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Miranda MNS, Pimentel V, Gomes P, Martins MDRO, Seabra SG, Kaiser R, Böhm M, Seguin-Devaux C, Paredes R, Bobkova M, Zazzi M, Incardona F, Pingarilho M, Abecasis AB. The Role of Late Presenters in HIV-1 Transmission Clusters in Europe. Viruses 2023; 15:2418. [PMID: 38140659 PMCID: PMC10746990 DOI: 10.3390/v15122418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/30/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Investigating the role of late presenters (LPs) in HIV-1 transmission is important, as they can contribute to the onward spread of HIV-1 virus before diagnosis, when they are not aware of their HIV status. OBJECTIVE To characterize individuals living with HIV-1 followed up in Europe infected with subtypes A, B, and G and to compare transmission clusters (TC) in LP vs. non-late presenter (NLP) populations. METHODS Information from a convenience sample of 2679 individuals living with HIV-1 was collected from the EuResist Integrated Database between 2008 and 2019. Maximum likelihood (ML) phylogenies were constructed using FastTree. Transmission clusters were identified using Cluster Picker. Statistical analyses were performed using R. RESULTS 2437 (91.0%) sequences were from subtype B, 168 (6.3%) from subtype A, and 74 (2.8%) from subtype G. The median age was 39 y/o (IQR: 31.0-47.0) and 85.2% of individuals were males. The main transmission route was via homosexual (MSM) contact (60.1%) and 85.0% originated from Western Europe. In total, 54.7% of individuals were classified as LPs and 41.7% of individuals were inside TCs. In subtype A, individuals in TCs were more frequently males and natives with a recent infection. For subtype B, individuals in TCs were more frequently individuals with MSM transmission route and with a recent infection. For subtype G, individuals in TCs were those with a recent infection. When analyzing cluster size, we found that LPs more frequently belonged to small clusters (<8 individuals), particularly dual clusters (2 individuals). CONCLUSION LP individuals are more present either outside or in small clusters, indicating a limited role of late presentation to HIV-1 transmission.
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Affiliation(s)
- Mafalda N. S. Miranda
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation towards Global Health (LA-REAL), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), 1349-008 Lisbon, Portugal; (V.P.); (M.d.R.O.M.); (S.G.S.); (M.P.); (A.B.A.)
| | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation towards Global Health (LA-REAL), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), 1349-008 Lisbon, Portugal; (V.P.); (M.d.R.O.M.); (S.G.S.); (M.P.); (A.B.A.)
| | - Perpétua Gomes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisbon, Portugal;
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, 2829-511 Costa da Caparica, Portugal
| | - Maria do Rosário O. Martins
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation towards Global Health (LA-REAL), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), 1349-008 Lisbon, Portugal; (V.P.); (M.d.R.O.M.); (S.G.S.); (M.P.); (A.B.A.)
| | - Sofia G. Seabra
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation towards Global Health (LA-REAL), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), 1349-008 Lisbon, Portugal; (V.P.); (M.d.R.O.M.); (S.G.S.); (M.P.); (A.B.A.)
| | - Rolf Kaiser
- Institute of Virology, University Hospital of Cologne, University of Cologne, 50923 Cologne, Germany; (R.K.); (M.B.)
- DZIF, Deutsches Zentrum für Infektionsforschung, German Center for Infection Research, Partner Site Bonn-Cologne, 50923 Cologne, Germany
| | - Michael Böhm
- Institute of Virology, University Hospital of Cologne, University of Cologne, 50923 Cologne, Germany; (R.K.); (M.B.)
- DZIF, Deutsches Zentrum für Infektionsforschung, German Center for Infection Research, Partner Site Bonn-Cologne, 50923 Cologne, Germany
| | - Carole Seguin-Devaux
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg;
| | - Roger Paredes
- Infectious Diseases Department, IrsiCaixa AIDS Research Institute, Hospital University Hospital Germans Trias i Pujol, 08916 Badalona, Spain;
| | - Marina Bobkova
- Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia;
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
| | - Francesca Incardona
- IPRO—InformaPRO S.r.l., 00152 Rome, Italy;
- EuResist Network, 00152 Rome, Italy
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation towards Global Health (LA-REAL), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), 1349-008 Lisbon, Portugal; (V.P.); (M.d.R.O.M.); (S.G.S.); (M.P.); (A.B.A.)
| | - Ana B. Abecasis
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation towards Global Health (LA-REAL), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), 1349-008 Lisbon, Portugal; (V.P.); (M.d.R.O.M.); (S.G.S.); (M.P.); (A.B.A.)
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Planinić A, Begovac J, Rokić F, Šimičić P, Oroz M, Jakovac K, Vugrek O, Zidovec-Lepej S. Characterization of Human Immunodeficiency Virus-1 Transmission Clusters and Transmitted Drug-Resistant Mutations in Croatia from 2019 to 2022. Viruses 2023; 15:2408. [PMID: 38140649 PMCID: PMC10747707 DOI: 10.3390/v15122408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Molecular epidemiology of HIV-1 infection is challenging due to the highly diverse HIV-genome. We investigated the genetic diversity and prevalence of transmitted drug resistance (TDR) followed by phylogenetic analysis in 270 HIV-1 infected, treatment-naïve individuals from Croatia in the period 2019-2022. The results of this research confirmed a high overall prevalence of TDR of 16.7%. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside RTIs (NNRTIs), and protease inhibitors (PIs) was found in 9.6%, 7.4%, and 1.5% of persons, respectively. No resistance to integrase strand-transfer inhibitors (INSTIs) was found. Phylogenetic analysis revealed that 173/229 sequences (75.5%) were part of transmission clusters, and the largest identified was T215S, consisting of 45 sequences. Forward transmission was confirmed in several clusters. We compared deep sequencing (DS) with Sanger sequencing (SS) on 60 randomly selected samples and identified additional surveillance drug resistance mutations (SDRMs) in 49 of them. Our data highlight the need for baseline resistance testing in treatment-naïve persons. Although no major INSTIs were found, monitoring of SDRMs to INSTIs should be continued due to the extensive use of first- and second-generation INSTIs.
