype C viruses. Here, we describe the development of a specific and sensitive PCR-based strategy to identify subtype C-viruses (C-PCR). The strategy is based on amplifying a region encompassing a long terminal repeat and gag in the first round, followed by two sets of nested primers; one amplifies multiple subtypes, while the other is specific to subtype C. The common HIV and subtype C-specific fragments are distinguishable by length differences in agarose gels and by the difference in the numbers of NF-B sites encoded in the subtype C-specific fragment. We implemented this method to screen 256 HIV-1-infected individuals from 35 towns and cities in four states in the south and a city in the east. With the exception of single samples of subtypes A and B and a B/C recombinant, we found all to be infected with subtype C viruses, and the subtype assignments were confirmed in a subset by using heteroduplex mobility assays and phylogenetic analysis of sequences. We propose the use of C-PCR to facilitate rapid molecular epidemiologic characterization to aid vaccine and therapeutic strategies.

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Section: Discussionmentioning

confidence: 99%

Identification of Subtype C Human Immunodeficiency Virus Type 1 by Subtype-Specific PCR and Its Use in the Characterization of Viruses Circulating in the Southern Parts of India

Siddappa

Dash

Mahadevan³

et al. 2004

J Clin Microbiol

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“…23 Briefly, PCR was performed for 31 cycles with oligonucleotides LTR1-SX and LTR4 (10 nM each). The following cycle was used: 95°C for 1 min, 55°C for 1 min, and 72°C for 1 min.…”

Section: Pcr Amplification Cloning and Sequence Analysismentioning

confidence: 99%

Long Terminal Repeat Promoter/Enhancer Activity of Different Subtypes of HIV Type 1

Naghavi

Schwartz

Sönnerborg

et al. 1999

AIDS Research and Human Retroviruses

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Transcription of the HIV-1 provirus genome is regulated by a complex interplay between viral regulatory proteins and cellular transcription factors that interact with the viral long terminal repeat (LTR) region of HIV-1. However, several cellular transcription factors have been identified that can interact with the HIV-1 LTR; the significance of all of these factors is not clearly understood. In this study we have characterized the LTR region of different subtypes of HIV-1 with regard to nucleotide sequence and promoter activity. The LTR regions of HIV-1 from peripheral blood mononuclear cells of 29 infected individuals originating from 10 different geographical regions were sequenced and further analyzed for promoter/enhancer activity in transient transfection of HeLa cells, in the context of a reporter gene and in the context of the complete virus genome. We found several subtype-specific LTR sequences of the various HIV-1 strains, such as an insertion that created a potential third NF-kappaB site in the LTR of the subtype C strains. The USF-binding site in the NRE also contained subtype-specific sequences. Interestingly, the promoter/enhancer activities of the subtype C LTRs were higher than the activities of the other subtypes analyzed here (subtypes A, B, D, E, and G), suggesting that the potential third NF-kappaB site may confer higher LTR activity or that the subtype C NRE may be less potent. Thus, our data suggest that genetic diversity of the LTR may result in HIV-1 subtypes with different replicative properties.

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“…The enhancer in most of the viral subtypes, including the prototype subtype B virus, consists of two identical and canonical B motifs with the exception of subtypes A/E and C. While in subtype A/E, the upstream NF-B site is replaced with a GA-binding protein-binding motif (14), the genetic variation within the subtype C enhancer is more complex. Although a large proportion of C-LTRs contains three NF-B sites (8,15,16), a small minority of these LTRs contains a fourth motif that is either a canonical B site or B-like site (8,(17)(18)(19)(20). Additionally, C-LTRs with only two B sites have also been reported (16,21).…”

mentioning

confidence: 99%

Multiple NF-κB Sites in HIV-1 Subtype C Long Terminal Repeat Confer Superior Magnitude of Transcription and Thereby the Enhanced Viral Predominance

Bachu

Swarupa

Asokan

et al. 2012

Journal of Biological Chemistry

137

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Background: Viral evolution of HIV-1 is dynamic and moving towards a higher order of replicative fitness. Results: HIV-1 subtype C acquires an extra (4th) NF-B site to achieve a higher degree of transcription and in turn enhances its replicative fitness and preponderance. Conclusion: Subtype C with an extra NF-B site adopts a novel strategy of strengthening its promoter to gain fitness. Significance: Learning how the new strains could impact viral prevalence, pathogenesis, and disease management strategies is critical.

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Multiple Enhancer Motifs in HIV Type 1 Strains from Ethiopia

Cited by 27 publications

References 10 publications

Identification of Subtype C Human Immunodeficiency Virus Type 1 by Subtype-Specific PCR and Its Use in the Characterization of Viruses Circulating in the Southern Parts of India

Identification of Subtype C Human Immunodeficiency Virus Type 1 by Subtype-Specific PCR and Its Use in the Characterization of Viruses Circulating in the Southern Parts of India

Long Terminal Repeat Promoter/Enhancer Activity of Different Subtypes of HIV Type 1

Multiple NF-κB Sites in HIV-1 Subtype C Long Terminal Repeat Confer Superior Magnitude of Transcription and Thereby the Enhanced Viral Predominance

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