1
|
Álvarez-Herrera M, Sevilla J, Ruiz-Rodriguez P, Vergara A, Vila J, Cano-Jiménez P, González-Candelas F, Comas I, Coscollá M. VIPERA: Viral Intra-Patient Evolution Reporting and Analysis. Virus Evol 2024; 10:veae018. [PMID: 38510921 PMCID: PMC10953798 DOI: 10.1093/ve/veae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/02/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Viral mutations within patients nurture the adaptive potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during chronic infections, which are a potential source of variants of concern. However, there is no integrated framework for the evolutionary analysis of intra-patient SARS-CoV-2 serial samples. Herein, we describe Viral Intra-Patient Evolution Reporting and Analysis (VIPERA), a new software that integrates the evaluation of the intra-patient ancestry of SARS-CoV-2 sequences with the analysis of evolutionary trajectories of serial sequences from the same viral infection. We have validated it using positive and negative control datasets and have successfully applied it to a new case, which revealed population dynamics and evidence of adaptive evolution. VIPERA is available under a free software license at https://github.com/PathoGenOmics-Lab/VIPERA.
Collapse
Affiliation(s)
- Miguel Álvarez-Herrera
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| | - Jordi Sevilla
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| | - Paula Ruiz-Rodriguez
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| | - Andrea Vergara
- Department of Clinical Microbiology, CDB, Hospital Clínic of Barcelona; University of Barcelona; ISGlobal, C. de Villarroel, 170, Barcelona 08007, Spain
- CIBER of Infectious Diseases (CIBERINFEC), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Jordi Vila
- Department of Clinical Microbiology, CDB, Hospital Clínic of Barcelona; University of Barcelona; ISGlobal, C. de Villarroel, 170, Barcelona 08007, Spain
- CIBER of Infectious Diseases (CIBERINFEC), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Pablo Cano-Jiménez
- Institute of Biomedicine of Valencia (IBV-CSIC), C/ Jaime Roig, 11, Valencia 46010, Spain
| | - Fernando González-Candelas
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Iñaki Comas
- Institute of Biomedicine of Valencia (IBV-CSIC), C/ Jaime Roig, 11, Valencia 46010, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Mireia Coscollá
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| |
Collapse
|
2
|
Graf C, Fuhrmann L, Lutz T, Stephan C, Knecht G, Gute P, Bickel M, Peiffer KH, Finkelmeier F, Dultz G, Mondorf A, Wetzstein N, Filmann N, Herrmann E, Zeuzem S, Beerenwinkel N, Dietz J, Sarrazin C. Expanding epidemic of recently acquired HCV in HIV-coinfected patients over a period of 10 years. JHEP Rep 2023; 5:100701. [PMID: 37305441 PMCID: PMC10250927 DOI: 10.1016/j.jhepr.2023.100701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/12/2023] [Accepted: 02/01/2023] [Indexed: 06/13/2023] Open
Abstract
Background & Aims Ongoing transmission of HCV infections is associated with risk factors such as drug injection, needlestick injuries, and men who have sex with men (MSM). Ways of transmission, the course of acute infection, changes of virologic features, and incidence over time are not well known. Methods Over a period of 10 years, n = 161 patients with recently acquired HCV infection (RAHC) (median follow-up 6.8 years) were prospectively enrolled. NS5B sequencing was performed to re-evaluate the HCV genotype (GT) and for phylogenetic analyses. Results Patients with RAHC were mainly male (92.5%), MSM (90.1%), and HIV-coinfected (86.3%). Transmission risk factors for MSM and non-MSM were sexual risk behaviour (100 and 6.3%, respectively), injection drug use (9.7 and 37.5%, respectively), and nasal drug use (15.2 and 0%, respectively). Spontaneous and interferon- or direct-acting antiviral-based clearance rates were 13.6, 84.3 and 93.4%, respectively. Mean RAHC declined from 19.8 in the first to 13.2 in the past five study years. Although the majority of infections was caused by HCV GT1a, the frequency of HCV GT4d and slightly HCV GT3a increased over time. No relevant clustering of HCV isolates was observed in non-MSM. However, 45% of HCV GT1a and 100% of HCV GT4d MSM cases clustered with MSM isolates from other countries. Travel-associated infections were supported by personal data in an MSM subgroup. No international clustering was detected in MSM with HCV GT1b or HCV GT3a. Conclusions RAHCs were mainly diagnosed in HIV-coinfected MSM patients and were associated with sexual risk behaviour. Spontaneous clearance rates were low, and phylogenetic clusters were observed in the majority of patients. Impact and Implications We evaluated the occurrence and transmission of recently acquired HCV infections (RAHCs) over a period of 10 years. Our data demonstrate that the presence of RAHC was mainly found in HIV-coinfected MSM, with internationally connected transmission networks being observed in the majority of patients. Spontaneous clearance rates were low, and reinfection rates increased mainly driven by a small subset of MSM patients with high-risk behaviour.
