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Gan SKE, Phua SX, Yeo JY. Sagacious epitope selection for vaccines, and both antibody-based therapeutics and diagnostics: tips from virology and oncology. Antib Ther 2022; 5:63-72. [PMID: 35372784 PMCID: PMC8972324 DOI: 10.1093/abt/tbac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/24/2022] [Accepted: 02/12/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
The target of an antibody plays a significant role in the success of antibody-based therapeutics and diagnostics, and vaccine development. This importance is focused on the target binding site—epitope, where epitope selection as a part of design thinking beyond traditional antigen selection using whole cell or whole protein immunization can positively impact success. With purified recombinant protein production and peptide synthesis to display limited/selected epitopes, intrinsic factors that can affect the functioning of resulting antibodies can be more easily selected for. Many of these factors stem from the location of the epitope that can impact accessibility of the antibody to the epitope at a cellular or molecular level, direct inhibition of target antigen activity, conservation of function despite escape mutations, and even non-competitive inhibition sites. By incorporating novel computational methods for predicting antigen changes to model-informed drug discovery and development, superior vaccines and antibody-based therapeutics or diagnostics can be easily designed to mitigate failures. With detailed examples, this review highlights the new opportunities, factors and methods of predicting antigenic changes for consideration in sagacious epitope selection.
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Affiliation(s)
- Samuel Ken-En Gan
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
- APD SKEG Pte Ltd, Singapore 439444, Singapore
| | - Ser-Xian Phua
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Joshua Yi Yeo
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
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Ahmad N, Ahmad AN, Ahmad SN. Features of Maternal HIV-1 Associated with Lack of Vertical Transmission. Open Virol J 2017; 11:8-14. [PMID: 28458735 PMCID: PMC5388788 DOI: 10.2174/1874357901710011008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/05/2017] [Accepted: 01/19/2017] [Indexed: 11/22/2022] Open
Abstract
HIV-1 is transmitted from mother-to-child (vertical transmission) at an estimated rate of approximately 30% without any antiretroviral therapy (ART). However, administration of ART during pregnancy considerably diminishes the rate of mother-to-child transmission of HIV-1, which has become a standard of perinatal care in HIV-infected pregnant females in developed countries. Moreover, a majority of children born to HIV-infected mothers are uninfected without any ART. In addition, characteristics of HIV-1 and/or cellular factors in the mothers may play a role in influencing or preventing vertical transmission. Several studies, including from our laboratory have characterized the properties of HIV-1 from infected mothers that transmitted HIV-1 to their infants (transmitting mothers) and compared with those mothers that failed to transmit HIV-1 to their infants (non-transmitting mothers) in the absence of ART. One of the striking differences observed was that the non-transmitting mothers harbored a less heterogeneous HIV-1 population than transmitting mothers in the analyzed HIV-1 regions of p17 gag, env V3, vif and vpr. The other significant and distinctive findings were that the functional domains of HIV-1 vif and vpr proteins were less conserved in non-transmitting mothers compared with transmitting mothers. Furthermore, there were differences seen in two important motifs of HIV-1 Gag p17, including conservation of QVSQNY motif and variation in KIEEEQN motif in non-transmitting mothers compared with transmitting mothers. Several of these distinguishing properties of HIV-1 in non-transmitting mothers provide insights in developing strategies for preventing HIV-1 vertical transmission.