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Affiliation(s)
- Ana Planinić
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases Dr. Fran Mihaljević, 10000 Zagreb, Croatia;
| | - Josip Begovac
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Filip Rokić
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Petra Šimičić
- Department of Oncology and Nuclear Medicine, Sestre Milosrdnice University Hospital Center, 10000 Zagreb, Croatia;
| | - Maja Oroz
- Cytogenetic Laboratory, Department of Obstetrics and Gynecology, Clinical Hospital Sveti Duh, 10000 Zagreb, Croatia;
| | - Katja Jakovac
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Oliver Vugrek
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Snjezana Zidovec-Lepej
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases Dr. Fran Mihaljević, 10000 Zagreb, Croatia;
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Limnaios S, Kostaki EG, Adamis G, Astriti M, Chini M, Mangafas N, Lazanas M, Patrinos S, Metallidis S, Tsachouridou O, Papastamopoulos V, Kakalou E, Chatzidimitriou D, Antoniadou A, Papadopoulos A, Psichogiou M, Basoulis D, Gova M, Pilalas D, Paraskeva D, Chrysos G, Paparizos V, Kourkounti S, Sambatakou H, Bolanos V, Sipsas NV, Lada M, Barbounakis E, Kantzilaki E, Panagopoulos P, Maltezos E, Drimis S, Sypsa V, Lagiou P, Magiorkinis G, Hatzakis A, Skoura L, Paraskevis D. Dating the Origin and Estimating the Transmission Rates of the Major HIV-1 Clusters in Greece: Evidence about the Earliest Subtype A1 Epidemic in Europe. Viruses 2022; 14:v14010101. [PMID: 35062305 PMCID: PMC8782043 DOI: 10.3390/v14010101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/20/2021] [Accepted: 12/30/2021] [Indexed: 12/16/2022] Open
Abstract
Our aim was to estimate the date of the origin and the transmission rates of the major local clusters of subtypes A1 and B in Greece. Phylodynamic analyses were conducted in 14 subtype A1 and 31 subtype B clusters. The earliest dates of origin for subtypes A1 and B were in 1982.6 and in 1985.5, respectively. The transmission rate for the subtype A1 clusters ranged between 7.54 and 39.61 infections/100 person years (IQR: 9.39, 15.88), and for subtype B clusters between 4.42 and 36.44 infections/100 person years (IQR: 7.38, 15.04). Statistical analysis revealed that the average difference in the transmission rate between the PWID and the MSM clusters was 6.73 (95% CI: 0.86 to 12.60; p = 0.026). Our study provides evidence that the date of introduction of subtype A1 in Greece was the earliest in Europe. Transmission rates were significantly higher for PWID than MSM clusters due to the conditions that gave rise to an extensive PWID HIV-1 outbreak ten years ago in Athens, Greece. Transmission rate can be considered as a valuable measure for public health since it provides a proxy of the rate of epidemic growth within a cluster and, therefore, it can be useful for targeted HIV prevention programs.
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Affiliation(s)
- Stefanos Limnaios
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.L.); (E.G.K.); (M.G.); (V.S.); (P.L.); (G.M.); (A.H.)
| | - Evangelia Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.L.); (E.G.K.); (M.G.); (V.S.); (P.L.); (G.M.); (A.H.)
| | - Georgios Adamis
- 1st Department of Internal Medicine, G. Gennimatas General Hospital, 11527 Athens, Greece; (G.A.); (M.A.)
| | - Myrto Astriti
- 1st Department of Internal Medicine, G. Gennimatas General Hospital, 11527 Athens, Greece; (G.A.); (M.A.)
| | - Maria Chini
- 3rd Department of Internal Medicine-Infectious Diseases Unit, “Korgialeneio-Benakeio” Red Cross General Hospital, 11526 Athens, Greece; (M.C.); (N.M.); (M.L.)
| | - Nikos Mangafas
- 3rd Department of Internal Medicine-Infectious Diseases Unit, “Korgialeneio-Benakeio” Red Cross General Hospital, 11526 Athens, Greece; (M.C.); (N.M.); (M.L.)
| | - Marios Lazanas
- 3rd Department of Internal Medicine-Infectious Diseases Unit, “Korgialeneio-Benakeio” Red Cross General Hospital, 11526 Athens, Greece; (M.C.); (N.M.); (M.L.)
| | | | - Simeon Metallidis
- 1st Department of Internal Medicine, AHEPA University Hospital, Medical School, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (S.M.); (O.T.)
| | - Olga Tsachouridou
- 1st Department of Internal Medicine, AHEPA University Hospital, Medical School, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (S.M.); (O.T.)
| | - Vasileios Papastamopoulos
- 5th Department of Internal Medicine and Infectious Diseases, Evaggelismos General Hospital, 10676 Athens, Greece; (V.P.); (E.K.)
| | - Eleni Kakalou
- 5th Department of Internal Medicine and Infectious Diseases, Evaggelismos General Hospital, 10676 Athens, Greece; (V.P.); (E.K.)
| | - Dimitrios Chatzidimitriou
- National AIDS Reference Centre of Northern Greece, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (D.C.); (L.S.)
| | - Anastasia Antoniadou
- 4th Department of Medicine, Attikon University General Hospital, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (A.A.); (A.P.)
| | - Antonios Papadopoulos
- 4th Department of Medicine, Attikon University General Hospital, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (A.A.); (A.P.)
| | - Mina Psichogiou
- 1st Department of Medicine, Laikon General Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (M.P.); (D.B.)
| | - Dimitrios Basoulis
- 1st Department of Medicine, Laikon General Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (M.P.); (D.B.)
| | - Maria Gova
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.L.); (E.G.K.); (M.G.); (V.S.); (P.L.); (G.M.); (A.H.)
| | - Dimitrios Pilalas
- Medical School, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Dimitra Paraskeva
- Department of Internal Medicine, Tzaneio General Hospital, 18536 Piraeus, Greece; (D.P.); (G.C.); (S.D.)
| | - Georgios Chrysos
- Department of Internal Medicine, Tzaneio General Hospital, 18536 Piraeus, Greece; (D.P.); (G.C.); (S.D.)
| | - Vasileios Paparizos
- HIV/AIDS Unit, A. Syngros Hospital of Dermatology and Venereology, 16121 Athens, Greece; (V.P.); (S.K.)
| | - Sofia Kourkounti
- HIV/AIDS Unit, A. Syngros Hospital of Dermatology and Venereology, 16121 Athens, Greece; (V.P.); (S.K.)
| | - Helen Sambatakou
- HIV Unit, 2nd Department of Internal Medicine, Hippokration General Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (H.S.); (V.B.)
| | - Vasileios Bolanos
- HIV Unit, 2nd Department of Internal Medicine, Hippokration General Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (H.S.); (V.B.)
| | - Nikolaos V. Sipsas
- Department of Pathophysiology, Laikon General Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Malvina Lada
- 2nd Department of Internal Medicine, Sismanogleion General Hospital, 15126 Marousi, Greece;
| | - Emmanouil Barbounakis
- Department of Internal Medicine, University Hospital of Heraklion “PAGNI”, Medical School, University of Crete, 71110 Heraklion, Greece; (E.B.); (E.K.)
| | - Evrikleia Kantzilaki
- Department of Internal Medicine, University Hospital of Heraklion “PAGNI”, Medical School, University of Crete, 71110 Heraklion, Greece; (E.B.); (E.K.)
| | - Periklis Panagopoulos
- Department of Internal Medicine, University General Hospital, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (P.P.); (E.M.)
| | - Efstratios Maltezos
- Department of Internal Medicine, University General Hospital, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (P.P.); (E.M.)
| | - Stelios Drimis
- Department of Internal Medicine, Tzaneio General Hospital, 18536 Piraeus, Greece; (D.P.); (G.C.); (S.D.)
| | - Vana Sypsa
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.L.); (E.G.K.); (M.G.); (V.S.); (P.L.); (G.M.); (A.H.)
| | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.L.); (E.G.K.); (M.G.); (V.S.); (P.L.); (G.M.); (A.H.)
