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Tshiabuila D, Choga W, James SE, Maponga T, Preiser W, van Zyl G, Moir M, van Wyk S, Giandhari J, Pillay S, Anyaneji UJ, Lessells RJ, Naidoo Y, Sanko TJ, Wilkinson E, Tegally H, Baxter C, Martin DP, de Oliveira T. An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable For Genomic Surveillance Within Clinical Diagnostic Settings. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.19.24301519. [PMID: 38293032 PMCID: PMC10827254 DOI: 10.1101/2024.01.19.24301519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Chronic hepatitis B virus (HBV) infection remains a significant public health concern, particularly in Africa, where there is a substantial burden. HBV is an enveloped virus, with isolates being classified into ten phylogenetically distinct genotypes (A - J) determined based on full-genome sequence data or reverse hybridization-based diagnostic tests. In practice, limitations are noted in that diagnostic sequencing, generally using Sanger sequencing, tends to focus only on the S-gene, yielding little or no information on intra-patient HBV genetic diversity with very low-frequency variants and reverse hybridization detects only known genotype-specific mutations. To resolve these limitations, we developed an Oxford Nanopore Technology (ONT)-based HBV genotyping protocol suitable for clinical virology, yielding complete HBV genome sequences and extensive data on intra-patient HBV diversity. Specifically, the protocol involves tiling-based PCR amplification of HBV sequences, library preparation using the ONT Rapid Barcoding Kit, ONT GridION sequencing, genotyping using Genome Detective software, recombination analysis using jpHMM and RDP5 software, and drug resistance profiling using Geno2pheno software. We prove the utility of our protocol by efficiently generating and characterizing high-quality near full-length HBV genomes from 148 left-over diagnostic Hepatitis B patient samples obtained in the Western Cape province of South Africa, providing valuable insights into the genetic diversity and epidemiology of HBV in this region of the world.
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Affiliation(s)
- Derek Tshiabuila
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Wonderful Choga
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - San E. James
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa & National Health Laboratory Service
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa & National Health Laboratory Service
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa & National Health Laboratory Service
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Stephanie van Wyk
- Collaborating Centre for Optimizing Antimalarial Therapy (CCOAT), Mitigating Antimalarial Resistance Consortium in South East Africa (MARC SEA), Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, South Africa
| | - Jennifer Giandhari
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Ugochukwu J. Anyaneji
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Richard J. Lessells
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Tomasz Janusz Sanko
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Darren P. Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
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Liu C, Yang J, Huang H, Zhan S, Xia X. Case report: Nocardia gipuzkoensis infection in an immunocompetent patient diagnosed by metagenomic next-generation sequencing and whole genome sequencing. Front Immunol 2022; 13:1053914. [PMID: 36569853 PMCID: PMC9780257 DOI: 10.3389/fimmu.2022.1053914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
The infection of Nocardia gipuzkoensis is a relatively uncommon form of pulmonary nocardiosis seen in clinical patients. In general, nocardiosis tends to occur in patients with immune deficiency. Here, we report a 23-year-old female who was admitted to the hospital due to cough and sputum production over 10 years, diagnosed with bronchiectasis. The N. gipuzkoensis infection was identified by metagenomic next-generation sequencing and whole genome sequencing. Imipenem/cilastatin and compound sulfamethoxazole tablets were used to control the infection and the pulmonary inflammation subsided gradually.
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Affiliation(s)
- Chengxin Liu
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China,The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Juhua Yang
- Vision Medicals Co., Ltd., Guangzhou, China
| | - Huiting Huang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shaofeng Zhan
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Shaofeng Zhan, ; Xintian Xia,
| | - Xintian Xia
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Shaofeng Zhan, ; Xintian Xia,
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Sandybayev N, Beloussov V, Strochkov V, Solomadin M, Granica J, Yegorov S. Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome. Microorganisms 2022; 10:microorganisms10122327. [PMID: 36557580 PMCID: PMC9785614 DOI: 10.3390/microorganisms10122327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic and heightened perception of the risk of emerging viral infections have boosted the efforts to better understand the virome or complete repertoire of viruses in health and disease, with a focus on infectious respiratory diseases. Next-generation sequencing (NGS) is widely used to study microorganisms, allowing the elucidation of bacteria and viruses inhabiting different body systems and identifying new pathogens. However, NGS studies suffer from a lack of standardization, in particular, due to various methodological approaches and no single format for processing the results. Here, we review the main methodological approaches and key stages for studies of the human virome, with an emphasis on virome changes during acute respiratory viral infection, with applications for clinical diagnostics and epidemiologic analyses.
