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Wang Y, Wang D, Zhang L, Sun W, Zhang Z, Chen W, Zhu A, Huang Y, Xiao F, Yao J, Gan M, Li F, Luo L, Huang X, Zhang Y, Wong SS, Cheng X, Ji J, Ou Z, Xiao M, Li M, Li J, Ren P, Deng Z, Zhong H, Xu X, Song T, Mok CKP, Peiris M, Zhong N, Zhao J, Li Y, Li J, Zhao J. Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients. Genome Med 2021; 13:30. [PMID: 33618765 PMCID: PMC7898256 DOI: 10.1186/s13073-021-00847-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/05/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Since early February 2021, the causative agent of COVID-19, SARS-CoV-2, has infected over 104 million people with more than 2 million deaths according to official reports. The key to understanding the biology and virus-host interactions of SARS-CoV-2 requires the knowledge of mutation and evolution of this virus at both inter- and intra-host levels. However, despite quite a few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and their evolutionary dynamics remain mostly unknown. METHODS Using high-throughput sequencing of metatranscriptomic and hybrid captured libraries, we characterized consensus genomes and intra-host single nucleotide variations (iSNVs) of serial samples collected from eight patients with COVID-19. The distribution of iSNVs along the SARS-CoV-2 genome was analyzed and co-occurring iSNVs among COVID-19 patients were identified. We also compared the evolutionary dynamics of SARS-CoV-2 population in the respiratory tract (RT) and gastrointestinal tract (GIT). RESULTS The 32 consensus genomes revealed the co-existence of different genotypes within the same patient. We further identified 40 intra-host single nucleotide variants (iSNVs). Most (30/40) iSNVs presented in a single patient, while ten iSNVs were found in at least two patients or identical to consensus variants. Comparing allele frequencies of the iSNVs revealed a clear genetic differentiation between intra-host populations from the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events during intra-host migrations. Compared to RT populations, the GIT populations showed a better maintenance and rapid development of viral genetic diversity following the suspected intra-host bottlenecks. CONCLUSIONS Our findings here illustrate the intra-host bottlenecks and evolutionary dynamics of SARS-CoV-2 in different anatomic sites and may provide new insights to understand the virus-host interactions of coronaviruses and other RNA viruses.
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Affiliation(s)
- Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Daxi Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Lu Zhang
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, 510060, Guangdong, China
| | - Wanying Sun
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Weijun Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen, Shenzhen, 518083, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Yongbo Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Fei Xiao
- Department of Infectious Diseases, Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong, China
| | - Jinxiu Yao
- Yangjiang People's Hospital, Yangjiang, Guangdong, China
| | - Mian Gan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Fang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Ling Luo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Xiaofang Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Sook-San Wong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Xinyi Cheng
- BGI-Shenzhen, Shenzhen, 518083, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jingkai Ji
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Zhihua Ou
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Minfeng Xiao
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Min Li
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Jiandong Li
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Peidi Ren
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ziqing Deng
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huanzi Zhong
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Tie Song
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, Guangdong, China
| | - Chris Ka Pun Mok
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
- The HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, 19406, China
| | - Malik Peiris
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
- The HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, 19406, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
| | - Yimin Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
| | - Junhua Li
- BGI-Shenzhen, Shenzhen, 518083, China.
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China.
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, 510060, Guangdong, China.
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2
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Alroy-Preis S, Daly ER, Adamski C, Dionne-Odom J, Talbot EA, Gao F, Cavallo SJ, Hansen K, Mahoney JC, Metcalf E, Loring C, Bean C, Drobeniuc J, Xia GL, Kamili S, Montero JT. Large Outbreak of Hepatitis C Virus Associated With Drug Diversion by a Healthcare Technician. Clin Infect Dis 2019; 67:845-853. [PMID: 29767683 DOI: 10.1093/cid/ciy193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/27/2018] [Indexed: 12/16/2022] Open
Abstract
Background In May 2012, the New Hampshire (NH) Division of Public Health Services (DPHS) was notified of 4 persons with newly diagnosed hepatitis C virus (HCV) infection at hospital X. Initial investigation suggested a common link to the hospital cardiac catheterization laboratory (CCL) because the infected persons included 3 CCL patients and a CCL technician. NH DPHS initiated an investigation to determine the source and control the outbreak. Methods NH DPHS conducted site visits, case patient and employee interviews, medical record and medication use review, and employee and patient HCV testing using enzyme immunoassay for anti-HCV, reverse-transcription polymerase chain reaction for HCV RNA, nonstructural 5B (NS5B) and hypervariable region 1 (HVR1) sequencing, and quasispecies analysis. Results HCV HVR1 analysis of the first 4 cases confirmed a common source of infection. HCV testing identified 32 of 1074 CCL patients infected with the outbreak strain, including 3 patients coinfected with >1 HCV strain. The epidemiologic investigation revealed evidence of drug diversion by the HCV-infected technician, evidenced by gaps in controlled medication control, higher fentanyl use during procedures for confirmed cases, and building card key access records documenting the presence of the technician during days when transmission occurred. The employee's status as a traveling technician led to a multistate investigation, which identified additional cases at prior employment sites. Conclusions This is the largest laboratory-confirmed drug diversion-associated HCV outbreak published to date. Recommendations to reduce drug diversion risk and to conduct outbreak investigations are provided.