Collapse
Affiliation(s)
- Christiana Graf
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
| | - Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Christoph Stephan
- HIVCENTER, Department of Infectious Diseases, University Hospital, Goethe University, Frankfurt, Germany
| | | | | | | | - Kai-Henrik Peiffer
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
| | - Fabian Finkelmeier
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
| | - Georg Dultz
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
| | - Antonia Mondorf
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
| | - Nils Wetzstein
- HIVCENTER, Department of Infectious Diseases, University Hospital, Goethe University, Frankfurt, Germany
| | - Natalie Filmann
- Institute of Biostatistics and Mathematical Modeling, Goethe University, Frankfurt, Germany
| | - Eva Herrmann
- Institute of Biostatistics and Mathematical Modeling, Goethe University, Frankfurt, Germany
| | - Stefan Zeuzem
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Julia Dietz
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
| | - Christoph Sarrazin
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt, Germany
- Medizinische Klinik II, St. Josefs-Hospital, Wiesbaden, Germany
| |
Collapse
|
3
|
Rockstroh JK. Hepatitis C Micro-elimination in Human Immunodeficiency Virus-Coinfected Men Who Have Sex With Men: A Low Hanging Fruit? Clin Infect Dis 2021; 73:e2203-e2204. [PMID: 32756972 DOI: 10.1093/cid/ciaa1113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/29/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jürgen Kurt Rockstroh
- Department of Medicine I, University Hospital Bonn, Bonn, Germany.,German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| |
Collapse
|
4
|
Comas I, Cancino-Muñoz I, Mariner-Llicer C, Goig GA, Ruiz-Hueso P, Francés-Cuesta C, García-González N, González-Candelas F. Use of next generation sequencing technologies for the diagnosis and epidemiology of infectious diseases. Enferm Infecc Microbiol Clin 2021; 38 Suppl 1:32-38. [PMID: 32111363 DOI: 10.1016/j.eimc.2020.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For the first time, next generation sequencing technologies provide access to genomic information at a price and scale that allow their implementation in routine clinical practice and epidemiology. While there are still many obstacles to their implementation, there are also multiple examples of their major advantages compared with previous methods. Their main advantage is that a single determination allows epidemiological information on the causative microorganism to be obtained simultaneously, as well as its resistance profile, although these advantages vary according to the pathogen under study. This review discusses several examples of the clinical and epidemiological use of next generation sequencing applied to complete genomes and microbiomes and reflects on its future in clinical practice.
Collapse
Affiliation(s)
- Iñaki Comas
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España; CIBER en Epidemiología y Salud Pública, Valencia, España.
| | | | | | - Galo A Goig
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España
| | - Paula Ruiz-Hueso
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Carlos Francés-Cuesta
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Neris García-González
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Fernando González-Candelas
- CIBER en Epidemiología y Salud Pública, Valencia, España; Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| |
Collapse
|
5
|
Impact of Sexualized Substance Use and Other Risk Practices on HCV Microelimination in gbMSM Living with HIV: Urgent Need for Targeted Strategies. Results of a Retrospective Cohort Study. Infect Dis Ther 2021; 10:1253-1266. [PMID: 33914265 PMCID: PMC8322221 DOI: 10.1007/s40121-021-00448-0] [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: 02/24/2021] [Accepted: 04/10/2021] [Indexed: 10/28/2022] Open
Abstract
INTRODUCTION The objective of the present study is to describe the incidence of recently acquired hepatitis C (RAHCV) in a large cohort of people living with HIV (PLWHIV) and sexualized drug use and other related risk behaviours. METHODS Observational study including all PLWHIV with a RAHCV episode between June 2005 and December 2019 at the Hospital Clinic of Barcelona, Spain. Incidence of RAHCV was determined per person calendar year (py) in those patients who were HCV RNA negative. Data were collected on high-risk sexual practices for HCV transmission focused on gay, bisexual and other men having sex with men (gbMSM). RESULTS A total of 340 RAHCV were diagnosed in 290 PLWHIV; 274 (94%) of them were gbMSM and developed 324 RAHCV, mainly since 2010 (90%). Overall incidence rate (IR) of RAHCV in gbMSM was 0.10 py (95% CI 0.09-0.11), with a 40% decreased observed since 2017 (IR 0.06, 95% CI 0.03-0.09 in 2019). Sixty reinfections were detected in 50 gbMSM (n = 244, 20%). The overall reinfection IR was 0.17 per py (95% CI 0.12-0.23) and the proportion of reinfection among total RAHCV increased to 47% cases in 2019, mainly in patients engaged in sexualized substance use (76%), unprotected anal intercourse (94%), sex partying (80%), fisting (43%), slamming (14%) and 60% of concomitant sexually transmitted infections (STIs). CONCLUSIONS Despite RAHCV incidence decline in our cohort since 2017, HCV reinfection increased. High sexualized substance use and other risk behaviours are described in this context, indicating the need for public health tailored strategies to reduce this transmission and achieve HCV microelimination in gbMSM living with HIV.