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Ahmad N. Molecular mechanisms of HIV-1 infection in neonatal target cells. Future Virol 2012. [DOI: 10.2217/fvl.12.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HIV-1-infected neonates and infants have a higher viral load and progress to symptomatic AIDS more rapidly than their own infected mothers, as well as other infected adults, with differences in clinical manifestations, recurrent bacterial infections and CNS disorders. Two major reasons have been attributed to this differential HIV pathogenesis and disease; the relative immaturity of the neonate’s immune system and it’s inability to contain the highly replicating and mutating HIV-1, and the more efficient replication of HIV-1 in neonatal cells than in adult target cells. In this context, it has been demonstrated that HIV-1 replicates more efficiently in neonatal (cord) blood monocytes/macrophages and T lymphocytes – including naive and memory T lymphocytes – compared with adult blood cells. We have also determined the mechanisms of the differential HIV-1 replication in cord versus adult blood monocytes/macrophages and T lymphocytes (naive and memory), finding that it was influenced at the level of HIV-1 gene expression. The increased HIV-1 gene expression in neonatal versus adult target cells was regulated by differential expression of host factors, transcription factors (NF-κB, E2F, HAT-1, TFIIE, Cdk9 and Cyclin T1), signal transducers (STAT3 and STAT5A) and cytokines (IL-1β, IL-6 and IL-10). We also showed that nuclear extracts from cord cells interacted with HIV-1 long terminal repeat cis-acting sequences, including NF-κB, NFAT, AP1 and NF-IL6, to a greater extent when compared with adult peripheral blood mononuclear cell nuclear extracts. Additionally, shRNA of retroviral origin for STAT3 and IL-6 downregulated both their own gene expression as well as that of HIV-1, indicating that these factors influenced the differential expression of HIV-1 genes in cord cells compared with adult cells. In addition, HIV-1 integration plays an important role in differential HIV-1 replication and gene expression in neonatal versus adult cells by integrating into more actively transcribed genes in neonates compared with adults. We characterized 468 HIV-1 integration sites within cord and adult blood T lymphocytes and monocytes/macrophages, including genes coding for cellular components, and those involved with maintenance of the intracellular environment, enzyme regulation, cellular metabolism, catalytic activity and cation transport, as well as several potential transcription factor binding sites at the sites of integration. Additionally, the genes at the integration sites, transcription factors and transcription binding sites were expressed at higher levels in cord than adult target cells. In summary, the increased HIV-1 gene expression and replication in neonatal target cells due to differential expression of host factors all contribute to an increased viral load and faster disease progression in neonates and infants when compared with similar situations in adult patients. Based on these findings, it may be possible to identify new viral and host targets for use in developing strategies for the treatment and prevention of HIV-1.
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Affiliation(s)
- Nafees Ahmad
- Department of Immunobiology, College of Medicine University of Arizona, Tucson, AZ 85724, USA
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Ahmad N. Molecular mechanisms of HIV-1 mother-to-child transmission and infection in neonatal target cells. Life Sci 2010; 88:980-6. [PMID: 20888841 DOI: 10.1016/j.lfs.2010.09.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 09/02/2010] [Accepted: 09/16/2010] [Indexed: 11/25/2022]
Abstract
HIV-1 mother-to-child transmission (MTCT) occurs mainly at three stages, including prepartum, intrapartum and postpartum. Several maternal factors, including low CD4+ lymphocyte counts, high viral load, immune response, advanced disease status, smoking and abusing drugs have been implicated in an increased risk of HIV-1 MTCT. While use of antiretroviral therapy (ART) during pregnancy has significantly reduced the rate of MTCT, selective transmission of ART resistant mutants has been reported. Based on HIV-1 sequence comparison, the maternal HIV-1 minor genotypes with R5 phenotypes are predominantly transmitted to their infants and initially maintained in the infants with the same properties. Several HIV-1 structural, regulatory and accessory genes were highly conserved following MTCT. In addition, HIV-1 sequences from non-transmitting mothers are less heterogeneous compared with transmitting mothers, suggesting that a higher level of viral heterogeneity influences MTCT. Analysis of the immunologically relevant epitopes showed that variants evolved to escape the immune response that influenced HIV-1 MTCT. Several cytotoxic T-lymphocyte (CTL) epitopes were identified in various HIV-1 genes that were conserved in HIV-1 mother-infant sequences, suggesting a role in MTCT. We have shown that HIV-1 replicates more efficiently in neonatal T-lymphocytes and monocytes/macrophages compared with adult cells, and this differential replication is influenced at the level of HIV-1 gene expression, which was due to differential expression of host factors, including transcriptional activators, signal transducers and cytokines in neonatal than adult cells. In addition, HIV-1 integration occurs in more actively transcribed genes in neonatal compared with adult cells, which may influence HIV-1 gene expression. The increased HIV-1 gene expression and replication in neonatal target cells contribute to a higher viral load and more rapid disease progression in neonates/infants than adults. These findings may identify targets, viral and host, for developing strategies for HIV-1 prevention and treatment.