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Affiliation(s)
- Sharon Alroy-Preis
- New Hampshire Department of Health and Human Services, Division of Public Health Services, Concord
| | - Elizabeth R Daly
- New Hampshire Department of Health and Human Services, Division of Public Health Services, Concord
| | - Christine Adamski
- New Hampshire Department of Health and Human Services, Division of Public Health Services, Concord
| | - Jodie Dionne-Odom
- New Hampshire Department of Health and Human Services, Division of Public Health Services, Concord.,Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Elizabeth A Talbot
- New Hampshire Department of Health and Human Services, Division of Public Health Services, Concord.,Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Fengxiang Gao
- New Hampshire Department of Health and Human Services, Division of Public Health Services, Concord
| | - Steffany J Cavallo
- New Hampshire Department of Health and Human Services, Division of Public Health Services, Concord
| | - Katrina Hansen
- New Hampshire Department of Health and Human Services, Division of Public Health Services, Concord
| | - Jennifer C Mahoney
- New Hampshire Department of Health and Human Services, Division of Public Health Services, Concord
| | - Erin Metcalf
- New Hampshire Department of Health and Human Services, Division of Public Health Services, Concord
| | - Carol Loring
- New Hampshire Department of Health and Human Services, Division of Public Health Services, Concord
| | - Christine Bean
- New Hampshire Department of Health and Human Services, Division of Public Health Services, Concord
| | - Jan Drobeniuc
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Guo-Liang Xia
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Saleem Kamili
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - José T Montero
- New Hampshire Department of Health and Human Services, Division of Public Health Services, Concord
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3
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Fernández-Caso B, Fernández-Caballero JÁ, Chueca N, Rojo E, de Salazar A, García Buey L, Cardeñoso L, García F. Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing. Sci Rep 2019; 9:9264. [PMID: 31239457 PMCID: PMC6592891 DOI: 10.1038/s41598-019-42605-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 04/01/2019] [Indexed: 12/21/2022] Open
Abstract
Current HCV genotyping methods may have some limitations in detecting mixed infections. We aimed to determine the accuracy of genotyping and the detection of mixed-genotype infections using the Abbott-RealTime HCV Genotype II assay (Abbott-RT-PCR) in comparison with a Roche-Next Generation Sequencing assay (Roche-NGS). Plasma samples collected from 139 HCV-infected patients tested with Abbott-RT-PCR, 114 with single genotype (GT) and 25 with mixed GTs were genotyped using Roche-NGS. Roche-NGS confirmed all single GTs obtained with Abbott-RT-PCR. One case of Abbott GT 4 was found as GT 1a using Roche-NGS. Genotype 5 was confirmed using Roche-NGS in 75% cases (3 out of 4 cases). Twenty-five patients were identified as having mixed HCVinfections using Abbott-RT-PCR. The concordance between Abbott-RT-PCR and Roche-NGS was 76% (19 out of 25 cases). Three mixed-GT infections identified with the Abbott assay (two (1b + 4); one (1a + 3)) were reported as pure 1b using Roche-NGS. Very divergent results were found for the other three samples. When compared to Roche-NGS, Abbott-RT-PCR has performed excellently for the determination of patients infected with single GTs. For patients that are categorized as having a mixed infection using Abbott-RT-PCR, we recommend an NGS assay as a confirmation test.
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Affiliation(s)
- Belén Fernández-Caso
- Servicio de Microbiologia, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria La Princesa, Madrid, Spain
| | - Jose Ángel Fernández-Caballero
- Unidad de Gestión Clinica de Microbiologia, Hospital Universitario San Cecilio; Instituto de Investigación Biosanitaria ibs.Granada; Red de Investigación en SIDA, RD16/0025/0040, Granada, Spain
| | - Natalia Chueca
- Unidad de Gestión Clinica de Microbiologia, Hospital Universitario San Cecilio; Instituto de Investigación Biosanitaria ibs.Granada; Red de Investigación en SIDA, RD16/0025/0040, Granada, Spain
| | - Eukene Rojo
- Servicio de Aparato Digestivo - Unidad de Hepatologia, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria La Princesa, Madrid, Spain
| | - Adolfo de Salazar
- Unidad de Gestión Clinica de Microbiologia, Hospital Universitario San Cecilio; Instituto de Investigación Biosanitaria ibs.Granada; Red de Investigación en SIDA, RD16/0025/0040, Granada, Spain
| | - Luisa García Buey
- Servicio de Aparato Digestivo - Unidad de Hepatologia, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria La Princesa, Madrid, Spain
| | - Laura Cardeñoso
- Servicio de Microbiologia, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria La Princesa, Madrid, Spain
| | - Federico García
- Unidad de Gestión Clinica de Microbiologia, Hospital Universitario San Cecilio; Instituto de Investigación Biosanitaria ibs.Granada; Red de Investigación en SIDA, RD16/0025/0040, Granada, Spain.
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4
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Nguyen DB, Bixler D, Patel PR. Transmission of hepatitis C virus in the dialysis setting and strategies for its prevention. Semin Dial 2018; 32:127-134. [PMID: 30569604 DOI: 10.1111/sdi.12761] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Hepatitis C virus (HCV) infection is more common among hemodialysis patients than the general population and transmission of HCV in dialysis clinics has been reported. In the context of the increased morbidity and mortality associated with HCV infection in the end stage renal disease population, it is important that dialysis clinics have processes in place for ensuring recommended infection control practices, including Standard Precautions, through regular audits and training of the staff. This review will summarize the epidemiology of HCV infection and risk factors for HCV transmission among hemodialysis patients. In addition, the proper protocols are required to investigate suspected cases of HCV transmission in dialysis facilities and recommendations for prevention of HCV transmission in will be reviewed.
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Affiliation(s)
- Duc B Nguyen
- Centers for Diseases Control and Prevention, Atlanta, Georgia
| | - Danae Bixler
- Centers for Diseases Control and Prevention, Atlanta, Georgia
| | - Priti R Patel
- Centers for Diseases Control and Prevention, Atlanta, Georgia
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5
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Paboriboune P, Vial T, Sitbounlang P, Bertani S, Trépo C, Dény P, Babin FX, Steenkeste N, Pineau P, Deharo E. Hepatitis C in Laos: A 7-Year Retrospective Study on 1765 Patients. Virol Sin 2018; 33:295-303. [PMID: 29948850 DOI: 10.1007/s12250-018-0039-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 05/25/2018] [Indexed: 12/29/2022] Open
Abstract
Hepatitis C virus (HCV) is a global health concern, notably in Southeast Asia, and in Laos the presentation of the HCV-induced liver disease is poorly known. Our objective was thus to describe a comprehensive HCV infection pattern in order to guide national health policies. A study on a group of 1765 patients formerly diagnosed by rapid test in health centres was conducted at the Centre of Infectiology Lao Christophe Merieux in Vientiane. The demographic information of patients, their infection status (viral load: VL), liver function (aminotransferases) and treatments were analysed. Results showed that gender distribution of infected people was balanced; with median ages of 53.8 for men and 51.6 years for women (13-86 years). The majority of patients (72%) were confirmed positive (VL > 50 IU/mL) and 28% of them had high VL (> 6log10). About 23% of patients had level of aminotransferases indicative of liver damage (> 40 IU/mL); but less than 20% of patients received treatment. Patients rarely received a second sampling or medical imaging. The survey also showed that cycloferon, pegylated interferon and ribavirin were the drugs prescribed preferentially by the medical staff, without following any international recommendations schemes. In conclusion, we recommend that a population screening policy and better management of patients should be urgently implemented in the country, respecting official guidelines. However, the cost of biological analysis and treatment are significant barriers that must be removed. Public health resolutions should be immediately enforced in the perspective of meeting the WHO HCV elimination deadline by 2030.
