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2. Unexpected rise in the circulation of complex HBV variants enriched of HBsAg vaccine-escape mutations in HBV genotype-D: potential impact on HBsAg detection/quantification and vaccination strategies

Author

Piermatteo, L, D'Anna, S, Bertoli, A, Bellocchi, M, Carioti, L, Fabeni, L, Alkhatib, M, Frazia, Sl, Lichtner, M, Mastroianni, C, Sanctis, Gd, Marignani, M, Pasquazzi, C, Iapadre, N, Parruti, G, Cappiello, G, Vecchiet, J, Malagnino, V, Grelli, S, Ceccherini-Silbertein, F, Andreoni, M, Sarmati, L, Svicher, V, and Salpini, R

Subjects
HBsAg, vaccine-escape mutations, HBsAg secretion, HBV, HBsAg antigenicity, Settore MED/07
Published
2023

3. Genetic intra-host variability of full-length MPXV genomes in multiple tissues over time

Author

Rueca, M., primary, Giombini, E., additional, Mazzotta, V., additional, Gramigna, G., additional, Gruber, CEM., additional, Pinnetti, C., additional, Fabeni, L., additional, Tucci, F., additional, Butera, O., additional, Matusali, G., additional, Mariano, A., additional, Mondi, A., additional, Lalle, E., additional, Forbici, F., additional, Girardi, E., additional, Vaia, F., additional, Nicastri, E., additional, Antinori, A., additional, and Maggi, F., additional

Published
2023
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5. Dynamics and phylogenetic relationships of HIV-1 transmitted drug resistance according to subtype in Italy over the years 2000–14

Author

Fabeni, L., Alteri, C., Di Carlo, D., Orchi, N., Carioti, L., Bertoli, A., Gori, C., Forbici, F., Continenza, F., Maffongelli, G., Pinnetti, C., Vergori, A., Mondi, A., Ammassari, A., Borghi, V., Giuliani, M., De Carli, G., Pittalis, S., Grisetti, S., Pennica, A., Mastroianni, C. M., Montella, F., Cristaudo, A., Mussini, C., Girardi, E., Andreoni, M., Antinori, A., Ceccherini-Silberstein, F., Perno, C. F., Santoro, M. M., Girardi, E., Capobianchi, M. R., Perno, C. F., Orchi, N., Navarra, A., Palummieri, A., Abbate, I., Ammassari, A., D’Arrigo, R., De Carli, G., Fabeni, L., Forbici, F., Fusco, F. M., Gori, C., Grisetti, S., Mariano, A., Nicastri, E., Nurra, G., Pinnetti, C., Pittalis, S., Puro, V., Sampaolesi, A., Sciarrone, M. R., Scognamiglio, P., Selleri, M., Sias, C., Zaccarelli, M., Di Carlo, A., Giuliani, M., Vullo, V., Falciano, M., Pennica, A., Errigo, F., Gattari, P., Spizzichino, L., Schito, S., Andreoni, M., Sarmati, L., Buonomini, A. R., Cerva, C., Mastroianni, C., Lichtner, M., Mercurio, V. S., Anzalone, E., Pitorri, A., Caterini, A., and Barbacci, S. Aviani

Published
2017
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6. Transmitted drug resistance to integrase based first-line HIV antiretroviral regimens in the Mediterranean Europe

Author

de Salazar, A, Viñuela, L, Fuentes, A, Teyssou, E, Charpentier, C, Lambert-Niclot, S, Serrano-Conde, E, Pingarilho, M, Fabeni, L, De Monte, A, Stefic, K, Perno, Cf, Aguilera, A, Falces, I, Delgado, R, Fernandes, S, Diogo, I, Gomes, P, Paraskevis, D, Santoro, M, Ceccherini-Silberstein, F, Marcelin, A, and Garcia, F

Subjects
resistance, transmission, HIV, Settore MED/07
Abstract

To study the prevalence of transmitted drug resistance (TDR) to INSTIs and NRTIs, and of clinically relevant resistance (CRR), in newly-diagnosed people with HIV (PWH) naïve to antiretroviral therapy (ART) in Europe.MeditRes HIV is a consortium that includes ART naïve PWH newly diagnosed in France, Greece, Italy, Portugal, and Spain during the years 2018-2021. Reverse transcriptase (RT) and Integrase (INSTI) sequences were provided by participating centers. To evaluate the prevalence of surveillance drug resistance mutations (SDRM) we used the CPR tools from Stanford HIV-website. To evaluate clinically relevant resistance (CRR), defined as any resistance level= 3, we used the Stanford v.9.1HIVDB Algorithm.We included 2705 PWH, 72% men, median age of 37 (IQR, 30-48); 43.7% infected by non-B subtypes. The prevalence of INSTI-SDRMs was 0.30% (T66I, T66A, E92Q, E138T, E138K, Y143R, S147G and R263K, all n = 1), and of NRTI-SDRMs was 5.77% (M184V n = 23, 0.85%; M184I n = 5, 0.18%; K65R/N n = 3, 0.11%; K70E n = 2, 0.07%; L74V/I n = 5, 0.18%; any TAMs n = 118, 4.36%). INSTI-CRR was 2.33% (0.15% dolutegravir/bictegravir; 2.29% raltegravir/elvitegravir), and 1.74% to first-line NRTIs (0.89% tenofovir/tenofovir alafenamide fumarate; 1.74% abacavir; 1.07% lamivudine/emtricitabine).We present the most recent data on TDR to integrase based first-line regimens in Europe. Given the low prevalence of CRR to second generation integrase inhibitors and to first-line NRTIs, in the years 2018-2021 it is unlikely that newly diagnosed PWH in MeditRes countries would present with baseline resistance to a first-line regimen based on second generation integrase inhibitors.