Collapse
|
6
|
Gonzalez-Serna A, Macias J, Palacios R, Gómez-Ayerbe C, Tellez F, Rivero-Juárez A, Fernandez M, Santos J, Real LM, Gonzalez-Domenech CM, Gomez-Mateos J, Pineda JA. Incidence of recently acquired hepatitis C virus infection among HIV-infected patients in southern Spain. HIV Med 2020; 22:379-386. [PMID: 33369104 DOI: 10.1111/hiv.13039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/20/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Spain is close to HCV microelimination, so rates of recently acquired HCV infection (RAHC) should decrease. Nowadays, men who have sex with men (MSM) carry the highest risk of HCV acquisition. Our aim was to estimate the incidence of and the factors associated with RAHC, together with reinfection rates, among patients sexually infected by HIV. METHODS Primary RAHC infection was diagnosed when anti-HCV antibody seroconversion was documented. In anti-HCV positive patients, initially without HCV viraemia, a diagnosis of reinfection was established if plasma HCV RNA was detected. RESULTS All 350 patients tested negative for anti-HCV at baseline and had at least one follow-up visit. Among them, there were 16 RAHC cases from 2016 to 2019. RAHC incidence rates [IR (95% confidence interval, CI)] per 100 person-years were 3.77 (0.5-12.9) in 2016, 1.85 (0.6-4.3) in 2017, 1.49 (0.4-3.8) in 2018 and 1.98 (0.6-4.5) in 2019. Only previous sexually transmitted infections [incidence rate ratio (IRR) = 18.23, 95% CI: 1.93-172.1; P = 0.011], male sex (IRR = 8.33, 95% CI: 1.38-54.15; P = 0.026) and sharing chem-sex drugs (IRR: 4.93, 95% CI: 1.17-20.76; P = 0.030), were independently associated with RAHC. Four out of 42 (9.5%) patients became reinfected. CONCLUSIONS The incidence of RAHC among HIV-infected patients showed a decrease after 2016, although a lower but steady incidence of residual cases still remains. HCV reinfections showed a similar pattern. New infections were associated with sharing chem-sex drugs among MSM.
Collapse
Affiliation(s)
- A Gonzalez-Serna
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de Valme, Sevilla, Spain
| | - J Macias
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de Valme, Sevilla, Spain
| | - R Palacios
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de la Victoria, Málaga, Spain
| | - C Gómez-Ayerbe
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de la Victoria, Málaga, Spain
| | - F Tellez
- UGC Enfermedades Infecciosas, Departamento Medicina, Universidad de Cádiz, Hospital Universitario de Puerto Real, Cádiz, Spain
| | - A Rivero-Juárez
- Unidad de Enfermedades Infecciosas, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - M Fernandez
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de Valme, Sevilla, Spain
| | - J Santos
- Unidad de Enfermedades Infecciosas, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - L M Real
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de Valme, Sevilla, Spain
| | - C M Gonzalez-Domenech
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de la Victoria, Málaga, Spain
| | - J Gomez-Mateos
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de Valme, Sevilla, Spain
| | - J A Pineda
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de Valme, Sevilla, Spain
| | | |
Collapse
|
7
|
Ramière C, Charre C, Miailhes P, Bailly F, Radenne S, Uhres AC, Brochier C, Godinot M, Chiarello P, Pradat P, Cotte L, Augustin-Normand C, François B, Biron F, Boibieux A, Brochier C, Braun E, Brunel F, Charre C, Chiarello P, Chidiac C, Cotte L, Ferry T, Godinot M, Guillaud O, Koffi J, Livrozet JM, Makhloufi D, Miailhes P, Perpoint T, Pradat P, Radenne S, Ramière C, Schlienger I, Scholtes C, Schuffenecker I, Tardy JC, Trabaud MA, Uhres AC. Patterns of Hepatitis C Virus Transmission in Human Immunodeficiency Virus (HIV)-infected and HIV-negative Men Who Have Sex With Men. Clin Infect Dis 2020; 69:2127-2135. [PMID: 30810158 DOI: 10.1093/cid/ciz160] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/22/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Sexually transmitted acute hepatitis C virus (HCV) infections (AHIs) have been mainly described in human immunodeficiency virus (HIV)-infected men who have sex with men (MSM). Cases in HIV-negative MSM are scarce. We describe the epidemic of AHI in HIV-infected and HIV-negative MSM in Lyon, France. METHODS All cases of AHI diagnosed in MSM in Lyon University Hospital from 2014 to 2017 were included. AHI incidence was determined in HIV-infected and in preexposure