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Affiliation(s)
| | - Thomas Vial
- UMR 152 PHARMADEV, IRD, Université de Toulouse, UPS, 31062, Toulouse, France
| | | | - Stéphane Bertani
- UMR 152 PHARMADEV, IRD, Université de Toulouse, UPS, 31062, Toulouse, France
| | - Christian Trépo
- INSERM U1052, CNRS, UMR 5286, Cancer Research Centre of Lyon, 69008, Lyon, France
| | - Paul Dény
- INSERM U1052, CNRS, UMR 5286, Cancer Research Centre of Lyon, 69008, Lyon, France.,Université Paris 13, Sorbonne Paris Cité, Hôpitaux Universitaires Paris Seine Saint Denis, 93000, Bobigny, France
| | | | | | - Pascal Pineau
- INSERM U993, Institut Pasteur Unité "Organisation Nucléaire et Oncogenèse", 75015, Paris, France
| | - Eric Deharo
- UMR 152 PHARMADEV, IRD, Université de Toulouse, UPS, 31062, Toulouse, France.
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6
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Gaivão M, Dionisio F, Gjini E. Transmission Fitness in Co-colonization and the Persistence of Bacterial Pathogens. Bull Math Biol 2017; 79:2068-2087. [PMID: 28741105 DOI: 10.1007/s11538-017-0320-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 07/03/2017] [Indexed: 01/18/2023]
Abstract
Humans are often colonized by polymorphic bacteria such as Streptococcus pneumoniae, Bordetella pertussis, Staphylococcus Aureus, and Haemophilus influenzae. Two co-colonizing pathogen clones may interact with each other upon host entry and during within-host dynamics, ranging from competition to facilitation. Here we examine the significance of these exploitation strategies for bacterial spread and persistence in host populations. We model SIS epidemiological dynamics to capture the global behavior of such multi-strain systems, focusing on different parameters of single and dual colonization. We analyze the impact of heterogeneity in clearance and transmission rates of single and dual colonization and find the criteria under which these asymmetries enhance endemic persistence. We obtain a backward bifurcation near [Formula: see text] if the reproductive value of the parasite in dually infected hosts is sufficiently higher than that in singly infected ones. In such cases, the parasite is able to persist even in sub-threshold conditions, and reducing the basic reproduction number below 1 would be insufficient for elimination. The fitness superiority in co-colonized hosts can be attained by lowering net parasite clearance rate ([Formula: see text]), by increasing transmission rate ([Formula: see text]), or both, and coupling between these traits critically constrains opportunities of pathogen survival in the [Formula: see text] regime. Finally, using an adaptive dynamics approach, we verify that despite their importance for sub-threshold endemicity, traits expressed exclusively in coinfection should generally evolve independently of single infection traits. In particular, for [Formula: see text] a saturating parabolic or hyperbolic function of [Formula: see text], co-colonization traits evolve to an intermediate optimum (evolutionarily stable strategy, ESS), determined only by host lifespan and the trade-off parameters linking [Formula: see text] and [Formula: see text]. Our study invites more empirical attention to the dynamics and evolution of parasite life-history traits expressed exclusively in coinfection.
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Affiliation(s)
- Maria Gaivão
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.,Departamento de Informática, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Francisco Dionisio
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.,CE3C - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Erida Gjini
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.
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7
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Characterization of Hepatitis C Virus (HCV) Envelope Diversification from Acute to Chronic Infection within a Sexually Transmitted HCV Cluster by Using Single-Molecule, Real-Time Sequencing. J Virol 2017; 91:JVI.02262-16. [PMID: 28077634 DOI: 10.1128/jvi.02262-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 12/29/2016] [Indexed: 12/18/2022] Open
Abstract
In contrast to other available next-generation sequencing platforms, PacBio single-molecule, real-time (SMRT) sequencing has the advantage of generating long reads albeit with a relatively higher error rate in unprocessed data. Using this platform, we longitudinally sampled and sequenced the hepatitis C virus (HCV) envelope genome region (1,680 nucleotides [nt]) from individuals belonging to a cluster of sexually transmitted cases. All five subjects were coinfected with HIV-1 and a closely related strain of HCV genotype 4d. In total, 50 samples were analyzed by using SMRT sequencing. By using 7 passes of circular consensus sequencing, the error rate was reduced to 0.37%, and the median number of sequences was 612 per sample. A further reduction of insertions was achieved by alignment against a sample-specific reference sequence. However, in vitro recombination during PCR amplification could not be excluded. Phylogenetic analysis supported close relationships among HCV sequences from the four male subjects and subsequent transmission from one subject to his female partner. Transmission was characterized by a strong genetic bottleneck. Viral genetic diversity was low during acute infection and increased upon progression to chronicity but subsequently fluctuated during chronic infection, caused by the alternate detection of distinct coexisting lineages. SMRT sequencing combines long reads with sufficient depth for many phylogenetic analyses and can therefore provide insights into within-host HCV evolutionary dynamics without the need for haplotype reconstruction using statistical algorithms.IMPORTANCE Next-generation sequencing has revolutionized the study of genetically variable RNA virus populations, but for phylogenetic and evolutionary analyses, longer sequences than those generated by most available platforms, while minimizing the intrinsic error rate, are desired. Here, we demonstrate for the first time that PacBio SMRT sequencing technology can be used to generate full-length HCV envelope sequences at the single-molecule level, providing a data set with large sequencing depth for the characterization of intrahost viral dynamics. The selection of consensus reads derived from at least 7 full circular consensus sequencing rounds significantly reduced the intrinsic high error rate of this method. We used this method to genetically characterize a unique transmission cluster of sexually transmitted HCV infections, providing insight into the distinct evolutionary pathways in each patient over time and identifying the transmission-associated genetic bottleneck as well as fluctuations in viral genetic diversity over time, accompanied by dynamic shifts in viral subpopulations.