Published
2022

7. Evaluation of HIV transmission clusters among natives and foreigners living in Italy

Author

Fabeni, L, Santoro, M, Lorenzini, P, Rusconi, S, Gianotti, N, Costantini, A, Sarmati, L, Antinori, A, Ceccherini-Silberstein, F, d'Arminio Monforte, A, Saracino, A, Girardi, E, Castagna, A, Castelli, F, Cauda, R, Di Perri, G, Galli, M, Iardino, R, Ippolito, G, Lazzarin, A, Marchetti, G, Rezza, G, von Schloesser, F, Viale, P, Cozzi-Lepri, A, Gori, A, Lo Caputo, S, Maggiolo, F, Mussini, C, Puoti, M, Perno, C, Bai, F, Bandera, A, Bonora, S, Borderi, M, Calcagno, A, Capobianchi, M, Cicalini, S, Cingolani, A, Cinque, P, Di Biagio, A, Gagliardini, R, Guaraldi, G, Lapadula, G, Lichtner, M, Lai, A, Madeddu, G, Merlini, E, Nozza, S, Piconi, S, Pinnetti, C, Quiros Roldan, E, Rossotti, R, Spagnuolo, V, Svicher, V, Taramasso, L, Fanti, I, Galli, L, Rodano, A, Macchia, M, Tavelli, A, Bove, A, Camposeragna, A, Errico, M, Manfredini, M, Perziano, A, Calvino, V, Carrara, S, Di Caro, A, Graziano, S, Petroni, F, Prota, G, Truffa, S, Giacometti, A, Barocci, V, Angarano, G, Monno, L, Milano, E, Suardi, C, Donati, V, Verucchi, G, Castelnuovo, F, Minardi, C, Menzaghi, B, Abeli, C, Chessa, L, Pes, F, Cacopardo, B, Celesia, B, Vecchiet, J, Falasca, K, Pan, A, Lorenzotti, S, Sighinolfi, L, Segala, D, Blanc, P, Vichi, F, Cassola, G, Bassetti, M, Alessandrini, A, Bobbio, N, Mazzarello, G, Fondaco, L, Bonfanti, P, Molteni, C, Chiodera, A, Milini, P, Nunnari, G, Pellicano, G, Rizzardini, G, Cannizzo, E, Moioli, M, Piolini, R, Bernacchia, D, Poli, A, Tincati, C, Puzzolante, C, Migliorino, C, Sangiovanni, V, Borgia, G, Esposito, V, Di Flumeri, G, Gentile, I, Rizzo, V, Cattelan, A, Marinello, S, Cascio, A, Trizzino, M, Francisci, D, Schiaroli, E, Parruti, G, Sozio, F, Lazzaretti, C, Corsini, R, Cristaudo, A, Vullo, V, Acinapura, R, Lamonica, S, Capozzi, M, Mondi, A, Rivano Capparuccia, M, Iaiani, G, Latini, A, Onnelli, G, Plazzi, M, de Girolamo, G, Vergori, A, Cecchetto, M, Viviani, F, de Vito, A, Rossetti, B, Montagnani, F, Franco, A, Fontana Del Vecchio, R, Di Giuli, C, Caramello, P, Orofino, G, Sciandra, M, Londero, A, Manfrin, V, Battagin, G, Starnini, G, Ialungo, A, Fabeni L., Santoro M. M., Lorenzini P., Rusconi S., Gianotti N., Costantini A., Sarmati L., Antinori A., Ceccherini-Silberstein F., d'Arminio Monforte A., Saracino A., Girardi E., Castagna A., Castelli F., Cauda R., Di Perri G., Galli M., Iardino R., Ippolito G., Lazzarin A., Marchetti G. C., Rezza G., von Schloesser F., Viale P., Cozzi-Lepri A., Gori A., Lo Caputo S., Maggiolo F., Mussini C., Puoti M., Perno C. F., Bai F., Bandera A., Bonora S., Borderi M., Calcagno A., Capobianchi M. R., Cicalini S., Cingolani A., Cinque P., Di Biagio A., Gagliardini R., Guaraldi G., Lapadula G., Lichtner M., Lai A., Madeddu G., Merlini E., Nozza S., Piconi S., Pinnetti C., Quiros Roldan E., Rossotti R., Spagnuolo V., Svicher V., Taramasso L., Fanti I., Galli L., Rodano A., Macchia M., Tavelli A., Bove A., Camposeragna A., Errico M., Manfredini M., Perziano A., Calvino V., Carrara S., Di Caro A., Graziano S., Petroni F., Prota G., Truffa S., Giacometti A., Barocci V., Angarano G., Monno L., Milano E., Suardi C., Donati V., Verucchi G., Castelnuovo F., Minardi C., Menzaghi B., Abeli C., Chessa L., Pes F., Cacopardo B., Celesia B., Vecchiet J., Falasca K., Pan A., Lorenzotti S., Sighinolfi L., Segala D., Blanc P., Vichi F., Cassola G., Bassetti M., Alessandrini A., Bobbio N., Mazzarello G., Fondaco L., Bonfanti P., Molteni C., Chiodera A., Milini P., Nunnari G., Pellicano G., Rizzardini G., Cannizzo E. S., Moioli M. C., Piolini R., Bernacchia D., Poli A., Tincati C., Puzzolante C., Migliorino C., Sangiovanni V., Borgia G., Esposito V., Di Flumeri G., Gentile I., Rizzo V., Cattelan A. M., Marinello S., Cascio A., Trizzino M., Francisci D., Schiaroli E., Parruti G., Sozio F., Lazzaretti C., Corsini R., Cristaudo A., Vullo V., Acinapura R., Lamonica S., Capozzi M., Mondi A., Rivano Capparuccia M., Iaiani G., Latini A., Onnelli G., Plazzi M. M., de Girolamo G., Vergori A., Cecchetto M., Viviani F., de Vito A., Rossetti B., Montagnani F., Franco A., Fontana Del Vecchio R., Di Giuli C., Caramello P., Orofino G. C., Sciandra M., Londero A., Manfrin V., Battagin G., Starnini G., Ialungo A., Fabeni, L, Santoro, M, Lorenzini, P, Rusconi, S, Gianotti, N, Costantini, A, Sarmati, L, Antinori, A, Ceccherini-Silberstein, F, d'Arminio Monforte, A, Saracino, A, Girardi, E, Castagna, A, Castelli, F, Cauda, R, Di Perri, G, Galli, M, Iardino, R, Ippolito, G, Lazzarin, A, Marchetti, G, Rezza, G, von Schloesser, F, Viale, P, Cozzi-Lepri, A, Gori, A, Lo Caputo, S, Maggiolo, F, Mussini, C, Puoti, M, Perno, C, Bai, F, Bandera, A, Bonora, S, Borderi, M, Calcagno, A, Capobianchi, M, Cicalini, S, Cingolani, A, Cinque, P, Di Biagio, A, Gagliardini, R, Guaraldi, G, Lapadula, G, Lichtner, M, Lai, A, Madeddu, G, Merlini, E, Nozza, S, Piconi, S, Pinnetti, C, Quiros Roldan, E, Rossotti, R, Spagnuolo, V, Svicher, V, Taramasso, L, Fanti, I, Galli, L, Rodano, A, Macchia, M, Tavelli, A, Bove, A, Camposeragna, A, Errico, M, Manfredini, M, Perziano, A, Calvino, V, Carrara, S, Di Caro, A, Graziano, S, Petroni, F, Prota, G, Truffa, S, Giacometti, A, Barocci, V, Angarano, G, Monno, L, Milano, E, Suardi, C, Donati, V, Verucchi, G, Castelnuovo, F, Minardi, C, Menzaghi, B, Abeli, C, Chessa, L, Pes, F, Cacopardo, B, Celesia, B, Vecchiet, J, Falasca, K, Pan, A, Lorenzotti, S, Sighinolfi, L, Segala, D, Blanc, P, Vichi, F, Cassola, G, Bassetti, M, Alessandrini, A, Bobbio, N, Mazzarello, G, Fondaco, L, Bonfanti, P, Molteni, C, Chiodera, A, Milini, P, Nunnari, G, Pellicano, G, Rizzardini, G, Cannizzo, E, Moioli, M, Piolini, R, Bernacchia, D, Poli, A, Tincati, C, Puzzolante, C, Migliorino, C, Sangiovanni, V, Borgia, G, Esposito, V, Di Flumeri, G, Gentile, I, Rizzo, V, Cattelan, A, Marinello, S, Cascio, A, Trizzino, M, Francisci, D, Schiaroli, E, Parruti, G, Sozio, F, Lazzaretti, C, Corsini, R, Cristaudo, A, Vullo, V, Acinapura, R, Lamonica, S, Capozzi, M, Mondi, A, Rivano Capparuccia, M, Iaiani, G, Latini, A, Onnelli, G, Plazzi, M, de Girolamo, G, Vergori, A, Cecchetto, M, Viviani, F, de Vito, A, Rossetti, B, Montagnani, F, Franco, A, Fontana Del Vecchio, R, Di Giuli, C, Caramello, P, Orofino, G, Sciandra, M, Londero, A, Manfrin, V, Battagin, G, Starnini, G, Ialungo, A, Fabeni L., Santoro M. M., Lorenzini P., Rusconi S., Gianotti N., Costantini A., Sarmati L., Antinori A., Ceccherini-Silberstein F., d'Arminio Monforte A., Saracino A., Girardi E., Castagna A., Castelli F., Cauda R., Di Perri G., Galli M., Iardino R., Ippolito G., Lazzarin A., Marchetti G. C., Rezza G., von Schloesser F., Viale P., Cozzi-Lepri A., Gori A., Lo Caputo S., Maggiolo F., Mussini C., Puoti M., Perno C. F., Bai F., Bandera A., Bonora S., Borderi M., Calcagno A., Capobianchi M. R., Cicalini S., Cingolani A., Cinque P., Di Biagio A., Gagliardini R., Guaraldi G., Lapadula G., Lichtner M., Lai A., Madeddu G., Merlini E., Nozza S., Piconi S., Pinnetti C., Quiros Roldan E., Rossotti R., Spagnuolo V., Svicher V., Taramasso L., Fanti I., Galli L., Rodano A., Macchia M., Tavelli A., Bove A., Camposeragna A., Errico M., Manfredini M., Perziano A., Calvino V., Carrara S., Di Caro A., Graziano S., Petroni F., Prota G., Truffa S., Giacometti A., Barocci V., Angarano G., Monno L., Milano E., Suardi C., Donati V., Verucchi G., Castelnuovo F., Minardi C., Menzaghi B., Abeli C., Chessa L., Pes F., Cacopardo B., Celesia B., Vecchiet J., Falasca K., Pan A., Lorenzotti S., Sighinolfi L., Segala D., Blanc P., Vichi F., Cassola G., Bassetti M., Alessandrini A., Bobbio N., Mazzarello G., Fondaco L., Bonfanti P., Molteni C., Chiodera A., Milini P., Nunnari G., Pellicano G., Rizzardini G., Cannizzo E. S., Moioli M. C., Piolini R., Bernacchia D., Poli A., Tincati C., Puzzolante C., Migliorino C., Sangiovanni V., Borgia G., Esposito V., Di Flumeri G., Gentile I., Rizzo V., Cattelan A. M., Marinello S., Cascio A., Trizzino M., Francisci D., Schiaroli E., Parruti G., Sozio F., Lazzaretti C., Corsini R., Cristaudo A., Vullo V., Acinapura R., Lamonica S., Capozzi M., Mondi A., Rivano Capparuccia M., Iaiani G., Latini A., Onnelli G., Plazzi M. M., de Girolamo G., Vergori A., Cecchetto M., Viviani F., de Vito A., Rossetti B., Montagnani F., Franco A., Fontana Del Vecchio R., Di Giuli C., Caramello P., Orofino G. C., Sciandra M., Londero A., Manfrin V., Battagin G., Starnini G., and Ialungo A.

Abstract

We aimed at evaluating the characteristics of HIV-1 molecular transmission clusters (MTCs) among natives and migrants living in Italy, diagnosed between 1998 and 2018. Phylogenetic analyses were performed on HIV-1 polymerase (pol) sequences to characterise subtypes and identify MTCs, divided into small (SMTCs, 2-3 sequences), medium (MMTCs, 4-9 sequences) and large (LMTCs, ≥10 sequences). Among 3499 drug-naïve individuals enrolled in the Italian Cohort Naive Antiretroviral (ICONA) cohort (2804 natives; 695 migrants), 726 (20.8%; 644 natives, 82 migrants) were involved in 228 MTCs (6 LMTCs, 36 MMTCs, 186 SMTCs). Migrants contributed 14.4% to SMTCs, 7.6% to MMTCs and 7.1% to LMTCs, respectively. HIV-1 non-B subtypes were found in 51 MTCs; noteworthy was that non-B infections involved in MTCs were more commonly found in natives (n = 47) than in migrants (n = 4). Factors such as Italian origin, being men who have sex with men (MSM), younger age, more recent diagnosis and a higher CD4 count were significantly associated with MTCs. Our findings show that HIV-1 clustering transmission among newly diagnosed individuals living in Italy is prevalently driven by natives, mainly MSM, with a more recent diagnosis and frequently infected with HIV-1 non-B subtypes. These results can contribute to monitoring of the HIV epidemic and guiding the public health response to prevent new HIV infections.

