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Gonçalves P, Barreto J, Santos M, Leal S, Marcelino J, Abecasis A, Palladino C, Taveira N. HIV-1 drug resistance and genetic diversity in people with HIV-1 in Cape Verde. AIDS 2024; 38:1101-1110. [PMID: 38349224 DOI: 10.1097/qad.0000000000003866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
OBJECTIVES To characterize the genetic diversity and drug resistance profiles of people with HIV-1 failing ART in Cape Verde (CV). DESIGN Cross-sectional study conducted between January 2019 and December 2021 in 24 health centres on the islands of Santiago and São Vicente. METHODS The HIV-1 pol gene was sequenced in individuals with a detectable viral load. HIV-1 genetic diversity was determined by phylogenetic analysis. Drug resistance mutation patterns and resistance phenotypes were estimated using the Stanford algorithm. RESULTS Viral load was detected in 73 of 252 (29%) enrolled participants and sequencing data were produced for 58 (79%) participants. CRF02 AG strains predominated (46.5%), followed by subtype G (22.4%). Most patients (80%) had mutations conferring resistance to nonnucleoside reverse transcriptase inhibitors (NNRTIs) (67%), nucleoside reverse transcriptase inhibitors (55%), integrase inhibitors (10%) and/or protease inhibitors (7%) used in Cape Verde, a significant increase compared with a study conducted in 2010-2011. The most common mutations were M184V/I (43%), K103N/S (36%) and G190A/S (19%). NNRTI resistance was associated with younger age and exposure to two or more drug regimens. CONCLUSION The HIV-1 epidemic in Cape Verde is mainly driven by CRF02_AG and subtype G. Resistance to NNRTIs and/or NRTIs is highly prevalent and resistance to LPV/r and DTG is emerging. Our results support the use of DTG-based first-line ART and protease inhibitor-based regimens for patients with virological failure, but emerging resistance to LPV/r and DTG is a concern. Continued monitoring of drug resistance is essential to ensure adequate healthcare for PWH in Cape Verde.
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Affiliation(s)
- Paloma Gonçalves
- Instituto de Investigação do Medicamento (iMed.Ulisboa), Faculdade de Farmácia de Lisboa, Lisbon, Portugal
| | | | - Menilita Santos
- Instituto Nacional de Saúde Pública de Cabo Verde, Praia, Cape Verde
| | - Silvania Leal
- Instituto Nacional de Saúde Pública de Cabo Verde, Praia, Cape Verde
| | - José Marcelino
- Instituto de Investigação do Medicamento (iMed.Ulisboa), Faculdade de Farmácia de Lisboa, Lisbon, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), Lisboa, Portugal
| | - Claudia Palladino
- Instituto de Investigação do Medicamento (iMed.Ulisboa), Faculdade de Farmácia de Lisboa, Lisbon, Portugal
| | - Nuno Taveira
- Instituto de Investigação do Medicamento (iMed.Ulisboa), Faculdade de Farmácia de Lisboa, Lisbon, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica
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Wieczorek L, Chang D, Sanders-Buell E, Zemil M, Martinez E, Schoen J, Chenine AL, Molnar S, Barrows B, Poltavee K, Charurat ME, Abimiku A, Blattner W, Iroezindu M, Kokogho A, Michael NL, Crowell TA, Ake JA, Tovanabutra S, Polonis VR. Differences in neutralizing antibody sensitivities and envelope characteristics indicate distinct antigenic properties of Nigerian HIV-1 subtype G and CRF02_AG. Virol J 2024; 21:148. [PMID: 38951814 PMCID: PMC11218331 DOI: 10.1186/s12985-024-02394-y] [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: 02/23/2024] [Accepted: 05/19/2024] [Indexed: 07/03/2024] Open
Abstract
The magnitude of the HIV-1 epidemic in Nigeria is second only to the subtype C epidemic in South Africa, yet the subtypes prevalent in Nigeria require further characterization. A panel of 50 subtype G and 18 CRF02_AG Nigerian HIV-1 pseudoviruses (PSV) was developed and envelope coreceptor usage, neutralization sensitivity and cross-clade reactivity were characterized. These PSV were neutralized by some antibodies targeting major neutralizing determinants, but potentially important differences were observed in specific sensitivities (eg. to sCD4, MPER and V2/V3 monoclonal antibodies), as well as in properties such as variable loop lengths, number of potential N-linked glycans and charge, demonstrating distinct antigenic characteristics of CRF02_AG and subtype G. There was preferential neutralization of the matched CRF/subtype when PSV from subtype G or CRF02_AG were tested using pooled plasma. These novel Nigerian PSV will be useful to study HIV-1 CRF- or subtype-specific humoral immune responses for subtype G and CRF02_AG.
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Affiliation(s)
- Lindsay Wieczorek
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - David Chang
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
- Present address: Office of AIDS Research, National Institutes of Health, Rockville, MD, 20852, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Michelle Zemil
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Elizabeth Martinez
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Jesse Schoen
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Agnes-Laurence Chenine
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
- Present address: Integrated Biotherapeutics, Rockville, MD, 20850, USA
| | - Sebastian Molnar
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Brittani Barrows
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
- Present address: Lentigen Technology, Gaithersburg, MD, 20878, USA
| | - Kultida Poltavee
- SEARCH, Insititute of HIV Research and Innovation (IHRI), Bangkok, Thailand
| | - Man E Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alash'le Abimiku
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - William Blattner
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael Iroezindu
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- HJF Medical Research International, Abuja, Nigeria
| | - Afoke Kokogho
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- HJF Medical Research International, Abuja, Nigeria
| | - Nelson L Michael
- Center for Infectious Disease Research, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
| | - Trevor A Crowell
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Julie A Ake
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Victoria R Polonis
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA.
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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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Herd CL, Mellet J, Mashingaidze T, Durandt C, Pepper MS. Consequences of HIV infection in the bone marrow niche. Front Immunol 2023; 14:1163012. [PMID: 37497228 PMCID: PMC10366613 DOI: 10.3389/fimmu.2023.1163012] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023] Open
Abstract
Dysregulation of the bone marrow niche resulting from the direct and indirect effects of HIV infection contributes to haematological abnormalities observed in HIV patients. The bone marrow niche is a complex, multicellular environment which functions primarily in the maintenance of haematopoietic stem/progenitor cells (HSPCs). These adult stem cells are responsible for replacing blood and immune cells over the course of a lifetime. Cells of the bone marrow niche support HSPCs and help to orchestrate the quiescence, self-renewal and differentiation of HSPCs through chemical and molecular signals and cell-cell interactions. This narrative review discusses the HIV-associated dysregulation of the bone marrow niche, as well as the susceptibility of HSPCs to infection by HIV.
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Mourik K, Boers SA, van Rijn AL, Thijssen JCP, Wessels E, Claas ECJ. Clinical performance of two new, fully integrated molecular platforms used for HIV-1, HBV and HCV viral load analysis, the NeuMoDx 288 and the Alinity m. J Clin Virol 2023; 160:105376. [PMID: 36640531 DOI: 10.1016/j.jcv.2022.105376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/20/2022] [Accepted: 12/31/2022] [Indexed: 01/04/2023]
Abstract
BACKGROUND Viral load (VL) determination in patients with human immunodeficiency virus type 1 (HIV-1), hepatitis B virus (HBV) and hepatitis C virus (HCV) is essential for proper patient management and follow-up. New molecular platforms have been developed to fully automate these diagnostic assays. OBJECTIVE Evaluation of the clinical performance of HIV-1, HBV and HCV VL assays on the Alinity m (Abbott) and NeuMoDx (Qiagen) molecular platforms. METHOD Test panels of the three viruses have been compiled of 100 plasma and/or serum samples per target containing non-detectable, non-quantifiable and quantifiable VLs. All samples were retrospectively tested on the Alinity m and NeuMoDx platforms according to manufacturers' instructions. RESULTS A total of 74, 86 and 66 samples with valid results for both platforms were included in the HIV-1, HBV and HCV analysis respectively. Overall qualitative agreement of the assays on both platforms was 78% for HIV-1, 93% for HBV and 100% for HCV. Quantitative agreement (less than 0.5 log difference) was shown to be 68% for HIV-1, 68% for HBV and 94% for HCV. CONCLUSION The Alinity m and NeuMoDx HCV assay have a comparable performance. Quantification differences in the HIV-1 assay were mostly apparent in the lower VLs and under-quantification of the NeuMoDx HBV assay was observed.
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Affiliation(s)
- K Mourik
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - S A Boers
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - A L van Rijn
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - J C P Thijssen
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - E Wessels
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - E C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.
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Datta J, Majumder S, Chaudhuri D, Giri K. In silico investigation of binding propensity of hematoxylin derivative and damnacanthal for their potential inhibitory effect on HIV-1 Vpr from different subtypes. J Biomol Struct Dyn 2023; 41:14977-14988. [PMID: 36858595 DOI: 10.1080/07391102.2023.2184634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/20/2023] [Indexed: 03/03/2023]
Abstract
HIV-1, the causative agent of AIDS leads to many deaths worldwide though few options are available as therapeutics. To deal with the continuous mutation in the virus genome, requirement of new drugs is always there. Subtype variation plays a crucial role in case of HIV-1 therapeutics development. In this study, we want to investigate some pre examined molecules that can be effective for HIV-1 VPR. Inhibition of several protein-protein interactions with the small molecules will lead to identify some molecules as therapeutics other than the conventional drugs. We retrieved the sequences of different subtypes from the database and representative sequences were identified. Representative structures were modelled and validated using MD simulations. Forty molecules, showing anti Vpr activity in vitro were identified from literature survey and those were docked with each subtype representative structures. Two molecules a stable Hematoxylin Derivative (SHD) and Damnacanthal (D3), these were shown to be bind more effectively for all the subtypes. The stability of the protein and those two small molecule complexes were identified again with MD simulation followed by the binding energy calculation. Thus, these molecules can be thought as any option other than the conventional drug targeting HIV-1 Vpr.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Joyeeta Datta
- Department of Life Sciences, Presidency University, Kolkata, India
| | | | | | - Kalyan Giri
- Department of Life Sciences, Presidency University, Kolkata, India
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HIV-1 subtype B spread through cross-border clusters in the Balkans: a molecular analysis in view of incidence trends. AIDS 2023; 37:125-135. [PMID: 36129113 DOI: 10.1097/qad.0000000000003394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVES To analyze phylogenetic relations and assess the role of cross-border clusters in the spread of HIV-1 subtype B across the Balkans, given the general trends of new HIV diagnoses in seven Balkan countries. DESIGN Retrospective phylogenetic and trend analysis. METHODS In-depth phylogenetic, phylodynamic and phylogeographic analysis performed on 2415 HIV-1 subtype B sequences from 1999 to 2019 using maximal likelihood and Bayesian methods. The joinpoint regression analysis of new HIV diagnoses by country and modes of transmission using 2004-2019 ECDC data. RESULTS Ninety-three HIV-1 Subtype B transmission clusters (68% of studied sequences) were detected of which four cross-border clusters (11% of studied sequences). Phylodynamic analysis showed activity of cross-border clusters up until the mid-2000s, with a subsequent stationary growth phase. Phylogeography analyses revealed reciprocal spread patterns between Serbia, Slovenia and Montenegro and several introductions to Romania from these countries and Croatia. The joinpoint analysis revealed a reduction in new HIV diagnoses in Romania, Greece and Slovenia, whereas an increase in Serbia, Bulgaria, Croatia and Montenegro, predominantly among MSM. CONCLUSION Differing trends of new HIV diagnoses in the Balkans mirror differences in preventive policies implemented in participating countries. Regional spread of HIV within the countries of former Yugoslavia has continued to play an important role even after country break-up, whereas the spread of subtype B through multiple introductions to Romania suggested the changing pattern of travel and migration linked to European integration of Balkan countries in the early 2000s.