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Affiliation(s)
- Nafees Ahmad
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, AZ, United States.
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Shanmugasundaram U, Solomon S, Murugavel KG, Nagalingeswaran K, Solomon SS, Mayer KH, Pachamuthu B. Short communication: Nucleotide variation and positively selected sites in HIV type 1 reverse transcriptase among heterosexual transmission pairs. AIDS Res Hum Retroviruses 2010; 26:895-9. [PMID: 20672974 DOI: 10.1089/aid.2010.0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mutations in the env gene of HIV-1 have been the primary focus in most epidemiologically related cohort studies of virus evolution and very limited studies have focused on the reverse transcriptase (RT) region, the primary target of antiretroviral therapy (ART). Hence, we measured the selection pressure and searched for the positively selected sites in the RT sequences amplified from HIV-1-infected heterosexual transmission pairs. Married couples (n = 10) who were ART naive were included in this study. Phylogenetic analysis, the measurement of synonymous and nonsynonymous ratio (dN/dS) and the interpatient nucleotide variation, was done. Phylogenetic analysis demonstrated distinct subclusters of the RT sequences from heterosexual transmission pairs and the median (IQR) nucleotide variation between the epidemiologically related transmission pairs was significantly (p < 0.001) lower [0.01% (0.01-0.02%)] compared to the epidemiologically unrelated transmission pairs [0.04% (0.03-0.04%)]. The ratio of dN/dS was <1 and codons 135, 162, 166, 207, and 211 were positively selected in >50% of the donor and recipient RT sequences. Purifying selection pressure and low nucleotide variation in the RT sequences between epidemiologically related transmission pairs highlight its essential role in HIV-1 replication. The effect of the RT positively selected mutations that persist over time following transmission between individuals needs to be studied to determine the fitness cost of the mutations in vivo, which may possibly represent good targets for inclusion in HIV-1 vaccines.
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Affiliation(s)
| | - Suniti Solomon
- Y.R. Gaitonde Centre for AIDS Research and Education, Chennai, India
| | | | | | - Sunil S. Solomon
- Y.R. Gaitonde Centre for AIDS Research and Education, Chennai, India
| | - Kenneth H. Mayer
- Warren Alpert School of Medicine, Brown University/Miriam Hospital, Providence, Rhode Island
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Abstract
OBJECTIVE Review the role and mechanism of in utero placental transmission of HIV-1. STUDY DESIGN A thorough review based on a literature search for publications relevant to this subject was performed using relevant search terms. Articles that describe the genetic and pathophysiology of vertical transmission have been acknowledged. The articles pertinent to the topic were selected to support the discussion. RESULTS Vertical transmission may occur through CD4+ endothelial tissues or CD4+ Hofbauer cells. Trophoblasts and villi have CD4 receptors, which make them potential candidates for HIV infection. Placental cytokines and chemokines influence HIV replication in trophoblasts. Genetic analysis of HIV-1 sequences verify the interaction of HIV-1 and placental tissue. The vertical transmission of HIV-1 characterized by selection of genotype variant that escape the mother's immune system. CONCLUSION Placental transmission of HIV-1 is a complex incompletely understood process which requires advanced studies. The available literature provides information with regards to the interactions of placental cells with HIV.
