Exceptional molecular and coreceptor-requirement properties of molecular clones isolated from an Human Immunodeficiency Virus Type-1 subtype C infection

Prasanta K. Dash, Nagadenahalli B. Siddappa, Asokan Mangaiarkarasi, Aruna V. Mahendarkar, Padmanabhan Roshan, Krishnamurthy Kumar Anand, Anita Mahadevan, Parthasarathy Satishchandra, Susarla K. Shankar, Vinayaka R. Prasad, Udaykumar Ranga

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Background: The pathogenic significance of coreceptor switch in the viral infection of HIV-1 is not completely understood. This situation is more complex in subtype C infection where coreceptor switch is either absent or extremely rare. To gain insights into the mechanisms that underlie coreceptor requirement of subtype C, we screened several primary viral isolates and identified a clinical sample that demonstrated a potential to grow on standard T-cell lines with no detectable CCR5 expression. The subject was diagnosed with HIV-1 associated dementia in the absence of opportunistic infections of the brain. To isolate molecular clones from this virus, we devised a novel strategy based on anchor primers that target a sequence in the reverse transcriptase, highly conserved among diverse subtypes of HIV-1. Results: Using this strategy, we isolated 8 full-length molecular clones from the donor. Two of the eight molecular clones, 03In94_D17 and 03In94_D24, (D17 and D24) generated replication-competent viruses. Phylogenetic analysis of the full-length viral sequences revealed that both clones were non-recombinant subtype C viruses. They contain intact open reading frames in all the viral proteins. Both the viral clones are endowed with several unique molecular and biological properties. The viral promoter of the clones is characterized by the presence of four NF-kB binding elements, a feature rarely seen in the subtype C HIV-1 LTR. Interestingly, we identified the coexistence of two different forms of Rev, a truncated form common to subtype C and a full-length form less common for this subtype, in both proviral and plasma virus compartments. An exceptional property of the viruses, atypical of subtype C, is their ability to use a wide range of coreceptors including CCR5, CXCR4, and several others tested. Sequence analysis of Env of D17 and D24 clones identified differences within the variable loops providing important clues for the expanded coreceptor use. The V1, V2 and V4 loops in both of the molecular clones are longer due to the insertion of several amino acid residues that generated potential N-linked glycosylation sites. Conclusion: The exceptional biological and molecular properties of these clones make them invaluable tools to understand the unique pathogenic characteristics of subtype C.

Original languageEnglish (US)
Article number25
JournalRetrovirology
Volume5
DOIs
StatePublished - Mar 7 2008

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HIV-1
Clone Cells
Infection
Viruses
HIV Long Terminal Repeat
Immunodeficiency without anhidrotic ectodermal dysplasia
Aptitude
NF-kappa B
RNA-Directed DNA Polymerase
Opportunistic Infections
Viral Proteins
Virus Diseases
Virus Replication
Glycosylation
Open Reading Frames
Sequence Analysis
Dementia
T-Lymphocytes
Amino Acids
Cell Line

ASJC Scopus subject areas

  • Virology

Cite this

Exceptional molecular and coreceptor-requirement properties of molecular clones isolated from an Human Immunodeficiency Virus Type-1 subtype C infection. / Dash, Prasanta K.; Siddappa, Nagadenahalli B.; Mangaiarkarasi, Asokan; Mahendarkar, Aruna V.; Roshan, Padmanabhan; Anand, Krishnamurthy Kumar; Mahadevan, Anita; Satishchandra, Parthasarathy; Shankar, Susarla K.; Prasad, Vinayaka R.; Ranga, Udaykumar.

In: Retrovirology, Vol. 5, 25, 07.03.2008.

Research output: Contribution to journalArticle

Dash, PK, Siddappa, NB, Mangaiarkarasi, A, Mahendarkar, AV, Roshan, P, Anand, KK, Mahadevan, A, Satishchandra, P, Shankar, SK, Prasad, VR & Ranga, U 2008, 'Exceptional molecular and coreceptor-requirement properties of molecular clones isolated from an Human Immunodeficiency Virus Type-1 subtype C infection', Retrovirology, vol. 5, 25. https://doi.org/10.1186/1742-4690-5-25
Dash, Prasanta K. ; Siddappa, Nagadenahalli B. ; Mangaiarkarasi, Asokan ; Mahendarkar, Aruna V. ; Roshan, Padmanabhan ; Anand, Krishnamurthy Kumar ; Mahadevan, Anita ; Satishchandra, Parthasarathy ; Shankar, Susarla K. ; Prasad, Vinayaka R. ; Ranga, Udaykumar. / Exceptional molecular and coreceptor-requirement properties of molecular clones isolated from an Human Immunodeficiency Virus Type-1 subtype C infection. In: Retrovirology. 2008 ; Vol. 5.
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AU - Siddappa, Nagadenahalli B.

AU - Mangaiarkarasi, Asokan

AU - Mahendarkar, Aruna V.

AU - Roshan, Padmanabhan

AU - Anand, Krishnamurthy Kumar

AU - Mahadevan, Anita

AU - Satishchandra, Parthasarathy

AU - Shankar, Susarla K.

AU - Prasad, Vinayaka R.

AU - Ranga, Udaykumar

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N2 - Background: The pathogenic significance of coreceptor switch in the viral infection of HIV-1 is not completely understood. This situation is more complex in subtype C infection where coreceptor switch is either absent or extremely rare. To gain insights into the mechanisms that underlie coreceptor requirement of subtype C, we screened several primary viral isolates and identified a clinical sample that demonstrated a potential to grow on standard T-cell lines with no detectable CCR5 expression. The subject was diagnosed with HIV-1 associated dementia in the absence of opportunistic infections of the brain. To isolate molecular clones from this virus, we devised a novel strategy based on anchor primers that target a sequence in the reverse transcriptase, highly conserved among diverse subtypes of HIV-1. Results: Using this strategy, we isolated 8 full-length molecular clones from the donor. Two of the eight molecular clones, 03In94_D17 and 03In94_D24, (D17 and D24) generated replication-competent viruses. Phylogenetic analysis of the full-length viral sequences revealed that both clones were non-recombinant subtype C viruses. They contain intact open reading frames in all the viral proteins. Both the viral clones are endowed with several unique molecular and biological properties. The viral promoter of the clones is characterized by the presence of four NF-kB binding elements, a feature rarely seen in the subtype C HIV-1 LTR. Interestingly, we identified the coexistence of two different forms of Rev, a truncated form common to subtype C and a full-length form less common for this subtype, in both proviral and plasma virus compartments. An exceptional property of the viruses, atypical of subtype C, is their ability to use a wide range of coreceptors including CCR5, CXCR4, and several others tested. Sequence analysis of Env of D17 and D24 clones identified differences within the variable loops providing important clues for the expanded coreceptor use. The V1, V2 and V4 loops in both of the molecular clones are longer due to the insertion of several amino acid residues that generated potential N-linked glycosylation sites. Conclusion: The exceptional biological and molecular properties of these clones make them invaluable tools to understand the unique pathogenic characteristics of subtype C.

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