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Transmitted HIV-1 is more virulent in heterosexual individuals than men-who-have-sex-with-men. PLoS Pathog 2022; 18:e1010319. [PMID: 35271687 PMCID: PMC8912199 DOI: 10.1371/journal.ppat.1010319] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 01/27/2022] [Indexed: 12/29/2022] Open
Abstract
Transmission bottlenecks introduce selection pressures on HIV-1 that vary with the mode of transmission. Recent studies on small cohorts have suggested that stronger selection pressures lead to fitter transmitted/founder (T/F) strains. Manifestations of this selection bias at the population level have remained elusive. Here, we analysed early CD4 cell count measurements reported from ∼340,000 infected heterosexual individuals (HET) and men-who-have-sex-with-men (MSM), across geographies, ethnicities and calendar years. The reduction in CD4 counts early in infection is reflective of the virulence of T/F strains. MSM and HET use predominant modes of transmission, namely, anal and penile-vaginal, with among the largest differences in the selection pressures at transmission across modes. Further, in most geographies, the groups show little inter-mixing, allowing for the differential selection bias to be sustained and amplified. We found that the early reduction in CD4 counts was consistently greater in HET than MSM (P<0.05). To account for inherent variations in baseline CD4 counts, we constructed a metric to quantify the extent of progression to AIDS as the ratio of the reduction in measured CD4 counts from baseline and the reduction associated with AIDS. We found that this progression corresponding to the early CD4 measurements was ∼68% for MSM and ∼87% for HET on average (P<10−4; Cohen’s d, ds = 0.36), reflecting the more severe disease caused by T/F strains in HET than MSM at the population level. Interestingly, the set-point viral load was not different between the groups (ds<0.12), suggesting that MSM were more tolerant and not more resistant to their T/F strains than HET. This difference remained when we controlled for confounding factors using multivariable regression. We concluded that the different selection pressures at transmission have resulted in more virulent T/F strains in HET than MSM. These findings have implications for our understanding of HIV-1 pathogenesis, evolution, and epidemiology. HIV-1 encounters a key bottleneck at the time of its transmission from one individual to another. This transmission bottleneck can differ between modes of transmission. The stronger this bottleneck is, the more fit the virus has to be to be successfully transmitted. Accordingly, the transmitted/founder (T/F) strains of HIV-1 may have different fitness in risk groups that use different modes of transmission. While studies on small cohorts do support this notion, observations of the manifestations of this differential selection bias at the population level have been lacking. Here, we examined reported early CD4 count measurements from ∼340,000 HET and MSM, across geographies, ethnicities, and calendar years. Early CD4 counts are a measure of the severity of the infection due to T/F strains. HET and MSM transmit predominantly via penile-vaginal and anal modes, respectively, and do not inter-mix significantly. Remarkably, we found that HET consistently had lower early CD4 counts than MSM. This difference could not be attributed to potential confounding factors, such as set-point viral load. The difference thus provided evidence that T/F strains had evolved to be more virulent in HET than MSM at the population level. Intervention strategies may benefit from accounting for this difference between risk groups.
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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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Duran Ramirez JJ, Ballouz T, Nguyen H, Kusejko K, Chaudron SE, Huber M, Hirsch HH, Perreau M, Ramette A, Yerly S, Cavassini M, Stöckle M, Furrer H, Vernazza P, Bernasconi E, Günthard HF, Kouyos RD. Increasing Frequency and Transmission of HIV-1 Non-B Subtypes among Men Who Have Sex with Men in the Swiss HIV Cohort Study. J Infect Dis 2021; 225:306-316. [PMID: 34260728 DOI: 10.1093/infdis/jiab360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/13/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND In Switzerland, HIV-1 transmission among men who have sex with men (MSM) has been dominated by subtype B, whilst non-B subtypes are commonly attributed to infections acquired abroad among heterosexuals. Here, we evaluated the temporal trends of non-B subtypes and the characteristics of molecular transmission clusters (MTCs) among MSM. METHODS Sociodemographic and clinical data and partial pol sequences were obtained from participants enrolled in the Swiss HIV Cohort Study (SHCS). For non-B subtypes, maximum likelihood trees were constructed, from which Swiss MTCs were identified and analysed by transmission group. RESULTS Non-B subtypes were identified in 8.1% (416/5,116) of MSM participants. CRF01_AE was the most prevalent strain (3.5%), followed by A (1.2%), F (1.1%), CRF02_AG (1.1%), C (0.9%), and G (0.3%). Between 1990 and 2019, an increase in the proportion of newly diagnosed individuals (0/123[0%] to 11/32 [34%]) with non-B subtypes in MSM was found. Across all non-B subtypes, the majority of MSM MTCs were European. Larger MTCs were observed for MSM than heterosexuals. CONCLUSIONS We found a substantial increase in HIV-1 non-B subtypes among MSM in Switzerland and the occurrence of large MTCs, highlighting the importance of molecular surveillance in guiding public health strategies targeting the HIV-1 epidemic.
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Affiliation(s)
- Jessy J Duran Ramirez
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Tala Ballouz
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland.,Epidemiology, Biostatistics and Prevention Institute, University of Zurich, 8001 Zurich, Switzerland
| | - Huyen Nguyen
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Sandra E Chaudron
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland.,Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, 4009 Basel, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, 1205 Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Pietro Vernazza
- Division of Infectious Diseases, Cantonal Hospital St. Gallen, 9007 St. Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, 6900 Lugano, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
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11
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Khatibi S, Sahebkar A, Aghaee-Bakhtiari SH. CRISPR Genome Editing Technology and its Application in Genetic Diseases: A Review. Curr Pharm Biotechnol 2021; 22:468-479. [PMID: 32564746 DOI: 10.2174/1389201021666200621161610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/29/2020] [Accepted: 05/18/2020] [Indexed: 11/22/2022]
Abstract
Gene therapy has been a long lasting goal for scientists, and there are many optimal methods and tools to correct disease-causing mutations in humans. Recently, the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology has been progressively adopted for the assessment a treatment of human diseases, including thalassemia, Parkinson's disease, cystic fibrosis, glaucoma, Huntington's disease, and Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome (HIV/AIDS). CRISPR sequences belong to the bacterial immune system, which includes the nuclease Cas enzyme and an RNA sequence. The RNA sequence is unique and pathogen-specific, and identifies and binds to the DNA of invasive viruses, allowing the nuclease Cas enzyme to cut the identified DNA and destroy the invasive viruses. This feature provides the possibility to edit mutations in the DNA sequence of live cells by replacing a specific targeted RNA sequence with the RNA sequence in the CRISPR system. Previous studies have reported the improvement steps in confrontation with human diseases caused by single-nucleotide mutations using this system. In this review, we first introduce CRISPR and its functions and then elaborate on the use of CRISPR in the treatment of human diseases.
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Affiliation(s)
- Sepideh Khatibi
- Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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12
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Visseaux B, Assoumou L, Mahjoub N, Grude M, Trabaud MA, Raymond S, Wirden M, Morand-Joubert L, Roussel C, Montes B, Bocket L, Fafi-Kremer S, Amiel C, De Monte A, Stefic K, Pallier C, Tumiotto C, Maillard A, Vallet S, Ferre V, Bouvier-Alias M, Dina J, Signori-Schmuck A, Carles MJ, Plantier JC, Meyer L, Descamps D, Chaix ML. Surveillance of HIV-1 primary infections in France from 2014 to 2016: toward stable resistance, but higher diversity, clustering and virulence? J Antimicrob Chemother 2021; 75:183-193. [PMID: 31641777 DOI: 10.1093/jac/dkz404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/19/2019] [Accepted: 08/23/2019] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES Patients with primary HIV-1 infection (PHI) are a particular population, giving important insight about ongoing evolution of transmitted drug resistance-associated mutation (TDRAM) prevalence, HIV diversity and clustering patterns. We describe these evolutions of PHI patients diagnosed in France from 2014 to 2016. METHODS A total of 1121 PHI patients were included. TDRAMs were characterized using the 2009 Stanford list and the French ANRS algorithm. Viral subtypes and recent transmission clusters (RTCs) were also determined. RESULTS Patients were mainly MSM (70%) living in the Paris area (42%). TDRAMs were identified among 10.8% of patients and rose to 18.6% when including etravirine and rilpivirine TDRAMs. Prevalences of PI-, NRTI-, first-generation NNRTI-, second-generation NNRTI- and integrase inhibitor-associated TDRAMs were 2.9%, 5.0%, 4.0%, 9.4% and 5.4%, respectively. In a multivariable analysis, age >40 years and non-R5 tropic viruses were associated with a >2-fold increased risk of TDRAMs. Regarding HIV diversity, subtype B and CRF02_AG (where CRF stands for circulating recombinant form) were the two main lineages (56% and 20%, respectively). CRF02_AG was associated with higher viral load than subtype B (5.83 versus 5.40 log10 copies/mL, P=0.004). We identified 138 RTCs ranging from 2 to 14 patients and including overall 41% from the global population. Patients in RTCs were younger, more frequently born in France and more frequently MSM. CONCLUSIONS Since 2007, the proportion of TDRAMs has been stable among French PHI patients. Non-B lineages are increasing and may be associated with more virulent CRF02_AG strains. The presence of large RTCs highlights the need for real-time cluster identification to trigger specific prevention action to achieve better control of the epidemic.
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Affiliation(s)
- Benoit Visseaux
- IAME, Université de Paris, AP-HP, UMR 1137, INSERM, Virology, Hôpital Bichat, AP-HP, Paris, France.,Centre National de Référence VIH, Paris, France
| | - Lambert Assoumou
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | | | - Maxime Grude
- AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | | | | | - Marc Wirden
- CHU Pitié-Salpêtrière, Virology, Paris, France
| | - Laurence Morand-Joubert
- AP-HP, Hôpital Saint-Antoine, Laboratoire de virologie, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, (iPLESP), Paris, France
| | | | | | | | | | | | | | - Karl Stefic
- INSERM U1259, Université de Tours, CHU Tours, Virology, Tours, France
| | | | | | | | | | | | | | | | | | | | - Jean-Christophe Plantier
- Normandie University, UNIROUEN Rouen, EA2656, Rouen University Hospital, Virology, Rouen, France
| | - Laurence Meyer
- INSERM SC10 US19, Villejuif, INSERM CESP U1018, Université Paris Sud, Université Paris Saclay, France
| | - Diane Descamps
- IAME, Université de Paris, AP-HP, UMR 1137, INSERM, Virology, Hôpital Bichat, AP-HP, Paris, France.,Centre National de Référence VIH, Paris, France
| | - Marie-Laure Chaix
- Centre National de Référence VIH, Paris, France.,Hopital Saint-Louis, Virology, Paris, France.,Université de Paris, INSERM U944, Paris, France
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13
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Parczewski M, Scheibe K, Witak-Jędra M, Pynka M, Aksak-Wąs B, Urbańska A. Infection with HIV-1 subtype D adversely affects the live expectancy independently of antiretroviral drug use. INFECTION GENETICS AND EVOLUTION 2021; 90:104754. [PMID: 33540086 DOI: 10.1016/j.meegid.2021.104754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/20/2021] [Accepted: 01/29/2021] [Indexed: 11/17/2022]
Abstract
INTRODUCTION HIV-1 subtypes have been associated with less favourable clinical profiles, differences in disease progression and higher risk of neurocognitive deficit. In this study we aimed to analyse the long term survival disparities between patients infected with the most common HIV-1 variants observed in Poland. METHODS For the study data from 518 Caucasian non-immigrant patients of Polish origin infected with divergent HIV subtypes and variants [subtype A (n = 35, 6.8%), subtype B (n = 386, 74.5%), subtype C (n = 13, 2.5%), subtype D (n = 58, 11.19%) or other non-A,B,C,D (n = 26, 5.01%)variants] were analysed. Subtyping was performed using the partial pol (reverse transcriptase and protease) sequencing. HIV variant was coupled with clinical, virologic and survival data censored at 20 years of observation. Overall survival and on antiretroviral treatment survival was analysed using Kaplan-Meyer as well as unadjusted and multivariate Cox proportional hazards models. RESULTS Significantly higher mortality was observed among subtype D (28.8%) infected subjects compared to subtype B (11.7%, p = 0.0004). Increased risk of death among subtype D cases remained significant when cART treated individuals were analysed, with on-treatment mortality of 26.9% for subtype D (p = 0.006) compared to 10.73% in subtype B infected cases. Kaplan-Meyer survival estimates differed significantly across all investigated HIV-1 variant groups when overall 20 year mortality was analysed (log rank p = 0.029), being non-significant for the cART treated group. In multivariate model of overall 20 year survival, adjusted for age at diagnosis, gender, HCV and AIDS status, lymphocyte CD4 count, transmission route and HIV viral load, only age and subtype D were independently associated with higher likelihood of death [HR: 1.08 (95%CI: 1.03-1.14, p = 0.002) and HR: 7.91 (95%CI:2.33-26.86), p < 0.001, respectively]. In the on-treatment (cART) multivariate model of 20 year survival adjusted for the same parameters only subtype D remained as the independent factor associated with higher mortality risk [HR: 4.24 (95%CI:1.31-13.7), p = 0.02]. CONCLUSIONS Subtype D has an independent deleterious effect of survival, even in the setting of antiretroviral treatment. Observed effect indicated higher clinical vigilance for patients infected with this subtype even after long time of stable antiretroviral treatment.
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Affiliation(s)
- Miłosz Parczewski
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland.
| | - Kaja Scheibe
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Magdalena Witak-Jędra
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Magdalena Pynka
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Bogusz Aksak-Wąs
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Anna Urbańska
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
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Adeniyi OV, Obi CL, Ter Goon D, Iweriebor B, Chitha W, Okoh A. Genetic Characterization of HIV-1 Subtype A1/C/D/B/K Unique Recombinant Form from Eastern Cape, South Africa. AIDS Res Hum Retroviruses 2021; 37:162-168. [PMID: 33076679 DOI: 10.1089/aid.2020.0160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 subtype C is the predominant circulating virus in South Africa. There are reports of non-C subtypes emerging in different regions of the country, however, very little information exists on the genetic diversity of HIV in the Eastern Cape Province, despite having the third largest HIV epidemic in the country. In the current study, a near full-length genomic sequence obtained from a heterosexual woman in the Eastern Cape (ADE/CMH/0032), was analyzed using two rapid online subtyping tools; REGA and the jumping Profile Hidden Markov Model (jpHMM). There was agreement between the two tools in the assignment of the pol, Vif, and vpr regions, identified as a C/D recombinant (pol) and subtype C (vif and vpr). Some degree of agreement existed in the assignment of the Gag region, as recombinant: A1/C/B/D by REGA, and A1/C/D by jPHMM, respectively. There was disparity between the two online tools in the subtype assignment of the remaining gene regions. Phylogenetic analysis with pure subtype reference sequences showed that the query sequence clustered with a subtype C reference strain, with a low bootstrap value of 43%. This is the first report from South Africa of a putative unique recombinant as classified by rapid online subtyping tools, involving subtype A1, C, D, B, and K. However, the clinical and epidemiological implications of this variant remain unclear. Further studies are needed to fully understand the genetic diversity of HIV in the Eastern Cape.