Published
2020

8. Evaluation of HIV transmission clusters among natives and foreigners living in Italy

Author

Fabeni L., Santoro M. M., Lorenzini P., Rusconi S., Gianotti N., Costantini A., Sarmati L., Antinori A., Ceccherini-Silberstein F., d'Arminio Monforte A., Saracino A., Girardi E., Castagna A., Castelli F., Cauda R., Di Perri G., Galli M., Iardino R., Ippolito G., Lazzarin A., Marchetti G. C., Rezza G., von Schloesser F., Viale P., Cozzi-Lepri A., Gori A., Lo Caputo S., Maggiolo F., Mussini C., Puoti M., Perno C. F., Bai F., Bandera A., Bonora S., Borderi M., Calcagno A., Capobianchi M. R., Cicalini S., Cingolani A., Cinque P., Di Biagio A., Gagliardini R., Guaraldi G., Lapadula G., Lichtner M., Lai A., Madeddu G., Merlini E., Nozza S., Piconi S., Pinnetti C., Quiros Roldan E., Rossotti R., Spagnuolo V., Svicher V., Taramasso L., Fanti I., Galli L., Rodano A., Macchia M., Tavelli A., Bove A., Camposeragna A., Errico M., Manfredini M., Perziano A., Calvino V., Carrara S., Di Caro A., Graziano S., Petroni F., Prota G., Truffa S., Giacometti A., Barocci V., Angarano G., Monno L., Milano E., Suardi C., Donati V., Verucchi G., Castelnuovo F., Minardi C., Menzaghi B., Abeli C., Chessa L., Pes F., Cacopardo B., Celesia B., Vecchiet J., Falasca K., Pan A., Lorenzotti S., Sighinolfi L., Segala D., Blanc P., Vichi F., Cassola G., Bassetti M., Alessandrini A., Bobbio N., Mazzarello G., Fondaco L., Bonfanti P., Molteni C., Chiodera A., Milini P., Nunnari G., Pellicano G., Rizzardini G., Cannizzo E. S., Moioli M. C., Piolini R., Bernacchia D., Poli A., Tincati C., Puzzolante C., Migliorino C., Sangiovanni V., Borgia G., Esposito V., Di Flumeri G., Gentile I., Rizzo V., Cattelan A. M., Marinello S., Cascio A., Trizzino M., Francisci D., Schiaroli E., Parruti G., Sozio F., Lazzaretti C., Corsini R., Cristaudo A., Vullo V., Acinapura R., Lamonica S., Capozzi M., Mondi A., Rivano Capparuccia M., Iaiani G., Latini A., Onnelli G., Plazzi M. M., de Girolamo G., Vergori A., Cecchetto M., Viviani F., de Vito A., Rossetti B., Montagnani F., Franco A., Fontana Del Vecchio R., Di Giuli C., Caramello P., Orofino G. C., Sciandra M., Londero A., Manfrin V., Battagin G., Starnini G., Ialungo A., Fabeni L., Santoro M.M., Lorenzini P., Rusconi S., Gianotti N., Costantini A., Sarmati L., Antinori A., Ceccherini-Silberstein F., d'Arminio Monforte A., Saracino A., Girardi E., Castagna A., Castelli F., Cauda R., Di Perri G., Galli M., Iardino R., Ippolito G., Lazzarin A., Marchetti G.C., Rezza G., von Schloesser F., Viale P., Cozzi-Lepri A., Gori A., Lo Caputo S., Maggiolo F., Mussini C., Puoti M., Perno C.F., Bai F., Bandera A., Bonora S., Borderi M., Calcagno A., Capobianchi M.R., Cicalini S., Cingolani A., Cinque P., Di Biagio A., Gagliardini R., Guaraldi G., Lapadula G., Lichtner M., Lai A., Madeddu G., Merlini E., Nozza S., Piconi S., Pinnetti C., Quiros Roldan E., Rossotti R., Spagnuolo V., Svicher V., Taramasso L., Fanti I., Galli L., Rodano A., Macchia M., Tavelli A., Bove A., Camposeragna A., Errico M., Manfredini M., Perziano A., Calvino V., Carrara S., Di Caro A., Graziano S., Petroni F., Prota G., Truffa S., Giacometti A., Barocci V., Angarano G., Monno L., Milano E., Suardi C., Donati V., Verucchi G., Castelnuovo F., Minardi C., Menzaghi B., Abeli C., Chessa L., Pes F., Cacopardo B., Celesia B., Vecchiet J., Falasca K., Pan A., Lorenzotti S., Sighinolfi L., Segala D., Blanc P., Vichi F., Cassola G., Bassetti M., Alessandrini A., Bobbio N., Mazzarello G., Fondaco L., Bonfanti P., Molteni C., Chiodera A., Milini P., Nunnari G., Pellicano G., Rizzardini G., Cannizzo E.S., Moioli M.C., Piolini R., Bernacchia D., Poli A., Tincati C., Puzzolante C., Migliorino C., Sangiovanni V., Borgia G., Esposito V., Di Flumeri G., Gentile I., Rizzo V., Cattelan A.M., Marinello S., Cascio A., Trizzino M., Francisci D., Schiaroli E., Parruti G., Sozio F., Lazzaretti C., Corsini R., Cristaudo A., Vullo V., Acinapura R., Lamonica S., Capozzi M., Mondi A., Rivano Capparuccia M., Iaiani G., Latini A., Onnelli G., Plazzi M.M., de Girolamo G., Vergori A., Cecchetto M., Viviani F., de Vito A., Rossetti B., Montagnani F., Franco A., Fontana Del Vecchio R., Di Giuli C., Caramello P., Orofino G.C., Sciandra M., Londero A., Manfrin V., Battagin G., Starnini G., Ialungo A., Fabeni, L., Santoro, M. M., Lorenzini, P., Rusconi, S., Gianotti, N., Costantini, A., Sarmati, L., Antinori, A., Ceccherini-Silberstein, F., d'Arminio Monforte, A., Saracino, A., Girardi, E., Castagna, A., Castelli, F., Cauda, R., Di Perri, G., Galli, M., Iardino, R., Ippolito, G., Lazzarin, A., Marchetti, G. C., Rezza, G., von Schloesser, F., Viale, P., Cozzi-Lepri, A., Gori, A., Lo Caputo, S., Maggiolo, F., Mussini, C., Puoti, M., Perno, C. F., Bai, F., Bandera, A., Bonora, S., Borderi, M., Calcagno, A., Capobianchi, M. R., Cicalini, S., Cingolani, A., Cinque, P., Di Biagio, A., Gagliardini, R., Guaraldi, G., Lapadula, G., Lichtner, M., Lai, A., Madeddu, G., Merlini, E., Nozza, S., Piconi, S., Pinnetti, C., Quiros Roldan, E., Rossotti, R., Spagnuolo, V., Svicher, V., Taramasso, L., Fanti, I., Galli, L., Rodano, A., Macchia, M., Tavelli, A., Bove, A., Camposeragna, A., Errico, M., Manfredini, M., Perziano, A., Calvino, V., Carrara, S., Di Caro, A., Graziano, S., Petroni, F., Prota, G., Truffa, S., Giacometti, A., Barocci, V., Angarano, G., Monno, L., Milano, E., Suardi, C., Donati, V., Verucchi, G., Castelnuovo, F., Minardi, C., Menzaghi, B., Abeli, C., Chessa, L., Pes, F., Cacopardo, B., Celesia, B., Vecchiet, J., Falasca, K., Pan, A., Lorenzotti, S., Sighinolfi, L., Segala, D., Blanc, P., Vichi, F., Cassola, G., Bassetti, M., Alessandrini, A., Bobbio, N., Mazzarello, G., Fondaco, L., Bonfanti, P., Molteni, C., Chiodera, A., Milini, P., Nunnari, G., Pellicano, G., Rizzardini, G., Cannizzo, E. S., Moioli, M. C., Piolini, R., Bernacchia, D., Poli, A., Tincati, C., Puzzolante, C., Migliorino, C., Sangiovanni, V., Borgia, G., Esposito, V., Di Flumeri, G., Gentile, I., Rizzo, V., Cattelan, A. M., Marinello, S., Cascio, A., Trizzino, M., Francisci, D., Schiaroli, E., Parruti, G., Sozio, F., Lazzaretti, C., Corsini, R., Cristaudo, A., Vullo, V., Acinapura, R., Lamonica, S., Capozzi, M., Mondi, A., Rivano Capparuccia, M., Iaiani, G., Latini, A., Onnelli, G., Plazzi, M. M., de Girolamo, G., Vergori, A., Cecchetto, M., Viviani, F., de Vito, A., Rossetti, B., Montagnani, F., Franco, A., Fontana Del Vecchio, R., Di Giuli, C., Caramello, P., Orofino, G. C., Sciandra, M., Londero, A., Manfrin, V., Battagin, G., Starnini, G., and Ialungo, A.

Subjects
0301 basic medicine, Male, lcsh:QR1-502, Subtype, HIV Infections, migrants, Bioinformatics, Cluster detection, Drug resistance testing, Human immunodeficiency virus (HIV), Migrants, Molecular epidemiology, Phylogenetic analysis, Risk factors, Subtypes, Transmission networks and clusters, Adult, Cohort Studies, Female, Genotype, HIV-1, Humans, Italy, Middle Aged, Sexual and Gender Minorities, pol Gene Products, Human Immunodeficiency Virus, Emigrants and Immigrants, Phylogeny, lcsh:Microbiology, Men who have sex with men, 0302 clinical medicine, human immunodeficiency virus (HIV), molecular epidemiology, phylogenetic analysis, cluster detection, transmission networks and clusters, subtypes, drug resistance testing, risk factors, bioinformatics, Medicine, 030212 general & internal medicine, pol Gene Products, Hiv transmission, Transmission (medicine), virus diseases, Infectious Diseases, Cohort, Human Immunodeficiency Virus, Cohort study, medicine.medical_specialty, Article, NO, 03 medical and health sciences, Phylogenetic analysi, Virology, Bioinformatic, business.industry, Public health, Migrant, Settore MED/17, 030104 developmental biology, Risk factor, business, Demography
Abstract

We aimed at evaluating the characteristics of HIV-1 molecular transmission clusters (MTCs) among natives and migrants living in Italy, diagnosed between 1998 and 2018. Phylogenetic analyses were performed on HIV-1 polymerase (pol) sequences to characterise subtypes and identify MTCs, divided into small (SMTCs, 2&ndash, 3 sequences), medium (MMTCs, 4&ndash, 9 sequences) and large (LMTCs, &ge, 10 sequences). Among 3499 drug-na&iuml, ve individuals enrolled in the Italian Cohort Naive Antiretroviral (ICONA) cohort (2804 natives, 695 migrants), 726 (20.8%, 644 natives, 82 migrants) were involved in 228 MTCs (6 LMTCs, 36 MMTCs, 186 SMTCs). Migrants contributed 14.4% to SMTCs, 7.6% to MMTCs and 7.1% to LMTCs, respectively. HIV-1 non-B subtypes were found in 51 MTCs, noteworthy was that non-B infections involved in MTCs were more commonly found in natives (n = 47) than in migrants (n = 4). Factors such as Italian origin, being men who have sex with men (MSM), younger age, more recent diagnosis and a higher CD4 count were significantly associated with MTCs. Our findings show that HIV-1 clustering transmission among newly diagnosed individuals living in Italy is prevalently driven by natives, mainly MSM, with a more recent diagnosis and frequently infected with HIV-1 non-B subtypes. These results can contribute to monitoring of the HIV epidemic and guiding the public health response to prevent new HIV infections.

Published
2020

10. Evaluation of HIV-1 integrase variability by combining computational and probabilistic approaches

Author

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, and Santoro, M

Subjects
Microbiology (medical), Hellinger distance, Bioinformatics, HIV Infections, HIV Integrase, Mutational rate, Integrase, Microbiology, Settore MED/07, Infectious Diseases, Drug Resistance, Viral, Mutation, Genetics, HIV-1, Humans, Genetic variability, HIV Integrase Inhibitors, Molecular Biology, Ecology, Evolution, Behavior and Systematics
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% to1% 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.

Published
2021

11. Phylogenetic analysis in the clinical risk management of an outbreak of hepatitis C virus infection among transfused thalassaemia patients in Italy

Author

Mazzucco, W., primary, Chiara di Maio, V., additional, Bronte, F., additional, Fabeni, L., additional, Pipitone, R.M., additional, Grimaudo, S., additional, Ferraro, D., additional, Marotta, C., additional, Aragri, M., additional, Macaluso, M., additional, Vitale, F., additional, Di Raimondo, F., additional, Ceccherini-Silberstein, F., additional, and Di Marco, V., additional

Published
2021
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12. HIV-1 integrase genotyping is reliable and reproducible for routine clinical detection of integrase resistance mutations even in patients with low-level viraemia

Author

Armenia, D., Fabeni, L., Alteri, C., Di Pinto, D., Di Carlo, D., Bertoli, A., Gori, C., Carta, S., Fedele, V., Forbici, F., DʼArrigo, R., Svicher, V., Berno, G., Pizzi, D., Nicastri, E., Sarmati, L., Pinnetti, C., Ammassari, A., DʼOffizi, G., Latini, A., Andreoni, M., Antinori, A., Ceccherini-Silberstein, F., Perno, C. F., and Santoro, M. M.

Published
2015
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13. The combined usage of accurate virological and serological HBV markers can help to identify HBsAg-negative/anti-HBc-positive patients at higher risk of HBV-reactivation and to optimize prophylaxis duration in oncohematological setting

Author

Salpini, R., primary, Alkhatib, M., additional, Cerva, C., additional, Piermatteo, L., additional, Battisti, A., additional, Malagnino, V., additional, Fabeni, L, additional, Cantonetti, M.L., additional, Arcese, W., additional, Ceccherini-Silberstein, F., additional, Perno, C.F., additional, Andreoni, M., additional, Sarmati, L., additional, and Svicher, V., additional

Published
2020
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14. Analysis of resistance and phylogenetic clusters in HCV-2c infected patients within the Italian network Vironet C

Author

Barbaliscia, S., primary, Di Maio, V.C., additional, Fabeni, L., additional, Teti, E., additional, Paolucci, S., additional, Minichini, C., additional, Aragri, M., additional, Rosa, K. Yu La, additional, Carioti, L., additional, Pasquazzi, C., additional, Milana, M., additional, Foroghi, L., additional, Pollicino, T., additional, Licata, A., additional, Pieri, A., additional, Palitti, V. Pace, additional, Bruzzone, B., additional, Micheli, V., additional, Bertoli, A., additional, Baiocchi, L., additional, Callegaro, A.P., additional, Pellicelli, A., additional, Morisco, F., additional, Gulminetti, R., additional, Novati, S., additional, Lichtner, M., additional, Mastroianni, C., additional, Di Lorenzo, F., additional, Andreone, P., additional, Rossetti, B., additional, Marenco, S., additional, Taliani, G., additional, Boeri, E., additional, Hasson, H., additional, Monno, L., additional, Nicolini, L.A., additional, Landonio, S., additional, Paternoster, C., additional, Puoti, M., additional, Babudieri, S., additional, Quartini, M., additional, Iapadre, N., additional, Cozzolongo, R., additional, Sangiovanni, V., additional, Parruti, G., additional, Sarmati, L., additional, Coppola, N., additional, Baldanti, F., additional, Marco, V. Di, additional, Zazzi, M., additional, Raimondo, G., additional, Angelico, M., additional, Perno, C.F., additional, Andreoni, M., additional, Craxì, A., additional, and Ceccherini-Silberstein, F., additional

