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Kottaridi C, Resta P, Leventakou D, Gioti K, Zygouras I, Gouloumi AR, Sakagiannis G, Alzahrani KJ, Venetikou MS, Anthouli-Anagnostopoulou F, Beloukas A. The T350G Variation of Human Papillomavirus 16 E6 Gene Prevails in Oropharyngeal Cancer from a Small Cohort of Greek Patients. Viruses 2022; 14:v14081724. [PMID: 36016346 PMCID: PMC9415711 DOI: 10.3390/v14081724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 12/04/2022] Open
Abstract
Recent trends have shown a dramatic rise in the incidence of oropharyngeal squamous cell carcinoma strongly associated with high-risk human papillomavirus (HPV) of type 16. The genetic variability of HPV16 has been extensively studied in cervical cancer but there are very limited published data concerning the genetic variations of this HPV type in oropharyngeal cancer. In the present study, the genetic variations of HPV16 E6 gene sequences originated from a small cohort of Greek patients diagnosed with oropharyngeal cancer were assessed. The vast majority of the sequences clustered within the European variant branch. The T350G variation was found to be the predominant one. This finding may indicate the need for further studies that could explain the possible impact of this variant in the pathomechanisms of oropharyngeal cancer.
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Affiliation(s)
- Christine Kottaridi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Correspondence: (C.K.); (A.B.)
| | - Panagiota Resta
- Department of Biomedical Sciences, University of West Attica, 122 43 Athens, Greece
- National AIDS Reference Centre of Southern Greece, Department of Public Health Policy, University of West Attica, 115 21 Athens, Greece
| | - Danai Leventakou
- 2nd Department of Pathology, University Hospital Attikon, School of Medicine, National and Kapodistrian University of Athens, 124 62 Athens, Greece
| | - Katerina Gioti
- Department of Biomedical Sciences, University of West Attica, 122 43 Athens, Greece
| | - Ioannis Zygouras
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Alina-Roxani Gouloumi
- 2nd Department of Pathology, University Hospital Attikon, School of Medicine, National and Kapodistrian University of Athens, 124 62 Athens, Greece
| | | | - Khalid J. Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Maria S. Venetikou
- Department of Biomedical Sciences, University of West Attica, 122 43 Athens, Greece
| | | | - Apostolos Beloukas
- Department of Biomedical Sciences, University of West Attica, 122 43 Athens, Greece
- National AIDS Reference Centre of Southern Greece, Department of Public Health Policy, University of West Attica, 115 21 Athens, Greece
- Correspondence: (C.K.); (A.B.)
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Gioti K, Kottaridi C, Voyiatzaki C, Chaniotis D, Rampias T, Beloukas A. Animal Coronaviruses Induced Apoptosis. Life (Basel) 2021; 11:life11030185. [PMID: 33652685 PMCID: PMC7996831 DOI: 10.3390/life11030185] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
Apoptosis is a form of programmed death that has also been observed in cells infected by several viruses. It is considered one of the most critical innate immune mechanisms that limits pathogen proliferation and propagation before the initiation of the adaptive immune response. Recent studies investigating the cellular responses to SARS-CoV and SARS-CoV-2 infection have revealed that coronaviruses can alter cellular homeostasis and promote cell death, providing evidence that the modulation of apoptotic pathways is important for viral replication and propagation. Despite the genetic diversity among different coronavirus clades and the infection of different cell types and several hosts, research studies in animal coronaviruses indicate that apoptosis in host cells is induced by common molecular mechanisms and apoptotic pathways. We summarize and critically review current knowledge on the molecular aspects of cell-death regulation during animal coronaviruses infection and the viral–host interactions to this process. Future research is expected to lead to a better understanding of the regulation of cell death during coronavirus infection. Moreover, investigating the role of viral proteins in this process will help us to identify novel antiviral targets related to apoptotic signaling pathways.
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Affiliation(s)
- Katerina Gioti
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece; (K.G.); (C.K.); (C.V.); (D.C.)
| | - Christine Kottaridi
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece; (K.G.); (C.K.); (C.V.); (D.C.)