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Affiliation(s)
- Oladele Vincent Adeniyi
- Department of Family Medicine & Rural Health, Faculty of Health Sciences, Walter Sisulu University/Cecilia Makiwane Hospital/East London Hospital Complex, East London, South Africa
| | - Chikwelu Larry Obi
- School of Science and Technology, Sefako Makgatho Health Sciences University, Ga-Rankuwa, Pretoria, South Africa
| | - Daniel Ter Goon
- Department of Public Health, Faculty of Health Sciences, University of Fort Hare, East London, South Africa
| | - Benson Iweriebor
- School of Science and Technology, Sefako Makgatho Health Sciences University, Ga-Rankuwa, Pretoria, South Africa
| | - Wezile Chitha
- Health Systems Enablement & Innovation Uni, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Anthony Okoh
- SAMRC Microbial Water Quality Monitoring Centre, Faculty of Science and Agriculture, University of Fort Hare, Alice, South Africa
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15
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Santos-Pereira A, Magalhães C, Araújo PMM, Osório NS. Evolutionary Genetics of Mycobacterium tuberculosis and HIV-1: "The Tortoise and the Hare". Microorganisms 2021; 9:147. [PMID: 33440808 PMCID: PMC7827287 DOI: 10.3390/microorganisms9010147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 12/24/2020] [Accepted: 01/06/2021] [Indexed: 12/16/2022] Open
Abstract
The already enormous burden caused by Mycobacterium tuberculosis and Human Immunodeficiency Virus type 1 (HIV-1) alone is aggravated by co-infection. Despite obvious differences in the rate of evolution comparing these two human pathogens, genetic diversity plays an important role in the success of both. The extreme evolutionary dynamics of HIV-1 is in the basis of a robust capacity to evade immune responses, to generate drug-resistance and to diversify the population-level reservoir of M group viral subtypes. Compared to HIV-1 and other retroviruses, M. tuberculosis generates minute levels of genetic diversity within the host. However, emerging whole-genome sequencing data show that the M. tuberculosis complex contains at least nine human-adapted phylogenetic lineages. This level of genetic diversity results in differences in M. tuberculosis interactions with the host immune system, virulence and drug resistance propensity. In co-infected individuals, HIV-1 and M. tuberculosis are likely to co-colonize host cells. However, the evolutionary impact of the interaction between the host, the slowly evolving M. tuberculosis bacteria and the HIV-1 viral "mutant cloud" is poorly understood. These evolutionary dynamics, at the cellular niche of monocytes/macrophages, are also discussed and proposed as a relevant future research topic in the context of single-cell sequencing.
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Affiliation(s)
- Ana Santos-Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Carlos Magalhães
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Pedro M. M. Araújo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.S.-P.); (C.M.); (P.M.M.A.)
- ICVS/3B’s-T Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
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16
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Amamuddy OS, Verkhivker GM, Bishop ÖT. Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M pro. J Chem Inf Model 2020; 60:5080-5102. [PMID: 32853525 PMCID: PMC7496595 DOI: 10.1021/acs.jcim.0c00634] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Indexed: 12/15/2022]
Abstract
A new coronavirus (SARS-CoV-2) is a global threat to world health and economy. Its dimeric main protease (Mpro), which is required for the proteolytic cleavage of viral precursor proteins, is a good candidate for drug development owing to its conservation and the absence of a human homolog. Improving our understanding of Mpro behavior can accelerate the discovery of effective therapies to reduce mortality. All-atom molecular dynamics (MD) simulations (100 ns) of 50 mutant Mpro dimers obtained from filtered sequences from the GISAID database were analyzed using root-mean-square deviation, root-mean-square fluctuation, Rg, averaged betweenness centrality, and geometry calculations. The results showed that SARS-CoV-2 Mpro essentially behaves in a similar manner to its SAR-CoV homolog. However, we report the following new findings from the variants: (1) Residues GLY15, VAL157, and PRO184 have mutated more than once in SARS CoV-2; (2) the D48E variant has lead to a novel "TSEEMLN"" loop at the binding pocket; (3) inactive apo Mpro does not show signs of dissociation in 100 ns MD; (4) a non-canonical pose for PHE140 widens the substrate binding surface; (5) dual allosteric pockets coinciding with various stabilizing and functional components of the substrate binding pocket were found to display correlated compaction dynamics; (6) high betweenness centrality values for residues 17 and 128 in all Mpro samples suggest their high importance in dimer stability-one such consequence has been observed for the M17I mutation whereby one of the N-fingers was highly unstable. (7) Independent coarse-grained Monte Carlo simulations suggest a relationship between the rigidity/mutability and enzymatic function. Our entire approach combining database preparation, variant retrieval, homology modeling, dynamic residue network (DRN), relevant conformation retrieval from 1-D kernel density estimates from reaction coordinates to other existing approaches of structural analysis, and data visualization within the coronaviral Mpro is also novel and is applicable to other coronaviral proteins.
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Affiliation(s)
- Olivier Sheik Amamuddy
- Research Unit in Bioinformatics, Department of Microbiology and Biochemistry, Rhodes University, Grahamstown 6140, South Africa
| | - Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics, Department of Microbiology and Biochemistry, Rhodes University, Grahamstown 6140, South Africa
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Kostaki EG, Gova M, Adamis G, Xylomenos G, Chini M, Mangafas N, Lazanas M, Metallidis S, Tsachouridou O, Papastamopoulos V, Chatzidimitriou D, Kakalou E, Antoniadou A, Papadopoulos A, Psichogiou M, Basoulis D, Pilalas D, Papageorgiou I, Paraskeva D, Chrysos G, Paparizos V, Kourkounti S, Sambatakou H, Bolanos V, Sipsas NV, Lada M, Barbounakis E, Kantzilaki E, Panagopoulos P, Petrakis V, Drimis S, Gogos C, Hatzakis A, Beloukas A, Skoura L, Paraskevis D. A Nationwide Study about the Dispersal Patterns of the Predominant HIV-1 Subtypes A1 and B in Greece: Inference of the Molecular Transmission Clusters. Viruses 2020; 12:E1183. [PMID: 33086773 PMCID: PMC7589601 DOI: 10.3390/v12101183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 01/22/2023] Open
Abstract
Our aim was to investigate the dispersal patterns and parameters associated with local molecular transmission clusters (MTCs) of subtypes A1 and B in Greece (predominant HIV-1 subtypes). The analysis focused on 1751 (28.4%) and 2575 (41.8%) sequences of subtype A1 and B, respectively. Identification of MTCs was based on phylogenetic analysis. The analyses identified 38 MTCs including 2-1518 subtype A1 sequences and 168 MTCs in the range of 2-218 subtype B sequences. The proportion of sequences within MTCs was 93.8% (1642/1751) and 77.0% (1982/2575) for subtype A1 and B, respectively. Transmissions within MTCs for subtype A1 were associated with risk group (Men having Sex with Men vs. heterosexuals, OR = 5.34, p < 0.001) and Greek origin (Greek vs. non-Greek origin, OR = 6.05, p < 0.001) and for subtype B, they were associated with Greek origin (Greek vs. non-Greek origin, OR = 1.57, p = 0.019), younger age (OR = 0.96, p < 0.001), and more recent sampling (time period: 2011-2015 vs. 1999-2005, OR = 3.83, p < 0.001). Our findings about the patterns of across and within country dispersal as well as the parameters associated with transmission within MTCs provide a framework for the application of the study of molecular clusters for HIV prevention.
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Affiliation(s)
- Evangelia Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.G.K.); (M.G.); (I.P.); (A.H.)
| | - Maria Gova
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.G.K.); (M.G.); (I.P.); (A.H.)
| | - Georgios Adamis
- 1st Department of Internal Medicine, G. Gennimatas General Hospital, 11527 Athens, Greece; (G.A.); (G.X.)
| | - Georgios Xylomenos
- 1st Department of Internal Medicine, G. Gennimatas General Hospital, 11527 Athens, Greece; (G.A.); (G.X.)
| | - 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.)
| | - Dimitrios Chatzidimitriou
- National AIDS Reference Centre of Northern Greece, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (D.C.); (D.P.); (L.S.)
| | - Eleni Kakalou
- 5th Department of Internal Medicine and Infectious Diseases, Evaggelismos General Hospital, 10676 Athens, Greece; (V.P.); (E.K.)
| | - Anastasia Antoniadou
- 4th Department of Medicine, Attikon General Hospital, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (A.A.); (A.P.)
| | - Antonios Papadopoulos
- 4th Department of Medicine, Attikon 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.)
| | - Dimitrios Pilalas
- National AIDS Reference Centre of Northern Greece, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (D.C.); (D.P.); (L.S.)
| | - Ifigeneia Papageorgiou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.G.K.); (M.G.); (I.P.); (A.H.)
| | - 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.); (V.P.)
| | - Vasilis Petrakis
- Department of Internal Medicine, University General Hospital, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (P.P.); (V.P.)
| | - Stelios Drimis
- Department of Internal Medicine, Tzaneio General Hospital, 18536 Piraeus, Greece; (D.P.); (G.C.); (S.D.)
| | - Charalambos Gogos
- Department of Internal Medicine and Infectious Diseases, University Hospital of Patras, 26504 Rio, Greece;
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.G.K.); (M.G.); (I.P.); (A.H.)
| | - Apostolos Beloukas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool L697BE, UK
- Department of Biomedical Sciences, School of Health Sciences, University of West Attica, 12243 Athens, Greece
| | - Lemonia Skoura
- National AIDS Reference Centre of Northern Greece, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (D.C.); (D.P.); (L.S.)
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.G.K.); (M.G.); (I.P.); (A.H.)
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18
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Vasylyeva TI, du Plessis L, Pineda-Peña AC, Kühnert D, Lemey P, Vandamme AM, Gomes P, Camacho RJ, Pybus OG, Abecasis AB, Faria NR. Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology. J Infect Dis 2020; 220:233-243. [PMID: 30805610 PMCID: PMC6581889 DOI: 10.1093/infdis/jiz085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/21/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Estimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies. METHODS Portuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. Bayesian birth-death models were used to estimate subtype-specific effective reproductive numbers (Re). Discrete trait analysis (DTA) was used to quantify mixing among transmission groups. RESULTS We identified 5 subtype B Portuguese clades (26-79 sequences) and a large monophyletic subtype G Portuguese clade (236 sequences). We estimated that major shifts in HIV-1 transmission occurred around 1999 (95% Bayesian credible interval [BCI], 1998-2000) and 2000 (95% BCI, 1998-2001) for subtypes B and G, respectively. For subtype B, Re dropped from 1.91 (95% BCI, 1.73-2.09) to 0.62 (95% BCI,.52-.72). For subtype G, Re decreased from 1.49 (95% BCI, 1.39-1.59) to 0.72 (95% BCI, .63-.8). The DTA suggests that people who inject drugs (PWID) and heterosexuals were the source of most (>80%) virus lineage transitions for subtypes G and B, respectively. CONCLUSIONS The estimated declines in Re coincide with the introduction of highly active antiretroviral therapy and the scale-up of harm reduction for PWID. Inferred transmission events across transmission groups emphasize the importance of prevention efforts for bridging populations.
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Affiliation(s)
- Tetyana I Vasylyeva
- Department of Zoology, University of Oxford, United Kingdom.,New College, University of Oxford, United Kingdom
| | | | - Andrea C Pineda-Peña
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa.,Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia.,Basic Sciences Department, Universidad del Rosario, Bogotá, Colombia
| | - Denise Kühnert
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Philippe Lemey
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Anne-Mieke Vandamme
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa.,Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Perpétua Gomes
- Laboratory of Molecular Biology, LMCBM, SPC, Hospital de Egas Moniz-Centro Hospitalar de Lisboa Ocidental, Lisbon.,Center for Interdisciplinary Research Egas Moniz, CiiEM, Almada, Portugal
| | - Ricardo J Camacho
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, United Kingdom
| | - Ana B Abecasis
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa
| | - Nuno R Faria
- Department of Zoology, University of Oxford, United Kingdom
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19
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Abstract
Human immunodeficiency virus-1 (HIV-1) is characterised by a vast genetic diversity classified into distinct phylogenetic strains and recombinant forms. We describe the HIV-1 molecular epidemiology and evolution of 129 consecutive HIV-1 positive migrants living in Milan (northern Italy). Polymerase gene sequences of 116 HIV-1 subtype-B positive patients were aligned with HIV-1 reference sequences (https://www.ncbi.nlm.nih.gov/) by using MAFFT alignment and edited by using Bioedit software. A maximum likelihood (ML) phylogenetic tree was performed by MEGA7 and was visualised by using FigTree v1.4.3. Of 129 migrants, 35 were born in Europe (28 in Eastern Europe), 70 in the Americas (67 in South America), 15 in Africa and nine in Asia; 76.4% were men who have sex with men (MSM). The serotype HIV-1-B prevailed (89.9%), followed by -C, -F1, -D and -A. Compared with 116 HIV-B patients, the 13 with HIV-non-B showed lower Nadir of CD4+ cell/mmc (P = 0.043), more frequently had sub Saharan origin (38.5 vs. 1.72%, P = 0.0001) and less frequently were MSM (40 vs. 74.5%, P = 0.02). The ML phylogenetic tree of the 116 HIV-1 subtype-B positive patients showed 13 statistically supported nodes (bootstrap > 70%). Most of the sequences included in these nodes have been isolated from male patients from the Americas and the most common risk factor was MSM. The low number of HIV-1 non-B subtype patients did not allow to perform this analysis. These results suggest a shift of HIV-1 prevention projects' focus and a continuous monitoring of HIV-1 molecular epidemiology among entry populations. Prevention efforts based on HIV molecular epidemiology may improve public health surveillance setting.