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.L.); (E.G.K.); (M.G.); (V.S.); (P.L.); (G.M.); (A.H.)
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.L.); (E.G.K.); (M.G.); (V.S.); (P.L.); (G.M.); (A.H.)
| | - Lemonia Skoura
- National AIDS Reference Centre of Northern Greece, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (D.C.); (L.S.)
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.L.); (E.G.K.); (M.G.); (V.S.); (P.L.); (G.M.); (A.H.)
- Correspondence:
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Molecular epidemiology and HIV-1 variant evolution in Poland between 2015 and 2019. Sci Rep 2021; 11:16609. [PMID: 34400726 PMCID: PMC8367969 DOI: 10.1038/s41598-021-96125-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/05/2021] [Indexed: 11/23/2022] Open
Abstract
The occurrence of HIV-1 subtypes differs worldwide and within Europe, with non-B variants mainly found across different exposure groups. In this study, we investigated the distribution and temporal trends in HIV-1 subtype variability across Poland between 2015 and 2019. Sequences of the pol gene fragment from 2518 individuals were used for the analysis of subtype prevalence. Subtype B was dominant (n = 2163, 85.90%). The proportion of subtype B-infected individuals decreased significantly, from 89.3% in 2015 to 80.3% in 2019. This was related to the increasing number of subtype A infections. In 355 (14.10%) sequences, non-B variants were identified. In 65 (2.58%) samples, recombinant forms (RFs) were noted. Unique recombinant forms (URFs) were found in 30 (1.19%) sequences. Three A/B recombinant clusters were identified of which two were A6/B mosaic viruses not previously described. Non-B clades were significantly more common among females (n = 81, 22.8%, p = 0.001) and heterosexually infected individuals (n = 45, 32.4%, p = 0.0031). The predominance of subtype B is evident, but the variability of HIV-1 in Poland is notable. Almost half of RFs (n = 65, 2.58%) was comprised of URFs (n = 30, 1.19%); thus those forms were common in the analyzed population. Hence, molecular surveillance of identified variants ensures recognition of HIV-1 evolution in Poland.
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Kantzanou M, Karalexi MA, Papachristou H, Vasilakis A, Rokka C, Katsoulidou A. Transmitted drug resistance among HIV-1 drug-naïve patients in Greece. Int J Infect Dis 2021; 105:42-48. [PMID: 33592343 DOI: 10.1016/j.ijid.2021.02.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/30/2021] [Accepted: 02/10/2021] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVES Despite the success of antiretroviral treatment (ART), the persisting transmitted drug resistance (TDR) and HIV genetic heterogeneity affect the efficacy of treatment. This study explored the prevalence of TDR among ART-naïve HIV patients in Greece during the period 2016-2019. METHODS Genotypic resistance testing was available for 438 ART-naïve HIV patients. Multivariable Poisson regression models were fitted. RESULTS The majority of patients were male, and there was a slight predominance of Hellenic (26.5%) over non-Hellenic (21.9%) nationality. The prevalence of TDR was 7.8%. There was a predominance of mutations for non-nucleoside reverse-transcriptase inhibitors (5.7%) over nucleoside reverse-transcriptase inhibitors (0.2%). No mutations to protease inhibitors were detected. The prevalence of resistance was 22.1% based on all mutations identified through the HIVdb interpretation system. The most frequent resistance sites were E138A (9.6%), K103N (6.4%), and K101E (2.1%). The majority of detected mutations were confined to subtype A (52.6%), followed by B (19.6%). Non-Hellenic nationality was significantly associated with an increased risk of TDR (relative risk 1.32, 95% confidence interval 1.04-1.69). CONCLUSIONS Non-B HIV infections predominate in Greece, with an increasing trend in recent years. The prevalence of TDR remains stable. Ongoing surveillance of resistance testing is needed to secure the long-term success of ART.
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Affiliation(s)
- Maria Kantzanou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527, Goudi, Athens, Greece; National Retrovirus Reference Center/NRRC, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527, Goudi, Athens, Greece
| | - Maria A Karalexi
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527, Goudi, Athens, Greece.
| | - Helen Papachristou
- National Retrovirus Reference Center/NRRC, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527, Goudi, Athens, Greece
| | - Alexis Vasilakis
- National Retrovirus Reference Center/NRRC, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527, Goudi, Athens, Greece
| | - Chrysoula Rokka
- National Retrovirus Reference Center/NRRC, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527, Goudi, Athens, Greece
| | - Antigoni Katsoulidou
- National Retrovirus Reference Center/NRRC, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527, Goudi, Athens, Greece
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Alexiev I, Campbell EM, Knyazev S, Pan Y, Grigorova L, Dimitrova R, Partsuneva A, Gancheva A, Kostadinova A, Seguin-Devaux C, Elenkov I, Yancheva N, Switzer WM. Molecular Epidemiological Analysis of the Origin and Transmission Dynamics of the HIV-1 CRF01_AE Sub-Epidemic in Bulgaria. Viruses 2021; 13:116. [PMID: 33467166 PMCID: PMC7829743 DOI: 10.3390/v13010116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/12/2022] Open
Abstract
HIV-1 subtype CRF01_AE is the second most predominant strain in Bulgaria, yet little is known about the molecular epidemiology of its origin and transmissibility. We used a phylodynamics approach to better understand this sub-epidemic by analyzing 270 HIV-1 polymerase (pol) sequences collected from persons diagnosed with HIV/AIDS between 1995 and 2019. Using network analyses at a 1.5% genetic distance threshold (d), we found a large 154-member outbreak cluster composed mostly of persons who inject drugs (PWID) that were predominantly men. At d = 0.5%, which was used to identify more recent transmission, the large cluster dissociated into three clusters of 18, 12, and 7 members, respectively, five dyads, and 107 singletons. Phylogenetic analysis of the Bulgarian sequences with publicly available global sequences showed that CRF01_AE likely originated from multiple Asian countries, with Vietnam as the likely source of the outbreak cluster between 1988 and 1990. Our findings indicate that CRF01_AE was introduced into Bulgaria multiple times since 1988, and infections then rapidly spread among PWID locally with bridging to other risk groups and countries. CRF01_AE continues to spread in Bulgaria as evidenced by the more recent large clusters identified at d = 0.5%, highlighting the importance of public health prevention efforts in the PWID communities.