Published
2020
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15. HIV MDR is still a relevant issue despite its dramatic drop over the years

Author

Armenia, D, primary, Di Carlo, D, primary, Flandre, P, primary, Bouba, Y, primary, Borghi, V, primary, Forbici, F, primary, Bertoli, A, primary, Gori, C, primary, Fabeni, L, primary, Gennari, W, primary, Pinnetti, C, primary, Mondi, A, primary, Cicalini, S, primary, Gagliardini, R, primary, Vergori, A, primary, Bellagamba, R, primary, Malagnino, V, primary, Montella, F, primary, Colafigli, M, primary, Latini, A, primary, Marocco, R, primary, Licthner, M, primary, Andreoni, M, primary, Mussini, C, primary, Ceccherini-Silberstein, F, primary, Antinori, A, primary, Perno, C F, primary, and Santoro, M M, primary

Published
2020
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16. NS5A gene analysis by next generation sequencing in HCV nosocomial transmission clusters of HCV genotype 1b infected patients

Author

Bellocchi, M.C., primary, Carioti, L., additional, Aragri, M., additional, Fabeni, L., additional, Pipitone, R., additional, Brancaccio, G., additional, Sorbo, M.C., additional, di Maio, V.C., additional, Bronte, F., additional, Grimaudo, S., additional, Rizzo, V., additional, Frigeri, F., additional, Cantone, M., additional, Genderini, F., additional, Pinto, A., additional, Perno, C.F., additional, Craxì, A., additional, Gaeta, G.B., additional, Di Marco, V., additional, and Ceccherini-Silberstein, F., additional

Published
2019
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17. Inferring the migration routes of hepatitis C virus subtype 1a lineages identifies a need for pan-European prevention strategies

Author

Cuypers, L., Vrancken, B., Fabeni, L., Di Maio, V. C., Cento, V., Baele, G., Parczewski, M., Chulanov, V., Gomes, P., Beloukas, A., Geretti, A. M., Dietz, J., Sarrazin, C., Neary, M., Degascun, C., Sierra, S., Kaiser, R., Jimenez, A. B. P., Garcia, F. G., Zazzi, M., Vandamme, A. -M., Silberstein, F. C., Cuypers, L., Vrancken, B., Fabeni, L., Di Maio, V. C., Cento, V., Baele, G., Parczewski, M., Chulanov, V., Gomes, P., Beloukas, A., Geretti, A. M., Dietz, J., Sarrazin, C., Neary, M., Degascun, C., Sierra, S., Kaiser, R., Jimenez, A. B. P., Garcia, F. G., Zazzi, M., Vandamme, A. -M., and Silberstein, F. C.

Published
2018

18. Inferring the migration routes of hepatitis C virus subtype 1a lineages identifies a need for pan-European prevention strategies

Author

Cuypers, L., primary, Vrancken, B., additional, Fabeni, L., additional, Di Maio, V.C., additional, Cento, V., additional, Baele, G., additional, Parczewski, M., additional, Chulanov, V., additional, Gomes, P., additional, Beloukas, A., additional, Geretti, A.M., additional, Dietz, J., additional, Sarrazin, C., additional, Neary, M., additional, Degascun, C., additional, Sierra, S., additional, Kaiser, R., additional, Jimenez, A.B.P., additional, Garcia, F.G., additional, Zazzi, M., additional, Vandamme, A.-M., additional, and Silberstein, F.C., additional

Published
2018
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19. A hyper-glycosylation of HBV surface antigen characterizes immunosuppression-driven HBV reactivation and hinders HBsAg recognition in vitro

Author

Salpini, R., primary, Piermatteo, L., additional, Battisti, A., additional, Colagrossi, L., additional, Aragri, M., additional, Fabeni, L., additional, Bertoli, A., additional, Mastroianni, C.M., additional, Marignani, M., additional, Maylin, S., additional, Delaugerre, C., additional, Morisco, F., additional, Nicola, C., additional, Marrone, A., additional, Iapadre, N., additional, Mario, A., additional, Sarmati, L., additional, Andreoni, M., additional, Verheyen, J., additional, Silberstein, F.C., additional, Levrero, M., additional, Perno, C.F., additional, Belloni, L., additional, and Svicher, V., additional

Published
2018
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20. Key mutational patterns in HBsAg C-terminus profoundly affect HBsAg levels in HBeAg-negative chronic HBV genotype D infection

Author

Salpini, R., primary, Battisti, A., additional, Carioti, L., additional, Carlo, D.D., additional, Anastasiou, O., additional, Gill, U.S., additional, Colagrossi, L., additional, Bertoli, A., additional, Aragri, M., additional, Fabeni, L., additional, Fini, V., additional, Piermatteo, L., additional, Iuvara, A., additional, Malagnino, V., additional, Cerva, C., additional, Lichtner, M., additional, Mastroianni, C.M., additional, Sanctis, G.M.D., additional, Maurizio, P., additional, Marignani, M., additional, Pasquazzi, C., additional, Iapadre, N., additional, Mari, T., additional, Parruti, G., additional, Vecchiet, J., additional, Sarmati, L., additional, Andreoni, M., additional, Angelico, M., additional, Grelli, S., additional, Kennedy, P., additional, Verheyen, J., additional, Silberstein, F.C., additional, Perno, C.F., additional, and Svicher, V., additional

Published
2018
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22. In HBeAg-negative chronic HBV infection, HBsAg levels profoundly differ among HBV-genotypes and can be affected by the extent of HBsAg variability: Can quantitative HBsAg truly reflect intra-hepatic HBV reservoir?

Author

Salpini, R., primary, Battisti, A., additional, Anastasiou, O., additional, Gill, U., additional, Colagrossi, L., additional, Bertoli, A., additional, Fabeni, L., additional, Fini, V., additional, Piermatteo, L., additional, Iuvara, A., additional, Malagnino, V., additional, Cerva, C., additional, Lichtner, M., additional, Mastroianni, C., additional, De Sanctis, G., additional, Paoloni, M., additional, Marignani, M., additional, Pasquazzi, C., additional, Iapadre, N., additional, Mari, T., additional, Parruti, G., additional, Vecchiet, I., additional, Sarmati, L., additional, Andreoni, M., additional, Angelico, M., additional, Grelli, S., additional, Kennedy, P., additional, Verheyen, J., additional, Perno, C.-F., additional, and Svicher, V., additional

Published
2017
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23. The circulation of specific vaccine-escape HBsAg mutations in HBV genotype D infected patients correlates with high viremia and affects HBsAg detection and quantification

Author

Salpini, R., primary, Piermatteo, L., additional, Di Carlo, D., additional, Battisti, A., additional, Colagrossi, L., additional, Bertoli, A., additional, Fabeni, L., additional, Fini, V., additional, Iuvara, A., additional, Ricciardi, A., additional, Cerva, C., additional, Sarrecchia, C., additional, Lichtner, M., additional, Mastroianni, C., additional, De Sanctis, G., additional, Paoloni, M., additional, Marignani, M., additional, Pasquazzi, C., additional, Iapadre, N., additional, Mari, T., additional, Parruti, G., additional, Romano, S., additional, Visca, M., additional, Moretti, A., additional, Vecchiet, J., additional, Sarmati, L., additional, Andreoni, M., additional, Cappiello, G., additional, Spanò, A., additional, Grelli, S., additional, Angelico, M., additional, Perno, C.F., additional, and Svicher, V., additional

Published
2017
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24. In HBeAg-negative chronic HBV infection, HBsAg levels profoundly vary among different HBV-genotypes and can be influenced by the degree of HBsAg variability: can quantitative HBsAg truly reflect intra-hepatic HBV reservoir?

Author

Salpini, R., primary, Battisti, A., additional, Anastasiou, O., additional, Gill, U., additional, Colagrossi, L., additional, Bertoli, A., additional, Fabeni, L., additional, Fini, V., additional, Piermatteo, L., additional, Iuvara, A., additional, Malagnino, V., additional, Cerva, C., additional, Lichtner, M., additional, Mastroianni, C., additional, De Sanctis, G., additional, Paoloni, M., additional, Marignani, M., additional, Pasquazzi, C., additional, Iapadre, N., additional, Mari, T., additional, Parruti, G., additional, Vecchiet, J., additional, Sarmati, L., additional, Andreoni, M., additional, Angelico, M., additional, Grelli, S., additional, Kennedy, P., additional, Verheyen, J., additional, Perno, C.F., additional, and Svicher, V., additional

Published
2017
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26. Gain of positively charged amino acids at specific positions of HBsAg C-terminus tightly correlates with HBV-induced hepatocellular carcinoma by altering the structural folding of this domain

Author

Salpini, R., primary, Carioti, L., additional, Aragri, M., additional, Di Carlo, D., additional, Colagrossi, L., additional, Battisti, A., additional, Piermatteo, L., additional, Bertoli, A., additional, Fabeni, L., additional, Ricciardi, A., additional, Longo, R., additional, Romano, S., additional, Cappiello, G., additional, Spanò, A., additional, Trimoulet, P., additional, Fleury, H., additional, Vecchiet, J., additional, Iapadre, N., additional, Barlattani, A., additional, Mari, T., additional, Pasquazzi, C., additional, Lenci, I., additional, Francioso, S., additional, Parruti, G., additional, Sarmati, L., additional, Andreoni, M., additional, Angelico, M., additional, Ceccherini-Silberstein, F., additional, Perno, C.F., additional, and Svicher, V., additional

Published
2017
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27. Vaccine-escape HBsAg mutants circulating among genotype D HBV-infected patients correlate with atypical serological profiles, high viremia and transaminases: Potential impact on vaccination strategies

Author

Salpini, R., primary, Battisti, A., additional, Colagrossi, L., additional, Alteri, C., additional, Bertoli, A., additional, Fabeni, L., additional, Sarrecchia, C., additional, Di Carlo, D., additional, Pollicita, M., additional, Lichtner, M., additional, Mastroianni, C., additional, De Sanctis, G., additional, Paoloni, M., additional, Marignani, M., additional, Pasquazzi, C., additional, Di Paolo, D., additional, Iapadre, N., additional, Mari, T., additional, Puoti, C., additional, Parruti, G., additional, Romano, S., additional, Visca, M., additional, Vecchiet, I., additional, Andreoni, M., additional, Cappiello, G., additional, Spanò, A., additional, Angelico, M., additional, Perno, C.F., additional, and Svicher, V., additional

Published
2016
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28. Vaccine-Escape HBsAg Mutations Circulating in a Relevant Proportion of HBV Genotype D Infected Patients Correlate with Atypical Serological Profiles, High Viremia and Transaminases: Potential Implication for Vaccine Success

Author

Salpini, R., primary, Battisti, A., additional, Colagrossi, L., additional, Alteri, C., additional, Bertoli, A., additional, Fabeni, L., additional, Sarrecchia, C., additional, Di Carlo, D., additional, Pollicita, M., additional, Lichtner, M., additional, Mastroianni, C., additional, De Sanctis, G., additional, Paoloni, M., additional, Marignani, M., additional, Pasquazzi, C., additional, Di Paolo, D., additional, Iapadre, N., additional, Mari, T., additional, Parruti, G., additional, Romano, S., additional, Visca, M., additional, Vecchiet, I., additional, Andreoni, M., additional, Cappiello, G., additional, Spanò, A., additional, Angelico, M., additional, Perno, C.F., additional, and Svicher, V., additional

Published
2016
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29. A recent epidemiological cluster of acute hepatitis B genotype F1b infection in a restricted geographical area of Italy

Author

Pollicita, M., primary, Alteri, C., additional, Bellocchi, M.C., additional, Armenia, D., additional, Carioti, L., additional, Salpini, R., additional, Colagrossi, L., additional, Battisti, A., additional, Aragri, M., additional, Fabeni, L., additional, Mariani, R., additional, Dalessandro, M., additional, Ranelli, A., additional, Paoloni, M., additional, Parruti, G., additional, Perno, C.F., additional, and Svicher, V., additional

Published
2015
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30. SAT-350 - A hyper-glycosylation of HBV surface antigen characterizes immunosuppression-driven HBV reactivation and hinders HBsAg recognition in vitro

Author

Salpini, R., Piermatteo, L., Battisti, A., Colagrossi, L., Aragri, M., Fabeni, L., Bertoli, A., Mastroianni, C.M., Marignani, M., Maylin, S., Delaugerre, C., Morisco, F., Nicola, C., Marrone, A., Iapadre, N., Mario, A., Sarmati, L., Andreoni, M., Verheyen, J., Silberstein, F.C., Levrero, M., Perno, C.F., Belloni, L., and Svicher, V.