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20
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Onoriode Digban T, Chucks Iweriebor B, Chikwelu Obi L, Nwodo U, Ifeanyi Okoh A. Analyses of HIV-1 integrase gene sequences among treatment-naive patients in the Eastern Cape, South Africa. J Med Virol 2020; 92:1165-1172. [PMID: 31889319 DOI: 10.1002/jmv.25661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/21/2019] [Indexed: 01/11/2023]
Abstract
Drug resistance has been recognized in all available therapeutic class of medications for the management of human immunodeficiency virus-1 (HIV-1) infected patients. This makes the continuous study of HIV drug resistance and new treatment options pertinent to patients and researchers globally. The aim of this study is to analyze the complete HIV-1 integrase gene for the possible occurrence of resistance mutations or polymorphisms. We performed genetic analyses on 48 treatment-naive HIV-1-infected patients using nested polymerase chain reaction. Integrase drug-related resistance mutation (DRMs) analysis was performed on all generated sequences according to Stanford HIV drug interpretation program and the International AIDS Society-USA guidelines while phylogenetic analysis was inferred using MEGA 6. The study revealed no major resistance-associated mutation. However, E157Q (2.1%), L74M/I (4.2%), and P142T (2.1%) were the observed accessory and polymorphic mutations. Naturally occurring polymorphism observed were E11D, K14R, D25E, V31I, M50I, V72I, P90T, F100Y, L101I, T124A, T125A, K136Q, D167E, V201I, L234I, A265V, A269K, D278A, and S283G. Phylogenetic analysis delineated all the sequences as HIV-1 subtype C. The study revealed the absence of major integrase inhibitors associated resistance mutations in a setting where integrase inhibitor is administered as salvage therapy in patients developing resistance to first and second-line antiretroviral treatment. However minor and natural polymorphisms were observed and thus may influence the outcome of each treatment regimen. However, additional studies are required to precisely evaluate the impact of these mutations on integrase inhibitors in the Eastern Cape of South Africa.
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Affiliation(s)
- Tennison Onoriode Digban
- South Africa Medical Research Council and Water Quality Monitoring Centre, University of Fort Hare, Alice, Eastern Cape, South Africa.,Applied Environmental and Microbiology Research Group, University of Fort Hare, Alice, Eastern Cape, South Africa.,Department of Microbiology and Biochemistry, University of Fort Hare, Alice, Eastern Cape, South Africa
| | - Benson Chucks Iweriebor
- School of Science and Technology, Sefako Makgatho Health Sciences University, Ga-Rankuwa, Pretoria, South Africa
| | - Larry Chikwelu Obi
- School of Science and Technology, Sefako Makgatho Health Sciences University, Ga-Rankuwa, Pretoria, South Africa
| | - Uchechuwku Nwodo
- South Africa Medical Research Council and Water Quality Monitoring Centre, University of Fort Hare, Alice, Eastern Cape, South Africa.,Applied Environmental and Microbiology Research Group, University of Fort Hare, Alice, Eastern Cape, South Africa.,Department of Microbiology and Biochemistry, University of Fort Hare, Alice, Eastern Cape, South Africa
| | - Anthony Ifeanyi Okoh
- South Africa Medical Research Council and Water Quality Monitoring Centre, University of Fort Hare, Alice, Eastern Cape, South Africa.,Applied Environmental and Microbiology Research Group, University of Fort Hare, Alice, Eastern Cape, South Africa.,Department of Microbiology and Biochemistry, University of Fort Hare, Alice, Eastern Cape, South Africa
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21
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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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22
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Analysis of HIV-1 diversity, primary drug resistance and transmission networks in Croatia. Sci Rep 2019; 9:17307. [PMID: 31754119 PMCID: PMC6872562 DOI: 10.1038/s41598-019-53520-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/31/2019] [Indexed: 01/23/2023] Open
Abstract
Molecular epidemiology of HIV-1 infection in treatment-naive HIV-1 infected persons from Croatia was investigated. We included 403 persons, representing 92.4% of all HIV-positive individuals entering clinical care in Croatia in 2014–2017. Overall prevalence of transmitted drug resistance (TDR) was estimated at 16.4%. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside RTI (NNRTIs) and protease inhibitors (PIs) was found in 11.4%, 6.7% and 2.5% of persons, respectively. Triple-class resistance was determined in 2.2% of individuals. In addition, a single case (1.0%) of resistance to integrase strand-transfer inhibitors (InSTIs) was found. Deep sequencing was performed on 48 randomly selected samples and detected additional TDR mutations in 6 cases. Phylogenetic inference showed that 347/403 sequences (86.1%) were part of transmission clusters and identified forward transmission of resistance in Croatia, even that of triple-class resistance. The largest TDR cluster of 53 persons with T215S was estimated to originate in the year 1992. Our data show a continuing need for pre-treatment HIV resistance testing in Croatia. Even though a low prevalence of resistance to InSTI was observed, surveillance of TDR to InSTI should be continued.
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23
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Araújo PMM, Martins JS, Osório NS. SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing. Virus Evol 2019; 5:vez050. [PMID: 31768265 PMCID: PMC6863187 DOI: 10.1093/ve/vez050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) genome sequencing is routinely done for drug resistance monitoring in hospitals worldwide. Subtyping these extensive datasets of HIV-1 sequences is a critical first step in molecular epidemiology and evolution studies. The clinical relevance of HIV-1 subtypes is increasingly recognized. Several studies suggest subtype-related differences in disease progression, transmission route efficiency, immune evasion, and even therapeutic outcomes. HIV-1 subtyping is mainly done using web-servers. These tools have limitations in scalability and potential noncompliance with data protection legislation. Thus, the aim of this work was to develop an efficient method for large-scale local HIV-1 subtyping. We designed SNAPPy: a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing. It contains several tasks of phylogenetic inference and BLAST queries, which can be executed sequentially or in parallel, taking advantage of multiple-core processing units. Although it was built for subtyping, SNAPPy is also useful to perform extensive HIV-1 alignments. This tool facilitates large-scale sequence-based HIV-1 research by providing a local, resource efficient and scalable alternative for HIV-1 subtyping. It is capable of analyzing full-length genomes or partial HIV-1 genomic regions (GAG, POL, and ENV) and recognizes more than ninety circulating recombinant forms. SNAPPy is freely available at: https://github.com/PMMAraujo/snappy/releases.
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Affiliation(s)
- Pedro M M Araújo
- Life and Health Sciences Research institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Joana S Martins
- Life and Health Sciences Research institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Nuno S Osório
- Life and Health Sciences Research institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
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24
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Abstract
Background Portugal has one of the most severe HIV-1 epidemics in Western Europe. Two subtypes circulate in parallel since the beginning of the epidemic. Comparing their transmission patterns and its association with transmitted drug resistance (TDR) is important to pinpoint transmission hotspots and to develop evidence-based treatment guidelines. Methods Demographic, clinical and genomic data were collected from 3599 HIV-1 naive patients between 2001 and 2014. Sequences obtained from drug resistance testing were used for subtyping, TDR determination and transmission clusters (TC) analyses. Results In Portugal, transmission of subtype B was significantly associated with young males, while transmission of subtype G was associated with older heterosexuals. In Portuguese originated people, there was a decreasing trend both for prevalence of subtype G and for number of TCs in this subtype. The active TCs that were identified (i.e. clusters originated after 2008) were associated with subtype B-infected males residing in Lisbon. TDR was significantly different when comparing subtypes B (10.8% [9.5–12.2]) and G (7.6% [6.4–9.0]) (p = 0.001). Discussion TC analyses shows that, in Portugal, the subtype B epidemic is active and fueled by young male patients residing in Lisbon, while transmission of subtype G is decreasing. Despite similar treatment rates for both subtypes in Portugal, TDR is significantly different between subtypes.
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25
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Budayanti NS, Merati TP, Bela B, Mahardika GN. Molecular Antiretroviral Resistance Markers of Human Immunodeficiency Virus-1 of CRF01_AE Subtype in Bali, Indonesia. Curr HIV Res 2019; 16:374-382. [PMID: 30714528 PMCID: PMC6446452 DOI: 10.2174/1570162x17666190204101154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/27/2019] [Accepted: 01/30/2019] [Indexed: 11/22/2022]
Abstract
Background: Molecular epidemiological study of human immunodeficiency virus drug-resistant (HIVDR) markers is challenging in areas where the dominant subtype is non-B. Objective: Here we provide molecular data for HIVDR in the CRF01_AE subtype in Bali, Indonesia. Method: Seventy patients were enrolled in this study and grouped into treatment failure and treatment naïve groups. The full-length pol gene was amplified using nested reverse transcriptase polymerase chain reaction and the product was then sequenced. The readable sequence was then subjected to Stan-ford HIV Drug Resistance Database genotyping. Results: We found that clinical classification was in accordance with the presence of HIVDR markers in the pol gene. Independent of therapy history, the treatment failure group showed resistance markers against nucleoside reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase in-hibitors (NNRTI), ranging from 72%–100% of patients. Only a small proportion of naïve patients harbored HIV with drug resistance markers to NNRTI. No protease inhibitor-resistant marker was found in either patient group. Molecular marker mutations, which were found in more than 50% of treatment failure patients, were M184V (100%), T215A/Y/F (88.2%), D67N/G (76.5%), and M41L (58.8%). Conclusion: The protocol used in this study to determine genetic markers of HIVDR based on sub-type B can be applied for the rapid determination of resistance of the CRF01_AE subtype. All patients with progressive clinical signs and increased viral load should be recommended to undergo second-line treatment of the ARV regimen.
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Affiliation(s)
- Nyoman Sri Budayanti
- Microbiology Department, Faculty of Medicine, Udayana University, Jl. PB Sudirman, Denpasar, Bali, Indonesia
| | - Tuti Parwati Merati
- Internal Medicine Department, Faculty of Medicine, Udayana University, Jl. PB Sudirman, Denpasar, Bali, Indonesia
| | - Budiman Bela
- Microbiology Department, Faculty of Medicine, Indonesia University, Jakarta, Indonesia
| | - Gusti Ngurah Mahardika
- Animal Biomedical and Molecular Biology Laboratory, Faculty of Veterinary Medicine, Udayana University, Jl. Sesetan-Markisa 6, Denpasar 80226, Bali, Indonesia
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26
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Ciccozzi M, Lai A, Zehender G, Borsetti A, Cella E, Ciotti M, Sagnelli E, Sagnelli C, Angeletti S. The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review. J Med Virol 2019; 91:1707-1724. [PMID: 31243773 DOI: 10.1002/jmv.25526] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/24/2019] [Indexed: 12/16/2022]
Abstract
In the last decade, the phylogenetic approach is recurrent in molecular evolutionary analysis. On 12 May, 2019, about 2 296 213 papers are found, but typing "phylogeny" or "epidemiology AND phylogeny" only 199 804 and 20 133 are retrieved, respectively. Molecular epidemiology in infectious diseases is widely used to define the source of infection as so as the ancestral relationships of individuals sampled from a population. Coalescent theory and phylogeographic analysis have had scientific application in several, recent pandemic events, and nosocomial outbreaks. Hepatitis viruses and immunodeficiency virus (human immunodeficiency virus) have been largely studied. Phylogenetic analysis has been recently applied on Polyomaviruses so as in the more recent outbreaks due to different arboviruses type as Zika and chikungunya viruses discovering the source of infection and the geographic spread. Data on sequences isolated by the microorganism are essential to apply the phylogenetic tools and research in the field of infectious disease phylodinamics is growing up. There is the need to apply molecular phylogenetic and evolutionary methods in areas out of infectious diseases, as translational genomics and personalized medicine. Lastly, the application of these tools in vaccine strategy so as in antibiotic and antiviral researchers are encouraged.