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Mehta R, Sundaravaradan V, Ahmad N. Mutations generated in human immunodeficiency virus type 1 long terminal repeat during vertical transmission correlate with viral gene expression. Virology 2008; 375:170-81. [PMID: 18313715 DOI: 10.1016/j.virol.2008.01.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 12/15/2007] [Accepted: 01/31/2008] [Indexed: 11/24/2022]
Abstract
We determined the effect of mutations generated in HIV-1 LTR on viral gene expression in six mother-infant pairs following vertical transmission. We show that the functional domains critical for LTR function, the promoter (TATAA), enhancers (three SpI and two NFkappaB sites), the modulatory region (two AP-I sites, two NFAT, one NF-IL6 site, one Ets-1, and one USF-1) and the TAR region were generally conserved among mother-infant pairs, although we observed several patient and pair specific mutations in these important domains. We then determined the promoter activity of our mother-infant LTR sequences by measuring CAT gene expression, which was driven by these LTRs and found that most of these HIV-1 LTRs derived from 6 mother-infant pairs were functional. However, mutations in the important transcription factor binding sites, including TATAA, SpI, NFkappaB, AP-I, NFAT, NF-IL6, Ets-1, USF-1 and TAR resulted in reduced LTR driven CAT gene expression. Taken together, conservation of functional domains in the LTR during vertical transmission supports the notion that a functional LTR is critical in viral replication and pathogenesis and mutations generated during the course of infection correlated with HIV-1 gene expression.
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Affiliation(s)
- Roshni Mehta
- Department of Immunobiology, College of Medicine, The University of Arizona, 1501 N. Campbell Avenue, Tucson, Arizona 85724, USA
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Mehta R, Ramakrishnan R, Doktor K, Sundaravaradan V, Ahmad N. Genetic characterization of HIV type 1 long terminal repeat following vertical transmission. AIDS Res Hum Retroviruses 2008; 24:437-45. [PMID: 18327987 DOI: 10.1089/aid.2007.0234] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) sequences were characterized from six mother-infant pairs following vertical transmission. The LTR sequences exhibited a low degree of heterogeneity within mothers, within infants, and between epidemiologically linked mother-infant pairs. However, LTR sequences were more heterogeneous between epidemiologically unlinked individuals compared with linked mother-infant pairs. These data were further supported by low estimates of genetic diversity and clustering of each mother-infant pair's sequences into a separate subtree as well as the presence of common signature sequences between mother-infant pairs. The functional domains essential for LTR (promoter) function, including the promoter (TATAA), enhancers (three Sp-I and two NF-kappaB), the modulatory regions (two AP-I sites, two NFAT, one NF-IL6 site, one Ets-1, and one USF-1), and the TAR region were generally conserved among mother-infant pairs. Taken together, limited heterogeneity and conservation of functional domains in the LTR following vertical transmission support the notion that a functional LTR is critical in viral replication and pathogenesis in HIV-1-infected mothers and their infected infants.
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Affiliation(s)
- Roshni Mehta
- Department of Immunobiology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona 85724
| | - Rajesh Ramakrishnan
- Department of Immunobiology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona 85724
| | - Katherine Doktor
- Department of Immunobiology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona 85724
| | - Vasudha Sundaravaradan
- Department of Immunobiology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona 85724
| | - Nafees Ahmad
- Department of Immunobiology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona 85724
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Ahmad N. Molecular Mechanisms of HIV-1 Vertical Transmission and Pathogenesis in Infants. HIV-1: MOLECULAR BIOLOGY AND PATHOGENESIS 2008; 56:453-508. [DOI: 10.1016/s1054-3589(07)56015-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Zhang H, Hoffmann F, He J, He X, Kankasa C, West JT, Mitchell CD, Ruprecht RM, Orti G, Wood C. Characterization of HIV-1 subtype C envelope glycoproteins from perinatally infected children with different courses of disease. Retrovirology 2006; 3:73. [PMID: 17054795 PMCID: PMC1635063 DOI: 10.1186/1742-4690-3-73] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Accepted: 10/20/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The causal mechanisms of differential disease progression