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Akand EH, Maher SJ, Murray JM. Mutational networks of escape from transmitted HIV-1 infection. PLoS One 2020; 15:e0243391. [PMID: 33284837 PMCID: PMC7721145 DOI: 10.1371/journal.pone.0243391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/19/2020] [Indexed: 02/08/2023] Open
Abstract
Human immunodeficiency virus (HIV) is subject to immune selective pressure soon after it establishes infection at the founder stage. As an individual progresses from the founder to chronic stage of infection, immune pressure forces a history of mutations that are embedded in envelope sequences. Determining this pathway of coevolving mutations can assist in understanding what is different with the founder virus and the essential pathways it takes to maintain infection. We have combined operations research and bioinformatics methods to extract key networks of mutations that differentiate founder and chronic stages for 156 subtype B and 107 subtype C envelope (gp160) sequences. The chronic networks for both subtypes revealed strikingly different hub-and-spoke topologies compared to the less structured transmission networks. This suggests that the hub nodes are impacted by the immune response and the resulting loss of fitness is compensated by mutations at the spoke positions. The major hubs in the chronic C network occur at positions 12, 137 (within the N136 glycan), and 822, and at position 306 for subtype B. While both founder networks had a more heterogeneous connected network structure, interestingly founder B subnetworks around positions 640 and 837 preferentially contained CD4 and coreceptor binding domains. Finally, we observed a differential effect of glycosylation between founder and chronic subtype B where the latter had mutational pathways significantly driven by N-glycosylation. Our study provides insights into the mutational pathways HIV takes to evade the immune response, and presents features more likely to establish founder infection, valuable for effective vaccine design.
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Affiliation(s)
- Elma H. Akand
- School of Mathematics and Statistics, UNSW Sydney, Kensington, NSW, Australia
| | - Stephen J. Maher
- College of Engineering, Mathematical and Physical Sciences, University of Exeter, Exeter, United Kingdom
| | - John M. Murray
- School of Mathematics and Statistics, UNSW Sydney, Kensington, NSW, Australia
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Sutar J, Padwal V, Nagar V, Patil P, Patel V, Bandivdekar A. Analysis of sequence diversity and selection pressure in HIV-1 clade C gp41 from India. Virusdisease 2020; 31:277-291. [PMID: 32904888 DOI: 10.1007/s13337-020-00595-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/28/2020] [Indexed: 01/31/2023] Open
Abstract
Evaluation of viral diversity is critical for the rational design of treatment modalities against Human immunodeficiency virus (HIV). Predominated by HIV-1 clade C (HIV-1C), the epidemic in India represents the third largest population infected with HIV-1 globally. Glycoprotein 41 (gp41) is critical for viral replication and is a target for the design of therapeutic strategies. However, documentation of viral diversity of gp41 gene in infected individuals from India remains limited. Present study employed high throughput sequencing to examine variation in gp41 amplicons generated from blood derived viruses in 24 HIV-1C infected individuals from Mumbai, India. Sequence diversity profiles were documented in different functional domains of gp41. Furthermore, through a meta-analysis approach, all reported gp41 sequences from India (N = 70) were compared with those from South Africa (N = 126), country with the largest HIV epidemic globally, also predominated by HIV-1C. A total of 44 positions displayed statistically significant differential (p < 0.05) Shannon entropy in the two regions. This comparison also identified 11 codon sites undergoing distinct selection, 8 of which remained differentially selected in an extended comparison of data from Asia (N = 137) and Africa(N = 383). Assessment of correlated mutation networks associated with differentially selected residues revealed common as well as distinct interaction networks. Furthermore, codon usage analysis revealed 17 differentially selected codons (Mann-Whitney test, p < 0.001) in Asia and Africa. Dissimilar trends in GC content across codon positions were also observed. In depth understanding of these divergent evolutionary signatures through extended analysis with larger data-sets would assist development of effective interventions being considered for HIV-1C.