prophylaxis (PrEP)-using MSM. Transmission clusters were identified by construction of phylogenetic trees based on HCV NS5B (genotype 1a/4d) or NS5A (genotype 3a) Sanger sequencing. RESULTS From 2014 to 2017, 108 AHIs (80 first infections, 28 reinfections) were reported in 96 MSM (HIV-infected, 72; HIV-negative, 24). AHI incidence rose from 1.1/100 person-years (95 confidence interval [CI], 0.7-1.7) in 2014 to 2.4/100 person-years (95 CI, 1.1-2.6) in 2017 in HIV-infected MSM (P = .05) and from 0.3/100 person-years (95 CI, 0.06-1.0) in 2016 to 3.4/100 person-years (95 CI, 2.0-5.5) in 2017 in PrEP users (P < .001). Eleven clusters were identified. All clusters included HIV-infected MSM; 6 also included HIV-negative MSM. All clusters started with ≥1 HIV-infected MSM. Risk factor distribution varied among clusters. CONCLUSIONS AHI incidence increased in both HIV-infected and HIV-negative MSM. Cluster analysis suggests initial transmission from HIV-infected to HIV-negative MSM through chemsex and traumatic sexual practices, leading to mixed patterns of transmission regardless of HIV status and no overlap with the general population.
Collapse
Affiliation(s)
- Christophe Ramière
- Virology Laboratory, Hospices Civils de Lyon, Hôpital de la Croix-Rousse, Lyon, France.,Centre International de Recherche en Infectiologie, INSERM, CNRS UMR, Lyon, France.,University of Lyon, Université Claude Bernard Lyon, Villeurbanne, France
| | - Caroline Charre
- Virology Laboratory, Hospices Civils de Lyon, Hôpital de la Croix-Rousse, Lyon, France.,University of Lyon, Université Claude Bernard Lyon, Villeurbanne, France.,INSERM U1052, Lyon, France
| | - Patrick Miailhes
- Infectious Diseases Department, Hospices Civils de Lyon, Hôpital de la Croix-Rousse, Lyon, France
| | - François Bailly
- Hepatology Department, Hospices Civils de Lyon, Hôpital de la Croix-Rousse, Lyon, France
| | - Sylvie Radenne
- Hepatology Department, Hospices Civils de Lyon, Hôpital de la Croix-Rousse, Lyon, France
| | - Anne-Claire Uhres
- Pharmacy, Hospices Civils de Lyon, Hôpital de la Croix-Rousse, Lyon, France
| | - Corinne Brochier
- Clinical Research Centre, Hospices Civils de Lyon, Hôpital de la Croix-Rousse, Lyon, France
| | - Matthieu Godinot
- Infectious Diseases Department, Hospices Civils de Lyon, Hôpital de la Croix-Rousse, Lyon, France
| | - Pierre Chiarello
- Infectious Diseases Department, Hospices Civils de Lyon, Hôpital de la Croix-Rousse, Lyon, France
| | - Pierre Pradat
- Clinical Research Centre, Hospices Civils de Lyon, Hôpital de la Croix-Rousse, Lyon, France
| | - Laurent Cotte
- Infectious Diseases Department, Hospices Civils de Lyon, Hôpital de la Croix-Rousse, Lyon, France.,INSERM U1052, Lyon, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Desdouits M, Wacrenier C, Ollivier J, Schaeffer J, Le Guyader FS. A Targeted Metagenomics Approach to Study the Diversity of Norovirus GII in Shellfish Implicated in Outbreaks. Viruses 2020; 12:E978. [PMID: 32899445 PMCID: PMC7552006 DOI: 10.3390/v12090978] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/20/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
Human noroviruses (NoV) cause epidemics of acute gastroenteritis (AGE) worldwide and can be transmitted through consumption of contaminated foods. Fresh products such as shellfish can be contaminated by human sewage during production, which results in the presence of multiple virus strains, at very low concentrations. Here, we tested a targeted metagenomics approach by deep-sequencing PCR amplicons of the capsid (VP1) and polymerase (RdRp) viral genes, on a set of artificial samples and on shellfish samples associated to AGE outbreaks, to evaluate its advantages and limitations in the identification of strains from the NoV genogroup (G) II. Using artificial samples, the method allowed the sequencing of most strains, but not all, and displayed variability between replicates especially with lower viral concentrations. Using shellfish samples, targeted metagenomics was compared to Sanger-sequencing of cloned amplicons and was able to identify a higher diversity of NoV GII and GIV strains. It allowed phylogenetic analyses of VP1 sequences and the identification, in most samples, of GII.17[P17] strains, also identified in related clinical samples. Despite several limitations, combining RdRp- and VP1-targeted metagenomics is a sensitive approach allowing the study NoV diversity in low-contaminated foods and the identification of NoV strains implicated in outbreaks.