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Affiliation(s)
- Ivailo Alexiev
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (L.G.); (R.D.); (A.P.); (A.G.); (A.K.)
| | - Ellsworth M. Campbell
- Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (E.M.C.); (S.K.); (Y.P.); (W.M.S.)
| | - Sergey Knyazev
- Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (E.M.C.); (S.K.); (Y.P.); (W.M.S.)
- Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
| | - Yi Pan
- Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (E.M.C.); (S.K.); (Y.P.); (W.M.S.)
| | - Lyubomira Grigorova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (L.G.); (R.D.); (A.P.); (A.G.); (A.K.)
| | - Reneta Dimitrova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (L.G.); (R.D.); (A.P.); (A.G.); (A.K.)
| | - Aleksandra Partsuneva
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (L.G.); (R.D.); (A.P.); (A.G.); (A.K.)
| | - Anna Gancheva
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (L.G.); (R.D.); (A.P.); (A.G.); (A.K.)
| | - Asya Kostadinova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (L.G.); (R.D.); (A.P.); (A.G.); (A.K.)
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Luxembourg, Luxembourg;
| | - Ivaylo Elenkov
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria; (I.E.); (N.Y.)
| | - Nina Yancheva
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria; (I.E.); (N.Y.)
| | - William M. Switzer
- Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (E.M.C.); (S.K.); (Y.P.); (W.M.S.)
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7
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Lebedev A, Pasechnik O, Ozhmegova E, Antonova A, Blokh A, Grezina L, Sandyreva T, Dementeva N, Kazennova E, Bobkova M. Prevalence and spatiotemporal dynamics of HIV-1 Circulating Recombinant Form 03_AB (CRF03_AB) in the Former Soviet Union countries. PLoS One 2020; 15:e0241269. [PMID: 33095842 PMCID: PMC7584246 DOI: 10.1371/journal.pone.0241269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/12/2020] [Indexed: 11/19/2022] Open
Abstract
Background HIV-1 circulating recombinant forms (CRFs) infections has been increasing in Former Soviet Union (FSU) countries in the recent decade. One is the CRF03_AB, which circulated in the region since late 1990s and probably became widespread in northwestern FSU countries. However, there is not much information provided about the dissemination of this recombinant. Here, we examine the prevalence, evolutionary dynamics and dispersion pattern of HIV-1 CRF03_AB recombinant. Methods We analyzed 32 independent studies and 151 HIV-1 CRF03_AB pol sequences isolated from different FSU countries over a period of 22 years. Pooled prevalence was estimated using a random effects model. Bayesian coalescent-based method was used to estimate the evolutionary, phylogeographic and demographic parameters. Results Our meta-analysis showed that the pooled prevalence of CRF03_AB infection in northwestern FSU region was 5.9% [95%CI: 4.1–7.8]. Lithuania (11.6%), Russia (5.9%) and Belarus (2.9%) were the most affected by CRF03_AB. We found that early region wide spread of HIV-1 CRF03_AB originated from one viral clade that arose in the city of Kaliningrad in 1992 [95%HPD: 1990–1995]. Fourteen migration route of this variant were found. The city of Kaliningrad is involved in most of these, confirming its leading role in CRF03_AB spread within FSU. Demographic reconstruction point to this is that CRF03_AB clade seems to have experienced an exponential growth until the mid-2000s and a decrease in recent years. Conclusion These data provide new insights into the molecular epidemiology of CRF03_AB as well as contributing to the fundamental understanding of HIV epidemic in FSU.
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Affiliation(s)
- Aleksey Lebedev
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
- * E-mail:
| | - Oksana Pasechnik
- Departments of Epidemiology, Omsk State Medical University, Omsk, Russia
| | - Ekaterina Ozhmegova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | - Anastasiia Antonova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | - Aleksey Blokh
- Departments of Epidemiology, Omsk State Medical University, Omsk, Russia
| | - Liliya Grezina
- Clinical Diagnostic Laboratory, Yamalo-Nenets Autonomous District Center for Prevention and Control of AIDS and Infectious Diseases, Noyabr'sk, Russia
| | - Tatiana Sandyreva
- Clinical Diagnostic Laboratory, Sverdlovsk Regional Center for Prevention and Control of AIDS and Infectious Diseases, Ekaterinburg, Russia
| | - Natalia Dementeva
- Clinical Diagnostic Laboratory, Saint-Petersburg Center for Prevention and Control of AIDS and Infectious Disease, Saint-Petersburg, Russia
| | - Elena Kazennova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | - Marina Bobkova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
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8
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Assoumou L, Bocket L, Pallier C, Grude M, Ait-Namane R, Izopet J, Raymond S, Charpentier C, Visseaux B, Wirden M, Trabaud MA, Le Guillou-Guillemette H, Allaoui C, Henquell C, Krivine A, Dos Santos G, Delamare C, Bouvier-Alias M, Montes B, Ferre V, De Monte A, Signori-Schmuck A, Maillard A, Morand-Joubert L, Tumiotto C, Fafi-Kremer S, Amiel C, Barin F, Marque-Juillet S, Courdavault L, Vallet S, Beby-Defaux A, de Rougemont A, Fenaux H, Avettand-Fenoel V, Allardet-Servent A, Plantier JC, Peytavin G, Calvez V, Chaix ML, Descamps D. Stable prevalence of transmitted drug resistance mutations and increased circulation of non-B subtypes in antiretroviral-naive chronically HIV-infected patients in 2015/2016 in France. J Antimicrob Chemother 2020; 74:1417-1424. [PMID: 30753724 DOI: 10.1093/jac/dkz011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/27/2018] [Accepted: 12/31/2018] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES We estimated the prevalence of transmitted-drug-resistance-associated mutations (TDRAMs) in antiretroviral-naive chronically HIV-1-infected patients. PATIENTS AND METHODS TDRAMs were sought in samples from 660 diagnosed HIV-1-infected individuals in 2015/2016 in 33 HIV clinical centres. Weighted analyses, considering the number of patients followed in each centre, were used to derive representative estimates of the percentage of individuals with TDRAMs. Results were compared with those of the 2010/2011 survey (n = 661) using the same methodology. RESULTS At inclusion, median CD4 cell counts and plasma HIV-1 RNA were 394 and 350/mm3 (P = 0.056) and 4.6 and 4.6 log10 copies/mL (P = 0.360) in the 2010/2011 survey and the 2015/2016 survey, respectively. The frequency of non-B subtypes increased from 42.9% in 2010/2011 to 54.8% in 2015/2016 (P < 0.001), including 23.4% and 30.6% of CRF02_AG (P = 0.004). The prevalence of virus with protease or reverse-transcriptase TDRAMs was 9.0% (95% CI = 6.8-11.2) in 2010/2011 and 10.8% (95% CI = 8.4-13.2) in 2015/2016 (P = 0.269). No significant increase was observed in integrase inhibitor TDRAMs (6.7% versus 9.2%, P = 0.146). Multivariable analysis showed that men infected with the B subtype were the group with the highest risk of being infected with a resistant virus compared with others (adjusted OR = 2.2, 95% CI = 1.3-3.9). CONCLUSIONS In France in 2015/2016, the overall prevalence of TDRAMs was 10.8% and stable compared with 9.0% in the 2010/2011 survey. Non-B subtypes dramatically increased after 2010. Men infected with B subtype were the group with the highest risk of being infected with a resistant virus, highlighting the need to re-emphasize safe sex messages.