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Affiliation(s)
- Jyoti Sutar
- Department of Biochemistry, National Institute for Research in Reproductive Health (NIRRH), Indian Council of Medical Research (ICMR), Parel, Mumbai, India
| | - Varsha Padwal
- Department of Biochemistry, National Institute for Research in Reproductive Health (NIRRH), Indian Council of Medical Research (ICMR), Parel, Mumbai, India
| | - Vidya Nagar
- Department of Medicine, Grant Government Medical College, Byculla, Mumbai, India
| | - Priya Patil
- Department of Medicine, Grant Government Medical College, Byculla, Mumbai, India
| | - Vainav Patel
- Department of Biochemistry, National Institute for Research in Reproductive Health (NIRRH), Indian Council of Medical Research (ICMR), Parel, Mumbai, India
| | - Atmaram Bandivdekar
- Department of Biochemistry, National Institute for Research in Reproductive Health (NIRRH), Indian Council of Medical Research (ICMR), Parel, Mumbai, India
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Minty M, Canceill T, Lê S, Dubois P, Amestoy O, Loubieres P, Christensen JE, Champion C, Azalbert V, Grasset E, Hardy S, Loubes JM, Mallet JP, Tercé F, Vergnes JN, Burcelin R, Serino M, Diemer F, Blasco-Baque V. Oral health and microbiota status in professional rugby players: A case-control study. J Dent 2018; 79:53-60. [PMID: 30292825 DOI: 10.1016/j.jdent.2018.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/29/2018] [Accepted: 10/03/2018] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Elite athletes are prone to develop oral diseases, which could increase the risk for injuries. The aim of this study was to evaluate the oral health and the composition of oral microbiota of elite rugby players compared to the general population. METHODS We set up a case-control study by screening 24 professional rugby players (PRG) and 22 control patients (CG) for dental and gingival examinations and performed a taxonomic analysis and a predicted functional analysis of oral microbiota. RESULTS The Decay, Missing and Filled (DMF) teeth index (5.54 ± 6.18 versus 2.14 ± 3.01; p = 0.01) and the frequency of gingivitis (58,33% versus 13.63%) were significantly increased in PRG compared to CG. PRG were characterized by a dysbiotic oral microbiota (Shannon Index: 3.32 ± 0.62 in PRG versus 3.79 ± 0.68 in CG; p = 0.03) with an increase of Streptococcus (58.43 ± 16.84 versus 42.60 ± 17.45; p = 0.005), the main genus implicated in caries. Predicted metagenomics of oral microbiota in rugby players was suggestive of a cariogenic metagenome favourable to the development of caries. CONCLUSIONS Our study shows that the oral health of PRG was poorer than the general population. PRG are characterized by a dysbiotic oral microbiota with an increase of the relative abundance of Streptococcus genus, positively correlated to the weight and negatively correlated to the diversity of oral microbiota. CLINICAL SIGNIFICANCE Dental screening should be included in the medical follow-up of professional rugby players as a part of their health management. New strategies such as using probiotics like Lactobacillus could help to control the dysbiosis of oral microbiota.
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Affiliation(s)
- Matthieu Minty
- INSERM U1048, F-31432 Toulouse, France, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), F-31432 Toulouse, France; Université Paul Sabatier III (UPS), F-31432 Toulouse, France; CHU Toulouse, Service d'Odontologie Toulouse, F-3100, France
| | - Thibault Canceill
- Université Paul Sabatier III (UPS), F-31432 Toulouse, France; CHU Toulouse, Service d'Odontologie Toulouse, F-3100, France
| | - Sylvie Lê
- INSERM U1048, F-31432 Toulouse, France, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), F-31432 Toulouse, France; Université Paul Sabatier III (UPS), F-31432 Toulouse, France; CHU Toulouse, Service d'Odontologie Toulouse, F-3100, France
| | - Pauline Dubois
- Université Paul Sabatier III (UPS), F-31432 Toulouse, France; CHU Toulouse, Service d'Odontologie Toulouse, F-3100, France
| | - Oihana Amestoy
- Université Paul Sabatier III (UPS), F-31432 Toulouse, France; CHU Toulouse, Service d'Odontologie Toulouse, F-3100, France
| | - Pascale Loubieres
- INSERM U1048, F-31432 Toulouse, France, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), F-31432 Toulouse, France; Université Paul Sabatier III (UPS), F-31432 Toulouse, France; CHU Toulouse, Service d'Odontologie Toulouse, F-3100, France
| | - Jeffrey E Christensen
- INSERM U1048, F-31432 Toulouse, France, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), F-31432 Toulouse, France; Université Paul Sabatier III (UPS), F-31432 Toulouse, France
| | - Camille Champion
- INSERM U1048, F-31432 Toulouse, France, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), F-31432 Toulouse, France; Université Paul Sabatier III (UPS), F-31432 Toulouse, France; Institut de Mathématiques de Toulouse, Université de Toulouse, 118, route de Narbonne, F-31062 Toulouse Cedex 9, France
| | - Vincent Azalbert
- INSERM U1048, F-31432 Toulouse, France, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), F-31432 Toulouse, France; Université Paul Sabatier III (UPS), F-31432 Toulouse, France
| | - Estelle Grasset
- INSERM U1048, F-31432 Toulouse, France, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), F-31432 Toulouse, France; Université Paul Sabatier III (UPS), F-31432 Toulouse, France
| | - Sara Hardy
- INSERM U1048, F-31432 Toulouse, France, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), F-31432 Toulouse, France; Université Paul Sabatier III (UPS), F-31432 Toulouse, France
| | - Jean-Michel Loubes
- Institut de Mathématiques de Toulouse, Université de Toulouse, 118, route de Narbonne, F-31062 Toulouse Cedex 9, France
| | - Jean-Philippe Mallet
- INSERM U1048, F-31432 Toulouse, France, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), F-31432 Toulouse, France; Université Paul Sabatier III (UPS), F-31432 Toulouse, France
| | - François Tercé