Published
2018
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31. FRI-293 - Key mutational patterns in HBsAg C-terminus profoundly affect HBsAg levels in HBeAg-negative chronic HBV genotype D infection

Author

Salpini, R., Battisti, A., Carioti, L., Carlo, D.D., Anastasiou, O., Gill, U.S., Colagrossi, L., Bertoli, A., Aragri, M., Fabeni, L., Fini, V., Piermatteo, L., Iuvara, A., Malagnino, V., Cerva, C., Lichtner, M., Mastroianni, C.M., Sanctis, G.M.D., Maurizio, P., Marignani, M., Pasquazzi, C., Iapadre, N., Mari, T., Parruti, G., Vecchiet, J., Sarmati, L., Andreoni, M., Angelico, M., Grelli, S., Kennedy, P., Verheyen, J., Silberstein, F.C., Perno, C.F., and Svicher, V.

Published
2018
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33. Performance of genotypic tropism testing on proviral DNAin clinical practice: results from the DIVA Study Group

Author

Svicher, V, Alteri, C, Montano, M, D'Arrigo, R, Andreoni, M, Angarano, G, Antinori, A, Antonelli, G, Allice, T, Bagnarelli, P, Baldanti, F, Bertoli, A, Borderi, M, Boeri, E, Bon, I, Bruzzone, B, Callegaro, Ap, Capobianchi, Mr, Carosi, G, Cauda, R, Ceccherini Silberstein, F, Clementi, M, Chirianni, A, Colafigli, M, D'Arminio Monforte, A, De Luca, A, Di Biagio, A, Di Nicuolo, G, Di Perri, G, Di Pietro, M, Di Santo, F, Fabeni, L, Fadda, G, Galli, M, Gennari, W, Ghisetti, V, Giacometti, A, Gori, C, Gori, A, Gulminetti, R, Leoncini, F, Maffongelli, G, Maggiolo, F, Manca, G, Gargiulo, F, Martinelli, C, Maserati, R, Mazzotta, F, Meini, G, Micheli, V, Monno, L, Mussini, C, Narciso, P, Nozza, S, Paolucci, S, Pal, G, Parisi, S, Parruti, G, Pignataro, Ar, Pollicita, M, Quirino, T, Re, Mc, Rizzardini, G, Santangelo, R, Scaggiante, R, Sterrantino, G, Turriziani, O, Vatteroni, Ml, Vecchi, L, Viscoli, Claudio, Vullo, V, Zazzi, M, Lazzarini, A, and Perno, Cf

Subjects
HIV, Proviral DNA, Tropism
Published
2012

37. Comparative replication capacity of raltegravir-resistant strains and antiviral activity of the new-generation integrase inhibitor dolutegravir in human primary macrophages and lymphocytes

Author

Pollicita, M., primary, Surdo, M., additional, Di Santo, F., additional, Cortese, M. F., additional, Fabeni, L., additional, Fedele, V., additional, Malet, I., additional, Marcelin, A.-G., additional, Calvez, V., additional, Ceccherini-Silberstein, F., additional, Perno, C. F., additional, and Svicher, V., additional

Published
2014
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38. Performance of genotypic tropism testing on proviral DNA in clinical practice: results from the DIVA study group

Author

Svicher, V, Alteri, C, Montano, M, D'Arrigo, R, Andreoni, M, Angarano, G, Antinori, A, Antonelli, G, Allice, T, Bagnarelli, P, Baldanti, F, Bertoli, A, Borderi, M, Boeri, E, Bon, I, Bruzzone, B, Callegaro, A, Capobianchi, M, Carosi, G, Cauda, R, Ceccherini Silberstein, F, Clementi, M, Chirianni, A, Colafigli, M, D'Arminio Monforte, A, De Luca, A, Di Biagio, A, Di Nicuolo, G, Di Perri, G, Di Pietro, M, Di Santo, F, Fabeni, L, Fadda, G, Galli, M, Gennari, W, Ghisetti, V, Giacometti, A, Gori, C, Gori, A, Gulminetti, R, Leoncini, F, Maffongelli, G, Maggiolo, F, Manca, G, Gargiulo, F, Martinelli, C, Maserati, R, Mazzotta, F, Meini, G, Micheli, V, Monno, L, Mussini, C, Narciso, P, Nozza, S, Paolucci, S, Pal, G, Parisi, S, Parruti, G, Pignataro, A, Pollicita, M, Quirino, T, Re, M, Rizzardini, G, Santangelo, R, Scaggiante, R, Sterrantino, G, Turriziani, O, Vatteroni, M, Vecchi, L, Viscoli, C, Vullo, V, Zazzi, M, Lazzarini, A, Perno, C, GORI, ANDREA, Perno, C., Svicher, V, Alteri, C, Montano, M, D'Arrigo, R, Andreoni, M, Angarano, G, Antinori, A, Antonelli, G, Allice, T, Bagnarelli, P, Baldanti, F, Bertoli, A, Borderi, M, Boeri, E, Bon, I, Bruzzone, B, Callegaro, A, Capobianchi, M, Carosi, G, Cauda, R, Ceccherini Silberstein, F, Clementi, M, Chirianni, A, Colafigli, M, D'Arminio Monforte, A, De Luca, A, Di Biagio, A, Di Nicuolo, G, Di Perri, G, Di Pietro, M, Di Santo, F, Fabeni, L, Fadda, G, Galli, M, Gennari, W, Ghisetti, V, Giacometti, A, Gori, C, Gori, A, Gulminetti, R, Leoncini, F, Maffongelli, G, Maggiolo, F, Manca, G, Gargiulo, F, Martinelli, C, Maserati, R, Mazzotta, F, Meini, G, Micheli, V, Monno, L, Mussini, C, Narciso, P, Nozza, S, Paolucci, S, Pal, G, Parisi, S, Parruti, G, Pignataro, A, Pollicita, M, Quirino, T, Re, M, Rizzardini, G, Santangelo, R, Scaggiante, R, Sterrantino, G, Turriziani, O, Vatteroni, M, Vecchi, L, Viscoli, C, Vullo, V, Zazzi, M, Lazzarini, A, Perno, C, GORI, ANDREA, and Perno, C.

Abstract

The DIVA study is aimed at setting up a standardized genotypic tropism-testing on proviral-DNA for the routine clinical diagnostic-laboratory. Methods: Twelve local centres and 5 reference centres (previously cross-validated) were identified. For inter-center validation-procedure, 60 peripheral-blood mononuclear cells (PBMCs) aliquots from 45 HAART-treated patients were randomly chosen for population V3 sequencing on proviral-DNA at local HIV centre and at reference-laboratory. Viral tropism was predicted by Geno2Pheno algorithm (False Positive Rate [FPR] = 20%) as proposed by the European-Guidelines. Quantification of total HIV-1 DNA was based on a method described by Viard (2004). Results: Quantification of HIV-1 DNA was available for 35/45 (77.8%) samples, and gave a median value of 598 (IQR:252- 1,203) copies/10 6 PBMCs. A total of 56/60 (93.3%) samples were successfully amplified by both the reference and the local virological centers. The overall concordance of tropism prediction between local and reference centers was 54/56 (96.4%). Results of tropism prediction by local centers were: 33/54 (61.1%) R5 and 21/54 (38.9%) X4/DM. Conclusion: There was high concordance in the genotypic tropism prediction based on proviral DNA among different virological centers throughout Italy. Our results are in line with other European studies, and support the use of genotypic tropism testing on proviral DNA in patients with suppressed plasma HIV-1 RNA candidate to CCR5-antagonist treatment.

Published
2012

39. THU-160 - Vaccine-Escape HBsAg Mutations Circulating in a Relevant Proportion of HBV Genotype D Infected Patients Correlate with Atypical Serological Profiles, High Viremia and Transaminases: Potential Implication for Vaccine Success

Author

Salpini, R., Battisti, A., Colagrossi, L., Alteri, C., Bertoli, A., Fabeni, L., Sarrecchia, C., Di Carlo, D., Pollicita, M., Lichtner, M., Mastroianni, C., De Sanctis, G., Paoloni, M., Marignani, M., Pasquazzi, C., Di Paolo, D., Iapadre, N., Mari, T., Parruti, G., Romano, S., Visca, M., Vecchiet, I., Andreoni, M., Cappiello, G., Spanò, A., Angelico, M., Perno, C.F., and Svicher, V.

Published
2016
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40. Performance of genotypic tropism testing in clinical practice using the enhanced sensitivity version of Trofile as reference assay: results from the OSCAR Study Group

Author

Svicher, V, D'Arrigo, R, Alteri, C, Andreoni, M, Angarano, G, Antinori, A, Antonelli, G, Bagnarelli, P, Baldanti, F, Bertoli, A, Borderi, M, Boeri, E, Bonn, I, Bruzzone, B, Callegaro, Ap, Cammarota, R, Canducci, F, Ceccherini Silberstein, F, Clementi, M, Monforte, Ad, De Luca, Andrea, Di Biagio, A, Di Giambenedetto, Simona, Di Perri, G, Di Pietro, M, Fabeni, L, Fadda, Giovanni, Galli, M, Gennari, W, Ghisetti, V, Giacometti, A, Gori, A, Leoncini, F, Maggiolo, F, Maserati, R, Mazzotta, F, Micheli, V, Meini, G, Monno, L, Mussini, C, Nozza, S, Paolucci, S, Parisi, S, Pecorari, M, Pizzi, D, Quirino, T, Re, Mc, Rizzardini, G, Santangelo, Rosaria, Soria, A, Stazi, F, Sterrantino, G, Turriziani, O, Viscoli, C, Vullo, V, Lazzarin, A, Perno, Cf, Oscar, Study Group, De Luca, Andrea (ORCID:0000-0002-8311-6935), Di Giambenedetto, Simona (ORCID:0000-0001-6990-5076), Santangelo, Rosaria (ORCID:0000-0002-8056-218X), Svicher, V, D'Arrigo, R, Alteri, C, Andreoni, M, Angarano, G, Antinori, A, Antonelli, G, Bagnarelli, P, Baldanti, F, Bertoli, A, Borderi, M, Boeri, E, Bonn, I, Bruzzone, B, Callegaro, Ap, Cammarota, R, Canducci, F, Ceccherini Silberstein, F, Clementi, M, Monforte, Ad, De Luca, Andrea, Di Biagio, A, Di Giambenedetto, Simona, Di Perri, G, Di Pietro, M, Fabeni, L, Fadda, Giovanni, Galli, M, Gennari, W, Ghisetti, V, Giacometti, A, Gori, A, Leoncini, F, Maggiolo, F, Maserati, R, Mazzotta, F, Micheli, V, Meini, G, Monno, L, Mussini, C, Nozza, S, Paolucci, S, Parisi, S, Pecorari, M, Pizzi, D, Quirino, T, Re, Mc, Rizzardini, G, Santangelo, Rosaria, Soria, A, Stazi, F, Sterrantino, G, Turriziani, O, Viscoli, C, Vullo, V, Lazzarin, A, Perno, Cf, Oscar, Study Group, De Luca, Andrea (ORCID:0000-0002-8311-6935), Di Giambenedetto, Simona (ORCID:0000-0001-6990-5076), and Santangelo, Rosaria (ORCID:0000-0002-8056-218X)

