1
|
de Carvalho Lima EN, Lima RSA, Arif MS, Piqueira JRC, Diaz RS. Evolutive Temporal Footprint of an HIV-1 Envelope Protein in an Epidemiologically Linked Cluster. Open AIDS J 2020. [DOI: 10.2174/1874613602014010041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background:
The C2V3C3 region of gp 120, encoded by the HIV-1 envelope gene (env), is an important antigenic target, a key determinant for viral evolution and essential for determining epitopes for vaccines.
Methods:
The relationships among genetic sequence diversity, selective pressure, constraints on HIV-1 envelope protein were explored and also correlated this analysis with information entropy; hypermutation; HIV tropism; CD4+ T cell counts or HIV viral load. A total of 179 HIV-1 C2V3C3 sequences derived from cell-free plasma were used, determined from serial samples, in four epidemiologically linked individuals (one infected blood donor, two transfusion recipients and a sexual partner infected by one of the recipients) over a maximum period of 8 years. This study is important because it considers the analysis of patterns in genomic sequences, without drugs and over time.
Results:
A temporal relationship among information entropy, hypermutation, tropism switch, viral load, and CD4+ T cell count was determined. Changes in information entropy were time-dependent, and an increase in entropy was observed in the C2V3C3 region at amino acids G313 and F317-I320 (related to the GPGR-motif and coreceptor tropism), and at amino acids A281 in C2 and A346 in C3, related to immune escape.
Conclusion:
The increase of information entropy over time was correlated with hypermutation and the emergence of nonR5- strains, which are both associated with more variable genomes.
Collapse
|
2
|
Alteri C, Surdo M, Bellocchi MC, Saccomandi P, Continenza F, Armenia D, Parrotta L, Carioti L, Costa G, Fourati S, Di Santo F, Scutari R, Barbaliscia S, Fedele V, Carta S, Balestra E, Alcaro S, Marcelin AG, Calvez V, Ceccherini-Silberstein F, Artese A, Perno CF, Svicher V. Incomplete APOBEC3G/F Neutralization by HIV-1 Vif Mutants Facilitates the Genetic Evolution from CCR5 to CXCR4 Usage. Antimicrob Agents Chemother 2015; 59:4870-81. [PMID: 26055363 PMCID: PMC4505216 DOI: 10.1128/aac.00137-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/30/2015] [Indexed: 11/20/2022] Open
Abstract
Incomplete APOBEC3G/F neutralization by a defective HIV-1Vif protein can promote genetic diversification by inducing G-to-A mutations in the HIV-1 genome. The HIV-1 Env V3 loop, critical for coreceptor usage, contains several putative APOBEC3G/F target sites. Here, we determined if APOBEC3G/F, in the presence of Vif-defective HIV-1 virus, can induce G-to-A mutations at V3 positions critical to modulation of CXCR4 usage. Peripheral blood mononuclear cells (PBMC) and monocyte-derived macrophages (MDM) from 2 HIV-1-negative donors were infected with CCR5-using 81.A-VifWT virus (i.e., with wild-type [WT] Vif protein), 81.A-VifE45G, or 81.A-VifK22E (known to incompletely/partially neutralize APOBEC3G/F). The rate of G-toA mutations was zero or extremely low in 81.A-VifWT- and 81.A-VifE45G-infected PBMC from both donors. Conversely, G-to-A enrichment was detected in 81.A-VifK22E-infected PBMC (prevalence ranging from 2.18% at 7 days postinfection [dpi] to 3.07% at 21 dpi in donor 1 and from 10.49% at 7 dpi to 8.69% at 21 dpi in donor 2). A similar scenario was found in MDM. G-to-A mutations occurred at 8 V3 positions, resulting in nonsynonymous amino acid substitutions. Of them, G24E and E25K strongly correlated with phenotypically/genotypically defined CXCR4-using viruses (P = 0.04 and 5.5e-7, respectively) and increased the CXCR4 N-terminal binding affinity for V3 (WT, -40.1 kcal/mol; G24E, -510 kcal/mol; E25K, -522 kcal/mol). The analysis of paired V3 and Vif DNA sequences from 84 HIV-1-infected patients showed that the presence of a Vif-defective virus correlated with CXCR4 usage in proviral DNA (P = 0.04). In conclusion, incomplete APOBEC3G/F neutralization by a single Vif amino acid substitution seeds a CXCR4-using proviral reservoir. This can have implications for the success of CCR5 antagonist-based therapy, as well as for the risk of disease progression.
Collapse
Affiliation(s)
- Claudia Alteri
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | - Matteo Surdo
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | | | - Patrizia Saccomandi
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | | | - Daniele Armenia
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | - Lucia Parrotta
- Università Magna Graecia di Catanzaro, Dipartimento di Scienze della Salute, Campus Universitario, Catanzaro, Italy
| | - Luca Carioti
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | - Giosuè Costa
- Università Magna Graecia di Catanzaro, Dipartimento di Scienze della Salute, Campus Universitario, Catanzaro, Italy
| | - Slim Fourati
- Department of Virology, Hospital "Pitie Salpietrere," Paris, France
| | - Fabiola Di Santo
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | - Rossana Scutari
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | - Silvia Barbaliscia
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | | | | | - Emanuela Balestra
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| | - Stefano Alcaro
- Università Magna Graecia di Catanzaro, Dipartimento di Scienze della Salute, Campus Universitario, Catanzaro, Italy
| | | | - Vincent Calvez
- Department of Virology, Hospital "Pitie Salpietrere," Paris, France
| | | | - Anna Artese
- Università Magna Graecia di Catanzaro, Dipartimento di Scienze della Salute, Campus Universitario, Catanzaro, Italy
| | - Carlo Federico Perno
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy INMI L. Spallanzani, Rome, Italy
| | - Valentina Svicher
- University of Rome "Tor Vergata," Department of Experimental Medicine and Surgery, Rome, Italy
| |
Collapse
|