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Affiliation(s)
- Lambert Assoumou
- INSERM, UMR 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | | | | | - Maxime Grude
- INSERM, UMR 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Rachid Ait-Namane
- INSERM, UMR 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | | | | | - Charlotte Charpentier
- Hopital Bichat Claude Bernard, Virology, Paris, France.,Univ Paris-Diderot, INSERM UMR 1137, CNR VIH, Paris, France
| | - Benoit Visseaux
- Hopital Bichat Claude Bernard, Virology, Paris, France.,Univ Paris-Diderot, INSERM UMR 1137, CNR VIH, Paris, France
| | - Marc Wirden
- INSERM, UMR 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France.,CHU Pitié-Salpêtrière, Virology, Paris, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Laurence Morand-Joubert
- INSERM, UMR 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France.,Hopital Saint-Antoine, Virology, Paris, France.,Sorbonne Université, Paris, France
| | | | | | | | | | | | | | | | | | | | | | - Véronique Avettand-Fenoel
- CHU Necker-Enfants Malades, Virology, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | | | | | - Gilles Peytavin
- Univ Paris-Diderot, INSERM UMR 1137, CNR VIH, Paris, France.,Hopital Bichat-Claude Bernard, Laboratoire de Pharmaco-Toxicologie, Paris, France
| | - Vincent Calvez
- INSERM, UMR 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France.,CHU Pitié-Salpêtrière, Virology, Paris, France.,Sorbonne Université, Paris, France
| | | | - Diane Descamps
- Hopital Bichat Claude Bernard, Virology, Paris, France.,Univ Paris-Diderot, INSERM UMR 1137, CNR VIH, Paris, France
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9
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Bagaglio S, Uberti-Foppa C, Sagnelli C, Lai A, Hasson H, Salpietro S, Messina E, Morsica G, Zaffina C, Sica A, Lazzarin A, Angeletti S, Sagnelli E, Foley B, Ciccozzi M. HIV-1 recombinant forms in immigrants regularly residing in Milan, northern Italy. Infection 2020; 48:553-558. [PMID: 32430647 DOI: 10.1007/s15010-020-01434-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 04/24/2020] [Indexed: 10/24/2022]
Abstract
To assess the HIV -1subtypes distribution in HIV-1 positive migrants living in Milan we studied 77 HIV-1 patients followed at the San Raffaele Hospital of Milan. Twenty subjects were born in Europe, 43 in the Americas, 10 in Africa and 4 in Asia. Unsafe heterosexual activity prevailed in migrants born in Africa and male homosexuality in those born in European, American and Asian countries (p = 0.05). The phylogeny showed that 38/77 (49.3%) subjects carried HIV-B subtype while the remaining strains were classified as not pure HIV-1 B subtypes 13/77 (16.9%) or recombinant forms 26/77 (33.8%). Female gender more frequently showed HIV-1 non-B strains and rarely HIV-1 B subtypes (12/39, 30.8% vs. 3/38, 7.9%, p = 0.02). Transmitted drug resistance was identified in 10/77 (13%) patients predominately with B subtype. Our data underscore a large heterogeneity in HIV-1 subtypes and a large proportion of recombinant forms.
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Affiliation(s)
- Sabrina Bagaglio
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy
| | - Caterina Uberti-Foppa
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy
| | - Caterina Sagnelli
- Section of Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania Luigi Vanvitelli, Via L. Armanni 5, 80131, Naples, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Hamid Hasson
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy
| | - Stefania Salpietro
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy
| | - Emanuela Messina
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Morsica
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Zaffina
- Medical Statistics and Epidemiology, Campus Bio-Medico University, Rome, Italy
| | - Antonello Sica
- Department of Precision Medicine, Campania University Luigi Vanvitelli, Naples, Italy
| | - Adriano Lazzarin
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Angeletti
- Laboratory Clinical Science, Campus Bio-Medico University, Rome, Italy
| | - Evangelista Sagnelli
- Department of Infectious Diseases, Vita-Salute University, San Raffaele Scientific Institute, Milan, Italy.
| | - Brian Foley
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Massimo Ciccozzi
- Laboratory Clinical Science, Campus Bio-Medico University, Rome, Italy
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10
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High HIV-1 diversity in immigrants resident in Italy (2008-2017). Sci Rep 2020; 10:3226. [PMID: 32094387 PMCID: PMC7039940 DOI: 10.1038/s41598-020-59084-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/23/2019] [Indexed: 02/02/2023] Open
Abstract
The proportion of new diagnoses of HIV infection in immigrants residing in Italy raised from 11% in 1992 to 29.7% in 2018. To investigate the HIV clades circulating in this community a retrospective study was performed in 557 HIV-infected immigrants living in 12 Italian cities. Immigrants originated from East-Europe and Central-Asia (11.7%), North Africa and Middle East (7.3%), South and South-East Asia (7.2%), Latin America and the Caribbean (14.4%), and sub-Saharan Africa (59.4%). More than 87% of immigrants were on antiretroviral therapy (ART), although 26.6% of them were viremic. A 22.0% of immigrants had hepatitis (HBV and/or HCV) and/or tuberculosis. HIV phylogenetic analysis on sequences from 192 immigrants showed the presence of clades B (23.4%), G (16.1%), C (10.4%), A1 (9.4%), F1 (5.2%), D (1.6%) and Circulating Recombinant Forms (CRFs) (33.9%). CRF02_AG represented 72.3% of the total CRFs. Clusters between immigrants and Italian natives were also present. Drug resistance mutations to NRTI, NNRTI, and PI drug classes occurred in 29.1% of ART-treated and in 12.9% of ART-naïve individuals. These data highlight the need for tailored public health interventions in immigrants to avoid spreading in Italy of HIV genetic forms and ART-resistant variants, as well as HIV co-morbidities.