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Affiliation(s)
- Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, Roma, Italy
| | - Eleonora Cella
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Marco Ciotti
- Laboratory of Molecular Virology, Polyclinic Tor Vergata Foundation, Rome, Italy
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
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27
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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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HIV-1 genetic diversity and demographic characteristics in Bulgaria. PLoS One 2019; 14:e0217063. [PMID: 31136611 PMCID: PMC6538145 DOI: 10.1371/journal.pone.0217063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/03/2019] [Indexed: 12/14/2022] Open
Abstract
HIV-1 strain diversity in Bulgaria is extensive and includes contributions from nearly all major subtypes and the Circulating Recombinant Forms (CRF): 01_AE, 02_AG, and 05_DF. Prior to this study, HIV-1 sequence information from Bulgaria has been based solely on the pro-RT gene, which represent less than 15% of the viral genome. To further characterize HIV-1 in Bulgaria, assess participant risk behaviors, and strengthen knowledge of circulating strains in the region, the study “Genetic Subtypes of HIV-1 in Bulgaria (RV240)” was conducted. This study employed the real time-PCR based Multi-region Hybridization Assay (MHA) B/non-B and HIV-1 sequencing to survey 215 of the approximately 1100 known HIV-1 infected Bulgarian adults (2008–2009) and determine if they were infected with subtype B HIV-1. The results indicated a subtype B prevalence of 40% and demonstrate the application of the MHA B/non-B in an area containing broad HIV-1 strain diversity. Within the assessed risk behaviors, the proportion of subtype B infection was greatest in men who have sex with men and lowest among those with drug use risk factors. During this study, 15 near full-length genomes and 22 envelope sequences were isolated from study participants. Phylogenetic analysis shows the presence of subtypes A1, B, C, F1, and G, CRF01_AE, CRF02_AG, CRF05_DF, and one unique recombinant form (URF). These sequences also show the presence of two strain groups containing participants with similar risk factors. Previous studies in African and Asian cohorts have shown that co-circulation of multiple subtypes can lead to viral recombination within super-infected individuals and the emergence of new URFs. The low prevalence of URFs in the presence of high subtype diversity in this study, may be the result of successful infection prevention and control programs. Continued epidemiological monitoring and support of infection prevention programs will help maintain control of the HIV-1 epidemic in Bulgaria.
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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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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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Vinken L, Fransen K, Cuypers L, Alexiev I, Balotta C, Debaisieux L, Seguin-Devaux C, García Ribas S, Gomes P, Incardona F, Kaiser R, Ruelle J, Sayan M, Paraschiv S, Paredes R, Peeters M, Sönnerborg A, Vancutsem E, Vandamme AM, Van den Wijngaert S, Van Ranst M, Verhofstede C, Stadler T, Lemey P, Van Laethem K. Earlier Initiation of Antiretroviral Treatment Coincides With an Initial Control of the HIV-1 Sub-Subtype F1 Outbreak Among Men-Having-Sex-With-Men in Flanders, Belgium. Front Microbiol 2019; 10:613. [PMID: 30972053 PMCID: PMC6443750 DOI: 10.3389/fmicb.2019.00613] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 03/11/2019] [Indexed: 11/17/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) non-B subtype infections occurred in Belgium since the 1980s, mainly amongst migrants and heterosexuals, whereas subtype B predominated in men-having-sex-with-men (MSM). In the last decade, the diagnosis of F1 sub-subtype in particular has increased substantially, which prompted us to perform a detailed reconstruction of its epidemiological history. To this purpose, the Belgian AIDS Reference Laboratories collected HIV-1 pol sequences from all sub-subtype F1-infected patients for whom genotypic drug resistance testing was requested as part of routine clinical follow-up. This data was complemented with HIV-1 pol sequences from countries with a high burden of F1 infections or a potential role in the global origin of sub-subtype F1. The molecular epidemiology of the Belgian subtype F1 epidemic was investigated using Bayesian phylogenetic inference and transmission dynamics were characterized based on birth-death models. F1 sequences were retained from 297 patients diagnosed and linked to care in Belgium between 1988 and 2015. Phylogenetic inference indicated that among the 297 Belgian F1 sequences, 191 belonged to a monophyletic group that mainly contained sequences from people likely infected in Belgium (OR 26.67, 95% CI 9.59–74.15), diagnosed in Flanders (OR 7.28, 95% CI 4.23–12.53), diagnosed at a recent stage of infection (OR 7.19, 95% CI 2.88-17.95) or declared to be MSM (OR 34.8, 95% CI 16.0–75.6). Together with a Spanish clade, this Belgian clade was embedded in the genetic diversity of Brazilian subtype F1 strains and most probably emerged after one or only a few migration events from Brazil to the European continent before 2002. The origin of the Belgian outbreak was dated back to 2002 (95% higher posterior density 2000–2004) and birth-death models suggested that its extensive growth had been controlled (Re < 1) by 2012, coinciding with a time period where delay in antiretroviral treatment initiation substantially declined. In conclusion, phylogenetic reconstruction of the Belgian HIV-1 sub-subtype F1 epidemic illustrates the introduction and substantial dissemination of viral strains in a geographically restricted risk group that was most likely controlled by effective treatment as prevention.
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Affiliation(s)
- Lore Vinken
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Katrien Fransen
- AIDS Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Lize Cuypers
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Ivailo Alexiev
- National Reference Confirmatory Laboratory of HIV, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Claudia Balotta
- Infectious Diseases and Immunopathology Section, 'L. Sacco' Department of Biomedical and Clinical Sciences, 'L. Sacco' Hospital, University of Milan, Milan, Italy
| | - Laurent Debaisieux
- AIDS Reference Laboratory, CUB-Hopital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Carole Seguin-Devaux
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Sergio García Ribas
- AIDS Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Perpétua Gomes
- Serviço de Patologia Clínica, Laboratorio de Biologia Molecular, LMCBM, Centro Hospitalar Lisboa Ocidental, Hospital Egas Moniz, Lisbon, Portugal.,Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Almada, Portugal
| | | | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Jean Ruelle
- Unit of Medical Microbiology, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Murat Sayan
- PCR Unit, Clinical Laboratory, Kocaeli University, İzmit, Turkey.,Research Center of Experimental Health Sciences, Near East University, Nicosia, Cyprus
| | - Simona Paraschiv
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases 'Matei Bals', Bucharest, Romania
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Martine Peeters
- UMI 233 TransVIHMI/INSERM1175, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ellen Vancutsem
- AIDS Reference Laboratory, Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Anne-Mieke Vandamme
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,Unidade de Microbiologia, Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Sigi Van den Wijngaert
- AIDS Reference Laboratory, Department of Microbiology, Saint-Pierre University Hospital, Brussels, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,AIDS Reference Laboratory, University Hospitals Leuven, Leuven, Belgium
| | - Chris Verhofstede
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Philippe Lemey
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Kristel Van Laethem
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,AIDS Reference Laboratory, University Hospitals Leuven, Leuven, Belgium
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Kostaki EG, Flampouris A, Karamitros T, Chueca N, Alvarez M, Casas P, Alejos B, Hatzakis A, Garcia F, Paraskevis D. Spatiotemporal Characteristics of the Largest HIV-1 CRF02_AG Outbreak in Spain: Evidence for Onward Transmissions. Front Microbiol 2019; 10:370. [PMID: 30915040 PMCID: PMC6421502 DOI: 10.3389/fmicb.2019.00370] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/12/2019] [Indexed: 01/25/2023] Open
Abstract
Background and Aim: The circulating recombinant form 02_AG (CRF02_AG) is the predominant clade among the human immunodeficiency virus type-1 (HIV-1) non-Bs with a prevalence of 5.97% (95% Confidence Interval-CI: 5.41–6.57%) across Spain. Our aim was to estimate the levels of regional clustering for CRF02_AG and the spatiotemporal characteristics of the largest CRF02_AG subepidemic in Spain. Methods: We studied 396 CRF02_AG sequences obtained from HIV-1 diagnosed patients during 2000–2014 from 10 autonomous communities of Spain. Phylogenetic analysis was performed on the 391 CRF02_AG sequences along with all globally sampled CRF02_AG sequences (N = 3,302) as references. Phylodynamic and phylogeographic analysis was performed to the largest CRF02_AG monophyletic cluster by a Bayesian method in BEAST v1.8.0 and by reconstructing ancestral states using the criterion of parsimony in Mesquite v3.4, respectively. Results: The HIV-1 CRF02_AG prevalence differed across Spanish autonomous communities we sampled from (p < 0.001). Phylogenetic analysis revealed that 52.7% of the CRF02_AG sequences formed 56 monophyletic clusters, with a range of 2–79 sequences. The CRF02_AG regional dispersal differed across Spain (p = 0.003), as suggested by monophyletic clustering. For the largest monophyletic cluster (subepidemic) (N = 79), 49.4% of the clustered sequences originated from Madrid, while most sequences (51.9%) had been obtained from men having sex with men (MSM). Molecular clock analysis suggested that the origin (tMRCA) of the CRF02_AG subepidemic was in 2002 (median estimate; 95% Highest Posterior Density-HPD interval: 1999–2004). Additionally, we found significant clustering within the CRF02_AG subepidemic according to the ethnic origin. Conclusion: CRF02_AG has been introduced as a result of multiple introductions in Spain, following regional dispersal in several cases. We showed that CRF02_AG transmissions were mostly due to regional dispersal in Spain. The hot-spot for the largest CRF02_AG regional subepidemic in Spain was in Madrid associated with MSM transmission risk group. The existence of subepidemics suggest that several spillovers occurred from Madrid to other areas. CRF02_AG sequences from Hispanics were clustered in a separate subclade suggesting no linkage between the local and Hispanic subepidemics.
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Affiliation(s)
- Evangelia-Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Flampouris
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Timokratis Karamitros
- Department of Zoology, University of Oxford, Oxford, United Kingdom.,Public Health Laboratories, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Natalia Chueca
- Department of Clinical Microbiology, Hospital Universitario San Cecilio, Instituto de Investigación Ibs, Granada, Spain
| | - Marta Alvarez
- Department of Clinical Microbiology, Hospital Universitario San Cecilio, Instituto de Investigación Ibs, Granada, Spain
| | - Paz Casas
- Department of Clinical Microbiology, Hospital Universitario San Cecilio, Instituto de Investigación Ibs, Granada, Spain
| | - Belen Alejos
- Centro Nacional de Epidemiología, Universidad de Alcalá de Henares, Madrid, Spain
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Federico Garcia
- Department of Clinical Microbiology, Hospital Universitario San Cecilio, Instituto de Investigación Ibs, Granada, Spain
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Kline RL, Saduvala N, Zhang T, Oster AM. Diversity and characterization of HIV-1 subtypes in the United States, 2008-2016. Ann Epidemiol 2019; 33:84-88. [PMID: 30961993 DOI: 10.1016/j.annepidem.2019.02.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/05/2019] [Accepted: 02/28/2019] [Indexed: 11/27/2022]
Abstract
PURPOSE This article describes subtype diversity among diagnosed HIV-1 infections in the United States during 2008-2016 by demographic or risk group and over time. METHODS HIV-1 polymerase sequences reported to the National HIV Surveillance System for persons in 17 U.S. states with HIV infection diagnosed during 2008-2016 were subtyped using COMET, an automated subtyping tool, and National HIV Surveillance System demographic data were analyzed. RESULTS Subtype B was identified in 93.6% of 121,793 reported sequences. The most common non-B subtypes and circulating recombinant forms (CRFs) were C, CRF02_AG, A, CRF01_AE, and G. Elevated percentages of non-B subtypes or CRFs were found in persons who were female, aged less than 13 years at diagnosis, Asian, or had transmission attributable to heterosexual contact (females only) or perinatal exposure. Foreign-born persons had a higher percentage of non-B subtypes. The prevalence of non-B subtypes and CRFs increased from 5.0% in 2008 to 8.5% in 2016; among specific subtypes and CRFs, subtype G and CRF01_AE increased. CONCLUSIONS Subtype B remains the predominant strain in the United States. Non-B subtypes and CRFs were not widespread, but diversity and numbers increased from 2008 through 2016, which could have consequences for clinical management, diagnostic testing, and vaccine development.
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Affiliation(s)
- Richard L Kline
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | | | | | - Alexandra M Oster
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA.
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Jovanović L, Šiljić M, Ćirković V, Salemović D, Pešić-Pavlović I, Todorović M, Ranin J, Jevtović D, Stanojević M. Exploring Evolutionary and Transmission Dynamics of HIV Epidemic in Serbia: Bridging Socio-Demographic With Phylogenetic Approach. Front Microbiol 2019; 10:287. [PMID: 30858834 PMCID: PMC6397891 DOI: 10.3389/fmicb.2019.00287] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 02/04/2019] [Indexed: 12/04/2022] Open
Abstract
Previous molecular studies of Serbian HIV epidemic identified the dominance of subtype B and presence of clusters related HIV-1 transmission, in particular among men who have sex with men (MSM). In order to get a deeper understanding of the complexities of HIV sub-epidemics in Serbia, epidemic trends, temporal origin and phylodynamic characteristics in general population and subpopulations were analyzed by means of mathematical modeling, phylogenetic analysis and latent class analysis (LCA). Fitting of the logistic curve of trends for a cumulative annual number of new HIV cases in 1984–2016, in general population and MSM transmission group, was performed. Both datasets fitted the logistic growth model, showing the early exponential phase of the growth curve. According to the suggested model, in the year 2030, the number of newly diagnosed HIV cases in Serbia will continue to grow, in particular in the MSM transmission group. Further, a detailed phylogenetic analysis was performed on 385 sequences from the period 1997–2015. Identification of transmission clusters, estimation of population growth (Ne), of the effective reproductive number (Re) and time of the most recent common ancestor (tMRCA) were estimated employing Bayesian and maximum likelihood methods. A substantial proportion of 53% of subtype B sequences was found within transmission clusters/network. Phylodynamic analysis revealed Re over one during the whole period investigated, with the steepest slopes and a recent tMRCA for MSM transmission group subtype B clades, in line with a growing trend in the number of transmissions in years approaching the end of the study period. Contrary, heterosexual clades in both studied subtypes – B and C – showed modest growth and stagnation. LCA analysis identified five latent classes, with transmission clusters dominantly present in 2/5 classes, linked to MSM transmission living in the capital city and with the high prevalence of co-infection with HBV and/or other STIs.Presented findings imply that HIV epidemic in Serbia is still in the exponential growth phase, in particular, related to the MSM transmission, with estimated steep growth curve until 2030. The obtained results imply that an average new HIV patient in Serbia is a young man with concomitant sexually transmitted infection.