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Affiliation(s)
- Nurlan Sandybayev
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Correspondence: ; Tel.: +7-778312-2058
| | - Vyacheslav Beloussov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Vitaliy Strochkov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
| | - Maxim Solomadin
- School of Pharmacy, Karaganda Medical University, Karaganda 100000, Kazakhstan
| | - Joanna Granica
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Sergey Yegorov
- Michael G. DeGroote Institute for Infectious Disease Research, Faculty of Health Sciences, McMaster University, Hamilton, ON L8S 4LB, Canada
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Metagenomic Sequencing for the Diagnosis of Plasmodium spp. with Different Levels of Parasitemia in EDTA Blood of Malaria Patients—A Proof-of-Principle Assessment. Int J Mol Sci 2022; 23:ijms231911150. [PMID: 36232449 PMCID: PMC9569645 DOI: 10.3390/ijms231911150] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Molecular diagnostic approaches are increasingly included in the diagnostic workup and even in the primary diagnosis of malaria in non-endemic settings, where it is difficult to maintain skillful microscopic malaria detection due to the rarity of the disease. Pathogen-specific nucleic acid amplification, however, bears the risk of overlooking other pathogens associated with febrile illness in returnees from the tropics. Here, we assessed the discriminatory potential of metagenomic sequencing for the identification of different Plasmodium species with various parasitemia in EDTA blood of malaria patients. Overall, the proportion of Plasmodium spp.-specific sequence reads in the assessed samples showed a robust positive correlation with parasitemia (Spearman r = 0.7307, p = 0.0001) and a robust negative correlation with cycle threshold (Ct) values of genus-specific real-time PCR (Spearman r = −0.8626, p ≤ 0.0001). Depending on the applied bioinformatic algorithm, discrimination on species level was successful in 50% (11/22) to 63.6% (14/22) instances. Limiting factors for the discrimination on species level were very low parasitemia, species-depending lacking availability of reliable reference genomes, and mixed infections with high variance of the proportion of the infecting species. In summary, metagenomic sequencing as performed in this study is suitable for the detection of malaria in human blood samples, but the diagnostic detection limit for a reliable discrimination on species level remains higher than for competing diagnostic approaches like microscopy and PCR.
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From Clinical Specimen to Whole Genome Sequencing of A(H3N2) Influenza Viruses: A Fast and Reliable High-Throughput Protocol. Vaccines (Basel) 2022; 10:vaccines10081359. [PMID: 36016246 PMCID: PMC9412868 DOI: 10.3390/vaccines10081359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
(1) Background: Over the last few years, there has been growing interest in the whole genome sequencing (WGS) of rapidly mutating pathogens, such as influenza viruses (IVs), which has led us to carry out in-depth studies on viral evolution in both research and diagnostic settings. We aimed at describing and determining the validity of a WGS protocol that can obtain the complete genome sequence of A(H3N2) IVs directly from clinical specimens. (2) Methods: RNA was extracted from 80 A(H3N2)-positive respiratory specimens. A one-step RT-PCR assay, based on the use of a single set of specific primers, was used to retro-transcribe and amplify the entire IV type A genome in a single reaction, thus avoiding additional enrichment approaches and host genome removal treatments. Purified DNA was quantified; genomic libraries were prepared and sequenced by using Illumina MiSeq platform. The obtained reads were evaluated for sequence quality and read-pair length. (3) Results: All of the study specimens were successfully amplified, and the purified DNA concentration proved to be suitable for NGS (at least 0.2 ng/µL). An acceptable coverage depth for all eight genes of influenza A(H3N2) virus was obtained for 90% (72/80) of the clinical samples with viral loads >105 genome copies/mL. The mean depth of sequencing ranged from 105 to 200 reads per position, with the majority of the mean depth values being above 103 reads per position. The total turnaround time per set of 20 samples was four working days, including sequence analysis. (4) Conclusions: This fast and reliable high-throughput sequencing protocol should be used for influenza surveillance and outbreak investigation.