in HIV-1 infected children remain poorly defined, and much of the accumulated knowledge comes from studies of subtype B infected individuals. The applicability of such findings to other subtypes, such as subtype C, remains to be substantiated. In this study, we longitudinally characterized the evolution of the Env V1-V5 region from seven subtype C HIV-1 perinatally infected children with different clinical outcomes. We investigated the possible influence of viral genotype and humoral immune response on disease progression in infants. RESULTS Genetic analyses revealed that rapid progressors (infants that died in the first year of life) received and maintained a genetically homogeneous viral population throughout the disease course. In contrast, slow progressors (infants that remained clinically asymptomatic for up to four years) also exhibited low levels variation initially, but attained higher levels of diversity over time. Genetic assessment of variation, as indicated by dN/dS, showed that particular regions of Env undergo selective changes. Nevertheless, the magnitude and distribution of these changes did not segregate slow and rapid progressors. Longitudinal trends in Env V1-V5 length and the number of potential N-glycosylation sites varied among patients but also failed to discriminate between fast and slow progressors. Viral isolates from rapid progressors and slow progressors displayed no significant growth properties differences in vitro. The neutralizing activity in maternal and infant baseline plasma also varied in its effectiveness against the initial virus from the infants but did not differentiate rapid from slow progressors. Quantification of the neutralization susceptibility of the initial infant viral isolates to maternal baseline plasma indicated that both sensitive and resistant viruses were transmitted, irrespective of disease course. We showed that humoral immunity, whether passively acquired or developed de novo in the infected children, varied but was not predictive of disease progression. CONCLUSION Our data suggest that neither genetic variation in env, or initial maternal neutralizing activity, or the level of passively acquired neutralizing antibody, or the level of the de novo neutralization response appear to be linked to differences in disease progression in subtype C HIV-1 infected children.
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Affiliation(s)
- Hong Zhang
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Federico Hoffmann
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Jun He
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Xiang He
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Chipepo Kankasa
- Department of Pediatrics, University Teaching Hospital, Lusaka, Zambia
| | - John T West
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Charles D Mitchell
- Department of Pediatrics, University of Miami School of Medicine, Miami, FL, USA
| | - Ruth M Ruprecht
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Guillermo Orti
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Charles Wood
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
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Ramakrishnan R, Ahmad N. Derivation of primary sequences and secondary structures of rev responsive element from HIV-1 infected mothers and infants following vertical transmission. Virology 2006; 359:201-11. [PMID: 17045321 DOI: 10.1016/j.virol.2006.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2006] [Revised: 09/01/2006] [Accepted: 09/05/2006] [Indexed: 11/15/2022]
Abstract
We have characterized the primary RRE sequences of HIV-1, including in vivo genetic variation and functional motifs required for Rev-RRE interactions as well as evaluated the RNA secondary structures of RRE derived from five mother-infant pairs following vertical transmission. Multiple (157) RRE sequences derived from mother-infant pairs showed that primary nucleotide sequences of RRE were highly conserved with a low degree of viral heterogeneity following vertical transmission. We found that the RRE sequences from mothers and infants folded and retained all the essential stem-loop formation required for Rev-RRE interactions. More importantly, a primary 9-nucleotide (5'-CACTATGGG-3') RRE sequence in the stem-loop B that is required for optimal Rev recognition and must be presented as a stem-bulge-stem structure was highly conserved in most of the sequences. The domains required for RRE-host protein interactions were also conserved in most of the RRE sequences. Taken together, the primary RRE sequences in the context of secondary structures were maintained and the Rev-RRE interaction domains were conserved following vertical transmission, which is consistent with a crucial role of RRE in HIV-1 pathogenesis.