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Affiliation(s)
- Luka Jovanović
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Marina Šiljić
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Valentina Ćirković
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Dubravka Salemović
- Infectious and Tropical Diseases University Hospital, Clinical Centre of Serbia, Belgrade, Serbia
| | - Ivana Pešić-Pavlović
- Virology Laboratory, Microbiology Department, Clinical Centre of Serbia, Belgrade, Serbia
| | - Marija Todorović
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jovan Ranin
- Infectious and Tropical Diseases University Hospital, Clinical Centre of Serbia, Belgrade, Serbia
| | - Djordje Jevtović
- Infectious and Tropical Diseases University Hospital, Clinical Centre of Serbia, Belgrade, Serbia
| | - Maja Stanojević
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
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35
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Paraskevis D, Beloukas A, Stasinos K, Pantazis N, de Mendoza C, Bannert N, Meyer L, Zangerle R, Gill J, Prins M, d'Arminio Montforte A, Kran AMB, Porter K, Touloumi G. HIV-1 molecular transmission clusters in nine European countries and Canada: association with demographic and clinical factors. BMC Med 2019; 17:4. [PMID: 30616632 PMCID: PMC6323837 DOI: 10.1186/s12916-018-1241-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 12/14/2018] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Knowledge of HIV-1 molecular transmission clusters (MTCs) is important, especially in large-scale datasets, for designing prevention programmes and public health intervention strategies. We used a large-scale HIV-1 sequence dataset from nine European HIV cohorts and one Canadian, to identify MTCs and investigate factors associated with the probability of belonging to MTCs. METHODS To identify MTCs, we applied maximum likelihood inferences on partial pol sequences from 8955 HIV-positive individuals linked to demographic and clinical data. MTCs were defined using two different criteria: clusters with bootstrap support >75% (phylogenetic confidence criterion) and clusters consisting of sequences from a specific region at a proportion of >75% (geographic criterion) compared to the total number of sequences within the network. Multivariable logistic regression analysis was used to assess factors associated with MTC clustering. RESULTS Although 3700 (41%) sequences belonged to MTCs, proportions differed substantially by country and subtype, ranging from 7% among UK subtype C sequences to 63% among German subtype B sequences. The probability of belonging to an MTC was independently less likely for women than men (OR = 0.66; P < 0.001), older individuals (OR = 0.79 per 10-year increase in age; P < 0.001) and people of non-white ethnicity (OR = 0.44; P < 0.001 and OR = 0.70; P = 0.002 for black and 'other' versus white, respectively). It was also more likely among men who have sex with men (MSM) than other risk groups (OR = 0.62; P < 0.001 and OR = 0.69; P = 0.002 for people who inject drugs, and sex between men and women, respectively), subtype B (ORs 0.36-0.70 for A, C, CRF01 and CRF02 versus B; all P < 0.05), having a well-estimated date of seroconversion (OR = 1.44; P < 0.001), a later calendar year of sampling (ORs 2.01-2.61 for all post-2002 periods versus pre-2002; all P < 0.01), and being naïve to antiretroviral therapy at sampling (OR = 1.19; P = 0.010). CONCLUSIONS A high proportion (>40%) of individuals belonged to MTCs. Notably, the HIV epidemic dispersal appears to be driven by subtype B viruses spread within MSM networks. Expansion of regional epidemics seems mainly associated with recent MTCs, rather than the growth of older, established ones. This information is important for designing prevention and public health intervention strategies.
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Affiliation(s)
- Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 115 27, Athens, Greece.
| | - Apostolos Beloukas
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 115 27, Athens, Greece.
- Institute of Infection and Global Health, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool, L69 7BE, UK.
- Department of Biomedical Sciences, School of Health Sciences, University of West Attica, Agiou Spiridonos Str (Campus 1), 12243, Athens, Greece.
| | - Kostantinos Stasinos
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 115 27, Athens, Greece
| | - Nikos Pantazis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 115 27, Athens, Greece
| | - Carmen de Mendoza
- Department of Internal Medicine, Puerta de Hierro Research Institute and University Hospital, Alle Manuel de Falla, 1, 28222, Madrid, Majadahonda, Spain
| | | | - Laurence Meyer
- Inserm, CESP U1018, Univ Paris-Sud, Department of Epidemiology and Population Health, APHP, Hôpital Bicêtre, 78 Rue du Général Leclerc, 94270, Le Kremlin-Bicêtre, France
| | - Robert Zangerle
- Department of Dermatology and Venerology, Innsbruck Medical University, Anichstraße 35, 6020, Innsbruck, Austria
| | - John Gill
- Department of Microbiology, Immunology and Infectious Diseases (MIID), University of Calgary, 269 Heritage Medical Research Building, 24 Ave NW, Calgary, Alberta, Canada
| | - Maria Prins
- Academic Medical Center, University of Amsterdam, Netherlands and Department of Infectious Diseases, Amsterdam Infection and Immunity Institute, Spui 21, 1012 WX, Amsterdam, Netherlands
| | | | - Anne-Marte Bakken Kran
- Department of Microbiology, Oslo University Hospital, OUS HF Rikshospitalet, Postboks 4950 Nydalen, 0424, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Sognsvannsveien 20, Rikshospitalet, 0372, Oslo, Norway
| | - Kholoud Porter
- University College London Institute for Global Health, Institute of Child Health, 3rd floor, 30 Guilford Street, London, WC1N 1EH, UK
| | - Giota Touloumi
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 115 27, Athens, Greece
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The N-Terminus of the HIV-1 p6 Gag Protein Regulates Susceptibility to Degradation by IDE. Viruses 2018; 10:v10120710. [PMID: 30545091 PMCID: PMC6316412 DOI: 10.3390/v10120710] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/07/2018] [Accepted: 12/09/2018] [Indexed: 12/14/2022] Open
Abstract
As part of the Pr55Gag polyprotein, p6 fulfills an essential role in the late steps of the replication cycle. However, almost nothing is known about the functions of the mature HIV-1 p6 protein. Recently, we showed that p6 is a bona fide substrate of the insulin-degrading enzyme (IDE), a ubiquitously expressed zinc metalloprotease. This phenomenon appears to be specific for HIV-1, since p6 homologs of HIV-2, SIV and EIAV were IDE-insensitive. Furthermore, abrogation of the IDE-mediated degradation of p6 reduces the replication capacity of HIV-1 in an Env-dependent manner. However, it remained unclear to which extent the IDE mediated degradation is phylogenetically conserved among HIV-1. Here, we describe two HIV-1 isolates with IDE resistant p6 proteins. Sequence comparison allowed deducing one single amino acid regulating IDE sensitivity of p6. Exchanging the N-terminal leucine residue of p6 derived from the IDE sensitive isolate HIV-1NL4-3 with proline enhances its stability, while replacing Pro-1 of p6 from the IDE insensitive isolate SG3 with leucine restores susceptibility towards IDE. Phylogenetic analyses of this natural polymorphism revealed that the N-terminal leucine is characteristic for p6 derived from HIV-1 group M except for subtype A, which predominantly expresses p6 with an N-terminal proline. Consequently, p6 peptides derived from subtype A are not degraded by IDE. Thus, IDE mediated degradation of p6 is specific for HIV-1 group M isolates and not occasionally distributed among HIV-1.
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Nicolás D, Ambrosioni J, de Lazzari E, Suarez A, Manzardo C, Agüero F, Mosquera MM, Costa J, Ligero C, Marcos MÁ, Sánchez-Palomino S, Fernández E, Plana M, Yerly S, Gatell JM, Miró JM. Epidemiological changes of acute/recent human immunodeficiency virus type 1 infection in Barcelona, Spain (1997-2015): a prospective cohort study. Clin Microbiol Infect 2018; 25:878-884. [PMID: 30472421 DOI: 10.1016/j.cmi.2018.10.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 10/27/2022]
Abstract
OBJECTIVE To describe the epidemiology of acute/recent human immunodeficiency virus (HIV) infection over two decades in Barcelona (Spain). METHODS Prospective, single-centre cohort including all patients with an acute/recent HIV infection (<180 days) since 1997. Patients were stratified into four periods. Phylogenetic analysis was performed to determine clusters of transmission. RESULTS A total of 346 consecutive acute/recently infected patients were included. The annual proportion of recent infections among total new HIV diagnoses increased over time from 1% (29 out of 1964) to 8% (112 out of 1474) (p <0.001). Proportion of men who have sex with men (MSM) in the cohort increased from 62% (18 out of 29) to 89% (100 out of 112) (p <0.001). The proportion of migrants showed a non-significant increasing trend (24% (7 of 29) to 40% (45 of 112)) likewise the non-B subtype (0% to 22% (22 of 112)). The mean time from infection to diagnosis was 53.6 days (interquartile range (IQR) 50-57), comparable among all periods. Mean time from infection to treatment decreased over the years from 575 (IQR 467-683) to 471 (IQR 394-549) days (p <0.001) without significant differences between migrants and non-migrants (133 (IQR 71-411) versus 208 (IQR 90-523) days p 0.089). Almost 50% (152 of 311) of recently infected individuals were included in a cluster of transmission, and 92% (137 of 149) of them were MSM. CONCLUSION The MSM population has progressively grown within acutely/recently infected patients in Barcelona, and is frequently involved in transmission clusters. Although the time between diagnosis and treatment has been reduced, the time between infection and diagnosis still needs to be shortened.
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Affiliation(s)
- D Nicolás
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - J Ambrosioni
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - E de Lazzari
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - A Suarez
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - C Manzardo
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - F Agüero
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - M M Mosquera
- Laboratory of Virology, Microbiology Service, Hospital Clinic Barcelona, CIBERehd, University of Barcelona, Barcelona, Spain
| | - J Costa
- Laboratory of Virology, Microbiology Service, Hospital Clinic Barcelona, CIBERehd, University of Barcelona, Barcelona, Spain
| | - C Ligero
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - M Á Marcos
- Laboratory of Virology, Microbiology Service, Hospital Clinic Barcelona, CIBERehd, University of Barcelona, Barcelona, Spain
| | - S Sánchez-Palomino
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, IDIBAPS, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - E Fernández
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - M Plana
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, IDIBAPS, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - S Yerly
- Laboratory of Virology, Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - J M Gatell
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - J M Miró
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain.
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Alteri C, Fabeni L, Scutari R, Berno G, Di Carlo D, Gori C, Bertoli A, Vergori A, Mastrorosa I, Bellagamba R, Mussini C, Colafigli M, Montella F, Pennica A, Mastroianni CM, Girardi E, Andreoni M, Antinori A, Svicher V, Ceccherini-Silberstein F, Perno CF, Santoro MM. Genetic divergence of HIV-1 B subtype in Italy over the years 2003-2016 and impact on CTL escape prevalence. Sci Rep 2018; 8:15739. [PMID: 30356083 PMCID: PMC6200748 DOI: 10.1038/s41598-018-34058-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/04/2018] [Indexed: 12/05/2022] Open
Abstract
HIV-1 is characterized by high genetic variability, with implications for spread, and immune-escape selection. Here, the genetic modification of HIV-1 B subtype over time was evaluated on 3,328 pol and 1,152 V3 sequences belonging to B subtype and collected from individuals diagnosed in Italy between 2003 and 2016. Sequences were analyzed for genetic-distance from consensus-B (Tajima-Nei), non-synonymous and synonymous rates (dN and dS), CTL escapes, and intra-host evolution over four time-spans (2003–2006, 2007–2009, 2010–2012, 2013–2016). Genetic-distance increased over time for both pol and V3 sequences (P < 0.0001 and 0.0003). Similar results were obtained for dN and dS. Entropy-value significantly increased at 16 pol and two V3 amino acid positions. Seven of them were CTL escape positions (protease: 71; reverse-transcriptase: 35, 162, 177, 202, 207, 211). Sequences with ≥3 CTL escapes increased from 36.1% in 2003–2006 to 54.0% in 2013–2016 (P < 0.0001), and showed better intra-host adaptation than those containing ≤2 CTL escapes (intra-host evolution: 3.0 × 10−3 [2.9 × 10−3–3.1 × 10−3] vs. 4.3 × 10−3 [4.0 × 10−3–5.0 × 10−3], P[LRT] < 0.0001[21.09]). These data provide evidence of still ongoing modifications, involving CTL escape mutations, in circulating HIV-1 B subtype in Italy. These modifications might affect the process of HIV-1 adaptation to the host, as suggested by the slow intra-host evolution characterizing viruses with a high number of CTL escapes.