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Chrysa Voyiatzaki
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece; (K.G.); (C.K.); (C.V.); (D.C.)
| | - Dimitrios Chaniotis
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece; (K.G.); (C.K.); (C.V.); (D.C.)
| | - Theodoros Rampias
- Biomedical Research Foundation of the Academy of Athens, Basic Research Center, 11527 Athens, Greece
- Correspondence: (T.R.); (A.B.)
| | - Apostolos Beloukas
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece; (K.G.); (C.K.); (C.V.); (D.C.)
- Institute of Infection & Global Health, University of Liverpool, Liverpool L69 7BE, UK
- Correspondence: (T.R.); (A.B.)
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Spatiotemporal Distribution and Genetic Characterization of Measles Strains Circulating in Greece during the 2017-2018 Outbreak. Viruses 2020; 12:v12101166. [PMID: 33076287 PMCID: PMC7602502 DOI: 10.3390/v12101166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 01/16/2023] Open
Abstract
Between May 2017 and November 2018, Greece has experienced a severe measles outbreak with a total of 3258 cases reported, after reaching its goal of eliminating measles since 2014-2015. In this study, we aimed to investigate the origin and the dispersal patterns of the measles strains that circulated in Greece during this outbreak and to identify possible transmission patterns of measles virus (MeV) in the country. Of the 832 measles suspect cases referred to the National Measles and Rubella Reference Laboratory for MeV RNA detection, 131 randomly selected positive samples, representative of the temporal and spatial distribution of the laboratory-confirmed measles cases in Greece, were processed for genotypic identification by an RT-PCR amplification of a 598 bp fragment containing the 450 bp hypervariable region of the measles virus N gene. Phylogenetic analysis was carried out by the approximate maximum likelihood method (ML) under the generalized time-reversible (GTR + cat) model. All samples analyzed were found to belong to genotype B3. Comparative analysis with other European and reference measles strains revealed three separate major clusters and other multiple viruses circulating simultaneously in Greece. They were all isolated from three main community groups, Greek-Roma children, non-minority Greek nationals and immigrants/refugees, a finding that is in accordance with what was also observed in the last two measles outbreaks in 2005-2006 and 2010-2011. Notably, for one of the three clusters, no similarity was detected with previously reported prototype strains. Our results indicate the need for a more intensive vaccination program against measles amongst minority populations and in refugee hot-spots as well as the importance of molecular surveillance as a tool for monitoring measles outbreaks.
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Karamitros T, Papadopoulou G, Bousali M, Mexias A, Tsiodras S, Mentis A. SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies. J Clin Virol 2020; 131:104585. [PMID: 32818852 PMCID: PMC7418792 DOI: 10.1016/j.jcv.2020.104585] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/05/2020] [Accepted: 08/09/2020] [Indexed: 12/19/2022]
Abstract
In December 2019, an outbreak of atypical pneumonia (Coronavirus disease 2019 -COVID-19) associated with a novel coronavirus (SARS-CoV-2) was reported in Wuhan city, Hubei province, China. The outbreak was traced to a seafood wholesale market and human to human transmission was confirmed. The rapid spread and the death toll of the new epidemic warrants immediate intervention. The intra-host genomic variability of SARS-CoV-2 plays a pivotal role in the development of effective antiviral agents and vaccines, as well as in the design of accurate diagnostics. We analyzed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify small- and large-scale intra-host variations in the viral genome. We identified tens of low- or higher- frequency single nucleotide variations (SNVs) with variable density across the viral genome, affecting 7 out of 10 protein-coding viral genes. The majority of these SNVs (72/104) corresponded to missense changes. The annotation of the identified SNVs but also of all currently circulating strain variations revealed colocalization of intra-host as well as strain specific SNVs with primers and probes currently used in molecular diagnostics assays. Moreover, we de-novo assembled the viral genome, in order to isolate and validate intra-host structural variations and recombination breakpoints. The bioinformatics analysis disclosed genomic rearrangements over poly-A / poly-U regions located in ORF1ab and spike (S) gene, including a potential recombination hot-spot within S gene. Our results highlight the intra-host genomic diversity and plasticity of SARS-CoV-2, pointing out genomic regions that are prone to alterations. The isolated SNVs and genomic rearrangements reflect the intra-patient capacity of the polymorphic quasispecies, which may arise rapidly during the outbreak, allowing immunological escape of the virus, offering resistance to anti-viral drugs and affecting the sensitivity of the molecular diagnostics assays.
