TY - JOUR
T1 - Exceptional molecular and coreceptor-requirement properties of molecular clones isolated from an Human Immunodeficiency Virus Type-1 subtype C infection
AU - Dash, Prasanta K.
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
N1 - Funding Information:
A number of reagents used in this study were obtained through the AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH, USA. This work was supported by grants to UR from The Department of Biotechnology, Government of India (Grant No. BT/PR5355/Med/14/623/ 2004), Indian Council of Medical Research, Government of India (Grant No. Immuno/18/11/19/2002-ECD-I). UR and NBS acknowledge support from the AIDS International Training and Research Program (NIH D43-TW01403) of the Albert Einstein College of Medicine. VP would like to acknowledge the Einstein/MMC Center for AIDS Research for the use of CFAR scientific core facilities. PKD, NBS, AM and KKA are recipients of the Council of Science and Industrial Research fellowship from the Government of India. The authors thank Pheroze Joshi and Elizabeth Hanna Luke for valuable assistance in sequencing of the viral DNAs.
PY - 2008/3/7
Y1 - 2008/3/7
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.
AB - 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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U2 - 10.1186/1742-4690-5-25
DO - 10.1186/1742-4690-5-25
M3 - Article
C2 - 18328091
AN - SCOPUS:42449103955
SN - 1742-4690
VL - 5
JO - Retrovirology
JF - Retrovirology
M1 - 25
ER -