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8
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Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes. J Clin Microbiol 2016; 54:2470-84. [PMID: 27385709 PMCID: PMC5035407 DOI: 10.1128/jcm.00330-16] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/28/2016] [Indexed: 12/14/2022] Open
Abstract
Affordable next-generation sequencing (NGS) technologies for hepatitis C virus (HCV) may potentially identify both viral genotype and resistance genetic motifs in the era of directly acting antiviral (DAA) therapies. This study compared the ability of high-throughput NGS methods to generate full-length, deep, HCV sequence data sets and evaluated their utility for diagnostics and clinical assessment. NGS methods using (i) unselected HCV RNA (metagenomics), (ii) preenrichment of HCV RNA by probe capture, and (iii) HCV preamplification by PCR implemented in four United Kingdom centers were compared. Metrics of sequence coverage and depth, quasispecies diversity, and detection of DAA resistance-associated variants (RAVs), mixed HCV genotypes, and other coinfections were compared using a panel of samples with different viral loads, genotypes, and mixed HCV genotypes/subtypes [geno(sub)types]. Each NGS method generated near-complete genome sequences from more than 90% of samples. Enrichment methods and PCR preamplification generated greater sequence depth and were more effective for samples with low viral loads. All NGS methodologies accurately identified mixed HCV genotype infections. Consensus sequences generated by different NGS methods were generally concordant, and majority RAVs were consistently detected. However, methods differed in their ability to detect minor populations of RAVs. Metagenomic methods identified human pegivirus coinfections. NGS provided a rapid, inexpensive method for generating whole HCV genomes to define infecting genotypes, RAVs, comprehensive viral strain analysis, and quasispecies diversity. Enrichment methods are particularly suited for high-throughput analysis while providing the genotype and information on potential DAA resistance.
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9
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Li H, Stoddard MB, Wang S, Giorgi EE, Blair LM, Learn GH, Hahn BH, Alter HJ, Busch MP, Fierer DS, Ribeiro RM, Perelson AS, Bhattacharya T, Shaw GM. Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification. J Virol 2016; 90:152-66. [PMID: 26468546 PMCID: PMC4702571 DOI: 10.1128/jvi.02156-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/02/2015] [Indexed: 01/06/2023] Open
Abstract
UNLABELLED Despite the recent development of highly effective anti-hepatitis C virus (HCV) drugs, the global burden of this pathogen remains immense. Control or eradication of HCV will likely require the broad application of antiviral drugs and development of an effective vaccine. A precise molecular identification of transmitted/founder (T/F) HCV genomes that lead to productive clinical infection could play a critical role in vaccine research, as it has for HIV-1. However, the replication schema of these two RNA viruses differ substantially, as do viral responses to innate and adaptive host defenses. These differences raise questions as to the certainty of T/F HCV genome inferences, particularly in cases where multiple closely related sequence lineages have been observed. To clarify these issues and distinguish between competing models of early HCV diversification, we examined seven cases of acute HCV infection in humans and chimpanzees, including three examples of virus transmission between linked donors and recipients. Using single-genome sequencing (SGS) of plasma vRNA, we found that inferred T/F sequences in recipients were identical to viral sequences in their respective donors. Early in infection, HCV genomes generally evolved according to a simple model of random evolution where the coalescent corresponded to the T/F sequence. Closely related sequence lineages could be explained by high multiplicity infection from a donor whose viral sequences had undergone a pretransmission bottleneck due to treatment, immune selection, or recent infection. These findings validate SGS, together with mathematical modeling and phylogenetic analysis, as a novel strategy to infer T/F HCV genome sequences. IMPORTANCE Despite the recent development of highly effective, interferon-sparing anti-hepatitis C virus (HCV) drugs, the global burden of this pathogen remains immense. Control or eradication of HCV will likely require the broad application of antiviral drugs and the development of an effective vaccine, which could be facilitated by a precise molecular identification of transmitted/founder (T/F) viral genomes and their progeny. We used single-genome sequencing to show that inferred HCV T/F sequences in recipients were identical to viral sequences in their respective donors and that viral genomes generally evolved early in infection according to a simple model of random sequence evolution. Altogether, the findings validate T/F genome inferences and illustrate how T/F sequence identification can illuminate studies of HCV transmission, immunopathogenesis, drug resistance development, and vaccine protection, including sieving effects on breakthrough virus strains.
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Affiliation(s)
- Hui Li
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mark B Stoddard
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shuyi Wang
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elena E Giorgi
- T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Lily M Blair
- T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA Department of Biology, Stanford University, Stanford, California, USA
| | - Gerald H Learn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Harvey J Alter
- Department of Transfusion Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael P Busch
- Blood Systems Research Institute, University of California San Francisco, San Francisco, California, USA
| | - Daniel S Fierer
- Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ruy M Ribeiro
- T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Tanmoy Bhattacharya
- T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA Santa Fe Institute, Santa Fe, New Mexico, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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10
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Tarr AW, Khera T, Hueging K, Sheldon J, Steinmann E, Pietschmann T, Brown RJP. Genetic Diversity Underlying the Envelope Glycoproteins of Hepatitis C Virus: Structural and Functional Consequences and the Implications for Vaccine Design. Viruses 2015; 7:3995-4046. [PMID: 26193307 PMCID: PMC4517138 DOI: 10.3390/v7072809] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/19/2015] [Accepted: 07/08/2015] [Indexed: 12/13/2022] Open
Abstract
In the 26 years since the discovery of Hepatitis C virus (HCV) a major global research effort has illuminated many aspects of the viral life cycle, facilitating the development of targeted antivirals. Recently, effective direct-acting antiviral (DAA) regimens with >90% cure rates have become available for treatment of chronic HCV infection in developed nations, representing a significant advance towards global eradication. However, the high cost of these treatments results in highly restricted access in developing nations, where the disease burden is greatest. Additionally, the largely asymptomatic nature of infection facilitates continued transmission in at risk groups and resource constrained settings due to limited surveillance. Consequently a prophylactic vaccine is much needed. The HCV envelope glycoproteins E1 and E2 are located on the surface of viral lipid envelope, facilitate viral entry and are the targets for host immunity, in addition to other functions. Unfortunately, the extreme global genetic and antigenic diversity exhibited by the HCV glycoproteins represents a significant obstacle to vaccine development. Here we review current knowledge of HCV envelope protein structure, integrating knowledge of genetic, antigenic and functional diversity to inform rational immunogen design.
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Affiliation(s)
- Alexander W Tarr
- School of Life Sciences, Nottingham Digestive Diseases Biomedical Research Unit, University of Nottingham, Nottingham NG7 2RD, UK.
| | - Tanvi Khera
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centrefor Infection Research (HZI), Hannover D-30625, Germany.
| | - Kathrin Hueging
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centrefor Infection Research (HZI), Hannover D-30625, Germany.
| | - Julie Sheldon
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centrefor Infection Research (HZI), Hannover D-30625, Germany.
| | - Eike Steinmann
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centrefor Infection Research (HZI), Hannover D-30625, Germany.
| | - Thomas Pietschmann
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centrefor Infection Research (HZI), Hannover D-30625, Germany.
