Genetic divergence of HIV-1 B subtype in Italy over the years 2003–2016 and impact on CTL escape prevalence View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-12

AUTHORS

Claudia Alteri, Lavinia Fabeni, Rossana Scutari, Giulia Berno, Domenico Di Carlo, Caterina Gori, Ada Bertoli, Alessandra Vergori, Ilaria Mastrorosa, Rita Bellagamba, Cristina Mussini, Manuela Colafigli, Francesco Montella, Alfredo Pennica, Claudio Maria Mastroianni, Enrico Girardi, Massimo Andreoni, Andrea Antinori, Valentina Svicher, Francesca Ceccherini-Silberstein, Carlo Federico Perno, Maria Mercedes Santoro

ABSTRACT

HIV-1 is characterized by high genetic variability, with implications for spread, and immune-escape selection. Here, the genetic modification of HIV-1 B subtype over time was evaluated on 3,328 pol and 1,152 V3 sequences belonging to B subtype and collected from individuals diagnosed in Italy between 2003 and 2016. Sequences were analyzed for genetic-distance from consensus-B (Tajima-Nei), non-synonymous and synonymous rates (dN and dS), CTL escapes, and intra-host evolution over four time-spans (2003-2006, 2007-2009, 2010-2012, 2013-2016). Genetic-distance increased over time for both pol and V3 sequences (P < 0.0001 and 0.0003). Similar results were obtained for dN and dS. Entropy-value significantly increased at 16 pol and two V3 amino acid positions. Seven of them were CTL escape positions (protease: 71; reverse-transcriptase: 35, 162, 177, 202, 207, 211). Sequences with ≥3 CTL escapes increased from 36.1% in 2003-2006 to 54.0% in 2013-2016 (P < 0.0001), and showed better intra-host adaptation than those containing ≤2 CTL escapes (intra-host evolution: 3.0 × 10-3 [2.9 × 10-3-3.1 × 10-3] vs. 4.3 × 10-3 [4.0 × 10-3-5.0 × 10-3], P[LRT] < 0.0001[21.09]). These data provide evidence of still ongoing modifications, involving CTL escape mutations, in circulating HIV-1 B subtype in Italy. These modifications might affect the process of HIV-1 adaptation to the host, as suggested by the slow intra-host evolution characterizing viruses with a high number of CTL escapes. More... »

PAGES

15739

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41598-018-34058-7

DOI

http://dx.doi.org/10.1038/s41598-018-34058-7

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1107713239

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30356083


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