Collapse
Affiliation(s)
- Marion Desdouits
- Laboratoire de Microbiologie (LSEM), Ifremer, rue de l’Ile d’Yeu, B.P. 21105, CEDEX 03, 44311 Nantes, France; (C.W.); (J.O.); (J.S.); (F.S.L.G.)
| | | | | | | | | |
Collapse
|
9
|
Shared HCV Transmission Networks Among HIV-1-Positive and HIV-1-Negative Men Having Sex With Men by Ultradeep Sequencing. J Acquir Immune Defic Syndr 2020; 82:105-110. [PMID: 31169768 DOI: 10.1097/qai.0000000000002099] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Several studies reported hepatitis C virus (HCV) transmission networks among men having sex with men (MSM) in Europe and the spread of HCV strains from HIV-HCV coinfected toward HCV monoinfected MSM. We aimed to investigate HCV transmission dynamics among HIV-positive and HIV-negative MSM by ultradeep sequencing (UDS). DESIGN AND METHODS NS5B fragment (388 bp) was sequenced from virus of 50 HIV-positive and 18 HIV-negative patients diagnosed with recent HCV infection. UDS data were analyzed by Geneious (version 10.3.2). Phylogenetic trees were constructed by FastTree (version 2.1) and submitted to ClusterPicker (version 1.2.3) for transmission chain detection at different thresholds of maximum genetic distance (MGD) (3% for Sanger, 3% and 4.5% for UDS). RESULTS Ten, 17, and 18 HCV transmission chains were identified by Sanger at 3%, UDS at 3% and at 4.5% of MGD, respectively. Of 68 subjects enrolled, 38 (55.9%), 38 (55.9%), and 43 (65.3%) individuals were involved in transmission networks found by Sanger at 3%, UDS at 3%, and at 4.5% of MGD, respectively. Mixed transmission chains including HIV-positive and HIV-negative subjects were detected for 8/10 chains by Sanger at 3%, for 9/17 by UDS at 3%, and for 10/18 by UDS at 4.5% of MGD. Overall, the number of HIV-negative individuals clustering with HIV-positive ones was 9/18 by Sanger, 9/18 by UDS at 3%, and 10/18 by UDS at 4.5% of MGD. CONCLUSIONS HIV-positive and HIV-negative MSM shared HCV transmission networks, which emphasizes the need for HCV surveillance and prevention measures in these communities regardless of the HIV status.
Collapse
|
10
|
Li WY, Huang SW, Wang SF, Liu HF, Chou CH, Wu SJ, Huang HD, Lu PL, Fann CSJ, Chen M, Chen YH, Chen YMA. Source identification of HIV-1 transmission in three lawsuits Using Ultra-Deep pyrosequencing and phylogenetic analysis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2020; 54:596-605. [PMID: 32067946 DOI: 10.1016/j.jmii.2019.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/21/2019] [Accepted: 12/26/2019] [Indexed: 12/01/2022]
Abstract
BACKGROUND/PURPOSE Intentional transmission of HIV-1 is a crime. Identifying the source of transmission between HIV-1 infected cases using phylogenetic analysis has limitations, including delayed examinations after the initiation of infection and ambiguity of phyletic relationships. This study was the first to introduce phylogenetic tree Results as forensic evidence in a trial in Taiwan. METHODS Three lawsuit cases from different district courts in Taiwan were chosen for this study. We identified the source of transmission between individuals in each lawsuit based on the maximum likelihood and Bayesian phylogenetic tree analyses using the HIV-1 sequences from molecular cloning and ultra-deep pyrosequencing (UDPS). Two gene regions of the HIV genome, env and gag, were involved. RESULTS The results of phylogenetic analysis using sequences from molecular cloning were clear and evidential enough in lawsuits 1 and 3. Due to the delayed sampling time, the result of sequences from molecular cloning in lawsuit 2 was ambiguous. Combined with the analyzed result of sequences from UDPS and epidemiological information, the source of transmission in lawsuit 2 was further identified. CONCLUSION Hence phylogenetic analyses cannot exclude the possibility of unsampled intermediaries, the data interpretation should be more careful and conservative, and it should not be considered as the only evidence for the source identification in a trial without epidemiological or serological information. The evaluation of the introduced UDPS method in the identification of transmission source has shown that the validity and evidential effects were still limited and need further optimization.