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig 38124, Germany.
| | - Richard J P Brown
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centrefor Infection Research (HZI), Hannover D-30625, Germany.
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11
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Modeling the effect of HIV coinfection on clearance and sustained virologic response during treatment for hepatitis C virus. Epidemics 2015; 12:1-10. [PMID: 26342237 DOI: 10.1016/j.epidem.2015.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 04/18/2015] [Accepted: 04/20/2015] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND HIV/hepatitis C (HCV) coinfection is a major concern in global health today. Each pathogen can exacerbate the effects of the other and affect treatment outcomes. Understanding the within-host dynamics of these coinfecting pathogens is crucial, particularly in light of new, direct-acting antiviral agents (DAAs) for HCV treatment that are becoming available. METHODS AND FINDINGS In this study, we construct a within-host mathematical model of HCV/HIV coinfection by adapting a previously published model of HCV monoinfection to include an immune system component in infection clearance. We explore the effect of HIV-coinfection on spontaneous HCV clearance and sustained virologic response (SVR) by building in decreased immune function with increased HIV viral load. Treatment is modeled by modifying HCV burst-size, and we use clinically-relevant parameter estimates. Our model replicates real-world patient outcomes; it outputs infected and uninfected target cell counts, and HCV viral load for varying treatment and coinfection scenarios. Increased HIV viral load and reduced CD4(+) count correlate with decreased spontaneous clearance and SVR chances. Treatment efficacy/duration combinations resulting in SVR are calculated for HIV-positive and negative patients, and crucially, we replicate the new findings that highly efficacious DAAs reduce treatment differences between HIV-positive and negative patients. However, we also find that if drug efficacy decays sufficiently over treatment course, SVR differences between HIV-positive and negative patients reappear. CONCLUSIONS Our model shows theoretical evidence of the differing outcomes of HCV infection in cases where the immune system is compromised by HIV. Understanding what controls these outcomes is especially important with the advent of efficacious but often prohibitively expensive DAAs. Using a model to predict patient response can lend insight into optimal treatment design, both in helping to identify patients who might respond well to treatment and in helping to identify treatment pathways and pitfalls.
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12
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Hajarizadeh B, Grady B, Page K, Kim AY, McGovern BH, Cox AL, Rice TM, Sacks-Davis R, Bruneau J, Morris M, Amin J, Schinkel J, Applegate T, Maher L, Hellard M, Lloyd AR, Prins M, Dore GJ, Grebely J. Patterns of hepatitis C virus RNA levels during acute infection: the InC3 study. PLoS One 2015; 10:e0122232. [PMID: 25837807 PMCID: PMC4383375 DOI: 10.1371/journal.pone.0122232] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 02/10/2015] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Understanding the patterns of HCV RNA levels during acute hepatitis C virus (HCV) infection provides insights into immunopathogenesis and is important for vaccine design. This study evaluated patterns of HCV RNA levels and associated factors among individuals with acute infection. METHODS Data were from an international collaboration of nine prospective cohorts of acute HCV (InC3 Study). Participants with well-characterized acute HCV infection (detected within three months post-infection and interval between the peak and subsequent HCV RNA levels ≤ 120 days) were categorised by a priori-defined patterns of HCV RNA levels: i) spontaneous clearance, ii) partial viral control with persistence (≥ 1 log IU/mL decline in HCV RNA levels following peak) and iii) viral plateau with persistence (increase or <1 log IU/mL decline in HCV RNA levels following peak). Factors associated with HCV RNA patterns were assessed using multinomial logistic regression. RESULTS Among 643 individuals with acute HCV, 162 with well-characterized acute HCV were identified: spontaneous clearance (32%), partial viral control with persistence (27%), and viral plateau with persistence (41%). HCV RNA levels reached a high viraemic phase within two months following infection, with higher levels in the spontaneous clearance and partial viral control groups, compared to the viral plateau group (median: 6.0, 6.2, 5.3 log IU/mL, respectively; P = 0.018). In the two groups with persistence, Interferon lambda 3 (IFNL3) CC genotype was independently associated with partial viral control compared to viral plateau (adjusted odds ratio [AOR]: 2.75; 95%CI: 1.08, 7.02). In the two groups with viral control, female sex was independently associated with spontaneous clearance compared to partial viral control (AOR: 2.86; 95%CI: 1.04, 7.83). CONCLUSIONS Among individuals with acute HCV, a spectrum of HCV RNA patterns is evident. IFNL3 CC genotype is associated with initial viral control, while female sex is associated with ultimate spontaneous clearance.
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Affiliation(s)
- Behzad Hajarizadeh
- The Kirby Institute, UNSW Australia (University of New South Wales), Sydney, NSW, Australia
| | - Bart Grady
- Cluster Infectious Diseases, GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Kimberly Page
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, United States of America
| | - Arthur Y. Kim
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Barbara H. McGovern
- Tufts Medical School, Boston, Massachusetts, United States of America
- Abbvie, Chicago, Illinois, United States of America
| | - Andrea L. Cox
- Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Thomas M. Rice
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, United States of America
| | - Rachel Sacks-Davis
- Burnet Institute, Melbourne, VIC, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia
| | - Julie Bruneau
- CRCHUM, Université de Montréal, Montreal, QC, Canada
| | - Meghan Morris
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, United States of America
| | - Janaki Amin
- The Kirby Institute, UNSW Australia (University of New South Wales), Sydney, NSW, Australia
| | | | - Tanya Applegate
- The Kirby Institute, UNSW Australia (University of New South Wales), Sydney, NSW, Australia
| | - Lisa Maher
- The Kirby Institute, UNSW Australia (University of New South Wales), Sydney, NSW, Australia
| | - Margaret Hellard
- Burnet Institute, Melbourne, VIC, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia
| | - Andrew R. Lloyd
- Inflammation and Infection Research Centre, School of Medical Sciences, UNSW Australia, Sydney, NSW, Australia
| | - Maria Prins
- Cluster Infectious Diseases, GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands
- Academic Medical Center, Amsterdam, The Netherlands
| | - Gregory J. Dore
- The Kirby Institute, UNSW Australia (University of New South Wales), Sydney, NSW, Australia
| | - Jason Grebely
- The Kirby Institute, UNSW Australia (University of New South Wales), Sydney, NSW, Australia
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13
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Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission. Nat Commun 2015; 6:6560. [PMID: 25814293 PMCID: PMC4389252 DOI: 10.1038/ncomms7560] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 02/06/2015] [Indexed: 12/18/2022] Open
Abstract
Genome sequencing is revolutionizing clinical microbiology and our understanding of infectious diseases. Previous studies have largely relied on the sequencing of a single isolate from each individual. However, it is not clear what degree of bacterial diversity exists within, and is transmitted between individuals. Understanding this ‘cloud of diversity’ is key to accurate identification of transmission pathways. Here, we report the deep sequencing of methicillin-resistant Staphylococcus aureus among staff and animal patients involved in a transmission network at a veterinary hospital. We demonstrate considerable within-host diversity and that within-host diversity may rise and fall over time. Isolates from invasive disease contained multiple mutations in the same genes, including inactivation of a global regulator of virulence and changes in phage copy number. This study highlights the need for sequencing of multiple isolates from individuals to gain an accurate picture of transmission networks and to further understand the basis of pathogenesis. Populations of bacterial pathogens can be diverse within colonized individuals. Here, the authors sequence the genomes of methicillin-resistant Staphylococcus aureus isolated from staff and animal patients at a veterinary hospital and show considerable within-host diversity that can rise and fall over time.