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11
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Lorenzin G, Gargiulo F, Caruso A, Caccuri F, Focà E, Celotti A, Quiros-Roldan E, Izzo I, Castelli F, De Francesco MA. Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis. Microorganisms 2019; 8:microorganisms8010036. [PMID: 31878069 PMCID: PMC7022943 DOI: 10.3390/microorganisms8010036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 11/16/2022] Open
Abstract
HIV-1 diversity is increasing in European countries due to immigration flows, as well as travels and human mobility, leading to the circulation of both new viral subtypes and new recombinant forms, with important implications for public health. We analyzed 710 HIV-1 sequences comprising protease and reverse-transcriptase (PR/RT) coding regions, sampled from 2011 to 2017, from naive patients in Spedali Civili Hospital, Brescia, Italy. Subtyping was performed by using a combination of different tools; the phylogenetic analysis with a structured coalescence model and Makarov Chain Monte Carlo was used on the datasets, to determine clusters and evolution. We detected 304 (43%) patients infected with HIV-1 non-B variants, of which only 293 sequences were available, with four pure subtypes and five recombinant forms; subtype F1 (17%) and CRF02_AG (51.1%) were most common. Twenty-five transmission clusters were identified, three of which included >10 patients, belonging to subtype CRF02_AG and subtype F. Most cases of alleged transmission were between heterosexual couples. Probably due to strong migratory flows, we have identified different subtypes with particular patterns of recombination or, as in the case of the subtype G (18/293, 6.1%), to a complete lack of relationship between the sequenced strains, revealing that they are all singletons. Continued HIV molecular surveillance is most important to analyze the dynamics of the boost of transmission clusters in order to implement public health interventions aimed at controlling the HIV epidemic.
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Affiliation(s)
- Giovanni Lorenzin
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia-Spedali Civili, 25123 Brescia, Italy; (G.L.); (F.G.); (A.C.); (F.C.)
- Institute of Microbiology and Virology, Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy
| | - Franco Gargiulo
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia-Spedali Civili, 25123 Brescia, Italy; (G.L.); (F.G.); (A.C.); (F.C.)
| | - Arnaldo Caruso
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia-Spedali Civili, 25123 Brescia, Italy; (G.L.); (F.G.); (A.C.); (F.C.)
| | - Francesca Caccuri
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia-Spedali Civili, 25123 Brescia, Italy; (G.L.); (F.G.); (A.C.); (F.C.)
| | - Emanuele Focà
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, 25123 Brescia, Italy; (E.F.); (A.C.); (E.Q.-R.); (I.I.); (F.C.)
| | - Anna Celotti
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, 25123 Brescia, Italy; (E.F.); (A.C.); (E.Q.-R.); (I.I.); (F.C.)
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, 25123 Brescia, Italy; (E.F.); (A.C.); (E.Q.-R.); (I.I.); (F.C.)
| | - Ilaria Izzo
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, 25123 Brescia, Italy; (E.F.); (A.C.); (E.Q.-R.); (I.I.); (F.C.)
| | - Francesco Castelli
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, 25123 Brescia, Italy; (E.F.); (A.C.); (E.Q.-R.); (I.I.); (F.C.)
| | - Maria A. De Francesco
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia-Spedali Civili, 25123 Brescia, Italy; (G.L.); (F.G.); (A.C.); (F.C.)
- Correspondence: ; Tel.: +39-030-399-5860
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12
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Reconstruction of the Genetic History and the Current Spread of HIV-1 Subtype A in Germany. J Virol 2019; 93:JVI.02238-18. [PMID: 30944175 DOI: 10.1128/jvi.02238-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 03/13/2019] [Indexed: 12/15/2022] Open
Abstract
HIV-1 non-B infections have been increasing in Europe for several years. In Germany, subtype A belongs to the most abundant non-B subtypes showing an increasing prevalence of 8.3% among new infections in 2016. Here we trace the origin and examine the current spread of the German HIV-1 subtype A epidemic. Bayesian coalescence and birth-death analyses were performed with 180 German HIV-1 pol sequences and 528 related and publicly available sequences to reconstruct the population dynamics and fluctuations for each of the transmission groups. Our reconstructions indicate two distinct sources of the German subtype A epidemic, with an Eastern European and an Eastern African lineage both cocirculating in the country. A total of 13 German-origin clusters were identified; among these, 6 clusters showed recent activity. Introductions leading to further countrywide spread originated predominantly from Eastern Africa when introduced before 2005. Since 2005, however, spreading introductions have occurred exclusively within the Eastern European clade. Moreover, we observed changes in the main route of subtype A transmission. The beginning of the German epidemic (1985 to 1995) was dominated by heterosexual transmission of the Eastern African lineage. Since 2005, transmissions among German men who have sex with men (MSM) have been increasing and have been associated with the Eastern European lineage. Infections among people who inject drugs dominated between 1998 and 2005. Our findings on HIV-1 subtype A infections provide new insights into the spread of this virus and extend the understanding of the HIV epidemic in Germany.IMPORTANCE HIV-1 subtype A is the second most prevalent subtype worldwide, with a high prevalence in Eastern Africa and Eastern Europe. However, an increase of non-B infections, including subtype A infections, has been observed in Germany and other European countries. There has simultaneously been an increased flow of refugees into Europe and especially into Germany, raising the question of whether the surge in non-B infections resulted from this increased immigration or whether German transmission chains are mainly involved. This study is the first comprehensive subtype A study from a western European country analyzing in detail its phylogenetic origin, the impact of various transmission routes, and its current spread. The results and conclusions presented provide new and substantial insights for virologists, epidemiologists, and the general public health sector. In this regard, they should be useful to those authorities responsible for developing public health intervention strategies to combat the further spread of HIV/AIDS.