Collapse
Affiliation(s)
- Wei-You Li
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Szu-Wei Huang
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Basic Research Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Sheng-Fan Wang
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hsin-Fu Liu
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Chih-Hung Chou
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan; Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Shang-Jung Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan; Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Po-Liang Lu
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Cathy S J Fann
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Marcelo Chen
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Urology, Mackay Memorial Hospital, Taipei, Taiwan; Department of Cosmetic Applications and Management, Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan
| | - Yen-Hsu Chen
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-Ming Arthur Chen
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Clinical Pharmacogenomics and Pharmacoproteomics Program, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.
| |
Collapse
|
11
|
Pérez-Losada M, Arenas M, Galán JC, Bracho MA, Hillung J, García-González N, González-Candelas F. High-throughput sequencing (HTS) for the analysis of viral populations. INFECTION GENETICS AND EVOLUTION 2020; 80:104208. [PMID: 32001386 DOI: 10.1016/j.meegid.2020.104208] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
Abstract
The development of High-Throughput Sequencing (HTS) technologies is having a major impact on the genomic analysis of viral populations. Current HTS platforms can capture nucleic acid variation across millions of genes for both selected amplicons and full viral genomes. HTS has already facilitated the discovery of new viruses, hinted new taxonomic classifications and provided a deeper and broader understanding of their diversity, population and genetic structure. Hence, HTS has already replaced standard Sanger sequencing in basic and applied research fields, but the next step is its implementation as a routine technology for the analysis of viruses in clinical settings. The most likely application of this implementation will be the analysis of viral genomics, because the huge population sizes, high mutation rates and very fast replacement of viral populations have demonstrated the limited information obtained with Sanger technology. In this review, we describe new technologies and provide guidelines for the high-throughput sequencing and genetic and evolutionary analyses of viral populations and metaviromes, including software applications. With the development of new HTS technologies, new and refurbished molecular and bioinformatic tools are also constantly being developed to process and integrate HTS data. These allow assembling viral genomes and inferring viral population diversity and dynamics. Finally, we also present several applications of these approaches to the analysis of viral clinical samples including transmission clusters and outbreak characterization.
Collapse
Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain; Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain.
| | - Juan Carlos Galán
- Microbiology Service, Hospital Ramón y Cajal, Madrid, Spain; CIBER in Epidemiology and Public Health, Spain.
| | - Mª Alma Bracho
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain.
| | - Julia Hillung
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Neris García-González
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Fernando González-Candelas
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| |
Collapse
|
12
|
Maisa A, Semple S, Griffiths A, Ngui SL, Verlander NQ, McCaughey C, Doherty L, Jessop L. Risk behaviours of homeless people who inject drugs during an outbreak of hepatitis C, Northern Ireland, 2016-2017. J Viral Hepat 2019; 26:1377-1387. [PMID: 31328838 DOI: 10.1111/jvh.13184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/25/2019] [Accepted: 06/25/2019] [Indexed: 12/14/2022]
Abstract
From July to August 2016, 4 homeless people who injected drugs (PWID) with acute or recent hepatitis C virus (HCV) infection were reported in Belfast. A multidisciplinary team including public health, homeless and addiction services undertook an investigation to identify risk behaviours and interrupt transmission chains. Recent HCV cases were defined as negative test within the previous year, or reported injecting for less than 1 year; acute cases had tested negative within the previous 6 months. Contacts in the injecting networks of cases were identified for testing. We undertook a cross-sectional survey using structured questionnaires to elicit risk behaviours for PWID and compare behaviours between self-reported hepatitis C positive and negative subjects. During the outbreak investigation until December 2017, 156 PWID were tested and 45 (29%) cases identified, including 7 (16%) recent and 13 (29%) acute infections. 68 PWID, including 12 cases, were interviewed. All respondents reported using heroin, with 76% injecting once or more daily. Sharing was reported for spoons (58%) and filters (53%), but also needles (27%) and syringes (29%). Hepatitis C positive individuals had higher odds to be injecting in public toilets (AOR 17, 95% CI 0.71-400, P < .05) when compared with hepatitis C negative individuals. Hepatitis C positive individuals were more likely to inject in public spaces, but all respondents indicated concerning risk behaviours. We recommend active surveillance with ongoing testing, expanding existing harm reduction programmes and access to bespoke services.