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14
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Identification, molecular cloning, and analysis of full-length hepatitis C virus transmitted/founder genotypes 1, 3, and 4. mBio 2015; 6:e02518. [PMID: 25714714 PMCID: PMC4358020 DOI: 10.1128/mbio.02518-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hepatitis C virus (HCV) infection is characterized by persistent replication of a complex mixture of viruses termed a “quasispecies.” Transmission is generally associated with a stringent population bottleneck characterized by infection by limited numbers of “transmitted/founder” (T/F) viruses. Characterization of T/F genomes of human immunodeficiency virus type 1 (HIV-1) has been integral to studies of transmission, immunopathogenesis, and vaccine development. Here, we describe the identification of complete T/F genomes of HCV by single-genome sequencing of plasma viral RNA from acutely infected subjects. A total of 2,739 single-genome-derived amplicons comprising 10,966,507 bp from 18 acute-phase and 11 chronically infected subjects were analyzed. Acute-phase sequences diversified essentially randomly, except for the poly(U/UC) tract, which was subject to polymerase slippage. Fourteen acute-phase subjects were productively infected by more than one genetically distinct virus, permitting assessment of recombination between replicating genomes. No evidence of recombination was found among 1,589 sequences analyzed. Envelope sequences of T/F genomes lacked transmission signatures that could distinguish them from chronic infection viruses. Among chronically infected subjects, higher nucleotide substitution rates were observed in the poly(U/UC) tract than in envelope hypervariable region 1. Fourteen full-length molecular clones with variable poly(U/UC) sequences corresponding to seven genotype 1a, 1b, 3a, and 4a T/F viruses were generated. Like most unadapted HCV clones, T/F genomes did not replicate efficiently in Huh 7.5 cells, indicating that additional cellular factors or viral adaptations are necessary for in vitro replication. Full-length T/F HCV genomes and their progeny provide unique insights into virus transmission, virus evolution, and virus-host interactions associated with immunopathogenesis. Hepatitis C virus (HCV) infects 2% to 3% of the world’s population and exhibits extraordinary genetic diversity. This diversity is mirrored by HIV-1, where characterization of transmitted/founder (T/F) genomes has been instrumental in studies of virus transmission, immunopathogenesis, and vaccine development. Here, we show that despite major differences in genome organization, replication strategy, and natural history, HCV (like HIV-1) diversifies essentially randomly early in infection, and as a consequence, sequences of actual T/F viruses can be identified. This allowed us to capture by molecular cloning the full-length HCV genomes that are responsible for infecting the first hepatocytes and eliciting the initial immune responses, weeks before these events could be directly analyzed in human subjects. These findings represent an enabling experimental strategy, not only for HCV and HIV-1 research, but also for other RNA viruses of medical importance, including West Nile, chikungunya, dengue, Venezuelan encephalitis, and Ebola viruses.
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15
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Hajarizadeh B, Grebely J, Applegate T, Matthews GV, Amin J, Petoumenos K, Hellard M, Rawlinson W, Lloyd A, Kaldor J, Dore GJ. Dynamics of HCV RNA levels during acute hepatitis C virus infection. J Med Virol 2014; 86:1722-9. [PMID: 25042465 DOI: 10.1002/jmv.24010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2014] [Indexed: 12/20/2022]
Abstract
Understanding viral dynamics during acute hepatitis C virus (HCV) infection can provide important insights into immunopathogenesis and guide early treatment. The aim of this study was to investigate the dynamics of HCV RNA and alanine transaminase (ALT) levels during recent HCV infection in the Australian Trial in Acute Hepatitis C (ATAHC). ATAHC was a prospective study of the natural history of recently acquired HCV infection. Longitudinal HCV RNA and ALT levels were compared among individuals with persistent infection and spontaneous clearance. Among those with HCV persistence (n = 104) and HCV clearance (n = 30), median HCV RNA (5.2 vs. 4.1 log IU/ml, respectively) and ALT levels (779 vs. 1,765 IU/L, respectively) were high during month two following infection, and then declined during months three and four in both groups. Among those with HCV persistence, median HCV RNA was 2.9 log IU/ml during months four, increased to 5.5 log IU/ml during month five, and remained subsequently relatively stable. Among those with HCV clearance, median HCV RNA was undetectable by month five. Median HCV RNA levels were comparable between individuals with HCV persistence and HCV clearance during month three following infection (3.2 vs. 3.5 log IU/ml, respectively; P = 0.935), but markedly different during month five (5.5 vs. 1.0 log IU/ml, respectively; P < 0.001). In conclusion, dynamics of HCV RNA levels in those with HCV clearance and HCV persistence diverged between months three and five following infection, with the latter time-point being potentially useful for commencing early treatment.