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Affiliation(s)
- Timokratis Karamitros
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece.
| | - Gethsimani Papadopoulou
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Maria Bousali
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Anastasios Mexias
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Sotirios Tsiodras
- 4(th) Academic Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Andreas Mentis
- Public Health Laboratories, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
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Rodger AJ, Cambiano V, Bruun T, Vernazza P, Collins S, Degen O, Corbelli GM, Estrada V, Geretti AM, Beloukas A, Raben D, Coll P, Antinori A, Nwokolo N, Rieger A, Prins JM, Blaxhult A, Weber R, Van Eeden A, Brockmeyer NH, Clarke A, Del Romero Guerrero J, Raffi F, Bogner JR, Wandeler G, Gerstoft J, Gutiérrez F, Brinkman K, Kitchen M, Ostergaard L, Leon A, Ristola M, Jessen H, Stellbrink HJ, Phillips AN, Lundgren J. Risk of HIV transmission through condomless sex in serodifferent gay couples with the HIV-positive partner taking suppressive antiretroviral therapy (PARTNER): final results of a multicentre, prospective, observational study. Lancet 2019; 393:2428-2438. [PMID: 31056293 PMCID: PMC6584382 DOI: 10.1016/s0140-6736(19)30418-0] [Citation(s) in RCA: 527] [Impact Index Per Article: 105.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/09/2019] [Accepted: 02/14/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND The level of evidence for HIV transmission risk through condomless sex in serodifferent gay couples with the HIV-positive partner taking virally suppressive antiretroviral therapy (ART) is limited compared with the evidence available for transmission risk in heterosexual couples. The aim of the second phase of the PARTNER study (PARTNER2) was to provide precise estimates of transmission risk in gay serodifferent partnerships. METHODS The PARTNER study was a prospective observational study done at 75 sites in 14 European countries. The first phase of the study (PARTNER1; Sept 15, 2010, to May 31, 2014) recruited and followed up both heterosexual and gay serodifferent couples (HIV-positive partner taking suppressive ART) who reported condomless sex, whereas the PARTNER2 extension (to April 30, 2018) recruited and followed up gay couples only. At study visits, data collection included sexual behaviour questionnaires, HIV testing (HIV-negative partner), and HIV-1 viral load testing (HIV-positive partner). If a seroconversion occurred in the HIV-negative partner, anonymised phylogenetic analysis was done to compare HIV-1 pol and env sequences in both partners to identify linked transmissions. Couple-years of follow-up were eligible for inclusion if condomless sex was reported, use of pre-exposure prophylaxis or post-exposure prophylaxis was not reported by the HIV-negative partner, and the HIV-positive partner was virally suppressed (plasma HIV-1 RNA <200 copies per mL) at the most recent visit (within the past year). Incidence rate of HIV transmission was calculated as the number of phylogenetically linked HIV infections that occurred during eligible couple-years of follow-up divided by eligible couple-years of follow-up. Two-sided 95% CIs for the incidence rate of transmission were calculated using exact Poisson methods. FINDINGS Between Sept 15, 2010, and July 31, 2017, 972 gay couples were enrolled, of which 782 provided 1593 eligible couple-years of follow-up with a median follow-up of 2·0 years (IQR 1·1-3·5). At baseline, median age for HIV-positive partners was 40 years (IQR 33-46) and couples reported condomless sex for a median of 1·0 years (IQR 0·4-2·9). During eligible couple-years of follow-up, couples reported condomless anal sex a total of 76 088 times. 288 (37%) of 777 HIV-negative men reported condomless sex with other partners. 15 new HIV infections occurred during eligible couple-years of follow-up, but none were phylogenetically linked within-couple transmissions, resulting in an HIV transmission rate of zero (upper 95% CI 0·23 per 100 couple-years of follow-up). INTERPRETATION Our results provide a similar level of evidence on viral suppression and HIV transmission risk for gay men to that previously generated for heterosexual couples and suggest that the risk of HIV transmission in gay couples through condomless sex when HIV viral load is suppressed is effectively zero. Our findings support the message of the U=U (undetectable equals untransmittable) campaign, and the benefits of early testing and treatment for HIV. FUNDING National Institute for Health Research.