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Affiliation(s)
- Claudia Alteri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy.
| | - Lavinia Fabeni
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Rossana Scutari
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Giulia Berno
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | - Domenico Di Carlo
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Milan, 20133, Italy
| | - Caterina Gori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | - Ada Bertoli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Alessandra Vergori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | - Ilaria Mastrorosa
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | - Rita Bellagamba
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | | | | | | | | | | | - Enrico Girardi
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | | | - Andrea Antinori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | - Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy
| | | | - Carlo Federico Perno
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy.,Department of Oncology, University of Milan, Milan, 20122, Italy
| | - Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy
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Patiño-Galindo JÁ, Domínguez F, Cuevas MT, Delgado E, Sánchez M, Pérez-Álvarez L, Thomson MM, Sanjuán R, González-Candelas F, Cuevas JM. Genome-scale analysis of evolutionary rate and selection in a fast-expanding Spanish cluster of HIV-1 subtype F1. INFECTION GENETICS AND EVOLUTION 2018; 66:43-47. [PMID: 30219320 DOI: 10.1016/j.meegid.2018.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/06/2018] [Accepted: 09/12/2018] [Indexed: 12/15/2022]
Abstract
This work is aimed at assessing the presence of positive selection and/or shifts of the evolutionary rate in a fast-expanding HIV-1 subtype F1 transmission cluster affecting men who have sex with men in Spain. We applied Bayesian coalescent phylogenetics and selection analyses to 23 full-coding region sequences from patients belonging to that cluster, along with other 19 F1 epidemiologically-unrelated sequences. A shift in the overall evolutionary rate of the virus, explained by positively selected sites in the cluster, was detected. We also found one substitution in Nef (H89F) that was specific to the cluster and experienced positive selection. These results suggest that fast transmission could have been facilitated by some inherent genetic properties of this HIV-1 variant.
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Affiliation(s)
- Juan Á Patiño-Galindo
- Joint Research Unit "Infection and Public Health" FISABIO-Universitat de València, València, Spain; CIBER in Epidemiology and Public Health, Madrid, Spain
| | - Francisco Domínguez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - María T Cuevas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Mónica Sánchez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València, Spain.; Department of Genetics, Universitat de València, València, Spain
| | - Fernando González-Candelas
- Joint Research Unit "Infection and Public Health" FISABIO-Universitat de València, València, Spain; CIBER in Epidemiology and Public Health, Madrid, Spain; Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València, Spain.; Department of Genetics, Universitat de València, València, Spain
| | - José M Cuevas
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València, Spain.; Department of Genetics, Universitat de València, València, Spain.
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Erlewein D, Bruni T, Gadebusch Bondio M. Is a shift from research on individual medical error to research on health information technology underway? A 40-year analysis of publication trends in medical journals. J Evid Based Med 2018; 11:184-190. [PMID: 29882339 DOI: 10.1111/jebm.12302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/22/2018] [Indexed: 01/11/2023]
Abstract
OBJECTIVE In 1983, McIntyre and Popper underscored the need for more openness in dealing with errors in medicine. Since then, much has been written on individual medical errors. Furthermore, at the beginning of the 21st century, researchers and medical practitioners increasingly approached individual medical errors through health information technology. Hence, the question arises whether the attention of biomedical researchers shifted from individual medical errors to health information technology. We ran a study to determine publication trends concerning individual medical errors and health information technology in medical journals over the last 40 years. METHODS We used the Medical Subject Headings (MeSH) taxonomy in the database MEDLINE. Each year, we analyzed the percentage of relevant publications to the total number of publications in MEDLINE. The trends identified were tested for statistical significance. RESULTS Our analysis showed that the percentage of publications dealing with individual medical errors increased from 1976 until the beginning of the 21st century but began to drop in 2003. Both the upward and the downward trends were statistically significant (P < 0.001). A breakdown by country revealed that it was the weight of the US and British publications that determined the overall downward trend after 2003. On the other hand, the percentage of publications dealing with health information technology doubled between 2003 and 2015. The upward trend was statistically significant (P < 0.001). CONCLUSIONS The identified trends suggest that the attention of biomedical researchers partially shifted from individual medical errors to health information technology in the USA and the UK.
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Affiliation(s)
- Daniel Erlewein
- Medizinhistorisches Institut, Universitätsklinikum Bonn, Bonn, Germany
| | - Tommaso Bruni
- Medizinhistorisches Institut, Universitätsklinikum Bonn, Bonn, Germany
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Paraskevis D, Kostaki E, Nikolopoulos GK, Sypsa V, Psichogiou M, Del Amo J, Hodges-Mameletzis I, Paraskeva D, Skoutelis A, Malliori M, Williams L, Friedman SR, Daikos GL, Hatzakis A. Molecular Tracing of the Geographical Origin of Human Immunodeficiency Virus Type 1 Infection and Patterns of Epidemic Spread Among Migrants Who Inject Drugs in Athens. Clin Infect Dis 2018; 65:2078-2084. [PMID: 29020180 DOI: 10.1093/cid/cix717] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/12/2017] [Indexed: 12/13/2022] Open
Abstract
Background High numbers of human immunodeficiency virus type 1 (HIV-1) infections among people who inject drugs (PWID) have been diagnosed in Athens, Greece, since 2011. We aimed to trace the geographic origin of HIV-1 infection for migrants who inject drugs and to investigate whether transmissions occur more frequently among migrants than among Greek nationals. Methods Multiple cross-sectional studies were pooled to assemble all persons diagnosed with HIV-1 in Greece between 1 January 2011 and 31 October 2014. Phylogenetic analyses used maximum likelihood estimation. The hypothesis of ethnic compartmentalization was tested by reconstructing ancestral states of characters at the tips using the criterion of parsimony over a set of bootstrap trees. Results Of 2274 persons, 38.4% were PWID. Phylogenetic analyses showed the existence of 4 major PWID-specific local transmission networks (LTNs): CRF14_BG (437 [58.6%]), CRF35_AD (139 [18.6%]), subtype B (116 [15.6%]), and subtype A (54 [7.2%]). Of 184 non-Greek PWID, 78.3% had been infected within the PWID-LTNs. For 173 (94.3%), the origin of their infection was assumed to be in Greece (postmigration). For PWID infected within LTNs, transmissions for subtype A and CRF14_BG occurred more frequently among migrants than would be expected by chance (phyloethnic study). Conclusions Our analysis showed that the majority of infections among migrants occurred postmigration. The existence of significant transmission networking among migrants highlights that this population is a priority for HIV prevention. As molecular analysis can estimate the probable country of HIV infection, it can help to inform the design of public health strategies.
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Affiliation(s)
- Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Evangelia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | | | - Vana Sypsa
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Mina Psichogiou
- First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Greece
| | - Julia Del Amo
- National Center for Epidemiology, Institute of Health Carlos III, Madrid, Spain
| | | | | | - Athanasios Skoutelis
- Fifth Department of Internal Medicine and Infectious Diseases Evangelismos Hospital Athens
| | - Meni Malliori
- Medical School, National and Kapodistrian University of Athens, Greece
| | - Leslie Williams
- National Development and Research Institutes, New York, New York
| | | | - Georgios L Daikos
- First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Greece
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
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Tumiotto C, Bellecave P, Recordon-Pinson P, Groppi A, Nikolski M, Fleury H. Diversity of HIV-1 in Aquitaine, Southwestern France, 2012-2016. AIDS Res Hum Retroviruses 2018; 34:471-473. [PMID: 29439582 DOI: 10.1089/aid.2017.0298] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have estimated the prevalence of the different viral subtypes between January 2012 and December 2016 in HIV-1-infected patients of the Aquitaine region (southwest part of France) who had a routine HIV-1 genotype resistance testing (GRT) centralized at the Bordeaux University Hospital. GRT was performed on viral RNA (1,784 samples) before treatment initiation or at failure, whereas proviral DNA was used as template (1,420 samples) in the event of a treatment switch in patients with viral load below 50 copies/mL. Pol and integrase sequences were obtained; subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) were assigned by combining the results of SCUEAL, REGA, COMET, and HIV BLAST. Globally, subtype B was predominant with 71.7%, whereas non-B subtypes accounted for 28.3%. Within the non-B viruses, CRF02_AG was the most prominent (11.6%) followed by non-B non-URF (13.5%), A, CRF01_AE, G, CRF06_cpx, F, C, D, H, J, and finally URF (3.2%). The analysis of the two compartments separately showed that RNA exhibits higher percentages of non-B viruses than DNA. This study reveals a high degree of diversity of HIV-1 non-B subtype strains in Aquitaine, with an increasing prevalence of CRF02_AG and URF in the population investigated for viral RNA, that is, including more recently detected HIV-1-infected patients. Future studies should attempt to identify the transmission clusters while paying special attention to URF, since they seem to be increasing in the population and could potentially host CRF.
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Affiliation(s)
- Camille Tumiotto
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
- CNRS UMR 5234 MFP, University of Bordeaux, Bordeaux, France
| | - Pantxika Bellecave
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
- CNRS UMR 5234 MFP, University of Bordeaux, Bordeaux, France
| | | | - Alexi Groppi
- Bordeaux Bioinformatics Center (CBiB), University of Bordeaux, Bordeaux, France
| | - Macha Nikolski
- Bordeaux Bioinformatics Center (CBiB), University of Bordeaux, Bordeaux, France
| | - Hervé Fleury
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
- CNRS UMR 5234 MFP, University of Bordeaux, Bordeaux, France
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Kostaki EG, Karamitros T, Bobkova M, Oikonomopoulou M, Magiorkinis G, Garcia F, Hatzakis A, Paraskevis D. Spatiotemporal Characteristics of the HIV-1 CRF02_AG/CRF63_02A1 Epidemic in Russia and Central Asia. AIDS Res Hum Retroviruses 2018; 34:415-420. [PMID: 29455562 DOI: 10.1089/aid.2017.0233] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Eastern European countries, including Russia, Ukraine, and other former Soviet Union (FSU) countries, have experienced a human immunodeficiency virus (HIV) epidemic spreading mostly among people who inject drugs (PWID). We aimed to investigate the origin and the dispersal patterns of HIV-1 CRF02_AG in Russia and other FSU countries. We studied 136 CRF02_AG sequences originating from Russia, and FSU countries along with a globally sampled dataset of 3,580 CRF02_AG sequences. Maximum-likelihood phylogeny reconstruction with bootstrap evaluation was conducted in RAxML. Bayesian phylogeographic analysis was performed in BEAST v1.8 using the discrete trait model. We found that all CRF02_AG sequences from Russia and other FSU countries formed a single monophyletic cluster within CRF02_AG radiation. The Russian/FSU clade was classified as CRF63_02A1. Sequences from the FSU countries clustered further within distinct subclades (two from Russia, three from Uzbekistan, and one Kazakhstan) according to the geographic origin of sampling. Molecular clock analysis revealed that the time to the most recent common ancestor (tMRCA) of the CRF63_02A1 epidemic was in 1996 [95% higher posterior density (95% HPD): 1992-1999], while for the two Russian subclades, tMRCA was estimated in 2003 (95% HPD: 2001-2004) and in 2007 (95% HPD: 2005-2008). Phylogeographic analysis suggested that the potential origin of the epidemic was in Uzbekistan. Early dispersal of CRF63_02A1 occurred in Kazakhstan and Uzbekistan and thereafter the epidemic spread to Russia. Notably, spillover transmissions to Russia kept occurring from both countries. Previous studies have shown that Russia and Ukraine have provided the source for the PWID-driven, HIV-1 subtype-A epidemic, spreading across the FSU countries (AFSU). In great contrast, CRF63_02A1 established an epidemic in central Asia (Uzbekistan and Kazakhstan), from where it subsequently disseminated to Russia. Our study suggests that cross-border transmissions among PWID occur bidirectionally between Russian and other FSU populations. These results are of public health importance and suggest that prevention actions have to be reinforced in this area to assist the management of high-risk practices.