Collapse
Affiliation(s)
- Anna Maisa
- Public Health Agency, Health Protection Service Northern Ireland, Belfast, Northern Ireland.,European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Susan Semple
- Homeless Public Health Nursing Service, Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | - Alison Griffiths
- Public Health Agency, Health Protection Service Northern Ireland, Belfast, Northern Ireland
| | - Siew Lin Ngui
- Virus Reference Department, National Infection Service, Public Health England, Colindale, London, UK
| | - Neville Q Verlander
- Statistics, Modelling and Economics Department, National Infection Service, Public Health England, London, UK
| | - Conall McCaughey
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | - Lorraine Doherty
- Public Health Agency, Health Protection Service Northern Ireland, Belfast, Northern Ireland
| | - Lucy Jessop
- Public Health Agency, Health Protection Service Northern Ireland, Belfast, Northern Ireland
| | | |
Collapse
|
13
|
Molecular surveillance of hepatitis C virus genotypes identifies the emergence of a genotype 4d lineage among men in Quebec, 2001-2017. ACTA ACUST UNITED AC 2019; 45:230-237. [PMID: 31650986 DOI: 10.14745/ccdr.v45i09a02] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Background Molecular phylogenetics are generally used to confirm hepatitis C virus (HCV) transmission events. In addition, the Laboratoire de santé publique du Québec (LSPQ) has been using molecular phylogenetics for surveillance of HCV genotyping since November 2001. Objectives To describe the emergence of a specific lineage of HCV genotype 4d (G4d) and its characteristics using molecular phylogenetics as a surveillance tool for identifying HCV strain clustering. Methods The LSPQ prospectively applied Sanger sequencing and phylogenetic analysis to determine the HCV genotype on samples collected from November 2001 to December 2017. When a major G4d cluster was identified, demographic information, HIV-infection status and syphilis test results were analyzed. Results Phylogenetic analyses performed on approximately 22,000 cases identified 122 G4d cases. One major G4d cluster composed of 37 cases was singled out. Two cases were identified in 2010, 10 from 2011-2014 and 25 from 2015-2017. Cases in the cluster were concentrated in two urban health regions. Compared to the other G4d cases, cluster cases were all male (p<0.001) and more likely to be HIV-positive (adjusted risk ratio: 4.4; 95% confidence interval: 2.5-7.9). A positive syphilis test result was observed for 27 (73%) of the cluster cases. The sequences in this cluster and of four outlier cases were located on the same monophyletic lineage as G4d sequences reported in HIV-positive men who have sex with men (MSM) in Europe. Conclusion Molecular phylogenetics enabled the identification and surveillance of ongoing transmission of a specific HCV G4d lineage in HIV-positive and HIV-negative men in Quebec and its cross-continental spread. This information can orient intervention strategies to avoid transmission of HCV in MSM.
Collapse
|
14
|
McNaughton AL, D’Arienzo V, Ansari MA, Lumley SF, Littlejohn M, Revill P, McKeating JA, Matthews PC. Insights From Deep Sequencing of the HBV Genome-Unique, Tiny, and Misunderstood. Gastroenterology 2019; 156:384-399. [PMID: 30268787 PMCID: PMC6347571 DOI: 10.1053/j.gastro.2018.07.058] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/27/2018] [Accepted: 07/23/2018] [Indexed: 12/13/2022]
Abstract
Hepatitis B virus (HBV) is a unique, tiny, partially double-stranded, reverse-transcribing DNA virus with proteins encoded by multiple overlapping reading frames. The substitution rate is surprisingly high for a DNA virus, but lower than that of other reverse transcribing organisms. More than 260 million people worldwide have chronic HBV infection, which causes 0.8 million deaths a year. Because of the high burden of disease, international health agencies have set the goal of eliminating HBV infection by 2030. Nonetheless, the intriguing HBV genome has not been well characterized. We summarize data on the HBV genome structure and replication cycle, explain and quantify diversity within and among infected individuals, and discuss advances that can be offered by application of next-generation sequencing technology. In-depth HBV genome analyses could increase our understanding of disease pathogenesis and allow us to better predict patient outcomes, optimize treatment, and develop new therapeutics.