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Maruapula D, Seatla KK, Morerinyane O, Molebatsi K, Giandhari J, de Oliveira T, Musonda RM, Leteane M, Mpoloka SW, Rowley CF, Moyo S, Gaseitsiwe S. Low-frequency HIV-1 drug resistance mutations in antiretroviral naïve individuals in Botswana. Medicine (Baltimore) 2022; 101:e29577. [PMID: 35838991 PMCID: PMC11132386 DOI: 10.1097/md.0000000000029577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/27/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Individuals living with human immunodeficiency virus (HIV) who experience virological failure (VF) after combination antiretroviral therapy (cART) initiation may have had low-frequency drug resistance mutations (DRMs) at cART initiation. There are no data on low-frequency DRMs among cART-naïve HIV-positive individuals in Botswana. METHODS We evaluated the prevalence of low-frequency DRMs among cART-naïve individuals previously sequenced using Sanger sequencing. The generated pol amplicons were sequenced by next-generation sequencing. RESULTS We observed low-frequency DRMs (detected at <20% in 33/103 (32%) of the successfully sequenced individuals, of whom four also had mutations detected at >20%. K65R was the most common low-frequency DRM detected in 8 individuals. Eighty-two of the 103 individuals had follow-up viral load data while on cART. Twenty-seven of the 82 individuals harbored low-frequency DRMs. Only 12 of 82 individuals experienced VF. The following low-frequency DRMs were observed in four individuals experiencing VF: K65R, K103N, V108I, and Y188C. No statistically significant difference was observed in the prevalence of low-frequency DRMs between individuals experiencing VF (4/12) and those not experiencing VF (23/70) (P = .97). However, individuals with non-nucleoside reverse transcriptase inhibitors-associated low-frequency DRMs were 2.68 times more likely to experience VF (odds ratio, 2.68; 95% confidential interval, 0.4-13.9) compared with those without (P = .22). CONCLUSION Next-generation sequencing was able to detect low-frequency DRMs in this cohort in Botswana, but these DRMs did not contribute significantly to VF.
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Affiliation(s)
- Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Kaelo K. Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- School of Allied Health Professions, University of Botswana, Gaborone, Botswana
| | | | - Kesaobaka Molebatsi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Statistics, University of Botswana, Gaborone, Botswana
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rosemary M. Musonda
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Melvin Leteane
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Sununguko W Mpoloka
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Christopher F. Rowley
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA
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Climaco-Arvizu S, Flores-López V, González-Torres C, Gaytán-Cervantes FJ, Hernández-García MC, Zárate-Segura PB, Chávez-Torres M, Tesoro-Cruz E, Pinto-Cardoso SM, Bekker-Méndez VC. Protease and gag diversity and drug resistance mutations among treatment-naive Mexican people living with HIV. BMC Infect Dis 2022; 22:447. [PMID: 35538426 PMCID: PMC9088029 DOI: 10.1186/s12879-022-07446-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/29/2022] [Indexed: 08/30/2023] Open
Abstract
Introduction In Mexico, HIV genotyping is performed in people living with HIV (PLWH) failing their first-line antiretroviral (ARV) regimen; it is not routinely done for all treatment-naive PLWH before ARV initiation. The first nationally representative survey published in 2016 reported that the prevalence of pretreatment drug mutations in treatment-naive Mexican PLWH was 15.5% to any antiretroviral drug and 10.6% to non-nucleoside reverse transcriptase inhibitors (NNRTIs) using conventional Sanger sequencing. Most reports in Mexico focus on HIV pol gene and nucleoside and non-nucleoside reverse transcriptase inhibitor (NRTI and NNRTI) drug resistance mutations (DRMs) prevalence, using Sanger sequencing, next-generation sequencing (NGS) or both. To our knowledge, NGS has not be used to detect pretreatment drug resistance mutations (DRMs) in the HIV protease (PR) gene and its substrate the Gag polyprotein. Methods Treatment-naive adult Mexican PLWH were recruited between 2016 and 2019. HIV Gag and protease sequences were obtained by NGS and DRMs were identified using the WHO surveillance drug resistance mutation (SDRM) list. Results One hundred PLWH attending a public national reference hospital were included. The median age was 28 years-old, and most were male. The median HIV viral load was 4.99 [4.39–5.40] log copies/mL and median CD4 cell count was 150 [68.0–355.78] cells/mm3. As expected, most sequences clustered with HIV-1 subtype B (97.9%). Major PI resistance mutations were detected: 8 (8.3%) of 96 patients at a detection threshold of 1% and 3 (3.1%) at a detection threshold of 20%. A total of 1184 mutations in Gag were detected, of which 51 have been associated with resistance to PI, most of them were detected at a threshold of 20%. Follow-up clinical data was available for 79 PLWH at 6 months post-ART initiation, seven PLWH failed their first ART regimen; however no major PI mutations were identified in these individuals at baseline. Conclusions The frequency of DRM in the HIV protease was 7.3% at a detection threshold of 1% and 3.1% at a detection threshold of 20%. NGS-based HIV drug resistance genotyping provide improved detection of DRMs. Viral load was used to monitor ARV response and treatment failure was 8.9%. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07446-8.