Published
2010

41. Prevalence of resistance mutations related to integrase inhibitor S/GSK1349572 in HIV-1 subtype B raltegravir-naive and -treated patients

Author

Malet, I., primary, Wirden, M., additional, Fourati, S., additional, Armenia, D., additional, Masquelier, B., additional, Fabeni, L., additional, Sayon, S., additional, Katlama, C., additional, Perno, C. F., additional, Calvez, V., additional, Marcelin, A.-G., additional, and Ceccherini-Silberstein, F., additional

Published
2011
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42. Study of genotypic and phenotypic HIV-1 dynamics of integrase mutations during raltegravir treatment: a refined analysis by ultra-deep 454 pyrosequencing.

Author

Armenia D, Vandenbroucke I, Fabeni L, Van Marck H, Cento V, D'Arrigo R, Van Wesenbeeck L, Scopelliti F, Micheli V, Bruzzone B, Lo Caputo S, Aerssens J, Rizzardini G, Tozzi V, Narciso P, Antinori A, Stuyver L, Perno CF, Ceccherini-Silberstein F, and Armenia, Daniele

Subjects
DOCUMENTATION, DRUG resistance in microorganisms, BIOLOGICAL evolution, HETEROCYCLIC compounds, HIV, HIV infections, MICROBIAL sensitivity tests, GENETIC mutation, PROTEINS, PHENOTYPES, SALVAGE therapy, ANTI-HIV agents, SEQUENCE analysis, GENOTYPES
Abstract

Background: The dynamics of raltegravir-resistant variants and their impact on virologic response in 23 HIV-1-infected patients, who started a salvage raltegravir-containing regimen, were investigated.Methods: Integrase population sequencing and Ultra-Deep-454 Pyrosequencing (UDPS) were performed on plasma samples at baseline and at raltegravir failure. All integrase mutations detected at a frequency ≥1% were considered to be reliable for the UDPS analyses. Phylogenetic and phenotypic resistance analyses were also performed.Results: At baseline, primary resistance mutations were not detected by both population and UDPS genotypic assays; few secondary mutations (T97A-V151I-G163R) were rarely detected and did not show any statistically association either with virologic response at 24-weeks or with the development of resistant variants at failure. At UDPS, not all resistant variants appearing early during treatment evolved as major populations during failure; only specific resistance pathways (Y143R-Q148H/R-N155H) associated with an increased rate of fitness and phenotypic resistance were selected.Conclusions: Resistance to raltegravir in integrase strand transfer inhibitor-naive patients remains today a rare event, which might be changed by future extensive use of such drugs. In our study, pathways of resistance at failure were not predicted by baseline mutations, suggesting that evolution plus stochastic selection plays a major role in the appearance of integrase-resistance mutations, whereas fitness and resistance are dominant factors acting for the late selection of resistant quasispecies. [ABSTRACT FROM AUTHOR]

Published
2012
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43. Performance of genotypic tropism testing in clinical practice using the enhanced sensitivity version of Trofile as reference assay: Results from the OSCAR Study Group

Author

Svicher V, D'Arrigo R, Alteri C, Andreoni M, Angarano G, Antinori A, Antonelli G, Bagnarelli P, Baldanti F, Bertoli A, Boeri E, Bruzzone B, Callegaro AP, Cammarota R, Canducci F, Ceccherini Silberstein F, Clementi M, Monforte AD, De Luca A, Di Biagio A, Di Gianbenedetto S, Di Perri G, Di Pietro M, Fabeni L, Fadda G, Galli M, Gennari W, Ghisetti V, Giacometti A, Gori A, Leoncini F, Maggiolo F, Maserati R, Mazzotta F, Micheli V, Meini G, Monno L, Mussini C, Nozza S, Paolucci S, Parisi S, Pecorari M, Pizzi D, Quirino T, Rizzardini G, Santangelo R, Soria A, Stazi F, Sterrantino G, Turriziani O, Viscoli C, Vullo V, Lazzarin A, Perno CF, OSCAR Study Group, BORDERI, MARCO, BON, ISABELLA, RE, MARIA CARLA, Svicher V, D'Arrigo R, Alteri C, Andreoni M, Angarano G, Antinori A, Antonelli G, Bagnarelli P, Baldanti F, Bertoli A, Borderi M, Boeri E, Bonn I, Bruzzone B, Callegaro AP, Cammarota R, Canducci F, Ceccherini-Silberstein F, Clementi M, Monforte AD, De Luca A, Di Biagio A, Di Gianbenedetto S, Di Perri G, Di Pietro M, Fabeni L, Fadda G, Galli M, Gennari W, Ghisetti V, Giacometti A, Gori A, Leoncini F, Maggiolo F, Maserati R, Mazzotta F, Micheli V, Meini G, Monno L, Mussini C, Nozza S, Paolucci S, Parisi S, Pecorari M, Pizzi D, Quirino T, Re MC, Rizzardini G, Santangelo R, Soria A, Stazi F, Sterrantino G, Turriziani O, Viscoli C, Vullo V, Lazzarin A, Perno CF, and OSCAR Study Group.

Subjects
Male, Protein Structure, trafile, Receptors, CCR5, Genotype, Settore MED/17 - Malattie Infettive, HIV, viral load, AIDS, hiv, HIV Infections, HIV Envelope Protein gp120, v3 loop, Receptors, Humans, Viral Tropism, Protein Structure, Tertiary, HIV-1, Female, Receptors, Virus, tropism, virus diseases, genotypic tropism testing, OSCAR Study Group, Settore MED/07 - Microbiologia e Microbiologia Clinica, Virus, genotypic tropism, CCR5 Receptor Antagonists, CCR5, Tertiary
Abstract

Objective: The goal of the OSCAR programme is to evaluate the performances of genotypic HIV-1 tropism testing in clinical practice using the enhanced sensitivity version of Trafile (ESTA) as reference-assay. Methods: HIV-1 coreceptor-usage was assessed using plasma samples from 406 HIV-1 infected patients by ESTA and by gp120 V3 population-sequencing followed by Geno2pheno (set at a False Positive Rate [FPR] of 10% and 5%). Results: ESTA was successful in 365 (89.9%) samples indicating R5 in 254 (69.6%), and DM/X4 in 111 (30.4% of samples (104 [28.5%] DM and 7 [1.9%] X4). Genotypic-testing successfully assessed viral tropism for all 406 samples, including the 41 with undetermined result by ESTA. Genotypic-tropism testing at a FPR of 5% and 10% was 81.1% and 78.4% concordant with ESTA, respectively. Despite a sensitivity of 48.7% and 55.9% at a FPR of 5% and 10%, respectively, a high concordance (specificity: 95.3% for FPR of 5% and 88.2% for FPR of 10%) between genotypic-tropism testing and ESTA was reached in the detection of R5-tropic viruses. Conclusion: Our results are in line with other European studies, and support the routine use of genotypic tropism testing in clinical-settings for monitoring of HIV-1 infected patients candidate to or failing CCR5-antagonists.

46. SARS-CoV-2 Serum Neutralization Assay: A Traditional Tool for a Brand-New Virus

Author

Matusali G., Colavita F., Lapa D., Meschi S., Bordi L., Piselli P., Gagliardini R., Corpolongo A., Nicastri E., Antinori A., Ippolito G., Capobianchi M. R., Castilletti C., Abbate I., Agrati C., Aleo L., Alonzi T., Amendola A., Apollonio C., Arduini N., Bartolini B., Berno G., Biancone S., Bibbo A., Brega C., Canali M., Cannas A., Carletti F., Carrara S., Casetti R., Castillettiy C., Chiappini R., Ciafrone L., Cimini E., Coen S., Condello R., Coppola A., D'arezzo S., Di Caro A., Di Filippo S., De Giuli C., Fabeni L., Felici L., Ferraioli V., Forbici F., Garbuglia A. R., Giombini E., Gruber C. E. M., Khouri D., Lalle E., Leone B., Mazzarelli A., Messina F., Minosse C., Montaldo C., Neri S., Nisii C., Petrivelli E., Petroni F., Petruccioli E., Pisciotta M., Pizzi D., Prota G., Rozera G., Rueca M., Sabatini R., Sarti S., Sberna G., Sciamanna R., Selleri M., Selvaggi C., Stellitano C., Toffoletti A., Truffa S., Turchi F., Valli M. B., Venditti C., Vincenti D., Vulcano A., Zambelli E., Bevilacqua N., Bordoni V., D'abramo A., Lepore L., Mariano A., Palazzolo C., Lorenzini P., Notari S., Sacchi A., Scorzolini L., Bettini A., Francalancia M., Specchiarello E., Federica M., Gaetano D., Luigi F., Barbara G., Roberto I., Giovanni M., Mirco M., Rachele S., Matusali, G., Colavita, F., Lapa, D., Meschi, S., Bordi, L., Piselli, P., Gagliardini, R., Corpolongo, A., Nicastri, E., Antinori, A., Ippolito, G., Capobianchi, M. R., Castilletti, C., Abbate, I., Agrati, C., Aleo, L., Alonzi, T., Amendola, A., Apollonio, C., Arduini, N., Bartolini, B., Berno, G., Biancone, S., Bibbo, A., Brega, C., Canali, M., Cannas, A., Carletti, F., Carrara, S., Casetti, R., Castillettiy, C., Chiappini, R., Ciafrone, L., Cimini, E., Coen, S., Condello, R., Coppola, A., D'Arezzo, S., Di Caro, A., Di Filippo, S., De Giuli, C., Fabeni, L., Felici, L., Ferraioli, V., Forbici, F., Garbuglia, A. R., Giombini, E., Gruber, C. E. M., Khouri, D., Lalle, E., Leone, B., Mazzarelli, A., Messina, F., Minosse, C., Montaldo, C., Neri, S., Nisii, C., Petrivelli, E., Petroni, F., Petruccioli, E., Pisciotta, M., Pizzi, D., Prota, G., Rozera, G., Rueca, M., Sabatini, R., Sarti, S., Sberna, G., Sciamanna, R., Selleri, M., Selvaggi, C., Stellitano, C., Toffoletti, A., Truffa, S., Turchi, F., Valli, M. B., Venditti, C., Vincenti, D., Vulcano, A., Zambelli, E., Bevilacqua, N., Bordoni, V., D'Abramo, A., Lepore, L., Mariano, A., Palazzolo, C., Lorenzini, P., Notari, S., Sacchi, A., Scorzolini, L., Bettini, A., Francalancia, M., Specchiarello, E., Federica, M., Gaetano, D., Luigi, F., Barbara, G., Roberto, I., Giovanni, M., Mirco, M., and Rachele, S.