Collapse
Affiliation(s)
- Anna L. McNaughton
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Valentina D’Arienzo
- Nuffield Department of Medicine, NDM Research Building, Oxford, United Kingdom
| | - M. Azim Ansari
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Sheila F. Lumley
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom,Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute of Infection and Immunity, Melbourne, Australia,Department of Microbiology and Immunology, University of Melbourne. Melbourne, Australia
| | - Peter Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute of Infection and Immunity, Melbourne, Australia,Department of Microbiology and Immunology, University of Melbourne. Melbourne, Australia
| | - Jane A. McKeating
- Nuffield Department of Medicine, NDM Research Building, Oxford, United Kingdom
| | - Philippa C. Matthews
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom,Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom,Reprint requests Address requests for reprints to: Philippa C. Matthews, BMBS, PhD, Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, United Kingdom.
| |
Collapse
|
15
|
Pradat P, Virlogeux V, Trépo E. Epidemiology and Elimination of HCV-Related Liver Disease. Viruses 2018; 10:E545. [PMID: 30301201 PMCID: PMC6213504 DOI: 10.3390/v10100545] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) infection, defined by active carriage of HCV RNA, affects nearly 1.0% of the worldwide population. The main risk factors include unsafe injection drug use and iatrogenic infections. Chronic HCV infection can promote liver damage, cirrhosis and hepatocellular carcinoma (HCC) in affected individuals. The advent of new second-generation, direct-acting antiviral (DAA) agents allow a virological cure in more than 90% of treated patients, and therefore prevent HCV-related complications. Recently, concerns have been raised regarding the safety of DAA-regimens in cirrhotic patients with respect to the occurrence and the recurrence of HCC. Here, we review the current available data on HCV epidemiology, the beneficial effects of therapy, and discuss the recent controversy with respect to the potential link with liver cancer. We also highlight the challenges that have to be overcome to achieve the ambitious World Health Organization objective of HCV eradication by 2030.
Collapse
Affiliation(s)
- Pierre Pradat
- Centre for Clinical Research, Groupement Hospitalier Nord, Hospices Civils de Lyon, 69004 Lyon, France.
- Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France.
- Lyon University, Lyon, France.
| | - Victor Virlogeux
- Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France.
- Lyon University, Lyon, France.
- Department of Hepatology, Croix-Rousse Hospital, Hospices Civils de Lyon, 69004 Lyon, France.
| | - Eric Trépo
- Liver Unit, Department of Gastroenterology and Hepatopancreatology and Digestive Oncology, CUB Hôpital Erasme, Université Libre de Bruxelles, 1070 Bruxelles, Belgium.
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, 1070 Bruxelles, Belgium.
| |
Collapse
|
16
|
Patiño-Galindo JÁ, González-Candelas F. Molecular evolution methods to study HIV-1 epidemics. Future Virol 2018; 13:399-404. [PMID: 29967650 DOI: 10.2217/fvl-2017-0159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 04/04/2018] [Indexed: 01/17/2023]
Abstract
Nucleotide sequences of HIV isolates are obtained routinely to evaluate the presence of resistance mutations to antiretroviral drugs. But, beyond their clinical use, these and other viral sequences include a wealth of information that can be used to better understand and characterize the epidemiology of HIV in relevant populations. In this review, we provide a brief overview of the main methods used to analyze HIV sequences, the data bases where reference sequences can be obtained, and some caveats about the possible applications for public health of these analyses, along with some considerations about their limitations and correct usage to derive robust and reliable conclusions.
Collapse
Affiliation(s)
- Juan Á Patiño-Galindo
- Department of Systems Biology, Columbia University, New York, NY 10032, USA.,Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Fernando González-Candelas
- Joint Research Unit "Infección y Salud Pública" FISABIO-Salud Pública/Universitat de València-Institute for Integrative Systems Biology (ISysBio, CSIC-UV) Valencia, Spain.,CIBER in Epidemiology & Public Health, Valencia, Spain.,Joint Research Unit "Infección y Salud Pública" FISABIO-Salud Pública/Universitat de València-Institute for Integrative Systems Biology (ISysBio, CSIC-UV) Valencia, Spain.,CIBER in Epidemiology & Public Health, Valencia, Spain
| |
Collapse
|