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Berkhout B, van Hemert FJ. Silent codon positions in the A-rich HIV RNA genome that do not easily become A: Restrictions imposed by the RNA sequence and structure. Virus Evol 2022; 8:veac072. [PMID: 36533144 PMCID: PMC9752802 DOI: 10.1093/ve/veac072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/13/2022] [Accepted: 08/04/2022] [Indexed: 07/30/2023] Open
Abstract
There is a strong evolutionary tendency of the human immunodeficiency virus (HIV) to accumulate A nucleotides in its RNA genome, resulting in a mere 40 per cent A count. This A bias is especially dominant for the so-called silent codon positions where any nucleotide can be present without changing the encoded protein. However, particular silent codon positions in HIV RNA refrain from becoming A, which became apparent upon genome analysis of many virus isolates. We analyzed these 'noA' genome positions to reveal the underlying reason for their inability to facilitate the A nucleotide. We propose that local RNA structure requirements can explain the absence of A at these sites. Thus, noA sites may be prominently involved in the correct folding of the viral RNA. Turning things around, the presence of multiple clustered noA sites may reveal the presence of important sequence and/or structural elements in the HIV RNA genome.
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Affiliation(s)
| | - Formijn J van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
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Lai A, Simonetti FR, Brindicci G, Bergna A, Di Giambenedetto S, Sterrantino G, Mussini C, Menzo S, Bagnarelli P, Zazzi M, Angarano G, Galli M, Monno L, Balotta C. Local Epidemics Gone Viral: Evolution and Diffusion of the Italian HIV-1 Recombinant Form CRF60_BC. Front Microbiol 2019; 10:769. [PMID: 31031735 PMCID: PMC6474184 DOI: 10.3389/fmicb.2019.00769] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/26/2019] [Indexed: 12/15/2022] Open
Abstract
The molecular epidemiology of HIV-1 in Italy is becoming increasingly complex, mainly due to the spread of non-B subtypes and the emergence of new recombinant forms. We previously characterized the outbreak of the first Italian circulating recombinant form (CRF60_BC), occurring among young MSM living in Apulia between the years 2009 and 2011. Here we show a 5-year follow-up surveillance to trace the evolution of CRF60_BC and to investigate its further spread in Italy. We collected additional sequences and clinical data from patients harboring CRF60_BC, enrolled at the Infectious Diseases Clinic of the University of Bari. In addition to the 24 previously identified sequences, we retrieved 27 CRF60_BC sequences from patients residing in Apulia, whose epidemiological and clinical features did not differ from those of the initial outbreak, i.e., the Italian origin, young age at HIV diagnosis (median: 24 years; range: 18–37), MSM risk factor (23/25, 92%) and recent infection (from 2008 to 2017). Sequence analysis revealed a growing overall nucleotide diversity, with few nucleotide changes that were fixed over time. Twenty-seven additional sequences were detected across Italy, spanning multiple distant regions. Using a BLAST search, we also identified a CRF60_BC sequence isolated in United Kingdom in 2013. Three patients harbored a unique second generation recombinant form in which CRF60_BC was one of the parental strains. Our data show that CRF60_BC gained epidemic importance, spreading among young MSM in multiple Italian regions and increasing its population size in few years, as the number of sequences identified so far has triplicated since our first report. The observed further divergence of CRF60_BC is likely due to evolutionary bottlenecks and host adaptation during transmission chains. Of note, we detected three second-generation recombinants, further supporting a widespread circulation of CRF60_BC and the increasing complexity of the HIV-1 epidemic in Italy.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetano Brindicci
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetana Sterrantino
- Division of Tropical and Infectious Diseases, Careggi Hospital, Florence, Italy
| | - Cristina Mussini
- Clinic of Infectious Diseases, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Menzo
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Patrizia Bagnarelli
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Massimo Galli
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Laura Monno
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Claudia Balotta
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
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Alteri C, Scutari R, Bertoli A, Armenia D, Gori C, Fabbri G, Mastroianni CM, Cerva C, Cristaudo A, Vicenti I, Bruzzone B, Zazzi M, Andreoni M, Antinori A, Svicher V, Ceccherini-Silberstein F, Perno CF, Santoro MM. Integrase strand transfer inhibitor-based regimen is related with a limited HIV-1 V3 loop evolution in clinical practice. Virus Genes 2019; 55:290-297. [PMID: 30796743 DOI: 10.1007/s11262-019-01649-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Abstract
Integrase-strand-transfer inhibitors (INSTIs) are known to rapidly reduce HIV-1 plasma viral load, replication cycles, and new viral integrations, thus potentially limiting viral evolution. Here, we assessed the role of INSTIs on HIV-1 V3 evolution in a cohort of 89 HIV-1-infected individuals starting an INSTI- (N = 41, [dolutegravir: N = 1; elvitegravir: N = 3; raltegravir: N = 37]) or a non-INSTI-based (N = 48) combined antiretroviral therapy (cART), with two plasma RNA V3 genotypic tests available (one before [baseline] and one during cART). V3 sequences were analysed for genetic distance (Tajima-Nei model) and positive selection (dN/dS ratio). Individuals were mainly infected by B subtype (71.9%). Median (interquartile-range, IQR) plasma viral load and CD4 + T cell count at baseline were 4.8 (3.5-5.5) log10 copies/mL and 207 (67-441) cells/mm3, respectively. Genetic distance (median, IQR) between the V3 sequences obtained during cART and those obtained at baseline was 0.04 (0.01-0.07). By considering treatment, genetic distance was significantly lower in INSTI-treated than in non-INSTI-treated individuals (median [IQR]: 0.03[0.01-0.04] vs. 0.05[0.02-0.08], p = 0.026). In line with this, a positive selection (defined as dN/dS ≥ 1) was observed in 36.6% of V3 sequences belonging to the INSTI-treated group and in 56.3% of non-INSTI group (p = 0.05). Multivariable logistic regression confirmed the independent correlation of INSTI-based regimens with a lower probability of both V3 evolution (adjusted odds-ratio: 0.35 [confidence interval (CI) 0.13-0.88], p = 0.027) and positive selection (even if with a trend) (adjusted odds-ratio: 0.46 [CI 0.19-1.11], p = 0.083). Overall, this study suggests a role of INSTI-based regimen in limiting HIV-1 V3 evolution over time. Further studies are required to confirm these findings.