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Affiliation(s)
- Alison J Rodger
- Institute for Global Health, University College London, London, UK.
| | | | - Tina Bruun
- Department of Infectious Diseases (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Pietro Vernazza
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital, St Gallen, Switzerland
| | | | - Olaf Degen
- University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | | | - Vicente Estrada
- Hospital Clinico San Carlos and Universidad Complutense, Madrid, Spain
| | - Anna Maria Geretti
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Apostolos Beloukas
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Department of Biomedical Sciences, University of West Attica, Athens, Greece
| | - Dorthe Raben
- Department of Infectious Diseases (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Pep Coll
- AIDS Research Institute-IrsiCaixa, Hospital Universitari Germans Trias i Pujol and BCN Checkpoint, Badalona and Barcelona, Spain
| | - Andrea Antinori
- Istituto Nazionale per le Malattie Infettive Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Nneka Nwokolo
- Chelsea and Westminster NHS Foundation Trust, London, UK
| | | | - Jan M Prins
- Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | | | - Rainer Weber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Norbert H Brockmeyer
- Centre for Sexual Health and Medicine, Walk in Ruhr, Ruhr University Bochum, Bochum, Germany
| | - Amanda Clarke
- Brighton and Sussex University Hospitals NHS Trust, and Brighton and Sussex Medical School, Brighton, UK
| | | | - Francois Raffi
- Infectious Diseases Department, University Hospital (Centre Hospitalier Universitaire de Nantes) Hotel-Dieu, and INSERM UIC 1413 Nantes University, Nantes, France
| | - Johannes R Bogner
- Medizinische Klinik und Poliklinik IV, University Hospital Munich, Munich, Germany
| | - Gilles Wandeler
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Felix Gutiérrez
- Hospital General de Elche and Universidad Miguel Hernández, Alicante, Spain
| | - Kees Brinkman
- Onze Lieve Vrouwe Gasthuis (OLVG), Amsterdam, Netherlands
| | | | | | - Agathe Leon
- Hospital Clinic - IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Matti Ristola
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | | | | | | | - Jens Lundgren
- Department of Infectious Diseases (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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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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Beloukas A, King S, Childs K, Papadimitropoulos A, Hopkins M, Atkins M, Agarwal K, Nelson M, Geretti A. Detection of the NS3 Q80K polymorphism by Sanger and deep sequencing in hepatitis C virus genotype 1a strains in the UK. Clin Microbiol Infect 2015; 21:1033-9. [DOI: 10.1016/j.cmi.2015.07.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/14/2015] [Accepted: 07/19/2015] [Indexed: 01/27/2023]
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Matthews PC, Beloukas A, Malik A, Carlson JM, Jooste P, Ogwu A, Shapiro R, Riddell L, Chen F, Luzzi G, Jaggernath M, Jesuthasan G, Jeffery K, Ndung’u T, Goulder PJR, Geretti AM, Klenerman P. Prevalence and Characteristics of Hepatitis B Virus (HBV) Coinfection among HIV-Positive Women in South Africa and Botswana. PLoS One 2015. [PMID: 26218239 PMCID: PMC4517770 DOI: 10.1371/journal.pone.0134037] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
There is progressive concern about the evolving burden of morbidity and mortality caused by coinfection with HIV-1 and hepatitis B virus (HBV) in sub-Saharan Africa, but the epidemiology and impact of this problem are not well defined. We therefore set out to assimilate more information about the nature of HBV/HIV coinfection in this region by undertaking a retrospective observational study of southern African adult women. We used samples from previously recruited HIV-1 positive women attending antenatal clinics in three settings in South Africa and Botswana (n = 950) and added a small cohort of HIV-negative antenatal South African women for comparison (n = 72). We tested for HBsAg and followed up HBsAg-positive samples by testing for HBeAg, HBV DNA, HBV genotype, presence of drug-resistance associated mutations (RAMs) and HDV. We identified HBsAg in 72 individuals (7% of the whole cohort), of whom 27% were HBeAg-positive, and the majority HBV genotypes A1 and A2. We did not detect any HDV coinfection. HBV prevalence was significantly different between geographically distinct cohorts, but did not differ according to HIV status. Among adults from South Africa, HBV/HIV coinfected patients had lower CD4+ T cell counts compared to those with HIV-monoinfection (p = 0.02), but this finding was not replicated in the cohort from Botswana. Overall, these data provide a snapshot of the coinfection problem at the heart of the HIV/HBV co-epidemic, and are important to inform public health policy, resource allocation, education, surveillance and clinical care.