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13
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Characterization of a large cluster of HIV-1 A1 infections detected in Portugal and connected to several Western European countries. Sci Rep 2019; 9:7223. [PMID: 31076722 PMCID: PMC6510806 DOI: 10.1038/s41598-019-43420-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 04/12/2019] [Indexed: 11/10/2022] Open
Abstract
HIV-1 subtypes associate with differences in transmission and disease progression. Thus, the existence of geographic hotspots of subtype diversity deepens the complexity of HIV-1/AIDS control. The already high subtype diversity in Portugal seems to be increasing due to infections with sub-subtype A1 virus. We performed phylogenetic analysis of 65 A1 sequences newly obtained from 14 Portuguese hospitals and 425 closely related database sequences. 80% of the A1 Portuguese isolates gathered in a main phylogenetic clade (MA1). Six transmission clusters were identified in MA1, encompassing isolates from Portugal, Spain, France, and United Kingdom. The most common transmission route identified was men who have sex with men. The origin of the MA1 was linked to Greece, with the first introduction to Portugal dating back to 1996 (95% HPD: 1993.6–1999.2). Individuals infected with MA1 virus revealed lower viral loads and higher CD4+ T-cell counts in comparison with those infected by subtype B. The expanding A1 clusters in Portugal are connected to other European countries and share a recent common ancestor with the Greek A1 outbreak. The recent expansion of this HIV-1 subtype might be related to a slower disease progression leading to a population level delay in its diagnostic.
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14
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Lai A, Simonetti FR, Brindicci G, Bergna A, Di Giambenedetto S, Sterrantino G, Mussini C, Menzo S, Bagnarelli P, Zazzi M, Angarano G, Galli M, Monno L, Balotta C. Local Epidemics Gone Viral: Evolution and Diffusion of the Italian HIV-1 Recombinant Form CRF60_BC. Front Microbiol 2019; 10:769. [PMID: 31031735 PMCID: PMC6474184 DOI: 10.3389/fmicb.2019.00769] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/26/2019] [Indexed: 12/15/2022] Open
Abstract
The molecular epidemiology of HIV-1 in Italy is becoming increasingly complex, mainly due to the spread of non-B subtypes and the emergence of new recombinant forms. We previously characterized the outbreak of the first Italian circulating recombinant form (CRF60_BC), occurring among young MSM living in Apulia between the years 2009 and 2011. Here we show a 5-year follow-up surveillance to trace the evolution of CRF60_BC and to investigate its further spread in Italy. We collected additional sequences and clinical data from patients harboring CRF60_BC, enrolled at the Infectious Diseases Clinic of the University of Bari. In addition to the 24 previously identified sequences, we retrieved 27 CRF60_BC sequences from patients residing in Apulia, whose epidemiological and clinical features did not differ from those of the initial outbreak, i.e., the Italian origin, young age at HIV diagnosis (median: 24 years; range: 18–37), MSM risk factor (23/25, 92%) and recent infection (from 2008 to 2017). Sequence analysis revealed a growing overall nucleotide diversity, with few nucleotide changes that were fixed over time. Twenty-seven additional sequences were detected across Italy, spanning multiple distant regions. Using a BLAST search, we also identified a CRF60_BC sequence isolated in United Kingdom in 2013. Three patients harbored a unique second generation recombinant form in which CRF60_BC was one of the parental strains. Our data show that CRF60_BC gained epidemic importance, spreading among young MSM in multiple Italian regions and increasing its population size in few years, as the number of sequences identified so far has triplicated since our first report. The observed further divergence of CRF60_BC is likely due to evolutionary bottlenecks and host adaptation during transmission chains. Of note, we detected three second-generation recombinants, further supporting a widespread circulation of CRF60_BC and the increasing complexity of the HIV-1 epidemic in Italy.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetano Brindicci
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetana Sterrantino
- Division of Tropical and Infectious Diseases, Careggi Hospital, Florence, Italy
| | - Cristina Mussini
- Clinic of Infectious Diseases, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Menzo
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Patrizia Bagnarelli
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Massimo Galli
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Laura Monno
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Claudia Balotta
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
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15
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Delgado E, Benito S, Montero V, Cuevas MT, Fernández-García A, Sánchez-Martínez M, García-Bodas E, Díez-Fuertes F, Gil H, Cañada J, Carrera C, Martínez-López J, Sintes M, Pérez-Álvarez L, Thomson MM. Diverse Large HIV-1 Non-subtype B Clusters Are Spreading Among Men Who Have Sex With Men in Spain. Front Microbiol 2019; 10:655. [PMID: 31001231 PMCID: PMC6457325 DOI: 10.3389/fmicb.2019.00655] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/15/2019] [Indexed: 11/23/2022] Open
Abstract
In Western Europe, the HIV-1 epidemic among men who have sex with men (MSM) is dominated by subtype B. However, recently, other genetic forms have been reported to circulate in this population, as evidenced by their grouping in clusters predominantly comprising European individuals. Here we describe four large HIV-1 non-subtype B clusters spreading among MSM in Spain. Samples were collected in 9 regions. A pol fragment was amplified from plasma RNA or blood-extracted DNA. Phylogenetic analyses were performed via maximum likelihood, including database sequences of the same genetic forms as the identified clusters. Times and locations of the most recent common ancestors (MRCA) of clusters were estimated with a Bayesian method. Five large non-subtype B clusters associated with MSM were identified. The largest one, of F1 subtype, was reported previously. The other four were of CRF02_AG (CRF02_1; n = 115) and subtypes A1 (A1_1; n = 66), F1 (F1_3; n = 36), and C (C_7; n = 17). Most individuals belonging to them had been diagnosed of HIV-1 infection in the last 10 years. Each cluster comprised viruses from 3 to 8 Spanish regions and also comprised or was related to viruses from other countries: CRF02_1 comprised a Japanese subcluster and viruses from 8 other countries from Western Europe, Asia, and South America; A1_1 comprised viruses from Portugal, United Kingom, and United States, and was related to the A1 strain circulating in Greece, Albania and Cyprus; F1_3 was related to viruses from Romania; and C_7 comprised viruses from Portugal and was related to a virus from Mozambique. A subcluster within CRF02_1 was associated with heterosexual transmission. Near full-length genomes of each cluster were of uniform genetic form. Times of MRCAs of CRF02_1, A1_1, F1_3, and C_7 were estimated around 1986, 1989, 2013, and 1983, respectively. MRCA locations for CRF02_1 and A1_1 were uncertain (however initial expansions in Spain in Madrid and Vigo, respectively, were estimated) and were most probable in Bilbao, Spain, for F1_3 and Portugal for C_7. These results show that the HIV-1 epidemic among MSM in Spain is becoming increasingly diverse through the expansion of diverse non-subtype B clusters, comprising or related to viruses circulating in other countries.