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Affiliation(s)
- Behzad Hajarizadeh
- The Kirby Institute, UNSW Australia (The University of New South Wales), Sydney, Australia
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16
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Culasso ACA, Baré P, Aloisi N, Monzani MC, Corti M, Campos RH. Intra-host evolution of multiple genotypes of hepatitis C virus in a chronically infected patient with HIV along a 13-year follow-up period. Virology 2013; 449:317-27. [PMID: 24418566 DOI: 10.1016/j.virol.2013.11.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/15/2013] [Accepted: 11/21/2013] [Indexed: 01/12/2023]
Abstract
The intra-host evolutionary process of hepatitis C virus (HCV) was analyzed by phylogenetic and coalescent methodologies in a patient co-infected with HCV-1a, HCV-2a, HCV-3a and human immunodeficiency virus (HIV) along a 13-year period. Direct sequence analysis of the E2 and NS5A regions showed diverse evolutionary dynamics, in agreement with different relationships between these regions and the host factors. The Bayesian Skyline Plot analyses of the E2 sequences (cloned) yielded different intra-host evolutionary patterns for each genotype: a steady state of a "consensus" sequence for HCV-1a; a pattern of lineage splitting and extinction for HCV-2a; and a two-phase (drift/diversification) process for HCV-3a. Each genotype evolving in the same patient and at the same time presents a different pattern apparently modulated by the immune pressure of the host. This study provides useful information for the management of co-infected patients and provides insights into the mechanisms behind the intra-host evolution of HCV.
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Affiliation(s)
- A C A Culasso
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Argentina
| | - P Baré
- Sección Virología, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - N Aloisi
- Sección Virología, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - M C Monzani
- Sección Virología, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - M Corti
- Departamento de Medicina Interna, Orientación Enfermedades Infecciosas, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina; División VIH/sida, Hospital de Infecciosas F.J. Muñiz, Ciudad Autónoma de Buenos Aires, Argentina; Jefe de Infectología, Fundación Argentina de la Hemofilia, Buenos Aires, Argentina
| | - R H Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Argentina.
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17
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Escobar-Gutiérrez A, Soudeyns H, Larouche A, Carpio-Pedroza JC, Martinez-Guarneros A, Vazquez-Chacon CA, Fonseca-Coronado S, Yamasaki LHT, Ruiz-Tovar K, Cruz-Rivera M. Vertical transmission of hepatitis C virus: a tale of multiple outcomes. INFECTION GENETICS AND EVOLUTION 2013; 20:465-70. [PMID: 24140559 DOI: 10.1016/j.meegid.2013.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 10/06/2013] [Accepted: 10/08/2013] [Indexed: 12/15/2022]
Abstract
Globally, hepatitis C virus (HCV) infection affects approximately 130 million people and 3 million new infections occur annually. HCV is also recognized as an important cause of chronic liver disease in children. The absence of proofreading properties of the HCV RNA polymerase leads to a highly error prone replication process, allowing HCV to escape host immune response. The adaptive nature of HCV evolution dictates the outcome of the disease in many ways. Here, we investigated the molecular evolution of HCV in three unrelated children who acquired chronic HCV infection as a result of mother-to-child transmission, two of whom were also coinfected with HIV-1. The persistence of discrete HCV variants and their population structure were assessed using median joining network and Bayesian approaches. While patterns of viral evolution clearly differed between subjects, immune system dysfunction related to HIV coinfection or persistent HCV seronegativity stand as potential mechanisms to explain the lack of molecular evolution observed in these three cases. In contrast, treatment of HCV infection with PegIFN, which did not lead to sustained virologic responses in all 3 cases, was not associated with commensurate variations in the complexity of the variant spectrum. Finally, the differences in the degree of divergence suggest that the mode of transmission of the virus was not the main factor driving viral evolution.
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18
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Edwards VC, McClure CP, Brown RJP, Thompson E, Irving WL, Ball JK. Use of short tandem repeat fingerprinting to validate sample origins in hepatitis C virus molecular epidemiology studies. J Gen Virol 2013; 95:66-70. [PMID: 24100764 PMCID: PMC3917063 DOI: 10.1099/vir.0.057828-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Sequence analysis is used to define the molecular epidemiology and evolution of the hepatitis C virus. Whilst most studies have shown that individual patients harbour viruses that are derived from a limited number of highly related strains, some recent reports have shown that some patients can be co-infected with very distinct variants whose frequency can fluctuate greatly. Whilst co-infection with highly divergent strains is possible, an alternative explanation is that such data represent contamination or sample mix-up. In this study, we have shown that DNA fingerprinting techniques can accurately assess sample provenance and differentiate between samples that are truly exhibiting mixed infection from those that harbour distinct virus populations due to sample mix-up. We have argued that this approach should be adopted routinely in virus sequence analyses to validate sample provenance.
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Affiliation(s)
- Victoria C Edwards
- Nottingham Digestive Diseases Centre Biomedical Research Unit, University of Nottingham, Queen's Medical Centre, Nottingham, UK.,School of Molecular Medical Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - C Patrick McClure
- Nottingham Digestive Diseases Centre Biomedical Research Unit, University of Nottingham, Queen's Medical Centre, Nottingham, UK.,School of Molecular Medical Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Richard J P Brown
- Nottingham Digestive Diseases Centre Biomedical Research Unit, University of Nottingham, Queen's Medical Centre, Nottingham, UK.,School of Molecular Medical Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Emma Thompson
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, Glasgow, UK
| | - William L Irving
- Nottingham Digestive Diseases Centre Biomedical Research Unit, University of Nottingham, Queen's Medical Centre, Nottingham, UK.,School of Molecular Medical Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Jonathan K Ball
- Nottingham Digestive Diseases Centre Biomedical Research Unit, University of Nottingham, Queen's Medical Centre, Nottingham, UK.,School of Molecular Medical Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
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19
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Li H, Stoddard MB, Wang S, Blair LM, Giorgi EE, Parrish EH, Learn GH, Hraber P, Goepfert PA, Saag MS, Denny TN, Haynes BF, Hahn BH, Ribeiro RM, Perelson AS, Korber BT, Bhattacharya T, Shaw GM. Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing. PLoS Pathog 2012; 8:e1002880. [PMID: 22927816 PMCID: PMC3426529 DOI: 10.1371/journal.ppat.1002880] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 06/27/2012] [Indexed: 02/07/2023] Open
Abstract
A precise molecular identification of transmitted hepatitis C virus (HCV) genomes could illuminate key aspects of transmission biology, immunopathogenesis and natural history. We used single genome sequencing of 2,922 half or quarter genomes from plasma viral RNA to identify transmitted/founder (T/F) viruses in 17 subjects with acute community-acquired HCV infection. Sequences from 13 of 17 acute subjects, but none of 14 chronic controls, exhibited one or more discrete low diversity viral lineages. Sequences within each lineage generally revealed a star-like phylogeny of mutations that coalesced to unambiguous T/F viral genomes. Numbers of transmitted viruses leading to productive clinical infection were estimated to range from 1 to 37 or more (median = 4). Four acutely infected subjects showed a distinctly different pattern of virus diversity that deviated from a star-like phylogeny. In these cases, empirical analysis and mathematical modeling suggested high multiplicity virus transmission from individuals who themselves were acutely infected or had experienced a virus population bottleneck due to antiviral drug therapy. These results provide new quantitative and qualitative insights into HCV transmission, revealing for the first time virus-host interactions that successful vaccines or treatment interventions will need to overcome. Our findings further suggest a novel experimental strategy for identifying full-length T/F genomes for proteome-wide analyses of HCV biology and adaptation to antiviral drug or immune pressures. Hepatitis C virus infects as many as 170 million people worldwide. Globally, there are seven major genotypes of HCV that differ by approximately 30% in nucleotide sequence. Importantly, the natural history of HCV infection is variable, ranging from spontaneous resolution to persistent viremia and chronic disease. Factors responsible for this variability in clinical outcome are unknown but likely involve a combination of viral and host determinants. To this end, a precise molecular identification of transmitted HCV genomes could illuminate key aspects of transmission biology, immunopathogenesis and natural history. We used single genome sequencing of plasma viral RNA to identify transmitted viral genomes and their progeny in 17 subjects with acute infection. Numbers of transmitted viruses leading to productive clinical infection ranged from 1 to 37 or more (median = 4). Surprisingly, we found evidence of high multiplicity acute-to-acute HCV transmission in 3 of 17 subjects, which suggests that clinical transmission of HCV, like that of HIV-1, may be enhanced in early infection when virus titers are highest and neutralizing antibodies are absent. These results provide novel insight into HCV transmission and early virus diversification key to our understanding of virus natural history and response to drug selection and immune pressure.