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Affiliation(s)
- Philippa C. Matthews
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- * E-mail:
| | - Apostolos Beloukas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Amna Malik
- Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Jonathan M. Carlson
- Microsoft Research, eScience Group, Redmond, Washington, United States of America
| | - Pieter Jooste
- Paediatric Department, Kimberley Hospital, Kimberley, Northern Cape, South Africa
| | - Anthony Ogwu
- Botswana Harvard AIDS Institute Partnership, Botswana
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Botswana
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Lynn Riddell
- Integrated Sexual Health Services, Northampton General Hospital, Cliftonville, Northampton, United Kingdom
| | - Fabian Chen
- Department of Sexual Health, Royal Berkshire Hospital, Reading, United Kingdom
| | - Graz Luzzi
- Department of Sexual Health, High Wycombe Hospital, High Wycombe, Buckinghamshire, United Kingdom
| | - Manjeetha Jaggernath
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Gerald Jesuthasan
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Katie Jeffery
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), University of KwaZulu-Natal, Durban, South Africa
- Max Planck Institute for Infection Biology, Chariteplatz, Berlin, Germany
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, Massachusetts, United States of America
| | - Philip J. R. Goulder
- Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Anna Maria Geretti
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- NIHR Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Headington, Oxford, United Kingdom
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Vrancken B, Rambaut A, Suchard MA, Drummond A, Baele G, Derdelinckx I, Van Wijngaerden E, Vandamme AM, Van Laethem K, Lemey P. The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates. PLoS Comput Biol 2014; 10:e1003505. [PMID: 24699231 PMCID: PMC3974631 DOI: 10.1371/journal.pcbi.1003505] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/15/2014] [Indexed: 11/23/2022] Open
Abstract
Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the ‘store and retrieve’ hypothesis positing that viruses stored early in latently infected cells preferentially transmit or establish new infections upon reactivation. Since its discovery three decades ago, the HIV epidemic has unfolded into one of the most devastating pandemics in human history. When HIV replication cannot be completely inhibited, the fast-evolving retrovirus continuously evades intra-host immune and drug selective pressure, but diversifies according to more neutral epidemiological dynamics at the interhost level. Limited evidence suggests that the virus may evolve faster in a single host than in a population of hosts, and various hypotheses have been put forward to explain this phenomenon. Here, we develop a new computational approach aimed at integrating host transmission information with pathogen genealogical reconstructions. We apply this approach to comprehensive sequence data sets sampled from a large HIV-1 subtype C transmission chain, and in addition to providing several insights into the reconstruction of HIV-1 transmissions histories and its associated population dynamics, we find that transmission decreases the HIV-1 evolutionary rate. The fact that we also identify this decline for substitutions that do not alter amino acid substitutions provides evidence against hypotheses that invoke selection forces. Instead, our findings support earlier reports that new infections start preferentially with less evolved variants, which may be stored in latently infected cells, and this may vary among different HIV-1 subtypes.
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Affiliation(s)
- Bram Vrancken
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- * E-mail:
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles Los Angeles, California, United States of America
| | - Alexei Drummond
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | | | | | - Anne-Mieke Vandamme
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Centro de Malária e Outras Doenças Tropicais Instituto de Higiene e Medicina Tropical and Unidade de Microbiologia, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Kristel Van Laethem
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
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