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Affiliation(s)
- Evangelia-Georgia Kostaki
- 1 Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, Greece
| | | | - Marina Bobkova
- 3 Ivanovsky Institute of Virology , FSBI "N.F. Gamaleya FRCEM" of the Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Martha Oikonomopoulou
- 1 Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, Greece
| | - Gkikas Magiorkinis
- 1 Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, Greece
- 2 Department of Zoology, University of Oxford , Oxford, United Kingdom
| | - Federico Garcia
- 4 Servicio de Microbiología, Hospital Universitario San Cecilio, Complejo Hospitalario Universitario Granada, Cohorte de Adultos de la Red de Investigación en SIDA-CoRIS, Instituto de Investigación Ibs , Granada, Granada (Andalucía), Spain
| | - Angelos Hatzakis
- 1 Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, Greece
| | - Dimitrios Paraskevis
- 1 Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens , Athens, Greece
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Lunar MM, Židovec Lepej S, Tomažič J, Vovko TD, Pečavar B, Turel G, Maver M, Poljak M. HIV-1 transmitted drug resistance in Slovenia and its impact on predicted treatment effectiveness: 2011-2016 update. PLoS One 2018; 13:e0196670. [PMID: 29698470 PMCID: PMC5919638 DOI: 10.1371/journal.pone.0196670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/17/2018] [Indexed: 01/30/2023] Open
Abstract
HIV-positive individuals that have a detected transmitted drug resistance (TDR) at baseline have a higher risk of virological failure with antiretroviral therapy (ART). This study offers an update on the prevalence of TDR in Slovenia, looks for onward transmission of TDR, and reassesses the need for baseline drug resistance testing. Blinded questionnaires and partial pol sequences were obtained from 54.5% (168/308) of all of the patients diagnosed with HIV-1 from 2011 to 2016. Subtype B was detected in 82.7% (139/168) of patients, followed by subtype A (8.3%), subtype C (2.4%), and CRF01_AE (1.8%). Surveillance drug resistance mutations (SDRMs) were found in four individuals (2.4%), all of them men who have sex with men (MSM) and infected with subtype B. K103N was detected in two patients and T68D and T215D in one person each, corresponding to a prevalence of 0%, 1.2%, and 1.2% of TDR to protease inhibitors (PIs), nucleoside reverse transcriptase inhibitors (NRTIs), and non-NRTIs (NNRTIs), respectively. The impact of mutations on drug susceptibility was found to be most pronounced for NNRTIs. No forward spread of TDR within the country was observed; however, phylogenetic analysis revealed several new introductions of HIV into Slovenia in recent years, possibly due to increased risky behavior by MSM. This was indirectly confirmed by a substantial increase in syphilis cases and HIV-1 non-B subtypes during the study period. A drug-resistant HIV variant with good transmission fitness is thus more likely to be imported into Slovenia in the near future, and so TDR should be closely monitored.
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Affiliation(s)
- Maja M. Lunar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | - Janez Tomažič
- Department of Infectious Diseases, Ljubljana University Medical Center, Ljubljana, Slovenia
| | - Tomaž D. Vovko
- Department of Infectious Diseases, Ljubljana University Medical Center, Ljubljana, Slovenia
| | - Blaž Pečavar
- Department of Infectious Diseases, Ljubljana University Medical Center, Ljubljana, Slovenia
| | - Gabriele Turel
- Department of Infectious Diseases, Ljubljana University Medical Center, Ljubljana, Slovenia
| | - Manja Maver
- Department of Infectious Diseases, Ljubljana University Medical Center, Ljubljana, Slovenia
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
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Abstract
A molecular epidemiology study of HIV-1 infection was conducted in one hundred diagnosed and untreated HIV-1-infected patients in Cyprus between 2010 and 2012, representing 65.4% of all the reported HIV-1 infections in Cyprus in this three-year period, using a previously defined enrolment strategy. Eighty-two patients were newly diagnosed (genotypic drug resistance testing within six months from diagnosis), and eighteen patients were HIV-1 diagnosed for a longer period or the diagnosis date was unknown. Phylogenetic trees of the pol sequences obtained in this study with reference sequences indicated that subtypes B and A1 were the most common subtypes present and accounted for 41.0 and 19.0% respectively, followed by subtype C (7.0%), F1 (8.0%), CRF02_AG (4.0%), A2 (2.0%), other circulating recombinant forms (CRFs) (7.0%) and unknown recombinant forms (URFs) (12%). Most of the newly-diagnosed study subjects were Cypriots (63%), males (78%) with median age 39 (Interquartile Range, IQR 33–48) reporting having sex with other men (MSM) (51%). A high rate of clustered transmission of subtype B drug-sensitive strains to reverse transcriptase and protease inhibitors was observed among MSM, twenty-eight out of forty-one MSM study subjects (68.0%) infected were implicated in five transmission clusters, two of which are sub-subtype A1 and three of which are subtype B strains. The two largest MSM subtype B clusters included nine and eight Cypriot men, respectively, living in all major cities in Cyprus. There were only three newly diagnosed patients with transmitted drug resistant HIV-1 strains, one study subject from the United Kingdom infected with subtype B strain and one from Romania with sub-subtype A2 strain, both with PI drug resistance mutation M46L and one from Greece with sub-subtype A1 with non-nucleoside reverse transcriptase inhibitors (NNRTI) drug resistance mutation K103N.
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Paraskevis D, Nikolopoulos GK, Sypsa V, Psichogiou M, Pantavou K, Kostaki E, Karamitros T, Paraskeva D, Schneider J, Malliori M, Friedman SR, Des Jarlais DC, Daikos GL, Hatzakis A. Molecular investigation of HIV-1 cross-group transmissions during an outbreak among people who inject drugs (2011-2014) in Athens, Greece. INFECTION GENETICS AND EVOLUTION 2018; 62:11-16. [PMID: 29653216 DOI: 10.1016/j.meegid.2018.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 03/31/2018] [Accepted: 04/07/2018] [Indexed: 01/12/2023]
Abstract
New diagnoses of HIV-1 infection among people who inject drugs (PWID) rocketed in Athens, Greece between 2011 and 2014 (HIV-1 outbreak). Our aim was to identify, during that period, potential cross-group transmissions between the within-Greece PWID and other risk or national groups using molecular methods. Sequences from 33 PWID were outside the PWID-outbreak networks in Greece (PWID-imported transmissions). Phylogenetic analyses on 28 of these sequences (subtypes A and B) showed that 11 subtype B infections originated from Greece, whereas 8 and 7 subtype A strains were from former Soviet Union countries (AFSU) and Greece, respectively. The putative source in half of the PWID-imported transmissions with Greek origin was an individual who acquired HIV via sexual contact. During four years of an HIV-1 outbreak among PWID in Athens, Greece, 33 individuals in this group (4.6% of all diagnoses with phylogenetic analyses) are likely to represent infections, sexually or injection-acquired, outside the within-Greece-PWID-outbreak networks. Combined molecular and traditional HIV surveillance to monitor introductions of new strains, and interventions that aim at reducing the rate of both injection and sexual risky practices are needed during drug injection-related HIV outbreaks.
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Affiliation(s)
- Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Vana Sypsa
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Mina Psichogiou
- First Department of Internal Medicine, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Evangelia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Timokratis Karamitros
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitra Paraskeva
- Hellenic Center for Disease Control and Prevention, Amarousio, Greece
| | - John Schneider
- Departments of Medicine and Public Health Sciences, and The Chicago Center for HIV Elimination, University of Chicago, Chicago, USA
| | - Melpomeni Malliori
- Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Don C Des Jarlais
- The Baron Edmond de Rothschild Chemical Dependency Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Georgios L Daikos
- First Department of Internal Medicine, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Phylogenetic analysis of the Belgian HIV-1 epidemic reveals that local transmission is almost exclusively driven by men having sex with men despite presence of large African migrant communities. INFECTION GENETICS AND EVOLUTION 2018. [PMID: 29522828 DOI: 10.1016/j.meegid.2018.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
To improve insight in the drivers of local HIV-1 transmission in Belgium, phylogenetic, demographic, epidemiological and laboratory data from patients newly diagnosed between 2013 and 2015 were combined and analyzed. Characteristics of clustered patients, paired patients and patients on isolated branches in the phylogenetic tree were compared. The results revealed an overall high level of clustering despite the short time frame of sampling, with 47.6% of all patients having at least one close genetic counterpart and 36.6% belonging to a cluster of 3 or more individuals. Compared to patients on isolated branches, patients in clusters more frequently reported being infected in Belgium (95.1% vs. 47.6%; p < 0.001), were more frequently men having sex with men (MSM) (77.9% vs. 42.8%; p < 0.001), of Belgian origin (68.2% vs. 32.9%; p < 0.001), male gender (92.6% vs. 65.8%; p < 0.001), infected with subtype B or F (87.8% vs. 43.4%; p < 0.001) and diagnosed early after infection (55.4% vs. 29.0%; p < 0.001). Strikingly, Sub-Saharan Africans (SSA), overall representing 27.1% of the population were significantly less frequently found in clusters than on individual branches (6.0% vs. 41.8%; p < 0.001). Of the SSA that participated in clustered transmission, 66.7% were MSM and this contrasts sharply with the overall 12.0% of SSA reporting MSM. Transmission clusters with SSA were more frequently non-B clusters than transmission clusters without SSA (44.4% versus 18.2%). MSM-driven clusters with patients of mixed origin may account, at least in part, for the increasing spread of non-B subtypes to the native MSM population, a cross-over that has been particularly successful for subtype F and CRF02_AG. The main conclusions from this study are that clustered transmission in Belgium remains almost exclusively MSM-driven with very limited contribution of SSA. There were no indications for local ongoing clustered transmission of HIV-1 among SSA.
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HIV-1 Infection in Cyprus, the Eastern Mediterranean European Frontier: A Densely Sampled Transmission Dynamics Analysis from 1986 to 2012. Sci Rep 2018; 8:1702. [PMID: 29374182 PMCID: PMC5786036 DOI: 10.1038/s41598-017-19080-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/21/2017] [Indexed: 11/09/2022] Open
Abstract
Since HIV-1 treatment is increasingly considered an effective preventionstrategy, it is important to study local HIV-1 epidemics to formulate tailored preventionpolicies. The prevalence of HIV-1 in Cyprus was historically low until 2005. To investigatethe shift in epidemiological trends, we studied the transmission dynamics of HIV-1 in Cyprususing a densely sampled Cypriot HIV-1 transmission cohort that included 85 percent ofHIV-1-infected individuals linked to clinical care between 1986 and 2012 based on detailedclinical, epidemiological, behavioral and HIV-1 genetic information. Subtyping andtransmission cluster reconstruction were performed using maximum likelihood and Bayesianmethods, and the transmission chain network was linked to the clinical, epidemiological andbehavioral data. The results reveal that for the main HIV-1 subtype A1 and B sub-epidemics,young and drug-naïve HIV-1-infected individuals in Cyprus are driving the dynamics of thelocal HIV-1 epidemic. The results of this study provide a better understanding of thedynamics of the HIV-1 infection in Cyprus, which may impact the development of preventionstrategies. Furthermore, this methodology for analyzing densely sampled transmissiondynamics is applicable to other geographic regions to implement effective HIV-1 preventionstrategies in local settings.
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van de Laar TJ, Van Gaever VA, Swieten PV, Muylaert A, Compernolle V, Zaaijer HL. Phylogenetic analysis reveals three distinct epidemiological profiles in Dutch and Flemish blood donors with hepatitis B virus infection. Virology 2018; 515:243-249. [PMID: 29324289 DOI: 10.1016/j.virol.2017.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 02/07/2023]
Abstract
During 2006-2016, hepatitis B virus (HBV) was detected in nearly 400 blood donors in the Netherlands and Flanders. Donor demographics and self-reported risk factors as disclosed during the donor exit interview were compared to HBV phylogenies of donor and reference sequences. First-time donors with chronic HBV-infection were often immigrants (67%) infected with genetically highly diverse strains of genotypes A (32%), B (8%), C (6%), D (53%) and E to H (1%). Each subtype was strongly associated with donor ethnicity. In contrast, 57/62 (93%) of acute/recent HBV infections occurred among indigenous donors, of whom 67% was infected with one specific widely circulating epidemic HBV-A2 lineage. HBV typing identified three distinct epidemiological profiles: the import of chronic HBV infections through migration, longstanding transmission of non-epidemic HBV-A2 strains within western-Europe, and the active transmission of one epidemic HBV-A2 strain most likely fueled by sexual risk behavior.
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Affiliation(s)
- Thijs J van de Laar
- Department op Blood-borne Infections, Sanquin Research, Amsterdam, The Netherlands.
| | | | - Peter van Swieten
- Department op Blood-borne Infections, Sanquin Research, Amsterdam, The Netherlands
| | - An Muylaert
- Blood Service, Belgian Red Cross-Flanders, Mechelen, Belgium
| | - Veerle Compernolle
- Blood Service, Belgian Red Cross-Flanders, Mechelen, Belgium; Faculty of Medicine and Health Sciences, University of Ghent, Ghent, Belgium
| | - Hans L Zaaijer
- Department op Blood-borne Infections, Sanquin Research, Amsterdam, The Netherlands; Department of Medical Microbiology (CINIMA), Academic Medical Center / University of Amsterdam, Amsterdam, The Netherlands
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Abstract
Human immunodeficiency virus (HIV) is a neurotropic virus that enters the central nervous system (CNS) early in the course of infection. Although highly active antiretroviral therapy (HAART) has resulted in remarkable decline in the morbidity and mortality in AIDS patients, controlling HIV infections still remains a global health priority. HIV access to the CNS serves as the natural viral preserve because most antiretroviral (ARV) drugs possess inadequate or zero delivery across the brain barriers. The structure of the blood-brain barrier (BBB), the presence of efflux pumps, and the expression of metabolic enzymes pose hurdles for ARV drug-brain entry. Thus, development of target-specific, effective, safe, and controllable drug delivery approach is an important health priority for global elimination of AIDS progression. Nanoformulations can circumvent the BBB to improve CNS-directed drug delivery by affecting such pumps and enzymes. Alternatively, they can be optimized to affect their size, shape, and protein and lipid coatings to facilitate drug uptake, release, and ingress across the barrier. Improved drug delivery to the CNS would affect pharmacokinetic and drug biodistribution properties. This review focuses on how nanotechnology can serve to improve the delivery of antiretroviral medicines, termed NanoART, across the BBB and affect the biodistribution and clinical benefit for NeuroAIDS.
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