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Affiliation(s)
- Samantha Climaco-Arvizu
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr Daniel Méndez Hernández", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, C.P. 02990, México.,Laboratorio de Medicina Traslacional, Instituto Politécnico Nacional, Ciudad de México, México
| | | | - Carolina González-Torres
- División de Desarrollo de La Investigación, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | | | - María Concepción Hernández-García
- Instituto Mexicano del Seguro Social (IMSS), Hospital de Infectología "Dr Daniel Méndez Hernández", Centro Médico Nacional (CMN), La Raza", Ciudad de México, México
| | | | - Monserrat Chávez-Torres
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, C.P. 14080, México
| | - Emiliano Tesoro-Cruz
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr Daniel Méndez Hernández", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, C.P. 02990, México
| | - Sandra María Pinto-Cardoso
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, C.P. 14080, México.
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr Daniel Méndez Hernández", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, C.P. 02990, México.
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Joussef-Piña S, Nankya I, Nalukwago S, Baseke J, Rwambuya S, Winner D, Kyeyune F, Chervenak K, Thiel B, Asaad R, Dobrowolski C, Luttge B, Lawley B, Kityo CM, Boom WH, Karn J, Quiñones-Mateu ME. Reduced and highly diverse peripheral HIV-1 reservoir in virally suppressed patients infected with non-B HIV-1 strains in Uganda. Retrovirology 2022; 19:1. [PMID: 35033105 PMCID: PMC8760765 DOI: 10.1186/s12977-022-00587-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Our understanding of the peripheral human immunodeficiency virus type 1 (HIV-1) reservoir is strongly biased towards subtype B HIV-1 strains, with only limited information available from patients infected with non-B HIV-1 subtypes, which are the predominant viruses seen in low- and middle-income countries (LMIC) in Africa and Asia. RESULTS In this study, blood samples were obtained from well-suppressed ART-experienced HIV-1 patients monitored in Uganda (n = 62) or the U.S. (n = 50), with plasma HIV-1 loads < 50 copies/ml and CD4+ T-cell counts > 300 cells/ml. The peripheral HIV-1 reservoir, i.e., cell-associated HIV-1 RNA and proviral DNA, was characterized using our novel deep sequencing-based EDITS assay. Ugandan patients were slightly younger (median age 43 vs 49 years) and had slightly lower CD4+ counts (508 vs 772 cells/ml) than U.S. individuals. All Ugandan patients were infected with non-B HIV-1 subtypes (31% A1, 64% D, or 5% C), while all U.S. individuals were infected with subtype B viruses. Unexpectedly, we observed a significantly larger peripheral inducible HIV-1 reservoir in U.S. patients compared to Ugandan individuals (48 vs. 11 cell equivalents/million cells, p < 0.0001). This divergence in reservoir size was verified measuring proviral DNA (206 vs. 88 cell equivalents/million cells, p < 0.0001). However, the peripheral HIV-1 reservoir was more diverse in Ugandan than in U.S. individuals (8.6 vs. 4.7 p-distance, p < 0.0001). CONCLUSIONS The smaller, but more diverse, peripheral HIV-1 reservoir in Ugandan patients might be associated with viral (e.g., non-B subtype with higher cytopathicity) and/or host (e.g., higher incidence of co-infections or co-morbidities leading to less clonal expansion) factors. This highlights the need to understand reservoir dynamics in diverse populations as part of ongoing efforts to find a functional cure for HIV-1 infection in LMICs.
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Affiliation(s)
- Samira Joussef-Piña
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Immaculate Nankya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Sophie Nalukwago
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Joy Baseke
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Sandra Rwambuya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Dane Winner
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Fred Kyeyune
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Keith Chervenak
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Bonnie Thiel
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Robert Asaad
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Curtis Dobrowolski
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Benjamin Luttge
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Blair Lawley
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland Street, P.O. Box 56, Dunedin, New Zealand
| | - Cissy M Kityo
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - W Henry Boom
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jonathan Karn
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Miguel E Quiñones-Mateu
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda.
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland Street, P.O. Box 56, Dunedin, New Zealand.
- Webster Centre for Infectious Diseases, University of Otago, Dunedin, New Zealand.