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Affiliation(s)
- Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mark B. Stoddard
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shuyi Wang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lily M. Blair
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Elena E. Giorgi
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Erica H. Parrish
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gerald H. Learn
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Peter Hraber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Paul A. Goepfert
- University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michael S. Saag
- University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Thomas N. Denny
- Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Barton F. Haynes
- Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Beatrice H. Hahn
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ruy M. Ribeiro
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan S. Perelson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Bette T. Korber
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tanmoy Bhattacharya
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - George M. Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Affiliation(s)
- Rebecca R. Gray
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marco Salemi
- Department of Pathology, Immunology & Laboratory Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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HAVCR1 gene haplotypes and infection by different viral hepatitis C virus genotypes. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2011; 19:223-7. [PMID: 22190394 DOI: 10.1128/cvi.05305-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The hepatitis A virus cellular receptor 1 (HAVCR1) gene is highly polymorphic, and several variants have been associated with susceptibility to allergic and autoimmune diseases. The HAVCR1 gene region was identified as a candidate for hepatitis C virus (HCV) natural clearance in a genotyping study of selected immune response genes in both European-American and African-American populations. The aim of the present study was to explore the influence of HAVCR1 in the outcome of HCV infection in the Spanish population. Three cohorts, consisting of 354 subjects with persistent HCV infection (285 with persistent HCV monoinfection and 69 with natural clearance), 182 coinfected HIV/HCV patients, and 320 controls, were included. Samples were genotyped in several polymorphic positions, insertion/deletion variants in exon 4 and tag single nucleotide polymorphisms (SNPs), in order to define previously described HAVCR1 haplotypes (haplotypes A to D). No statistically significant differences were observed with spontaneous resolution of infection or with viral clearance after treatment. Nevertheless, different rates of infection by viral genotypes (G's) were observed among the HAVCR1 haplotypes. Individuals bearing haplotype C had the highest viral G1 infection rate when compared to individuals bearing other haplotypes (75.82% versus 57.72%, respectively; corrected P value [P(c)], 3.2 × 10(-4); odds ratio [OR], 2.30; 95% confidence interval [CI], 1.51 to 3.47). Thus, HAVCR1 could be involved in susceptibility or resistance to infection by a particular HCV genotype.
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Alarming incidence of hepatitis C virus re-infection after treatment of sexually acquired acute hepatitis C virus infection in HIV-infected MSM. AIDS 2011; 25:F21-7. [PMID: 21857492 DOI: 10.1097/qad.0b013e32834bac44] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Recent data indicate that seroprevalence of sexually transmitted hepatitis C virus (HCV) infection among MSM is stabilizing in Amsterdam. However, little is known about the incidence of HCV re-infection in MSM who have cleared their HCV infection. We, therefore, studied the incidence of re-infection in HIV-infected MSM who were HCV RNA-negative following HCV treatment of acute primary infection. METHODS Our study population comprised HIV-infected MSM at two large HIV outpatient clinics in Amsterdam, who were previously diagnosed with a sexually transmitted acute HCV infection and tested HCV RNA-negative at the end of treatment. We defined HCV re-infection as detectable HCV RNA in individuals with an undetectable HCV RNA at the end of treatment accompanied by a switch in HCV genotype or clade. Person-time methods were used to calculate the incidence of re-infection. RESULTS Fifty-six persons who became HCV RNA-negative during primary acute HCV treatment were included. Five of the 56 cases relapsed and were not analysed. Eleven persons were re-infected. The incidence of HCV re-infection in this group was 15.2 per 100 person-years (95% confidence interval 8.0-26.5). The cumulative incidence was 33% within 2 years. DISCUSSION An alarmingly high incidence of HCV re-infection was found in this group. This high re-infection rate indicates that current prevention measures should be discussed, frequent HCV RNA testing should be continued after successful treatment and, in case of possible relapse, clade typing should be performed to exclude re-infection.
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Thomson EC, Smith JA, Klenerman P. The natural history of early hepatitis C virus evolution; lessons from a global outbreak in human immunodeficiency virus-1-infected individuals. J Gen Virol 2011; 92:2227-2236. [PMID: 21775583 PMCID: PMC3347798 DOI: 10.1099/vir.0.033910-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
New insights into the early viral evolution and cellular immune response during acute hepatitis C virus (HCV) infection are being gained following a global outbreak in human immunodeficiency virus-1 (HIV)-positive men who have sex with men. Cross-sectional and longitudinal sequence analysis at both the population and individual level have facilitated tracking of the HCV epidemic across the world and enabled the development of tests of viral diversity in individual patients in order to predict spontaneous clearance of HCV and response to treatment. Immunological studies in HIV-positive cohorts have highlighted the role of the CD4+ T-cell response in the control of early HCV infection and will increase the opportunity for the identification of protective epitopes that could be used in future vaccine development.
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Affiliation(s)
- Emma C Thomson
- Department of Hepatology, Imperial College London, Norfolk Place, London W2 1PG, UK.,Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Jennifer A Smith
- Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
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