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Affiliation(s)
- Rajesh Ramakrishnan
- Department of Immunobiology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, AZ 85724, USA
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Ramakrishnan R, Mehta R, Sundaravaradan V, Davis T, Ahmad N. Characterization of HIV-1 envelope gp41 genetic diversity and functional domains following perinatal transmission. Retrovirology 2006; 3:42. [PMID: 16820061 PMCID: PMC1526753 DOI: 10.1186/1742-4690-3-42] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Accepted: 07/04/2006] [Indexed: 01/17/2023] Open
Abstract
Background HIV-1 envelope gp41 is a transmembrane protein that promotes fusion of the virus with the plasma membrane of the host cells required for virus entry. In addition, gp41 is an important target for the immune response and development of antiviral and vaccine strategies, especially when targeting the highly variable envelope gp120 has not met with resounding success. Mutations in gp41 may affect HIV-1 entry, replication, pathogenesis, and transmission. We, therefore, characterized the molecular properties of gp41, including genetic diversity, functional motifs, and evolutionary dynamics from five mother-infant pairs following perinatal transmission. Results The gp41 open reading frame (ORF) was maintained with a frequency of 84.17% in five mother-infant pairs' sequences following perinatal transmission. There was a low degree of viral heterogeneity and estimates of genetic diversity in gp41 sequences. Both mother and infant gp41 sequences were under positive selection pressure, as determined by ratios of non-synonymous to synonymous substitutions. Phylogenetic analysis of 157 mother-infant gp41 sequences revealed distinct clusters for each mother-infant pair, suggesting that the epidemiologically linked mother-infant pairs were evolutionarily closer to each other as compared with epidemiologically unlinked sequences. The functional domains of gp41, including fusion peptide, heptad repeats, glycosylation sites and lentiviral lytic peptides were mostly conserved in gp41 sequences analyzed in this study. The CTL recognition epitopes and motifs recognized by fusion inhibitors were also conserved in the five mother-infant pairs. Conclusion The maintenance of an intact envelope gp41 ORF with conserved functional domains and a low degree of genetic variability as well as positive selection pressure for adaptive evolution following perinatal transmission is consistent with an indispensable role of envelope gp41 in HIV-1 replication and pathogenesis.
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Affiliation(s)
- Rajesh Ramakrishnan
- Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona 85724, USA
- Current Address : Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Roshni Mehta
- Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona 85724, USA
| | - Vasudha Sundaravaradan
- Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona 85724, USA
| | - Tiffany Davis
- Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona 85724, USA
| | - Nafees Ahmad
- Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona 85724, USA
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Wellensiek BP, Sundaravaradan V, Ramakrishnan R, Ahmad N. Molecular characterization of the HIV-1 gag nucleocapsid gene associated with vertical transmission. Retrovirology 2006; 3:21. [PMID: 16600029 PMCID: PMC1459197 DOI: 10.1186/1742-4690-3-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Accepted: 04/06/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The human immunodeficiency virus type 1 (HIV-1) nucleocapsid (NC) plays a pivotal role in the viral lifecycle: including encapsulating the viral genome, aiding in strand transfer during reverse transcription, and packaging two copies of the viral genome into progeny virions. Another gag gene product, p6, plays an integral role in successful viral budding from the plasma membrane and inclusion of the accessory protein Vpr within newly budding virions. In this study, we have characterized the gag NC and p6 genes from six mother-infant pairs following vertical transmission by performing phylogenetic analysis and by analyzing the degree of genetic diversity, evolutionary dynamics, and conservation of functional domains. RESULTS Phylogenetic analysis of 168 gag NC and p6 genes sequences revealed six separate subtrees that corresponded to each mother-infant pair, suggesting that epidemiologically linked individuals were closer to each other than epidemiologically unlinked individuals. A high frequency (92.8%) of intact open reading frames of NC and p6 with patient and pair specific sequence motifs were conserved in mother-infant pairs' sequences. Nucleotide and amino acid distances showed a lower degree of viral heterogeneity, and a low degree of estimates of genetic diversity was also found in NC and p6 sequences. The NC and p6 sequences from both mothers and infants were found to be under positive selection pressure. The two important functional motifs within NC, the zinc-finger motifs, were highly conserved in most of the sequences, as were the gag p6 Vpr binding, AIP1 and late binding domains. Several CTL recognition epitopes identified within the NC and p6 genes were found to be mostly conserved in 6 mother-infant pairs' sequences. CONCLUSION These data suggest that the gag NC and p6 open reading frames and functional domains were conserved in mother-infant pairs' sequences following vertical transmission, which confirms the critical role of these gene products in the viral lifecycle.
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Affiliation(s)
- Brian P Wellensiek
- Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona, USA
| | - Vasudha Sundaravaradan
- Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona, USA
| | - Rajesh Ramakrishnan
- Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona, USA
| | - Nafees Ahmad
- Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona, USA
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