Identification of a new HIV-1 BC circulating recombinant form (CRF60_BC) in Italian young men having sex with men

Simonetti, Francesco R.; Lai, Alessia; Monno, Laura; Binda, Francesca; Brindicci, Gaetano; Punzi, Grazia; Bozzi, Giorgio; Violin, Michela; Galli, Massimo; Zazzi, Maurizio; Angarano, Gioacchino; Balotta, Claudia

doi:10.1016/j.meegid.2014.02.007

Cited by 32 publications

(30 citation statements)

References 25 publications

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“…Subtype B was found to be most prevalent and determined significantly more often among MSM compared to IDUs and heterosexuals; however, the authors anticipated an influx of different subtypes into Europe in the near future [ 26 ]. Dispersal of non-B subtypes within a local (native) population was already observed in various central and western European countries; for example, subtype G in Portugal, subtype A in Greece, and subtype C in the UK [ 27 – 33 ]. Consistent with these findings are more non-B infections observed among MSM in 2011–2016 as opposed to 2005–2010; namely, 6.2% vs. 2.5% [ 9 ].…”

Section: Discussionmentioning

confidence: 99%

HIV-1 transmitted drug resistance in Slovenia and its impact on predicted treatment effectiveness: 2011–2016 update

et al. 2018

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HIV-positive individuals that have a detected transmitted drug resistance (TDR) at baseline have a higher risk of virological failure with antiretroviral therapy (ART). This study offers an update on the prevalence of TDR in Slovenia, looks for onward transmission of TDR, and reassesses the need for baseline drug resistance testing. Blinded questionnaires and partial pol sequences were obtained from 54.5% (168/308) of all of the patients diagnosed with HIV-1 from 2011 to 2016. Subtype B was detected in 82.7% (139/168) of patients, followed by subtype A (8.3%), subtype C (2.4%), and CRF01_AE (1.8%). Surveillance drug resistance mutations (SDRMs) were found in four individuals (2.4%), all of them men who have sex with men (MSM) and infected with subtype B. K103N was detected in two patients and T68D and T215D in one person each, corresponding to a prevalence of 0%, 1.2%, and 1.2% of TDR to protease inhibitors (PIs), nucleoside reverse transcriptase inhibitors (NRTIs), and non-NRTIs (NNRTIs), respectively. The impact of mutations on drug susceptibility was found to be most pronounced for NNRTIs. No forward spread of TDR within the country was observed; however, phylogenetic analysis revealed several new introductions of HIV into Slovenia in recent years, possibly due to increased risky behavior by MSM. This was indirectly confirmed by a substantial increase in syphilis cases and HIV-1 non-B subtypes during the study period. A drug-resistant HIV variant with good transmission fitness is thus more likely to be imported into Slovenia in the near future, and so TDR should be closely monitored.

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Section: Discussionmentioning

confidence: 99%

HIV-1 transmitted drug resistance in Slovenia and its impact on predicted treatment effectiveness: 2011–2016 update

et al. 2018

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“…Non-B and/or CRF clades have been introduced mainly through waves of migration from areas where are predominant and have been spread through population mobility between European countries. Subsequently their prevalence in the Central and Western European region have been increased, because of dispersal through European and mainly regionally restricted MSM, PWID and heterosexual transmission networks increasing the complexity of the epidemic de Oliveira et al, 2010;Fabeni et al, 2015;Fox et al, 2010;Hemelaar et al, 2011;Hoenigl et al, 2016;Simonetti et al, 2014;Tamalet et al, 2015). Subtype B clade still predominates in Western and Central European countries, but each country has a unique pattern shaped by different regional circumstances and high prevalent local transmission routes.…”

Section: Overview Of Hiv-1 Diversity In Europementioning

confidence: 99%

“…6% in 1980-1992 to 18.9% in 1993-2008, affecting mostly heterosexuals (77.2%) and people of African origin (94.8% of African people carried a non-B strain) (Lai et al, 2010). Nevertheless, MSM transmission networks have been reported recently to drive the expansion of non-B Italian regional sub-epidemics (Fabeni et al, 2015;Simonetti et al, 2014).…”

Section: Western Europementioning

confidence: 99%

Molecular epidemiology of HIV-1 infection in Europe: An overview

Beloukas

Psarris

Giannelou

et al. 2016

Infection, Genetics and Evolution

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“…This new heterogeneity has resulted in the description of an increasing number of CRFs in Western Europe, which traditionally were restricted to regional hotspots with great co-circulation of variants–like sub-Saharan Africa, South-East Asia and parts of South America. These new European recombinants include CRF47_BF and CRF73_BG in Spain and Portugal [ 6 , 7 ], CRF50_A1D in the UK [ 8 ], CRF56_cpx in France [ 9 ], and CRF60_BC in Italy [ 10 ], as well as second-generation complex recombinant strains [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project

Yebra

Frampton²,

Cassarino³

et al. 2018

PLoS ONE

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Background & methodsThe ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospitals NHS Trust and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker.ResultsThe pipeline generated sequences of at least 1Kb of length (median = 7.46Kb, IQR = 4.01Kb) for 375 out of the 420 samples (89%), with 174 (46.4%) being NFLG. A total of 365 sequences (169 of them NFLG) corresponded to unique subjects and were included in the down-stream analyses. The most frequent HIV subtypes were B (n = 149, 40.8%) and C (n = 77, 21.1%) and the circulating recombinant form CRF02_AG (n = 32, 8.8%). We found 14 different CRFs (n = 66, 18.1%) and multiple URFs (n = 32, 8.8%) that involved recombination between 12 different subtypes/CRFs. The most frequent URFs were B/CRF01_AE (4 cases) and A1/D, B/C, and B/CRF02_AG (3 cases each). Most URFs (19/26, 73%) lacked breakpoints in the PR+RT pol region, rendering them undetectable if only that was sequenced. Twelve (37.5%) of the URFs could have emerged within the UK, whereas the rest were probably imported from sub-Saharan Africa, South East Asia and South America. For 2 URFs we found highly similar pol sequences circulating in the UK. We detected 31 phylogenetic clusters using the full dataset: 25 pairs (mostly subtypes B and C), 4 triplets and 2 quadruplets. Some of these were not consistent across different genes due to inter- and intra-subtype recombination. Clusters involved 70 sequences, 19.2% of the dataset.ConclusionsThe initial analysis of genome sequences detected substantial hidden variability in the London HIV epidemic. Analysing full genome sequences, as opposed to only PR+RT, identified previously undetected recombinants. It provided a more reliable description of CRFs (that would be otherwise misclassified) and transmission clusters.

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Identification of a new HIV-1 BC circulating recombinant form (CRF60_BC) in Italian young men having sex with men

Cited by 32 publications

References 25 publications

HIV-1 transmitted drug resistance in Slovenia and its impact on predicted treatment effectiveness: 2011–2016 update

HIV-1 transmitted drug resistance in Slovenia and its impact on predicted treatment effectiveness: 2011–2016 update

Molecular epidemiology of HIV-1 infection in Europe: An overview

A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project

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