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Affiliation(s)
- Claudia Alteri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy. .,Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122, Milano, Italia.
| | - Rossana Scutari
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Ada Bertoli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Daniele Armenia
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.,UniCamillus, Saint Camillus International University of Health Sciences, Via di Sant'Alessandro, 8, 00131, Rome, Italy
| | - Caterina Gori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149, Rome, Italy
| | - Gabriele Fabbri
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149, Rome, Italy
| | | | - Carlotta Cerva
- Infectious Diseases Unit, University Hospital of Rome "Tor Vergata", Viale Oxford 81, 00133, Rome, Italy
| | - Antonio Cristaudo
- Infectious Dermatology and Allergology Unit, San Gallicano Dermatological Institute, IFO-IRCCS, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnology, University of Siena, Viale Bracci 2, 53100, Siena, Italy
| | - Bianca Bruzzone
- Hygiene Unit, IRCCS AOU San Martino - IST, Largo R. Benzi 10, 16132, Genoa, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, Viale Bracci 2, 53100, Siena, Italy
| | - Massimo Andreoni
- Infectious Diseases Unit, University Hospital of Rome "Tor Vergata", Viale Oxford 81, 00133, Rome, Italy
| | - Andrea Antinori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149, Rome, Italy
| | - Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | | | - Carlo Federico Perno
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122, Milano, Italia.,National Institute for Infectious Diseases L. Spallanzani, IRCCS, Via Portuense 292, 00149, Rome, Italy
| | - Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
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Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Pérez-Losada M. Mutation and recombination in pathogen evolution: Relevance, methods and controversies. Infect Genet Evol 2017; 63:295-306. [PMID: 28951202 DOI: 10.1016/j.meegid.2017.09.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
Abstract
Mutation and recombination drive the evolution of most pathogens by generating the genetic variants upon which selection operates. Those variants can, for example, confer resistance to host immune systems and drug therapies or lead to epidemic outbreaks. Given their importance, diverse evolutionary studies have investigated the abundance and consequences of mutation and recombination in pathogen populations. However, some controversies persist regarding the contribution of each evolutionary force to the development of particular phenotypic observations (e.g., drug resistance). In this study, we revise the importance of mutation and recombination in the evolution of pathogens at both intra-host and inter-host levels. We also describe state-of-the-art analytical methodologies to detect and quantify these two evolutionary forces, including biases that are often ignored in evolutionary studies. Finally, we present some of our former studies involving pathogenic taxa where mutation and recombination played crucial roles in the recovery of pathogenic fitness, the generation of interspecific genetic diversity, or the design of centralized vaccines. This review also illustrates several common controversies and pitfalls in the analysis and in the evaluation and interpretation of mutation and recombination outcomes.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain; Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Catarina Branco
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Nadine Castelhano
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago, Chile.
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, Washington, DC, United States; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal.
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Klaver B, van der Velden Y, van Hemert F, van der Kuyl AC, Berkhout B. HIV-1 tolerates changes in A-count in a small segment of the pol gene. Retrovirology 2017; 14:43. [PMID: 28870251 PMCID: PMC5583962 DOI: 10.1186/s12977-017-0367-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/30/2017] [Indexed: 11/21/2022] Open
Abstract
Background The HIV-1 RNA genome has a biased nucleotide composition with a surplus of As. Several hypotheses have been put forward to explain this striking phenomenon, but the A-count of the HIV-1 genome has thus far not been systematically manipulated. The reason for this reservation is the likelihood that known and unknown sequence motifs will be affected by such a massive mutational approach, thus resulting in replication-impaired virus mutants. We present the first attempt to increase and decrease the A-count in a relatively small polymerase (pol) gene segment of HIV-1 RNA. Results To minimize the mutational impact, a new mutational approach was developed that is inspired by natural sequence variation as present in HIV-1 isolates. This phylogeny-instructed mutagenesis allowed us to create replication-competent HIV-1 mutants with a significantly increased or decreased local A-count. The local A-count of the wild-type (wt) virus (40.2%) was further increased to 46.9% or reduced to 31.7 and 26.3%. These HIV-1 variants replicate efficiently in vitro, despite the fact that the pol changes cause a quite profound move in HIV–SIV sequence space. Conclusions Extrapolating these results to the complete 9 kb RNA genome, we may cautiously suggest that the A-rich signature does not have to be maintained. This survey also provided clues that silent codon changes, in particular from G-to-A, determine the subtype-specific sequence signatures.
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Affiliation(s)
- Bep Klaver
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Yme van der Velden
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Formijn van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
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