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Affiliation(s)
- Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sonia Benito
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Vanessa Montero
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María Teresa Cuevas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Aurora Fernández-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Mónica Sánchez-Martínez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Elena García-Bodas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco Díez-Fuertes
- AIDS Immunopathogenesis Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Horacio Gil
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,European Program for Public Health Microbiology Training, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Javier Cañada
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Carrera
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Martínez-López
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Marcos Sintes
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Michael M Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
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16
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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 CM, Montella F, Cristaudo A, Mussini C, Girardi E, Andreoni M, Antinori A, Ceccherini-Silberstein F, Perno CF, Santoro MM. Dynamics and phylogenetic relationships of HIV-1 transmitted drug resistance according to subtype in Italy over the years 2000-14. J Antimicrob Chemother 2018; 72:2837-2845. [PMID: 29091206 DOI: 10.1093/jac/dkx231] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/09/2017] [Indexed: 11/14/2022] Open
Abstract
Background Transmitted drug-resistance (TDR) remains a critical aspect for the management of HIV-1-infected individuals. Thus, studying the dynamics of TDR is crucial to optimize HIV care. Methods In total, 4323 HIV-1 protease/reverse-transcriptase sequences from drug-naive individuals diagnosed in north and central Italy between 2000 and 2014 were analysed. TDR was evaluated over time. Maximum-likelihood and Bayesian phylogenetic trees with bootstrap and Bayesian-probability supports defined transmission clusters. Results Most individuals were males (80.2%) and Italian (72.1%), with a median (IQR) age of 37 (30-45) years. MSM accounted for 42.2% of cases, followed by heterosexuals (36.4%). Non-B subtype infections accounted for 30.8% of the overall population and increased over time (<2005-14: 19.5%-38.5%, P < 0.0001), particularly among Italians (<2005-14: 6.5%-28.8%, P < 0.0001). TDR prevalence was 8.8% and increased over time in non-B subtypes (<2005-14: 2%-7.1%, P = 0.018). Overall, 467 transmission clusters (involving 1207 individuals; 27.9%) were identified. The prevalence of individuals grouping in transmission clusters increased over time in both B (<2005-14: 12.9%-33.5%, P = 0.001) and non-B subtypes (<2005-14: 18.4%-41.9%, P = 0.006). TDR transmission clusters were 13.3% within the overall cluster observed and dramatically increased in recent years (<2005-14: 14.3%-35.5%, P = 0.005). This recent increase was mainly due to non-B subtype-infected individuals, who were also more frequently involved in large transmission clusters than those infected with a B subtype [median number of individuals in transmission clusters: 7 (IQR 6-19) versus 4 (3-4), P = 0.047]. Conclusions The epidemiology of HIV transmission changed greatly over time; the increasing number of transmission clusters (sometimes with drug resistance) shows that detection and proper treatment of the multi-transmitters is a major target for controlling HIV spread.
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Affiliation(s)
- L Fabeni
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - C Alteri
- University of Rome Tor Vergata, Rome, Italy
| | - D Di Carlo
- University of Rome Tor Vergata, Rome, Italy
| | - N Orchi
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - L Carioti
- University of Rome Tor Vergata, Rome, Italy
| | - A Bertoli
- University of Rome Tor Vergata, Rome, Italy
| | - C Gori
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - F Forbici
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - F Continenza
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | - C Pinnetti
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - A Vergori
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - A Mondi
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - A Ammassari
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - V Borghi
- Modena University Hospital, Modena, Italy
| | - M Giuliani
- San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - G De Carli
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - S Pittalis
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - S Grisetti
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | | | - F Montella
- S. Giovanni Addolorata Hospital, Rome, Italy
| | - A Cristaudo
- San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - C Mussini
- Modena University Hospital, Modena, Italy
| | - E Girardi
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - M Andreoni
- University Hospital Tor Vergata, Rome, Italy
| | - A Antinori
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | - C F Perno
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
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Abstract
The HIV pandemic has disproportionately impacted sub-Saharan Africa and Southern Africa in particular. The concurrent presence of overlapping epidemic drivers likely underpins how and why the HIV epidemic is so explosive in this region, with implications for understanding approaches to reduce transmission. In this review, we discuss the relative contribution and interaction between epidemic drivers in the Southern African context, including factors both distally and proximally associated with the likelihood and degree of exposure to HIV and factors that increase the probability of transmission when exposure occurs. In particular, we focus on young women as a key population in need of HIV prevention and highlight factors that increase their risk on several levels.
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Affiliation(s)
- Lyle R McKinnon
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Nelson R Mandela School of Medicine, 719 Umbilo Road, Private Bag X7, Congella, Durban, 4013, South Africa. .,Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada.
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Nelson R Mandela School of Medicine, 719 Umbilo Road, Private Bag X7, Congella, Durban, 4013, South Africa.,Department of Epidemiology, Columbia University, New York, USA
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18
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Nikolopoulos GK, Kostaki EG, Paraskevis D. Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia. INFECTION GENETICS AND EVOLUTION 2016; 46:256-268. [PMID: 27287560 DOI: 10.1016/j.meegid.2016.06.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 01/14/2023]
Abstract
HIV strains continuously evolve, tend to recombine, and new circulating variants are being discovered. Novel strains complicate efforts to develop a vaccine against HIV and may exhibit higher transmission efficiency and virulence, and elevated resistance to antiretroviral agents. The United Nations Joint Programme on HIV/AIDS (UNAIDS) set an ambitious goal to end HIV as a public health threat by 2030 through comprehensive strategies that include epidemiological input as the first step of the process. In this context, molecular epidemiology becomes invaluable as it captures trends in HIV evolution rates that shape epidemiological pictures across several geographical areas. This review briefly summarizes the molecular epidemiology of HIV among people who inject drugs (PWID) in Europe and Asia. Following high transmission rates of subtype G and CRF14_BG among PWID in Portugal and Spain, two European countries, Greece and Romania, experienced recent HIV outbreaks in PWID that consisted of multiple transmission clusters including subtypes B, A, F1, and recombinants CRF14_BG and CRF35_AD. The latter was first identified in Afghanistan. Russia, Ukraine, and other Former Soviet Union (FSU) states are still facing the devastating effects of epidemics in PWID produced by AFSU (also known as IDU-A), BFSU (known as IDU-B), and CRF03_AB. In Asia, CRF01_AE and subtype B (Western B and Thai B) travelled from PWID in Thailand to neighboring countries. Recombination hotspots in South China, Northern Myanmar, and Malaysia have been generating several intersubtype and inter-CRF recombinants (e.g. CRF07_BC, CRF08_BC, CRF33_01B etc.), increasing the complexity of HIV molecular patterns.
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Affiliation(s)
- Georgios K Nikolopoulos
- Hellenic Centre for Diseases Control and Prevention, Amarousio, Greece; Hellenic Scientific Society for the Study of AIDS and Sexually Transmitted Diseases, Transmission Reduction Intervention Project-Athens site, Athens, Greece.
| | - Evangelia-Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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