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Vergni D, Santoni D, Bouba Y, Lemme S, Fabeni L, Carioti L, Bertoli A, Gennari W, Forbici F, Perno CF, Gagliardini R, Ceccherini-Silberstein F, Santoro MM. Evaluation of HIV-1 integrase variability by combining computational and probabilistic approaches. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 101:105294. [PMID: 35513162 DOI: 10.1016/j.meegid.2022.105294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/24/2022] [Accepted: 04/28/2022] [Indexed: 10/18/2022]
Abstract
This study aimed at updating previous data on HIV-1 integrase variability, by using effective bioinformatics methods combining different statistical instruments from simple entropy and mutation rate to more specific approaches such as Hellinger distance. A total of 2133 HIV-1 integrase sequences were analyzed in: i) 1460 samples from drug-naïve [DN] individuals; ii) 386 samples from drug-experienced but INI-naïve [IN] individuals; iii) 287 samples from INI-experienced [IE] individuals. Within the three groups, 76 amino acid positions were highly conserved (≤0.2% variation, Hellinger distance: <0.25%), with 35 fully invariant positions; while, 80 positions were conserved (>0.2% to <1% variation, Hellinger distance: <1%). The H12-H16-C40-C43 and D64-D116-E152 motifs were all well conserved. Some residues were affected by dramatic changes in their mutation distributions, especially between DN and IE samples (Hellinger distance ≥1%). In particular, 15 positions (D6, S24, V31, S39, L74, A91, S119, T122, T124, T125, V126, K160, N222, S230, C280) showed a significant decrease of mutation rate in IN and/or IE samples compared to DN samples. Conversely, 8 positions showed significantly higher mutation rate in samples from treated individuals (IN and/or IE) compared to DN. Some of these positions, such as E92, T97, G140, Y143, Q148 and N155, were already known to be associated with resistance to integrase inhibitors; other positions including S24, M154, V165 and D270 are not yet documented to be associated with resistance. Our study confirms the high conservation of HIV-1 integrase and identified highly invariant positions using robust and innovative methods. The role of novel mutations located in the critical region of HIV-1 integrase deserves further investigation.
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Affiliation(s)
- Davide Vergni
- Istituto per le Applicazioni del Calcolo "Mauro Picone" - CNR, Rome, Italy.
| | - Daniele Santoni
- Istituto di Analisi dei Sistemi ed. Informatica "Antonio Ruberti" - CNR, Rome, Italy
| | - Yagai Bouba
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon; Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Saverio Lemme
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology, IRCCS, National Institute for Infectious Diseases "Lazzaro Spallanzani", Rome, Italy
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Ada Bertoli
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy; Laboratory of Virology, University Hospital "Tor Vergata", Rome, Italy
| | - William Gennari
- Microbiology and Virology Unit, University Hospital, University of Modena and Reggio Emilia, Modena, Italy
| | - Federica Forbici
- Laboratory of Virology, IRCCS, National Institute for Infectious Diseases "Lazzaro Spallanzani", Rome, Italy
| | - Carlo Federico Perno
- Multimodal Laboratory Research Department, Children Hospital Bambino Gesù, IRCCS, Rome, Italy
| | - Roberta Gagliardini
- HIV/AIDS Department, IRCCS, National Institute for Infectious Diseases "Lazzaro Spallanzani", Rome, Italy
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