- INSERM U1048, F-31432 Toulouse, France, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), F-31432 Toulouse, France; Université Paul Sabatier III (UPS), F-31432 Toulouse, France
| | - Jean-Noël Vergnes
- INSERM U1048, F-31432 Toulouse, France, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), F-31432 Toulouse, France; Université Paul Sabatier III (UPS), F-31432 Toulouse, France; CHU Toulouse, Service d'Odontologie Toulouse, F-3100, France
| | - Rémy Burcelin
- INSERM U1048, F-31432 Toulouse, France, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), F-31432 Toulouse, France; Université Paul Sabatier III (UPS), F-31432 Toulouse, France
| | - Matteo Serino
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Franck Diemer
- Université Paul Sabatier III (UPS), F-31432 Toulouse, France; CHU Toulouse, Service d'Odontologie Toulouse, F-3100, France; Clément Ader Institute, UMR-CNRS 5312, Toulouse, France
| | - Vincent Blasco-Baque
- INSERM U1048, F-31432 Toulouse, France, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), F-31432 Toulouse, France; Université Paul Sabatier III (UPS), F-31432 Toulouse, France; CHU Toulouse, Service d'Odontologie Toulouse, F-3100, France.
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DeLeon O, Hodis H, O’Malley Y, Johnson J, Salimi H, Zhai Y, Winter E, Remec C, Eichelberger N, Van Cleave B, Puliadi R, Harrington RD, Stapleton JT, Haim H. Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model. PLoS Biol 2017; 15:e2001549. [PMID: 28384158 PMCID: PMC5383018 DOI: 10.1371/journal.pbio.2001549] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 01/08/2023] Open
Abstract
The envelope glycoproteins (Envs) of HIV-1 continuously evolve in the host by random mutations and recombination events. The resulting diversity of Env variants circulating in the population and their continuing diversification process limit the efficacy of AIDS vaccines. We examined the historic changes in Env sequence and structural features (measured by integrity of epitopes on the Env trimer) in a geographically defined population in the United States. As expected, many Env features were relatively conserved during the 1980s. From this state, some features diversified whereas others remained conserved across the years. We sought to identify “clues” to predict the observed historic diversification patterns. Comparison of viruses that cocirculate in patients at any given time revealed that each feature of Env (sequence or structural) exists at a defined level of variance. The in-host variance of each feature is highly conserved among individuals but can vary between different HIV-1 clades. We designate this property “volatility” and apply it to model evolution of features as a linear diffusion process that progresses with increasing genetic distance. Volatilities of different features are highly correlated with their divergence in longitudinally monitored patients. Volatilities of features also correlate highly with their population-level diversification. Using volatility indices measured from a small number of patient samples, we accurately predict the population diversity that developed for each feature over the course of 30 years. Amino acid variants that evolved at key antigenic sites are also predicted well. Therefore, small “fluctuations” in feature values measured in isolated patient samples accurately describe their potential for population-level diversification. These tools will likely contribute to the design of population-targeted AIDS vaccines by effectively capturing the diversity of currently circulating strains and addressing properties of variants expected to appear in the future. HIV-1 is the causative agent of the global AIDS pandemic. The envelope glycoproteins (Envs) of HIV-1 constitute a primary target for antibody-based vaccines. However, the diversity of Envs in the population limits the potential efficacy of this approach. Accurate estimates of the range of variants that currently infect patients and those expected to appear in the future will likely contribute to the design of population-targeted immunogens. We found that different properties (features) of Env have different propensities for small “fluctuations” in their values among viruses that infect patients at any given time point. This propensity of each feature for in-host variance, which we designate “volatility”, is conserved among patients. We apply this parameter to model the evolution of features (in patients and population) as a diffusion process driven by their “diffusion coefficients” (volatilities). Using volatilities measured from a few patient samples from the 1980s, we accurately predict properties of viruses that evolved in the population over the course of 30 years. The diffusion-based model described here efficiently captures evolution of phenotypes in biological systems controlled by a dominant random component.
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Affiliation(s)
- Orlando DeLeon
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Hagit Hodis
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Yunxia O’Malley
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Jacklyn Johnson
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Hamid Salimi
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Yinjie Zhai
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Elizabeth Winter
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Claire Remec
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Noah Eichelberger
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Brandon Van Cleave
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Ramya Puliadi
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Robert D. Harrington
- Center for AIDS Research (CFAR) at the University of Washington, Seattle, Washington, United States of America
| | - Jack T. Stapleton
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Veterans Affairs Medical Center, Iowa City, Iowa, United States of America
| | - Hillel Haim
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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