Subjects
0301 basic medicine, Male, lcsh:QR1-502, serology, Antibodies, Viral, lcsh:Microbiology, Serology, protective immunity, 0302 clinical medicine, Medicine, 030212 general & internal medicine, Neutralizing antibody, biology, Middle Aged, 3. Good health, Algorithm, Titer, Infectious Diseases, Female, Neutralization Test, Algorithms, Human, Adult, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Protective immunity, Article, Virus, COVID-19 Serological Testing, 03 medical and health sciences, Neutralization Tests, Immunity, Virology, Neutralizing antibodie, Humans, neutralizing antibodies, Kinetic, Receiver operating characteristic, business.industry, SARS-CoV-2, COVID-19, Gold standard (test), Antibodies, Neutralizing, Kinetics, 030104 developmental biology, ROC Curve, Immunoglobulin G, Immunology, biology.protein, business
Abstract

SARS-CoV-2 serum neutralization assay represents the gold standard for assessing antibody-mediated protection in naturally infected and vaccinated individuals. In the present study, 662 serum samples collected from February 2020 to January 2021 from acute and convalescent COVID-19 patients were tested to determine neutralizing antibody (NAb) titers using a microneutralization test (MNT) for live SARS-CoV-2. Moreover, anti-SARS-CoV-2 IgG, IgA, and IgM directed against different viral antigens were measured by high-throughput automated platforms. We observed higher levels of NAbs in elderly (&gt, 60 years old) individuals and in patients presenting acute respiratory distress syndrome. SARS-CoV-2 NAbs develop as soon as five days from symptom onset and, despite a decline after the second month, persist for over 11 months, showing variable dynamics. Through correlation and receiver operating characteristic (ROC) curve analysis, we set up a testing algorithm, suitable for the laboratory workload, by establishing an optimal cutoff value of anti-SARS-CoV-2 IgG for convalescent plasma donors to exclude from MNT samples foreseen to have low/negative NAb titers and ineligible for plasma donation. Overall, MNT, although cumbersome and not suitable for routine testing of large sample sizes, remains the reference tool for the assessment of antibody-mediated immunity after SARS-CoV-2 infection. Smart testing algorithms may optimize the laboratory workflow to monitor antibody-mediated protection in COVID-19 patients, plasma donors, and vaccinated individuals.

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47. A snapshot of virological presentation and outcome of immunosuppression-driven HBV reactivation from real clinical practice: Evidence of a relevant risk of death and evolution from silent to chronic infection

Author

Romina Salpini, Arianna Battisti, Luna Colagrossi, Domenico Di Carlo, Lavinia Fabeni, Lorenzo Piermatteo, Carlotta Cerva, Miriam Lichtner, Claudio Mastroianni, Massimo Marignani, Sarah Maylin, Constance Delaugerre, Filomena Morisco, Nicola Coppola, Aldo Marrone, Mario Angelico, Loredana Sarmati, Massimo Andreoni, Carlo‐Federico Perno, Francesca Ceccherini‐Silberstein, Valentina Svicher, Ada Bertoli, Vanessa Fini, Michela Pollicita, Gaetano Maffongelli, Alessandra Ricciardi, Cesare Sarrecchia, Leonardo Baiocchi, Arianna Brega, null Daniele Di Paolo, Simona Francioso, Ilaria Lenci, William Arcese, Laura Cudillo, Benedetta Mariotti, null Claudio Miriam Lichtner, Raffaella Marocco, Maria Mastroianni, Gloria Taliani, Tiziana Tieghi, Maria Rosaria Esposito, Terenzio Mari, Ettore Mazzoni, Fabrizio Spaziani, Katia Casinelli, Maurizio Paoloni, Nerio Iapadre, Alessandro Grimaldi, Paola Begini, Barbara Imperatrice, Luigi Vanvitelli, Margherita Macera, Mariantonietta Pisaturo, Chiara more, Isabella Siniscalchi, Salpini, R, Battisti, A, Colagrossi, L, Di Carlo, D, Fabeni, L, Piermatteo, L, Cerva, C, Lichtner, M, Mastroianni, C, Marignani, M, Maylin, S, Delaugerre, C, Morisco, F, Coppola, N, Marrone, A, Angelico, M, Sarmati, L, Andreoni, M, Perno, Cf, Ceccherini-Silberstein, F, Svicher, V, Salpini, R., Battisti, A., Colagrossi, L., Di Carlo, D., Fabeni, L., Piermatteo, L., Cerva, C., Lichtner, M., Mastroianni, C., Marignani, M., Maylin, S., Delaugerre, C., Morisco, F., Coppola, N., Marrone, A., Angelico, M., Sarmati, L., Andreoni, M., Perno, C. -F., Ceccherini-Silberstein, F., and Svicher, V.

Subjects
Male, Hepatitis B virus, HBsAg, medicine.medical_specialty, Genotype, Settore MED/17 - Malattie Infettive, medicine.medical_treatment, Treatment outcome, Hbv reactivation, HBV reactivation, Immunocompromised Host, 03 medical and health sciences, Hepatitis B, Chronic, HBV chronicity, Immunosuppression, antiviral prophylaxis, 0302 clinical medicine, Virology, Internal medicine, Humans, Medicine, 030212 general & internal medicine, Hepatitis B Surface Antigens, Hepatology, business.industry, Genetic Variation, virus diseases, Viral Load, Hepatitis B, digestive system diseases, Clinical Practice, Chronic infection, Treatment Outcome, Infectious Diseases, Disease Progression, Female, Virus Activation, 030211 gastroenterology & hepatology, Rituximab, antiviral prophylaxi, Risk of death, business, hbv chronicity, hbv reactivation, immunosuppression, Immunosuppressive Agents, medicine.drug
Abstract

The study was undertaken in order to provide a snapshot from real clinical practice of virological presentation and outcome of patients developing immunosuppression-driven HBV reactivation. Seventy patients with HBV reactivation were included (66.2% treated with rituximab, 10% with corticosteroids and 23.8% with other immunosuppressive drugs). Following HBV reactivation, patients received anti-HBV treatment for a median (IQR) follow-up of 31(13-47) months. At baseline-screening, 72.9% of patients were HBsAg-negative and 27.1% HBsAg-positive. About 71.4% had a diagnosis of biochemical reactivation [median (IQR) HBV DNA and ALT: 6.9 (5.4-7.8) log IU/mL and 359 (102-775) U/L]. Moreover, 10% of patients died from hepatic failure. Antiviral prophylaxis was documented in 57.9% and 15.7% of HBsAg-positive and HBsAg-negative patients at baseline-screening (median [IQR] prophylaxis duration: 24[15-33] and 25[17-36] months, respectively). Notably, HBV reactivation occurred 2-24 months after completing the recommended course of anti-HBV prophylaxis in 35.3% of patients. By analysing treatment outcome, the cumulative probability of ALT normalization and of virological suppression was 97% and 69%, respectively. Nevertheless, in patients negative to HBsAg at baseline-screening, only 27% returned to HBsAg-negative status during prolonged follow-up, suggesting the establishment of chronic infection. In conclusion, most patients received a diagnosis of HBV reactivation accompanied by high ALT and 10% died for hepatic failure, supporting the importance of strict monitoring for an early HBV reactivation diagnosis. Furthermore, HBV reactivation correlates with high risk of HBV chronicity in patients negative for HBsAg at baseline-screening, converting a silent into a chronic infection, requiring long-term antiviral treatment. Finally, a relevant proportion of patients experienced HBV reactivation after completing the recommended course of anti-HBV prophylaxis, suggesting the need to reconsider proper duration of prophylaxis particularly in profound immunosuppression.

Published
2019

48. Phylogenetic analysis in the clinical risk management of an outbreak of hepatitis C virus infection among transfused thalassaemia patients in Italy

Author

Stefania Grimaudo, Francesca Ceccherini-Silberstein, Lavinia Fabeni, V. Di Marco, Marianna Aragri, F. Di Raimondo, Claudia Marotta, Mazzucco W, Fabrizio Bronte, Maurizio Macaluso, Francesco Vitale, V. Chiara di Maio, Donatella Ferraro, Rosaria Maria Pipitone, Mazzucco W., Chiara di Maio V., Bronte F., Fabeni L., Pipitone R.M., Grimaudo S., Ferraro D., Marotta C., Aragri M., Macaluso M., Vitale F., Di Raimondo F., Ceccherini-Silberstein F., and Di Marco V.

Subjects
Sofosbuvir, Clinical risk management, Hepatitis C virus (HCV), Molecular epidemiology, Nosocomial outbreak, Phylogenetic analysis, Antiviral Agents, Bayes Theorem, Disease Outbreaks, Genotype, Hepacivirus, Humans, Italy, Phylogeny, Risk Management, Hepatitis C, Thalassemia, Hepacivirus, 030501 epidemiology, Settore MED/42 - Igiene Generale E Applicata, medicine.disease_cause, Disease Outbreaks, Settore MED/07, chemistry.chemical_compound, Settore BIO/13 - Biologia Applicata, Epidemiology, Medicine, Phylogeny, Settore MED/12 - Gastroenterologia, 0303 health sciences, Clinical risk management, Phylogenetic analysis, biology, Transmission (medicine), virus diseases, General Medicine, Hepatitis C, Hepatitis C virus (HCV), Infectious Diseases, Italy, Molecular epidemiology, Thalassemia, 0305 other medical science, medicine.drug, Microbiology (medical), Ledipasvir, medicine.medical_specialty, Genotype, Hepatitis C virus, Antiviral Agents, 03 medical and health sciences, Phylogenetic analysi, Internal medicine, Humans, Risk Management, 030306 microbiology, business.industry, Nosocomial outbreak, Bayes Theorem, biology.organism_classification, medicine.disease, digestive system diseases, Chronic infection, chemistry, business
Abstract

Background: Occurrence of hepatitis C virus (HCV) infection is reduced by effective risk management procedures, but patient-to-patient transmission continues to be reported in healthcare settings. Aim: To report the use of phylogenetic analysis in the clinical risk management of an HCV outbreak among 128 thalassaemia outpatients followed at a thalassaemia centre of an Italian hospital. Methods: Epidemiological investigation and root-cause analysis were performed. All patients with acute hepatitis and known chronic infection were tested for HCV RNA, HCV genotyping, and NS3, NS5A, and NS5B HCV genomic region sequencing. To identify transmission clusters, phylogenetic trees were built for each gene employing Bayesian methods. Findings: All patients with acute hepatitis were infected with HCV genotype 1b. Root-cause analysis, including a lookback procedure, excluded blood donors as the source of HCV transmission. The phylogenetic analysis, conducted on seven patients with acute infection and eight patients with chronic infection, highlighted four transmission clusters including at least one patient with chronic and one patient with acute HCV infection. All patients in the same cluster received a blood transfusion during the same day. Two patients with acute hepatitis spontaneously cleared HCV within four weeks and nine patients received ledipasvir plus sofosbuvir for six weeks, all achieving a sustained virological response. Conclusion: Combined use of root-cause analysis and molecular epidemiology was effective in ascertaining the origin of the HCV outbreak. Antiviral therapy avoided the chronic progression of the infection and further spread in care units and in the family environment.

Published
2021

49. HDV can constrain HBV genetic evolution in hbsag: Implications for the identification of innovative pharmacological targets

Author

A. Battisti, Alberto Spanò, G. Stornaiuolo, L. Colagrossi, Francesca Ceccherini-Silberstein, Ada Bertoli, Ilaria Lenci, Carmine Minichini, Rossana Scutari, A. Barlattani, Valentina Svicher, T. Mari, Vincenzo Malagnino, Maria De Cristofaro, Lavinia Fabeni, Nicola Coppola, Giuseppina Cappiello, Carlo Federico Perno, Massimo Marignani, Pascale Trimoulet, Alfonso Galeota Lanza, Romina Salpini, L. Carioti, Hervé Fleury, L. Piermatteo, Massimo Andreoni, Mario Angelico, N. Iapadre, Loredana Sarmati, E. Nebuloso, Maria Stanzione, Giuseppe Maria De Sanctis, Miriam Lichtner, Caterina Pasquazzi, Claudio Maria Mastroianni, Colagrossi, L, Salpini, R, Scutari, R, Carioti, L, Battisti, A, Piermatteo, L, Bertoli, A, Fabeni, L, Minichini, C, Trimoulet, P, Fleury, H, Nebuloso, E, De Cristofaro, M, Cappiello, G, Spano', Antonio, Malagnino, V, Mari, T, Barlattani, A, Iapadre, N, Lichtner, M, Mastroianni, C, Lenci, I, Pasquazzi, C, De Sanctis, Gm, Galeota Lanza, A, Stanzione, M, Stornaiuolo, G, Marignani, M, Sarmati, L, Andreoni, M, Angelico, M, Ceccherini-Silberstein, F, Perno, Cf, Coppola, N, and Svicher, V.

Subjects
0301 basic medicine, Models, Molecular, Male, HBsAg, Cirrhosis, HDV-RNA, Protein Conformation, viruses, lcsh:QR1-502, lcsh:Microbiology, Models, Genotype, Viral, Phylogeny, Coinfection, virus diseases, Middle Aged, Hepatitis B, Clinical Practice, Infectious Diseases, Hepatocellular carcinoma, RNA, Viral, HDAg, Adult, Antiviral Agents, Female, Genetic Variation, Hepatitis B Surface Antigens, Hepatitis B virus, Hepatitis Delta Virus, Humans, Mutation, Viral Proteins, Evolution, Molecular, Microbial Interactions, Settore MED/17 - Malattie Infettive, Evolution, Biology, Article, 03 medical and health sciences, Genetic Evolution, Virology, medicine, infectious diseases, virology, Molecular, biochemical phenomena, metabolism, and nutrition, medicine.disease, digestive system diseases, 030104 developmental biology, Structural plasticity, RNA, Hepatic decompensation
Abstract

Chronic HBV + HDV infection is associated with greater risk of liver fibrosis, earlier hepatic decompensation, and liver cirrhosis hepatocellular carcinoma compared to HBV mono-infection. However, to-date no direct anti-HDV drugs are available in clinical practice. Here, we identified conserved and variable regions in HBsAg and HDAg domains in HBV + HDV infection, a critical finding for the design of innovative therapeutic agents. The extent of amino-acid variability was measured by Shannon-Entropy (Sn) in HBsAg genotype-d sequences from 31 HBV + HDV infected and 62 HBV mono-infected patients (comparable for demographics and virological-parameters), and in 47 HDAg genotype-1 sequences. Positions with Sn = 0 were defined as conserved. The percentage of conserved HBsAg-positions was significantly higher in HBV + HDV infection than HBV mono-infection (p = 0.001). Results were confirmed after stratification for HBeAg-status and patients&rsquo, age. A Sn = 0 at specific positions in the C-terminus HBsAg were correlated with higher HDV-RNA, suggesting that conservation of these positions can preserve HDV-fitness. Conversely, HDAg was characterized by a lower percentage of conserved-residues than HBsAg (p &lt, 0.001), indicating higher functional plasticity. Furthermore, specific HDAg-mutations were significantly correlated with higher HDV-RNA, suggesting a role in conferring HDV replicative-advantage. Among HDAg-domains, only the virus-assembly signal exhibited a high genetic conservation (75% of conserved-residues). In conclusion, HDV can constrain HBsAg genetic evolution to preserve its fitness. The identification of conserved regions in HDAg poses the basis for designing innovative targets against HDV-infection.

Published
2018

50. Performance of genotypic tropism testing on proviral DNA in clinical practice: Results from the DIVA study group

Author

Svicher, Valentina, Alteri, Claudia, Montano, Marco, D Arrigo, Roberta, Andreoni, Massimo, Angarano, Gioacchino, Antinori, Andrea, Antonelli, Guido, Allice, Tiziano, Bagnarelli, Patrizia, Baldanti, Fausto, Bertoli, Ada, Borderi, Marco, Boeri, Enzo, Bon, Isabella, Bruzzone, Bianca, Callegaro, Anna Paola, Capobianchi, Maria Rosaria, Carosi, Giampiero, Cauda, Roberto, Ceccherini-Silberstein, Francesca, Clementi, Massimo, Chirianni, Antonio, Manuela Colafigli, Monforte, Antonella D. Arminio, Luca, Andrea, Di Biagio, Antonio, Di Nicuolo, Giuseppe, Di Perri, Giovanni, Di Pietro, Massimo, Di Santo, Fabiola, Fabeni, Lavinia, Fadda, Giovanni, Galli, Massimo, Gennari, William, Ghisetti, Valeria, Giacometti, Andrea, Gori, Caterina, Gori, Andrea, Gulminetti, Roberto, Leoncini, Francesco, Maffongelli, Gaetano, Maggiolo, Franco, Manca, Giuseppe, Gargiulo, Franco, Martinelli, Canio, Maserati, Renato, Mazzotta, Francesco, Meini, Genny, Micheli, Valeria, Monno, Laura, Mussini, Cristina, Narciso, Pasquale, Nozza, Silvia, Paolucci, Stefania, Palu, Giorgio, Parisi, Saverio, Parruti, Giustino, Pignataro, Angela Rosa, Pollicita, Michela, Quirino, Tiziana, Re, Maria Carla, Rizzardini, Giuliano, Santangelo, Rosaria, Scaggiante, Renzo, Sterrantino, Gaetana, Turriziani, Ombretta, Vatteroni, Maria Linda, Vecchi, Laura, Viscoli, Claudio, Vullo, Vincenzo, Zazzi, Maurizio, Lazzarin, Adriano, Perno, Carlo Federico, Diva, Grp, Svicher V, Alteri C, Montano M, D'Arrigo R, Andreoni M, Angarano G, Antinori A, Antonelli G, Allice T, Bagnarelli P, Baldanti F, Bertoli A, Borderi M, Boeri E, Bon I, Bruzzone B, Callegaro AP, Capobianchi MR, Carosi G, Cauda R, Ceccherini-Silberstein F, Clementi M, Chirianni A, Colafigli M, D'Arminio Monforte A, De Luca A, Di Biagio A, Di Nicuolo G, Di Perri G, Di Pietro M, Di Santo F, Fabeni L, Fadda G, Galli M, Gennari W, Ghisetti V, Giacometti A, Gori C, Gori A, Gulminetti R, Leoncini F, Maffongelli G, Maggiolo F, Manca G, Gargiulo F, Martinelli C, Maserati R, Mazzotta F, Meini G, Micheli V, Monno L, Mussini C, Narciso P, Nozza S, Paolucci S, Pal G, Parisi S, Parruti G, Pignataro AR, Pollicita M, Quirino T, Re MC, Rizzardini G, Santangelo R, Scaggiante R, Sterrantino G, Turriziani O, Vatteroni ML, Vecchi L, Viscoli C, Vullo V, Zazzi M, Lazzarini A, Perno CF., Svicher, V, Alteri, C, Montano, M, D'Arrigo, R, Andreoni, M, Angarano, G, Antinori, A, Antonelli, G, Allice, T, Bagnarelli, P, Baldanti, F, Bertoli, A, Borderi, M, Boeri, E, Bon, I, Bruzzone, B, Callegaro, Ap, Capobianchi, Mr, Carosi, G, Cauda, R, Ceccherini Silberstein, F, Clementi, Massimo, Chirianni, A, Colafigli, M, Monforte, Ad, De Luca, A, Di Biagio, A, Di Nicuolo, G, Di Perri, G, Di Pietro, M, Di Santo, F, Fabeni, L, Fadda, G, Galli, M, Gennari, W, Ghisetti, V, Giacometti, A, Gori, C, Gori, A, Gulminetti, R, Leoncini, F, Maffongelli, G, Maggiolo, F, Manca, G, Gargiulo, F, Martinelli, C, Maserati, R, Mazzotta, F, Meini, G, Micheli, V, Monno, L, Mussini, C, Narciso, P, Nozza, S, Paolucci, S, Palu, G, Parisi, S, Parruti, G, Pignataro, Ar, Pollicita, M, Quirino, T, Re, Mc, Rizzardini, G, Santangelo, R, Scaggiante, R, Sterrantino, G, Turriziani, O, Vatteroni, Ml, Vecchi, L, Viscoli, C, Vullo, V, Zazzi, M, Lazzarin, Adriano, Perno, Cf, Callegaro, A, Capobianchi, M, Clementi, M, D'Arminio Monforte, A, Pal, G, Pignataro, A, Re, M, Vatteroni, M, Lazzarini, A, and Perno, C

Subjects
Male, Genotype, Genotyping Techniques, IMPACT, Mononuclear, HIV-1 TROPISM, Proviral DNA, Reproducibility of Result, HIV Infections, CORECEPTOR SWITCH, HIV Envelope Protein gp120, FREQUENCY, Tropism, CXCR4-USING HIV, HIV, AIDS, DNA provirale, ANTIRETROVIRAL THERAPY, Proviruses, INFECTION, Leukocytes, Humans, HIV Infection, CD4 CELL COUNT, PLASMA RNA, MARAVIROC, Proviruse, hiv, tropism, proviral dna, virus diseases, Reproducibility of Results, Viral Load, Settore MED/07 - Microbiologia e Microbiologia Clinica, Viral Tropism, HIV-1, Leukocytes, Mononuclear, Female, Genotyping Technique, Human
Abstract

"Objective: The DIVA study is aimed at setting up a standardized genotypic tropism-testing on proviral-DNA for the routine clinical diagnostic-laboratory Methods: Twelve local centres and 5 reference centres (previously cross-validated) were identified. For inter-center validation-procedure, 60 peripheral-blood mononuclear cells (PBMCs) aliquots from 45 HAART-treated patients were randomly chosen for population V3 sequencing on proviral-DNA at local HIV centre and at reference-laboratory Viral tropism was predicted by Geno2Pheno algorithm (False Positive Rate [FPR] = 20%) as proposed by the European-Guidelines. Quantification of total HIV-1 DNA was based on a method described by Viard (2004). Results: Quantification of HIV-1 DNA was available for 35\/45 (77.8%) samples, and gave a median value of 598 (IQR:252-1,203) copies\/10(6) PBMCs. A total of 56\/60 (93.3%) samples were successfully amplified by both the reference and the local virological centers. The overall concordance of tropism prediction between local and reference centers was 54\/56 (96.4%). Results of tropism prediction by local centers were: 33\/54 (61.1%) R5 and 21\/54 (38.9%) X4\/DM. Conclusion: There was high concordance in the genotypic tropism prediction based on proviral DNA among different virological centers throughout Italy. Our results are in line with other European studies, and support the use of genotypic tropism testing on proviral DNA in patients with suppressed plasma HIV-1 RNA candidate to CCR5-antagonist treatment."

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