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Fogel JM, Bonsall D, Cummings V, Bowden R, Golubchik T, de Cesare M, Wilson EA, Gamble T, Del Rio C, Batey DS, Mayer KH, Farley JE, Hughes JP, Remien RH, Beyrer C, Fraser C, Eshleman SH. Performance of a high-throughput next-generation sequencing method for analysis of HIV drug resistance and viral load. J Antimicrob Chemother 2021; 75:3510-3516. [PMID: 32772080 DOI: 10.1093/jac/dkaa352] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/13/2020] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES To evaluate the performance of a high-throughput research assay for HIV drug resistance testing based on whole genome next-generation sequencing (NGS) that also quantifies HIV viral load. METHODS Plasma samples (n = 145) were obtained from HIV-positive MSM (HPTN 078). Samples were analysed using clinical assays (the ViroSeq HIV-1 Genotyping System and the Abbott RealTime HIV-1 Viral Load assay) and a research assay based on whole-genome NGS (veSEQ-HIV). RESULTS HIV protease and reverse transcriptase sequences (n = 142) and integrase sequences (n = 138) were obtained using ViroSeq. Sequences from all three regions were obtained for 100 (70.4%) of the 142 samples using veSEQ-HIV; results were obtained more frequently for samples with higher viral loads (93.5% for 93 samples with >5000 copies/mL; 50.0% for 26 samples with 1000-5000 copies/mL; 0% for 23 samples with <1000 copies/mL). For samples with results from both methods, drug resistance mutations (DRMs) were detected in 33 samples using ViroSeq and 42 samples using veSEQ-HIV (detection threshold: 5.0%). Overall, 146 major DRMs were detected; 107 were detected by both methods, 37 were detected by veSEQ-HIV only (frequency range: 5.0%-30.6%) and two were detected by ViroSeq only. HIV viral loads estimated by veSEQ-HIV strongly correlated with results from the Abbott RealTime Viral Load assay (R2 = 0.85; n = 142). CONCLUSIONS The NGS-based veSEQ-HIV method provided results for most samples with higher viral loads, was accurate for detecting major DRMs, and detected mutations at lower levels compared with a method based on population sequencing. The veSEQ-HIV method also provided HIV viral load data.
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Affiliation(s)
- Jessica M Fogel
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David Bonsall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Vanessa Cummings
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Ethan A Wilson
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Carlos Del Rio
- Hubert Department of Global Health, Emory University Rollins School of Public Health, Atlanta, GA, USA.,Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - D Scott Batey
- Department of Social Work, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kenneth H Mayer
- Department of Medicine, Harvard Medical School, Boston, MA, USA.,Fenway Institute, Boston, MA, USA
| | - Jason E Farley
- The REACH Initiative, Johns Hopkins University School of Nursing, Baltimore, MD, USA
| | - James P Hughes
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Robert H Remien
- HIV Center for Clinical and Behavioral Studies, NY State Psychiatric Institute, New York, NY, USA.,Department of Psychiatry, Columbia University, New York, NY, USA
| | - Chris Beyrer
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susan H Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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10
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Rfaki A, Touil N, Hemlali M, Alaoui Amine S, Melloul M, El Alaoui MA, Elannaz H, Lahlou AI, Elouennass M, Ennibi K, El Fahime E. Complete Genome Sequence of a SARS-CoV-2 Strain Sampled in Morocco in May 2020, Obtained Using Sanger Sequencing. Microbiol Resour Announc 2021; 10:e00387-21. [PMID: 34016683 PMCID: PMC8188342 DOI: 10.1128/mra.00387-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 04/30/2021] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain was obtained. The strain was isolated from a nasopharyngeal swab specimen from a female patient in Rabat, Morocco, with coronavirus disease 2019 (COVID-19). This strain belongs to clade 20A and has 12 mutations and 8 amino acid substitutions compared to the reference strain Wuhan/Hu-1/2019.
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Affiliation(s)
- Abderrazak Rfaki
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Nadia Touil
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
- Unité de Culture Cellulaire, CVMIT, HMI Med V, Rabat, Morocco
| | - Mouhssine Hemlali
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Sanaâ Alaoui Amine
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Marouane Melloul
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Moulay Abdelaziz El Alaoui
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
- Laboratoire de Botanique et de Protection des Plantes, UFR de Mycologie, Département de Biologie, Faculté des Sciences, Université Ibn Tofail, Kenitra, Morocco
| | - Hicham Elannaz
- Unité de Culture Cellulaire, CVMIT, HMI Med V, Rabat, Morocco
| | | | | | - Khalid Ennibi
- Unité de Culture Cellulaire, CVMIT, HMI Med V, Rabat, Morocco
| | - Elmostafa El Fahime
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
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11
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Ben Chehida S, Filloux D, Fernandez E, Moubset O, Hoareau M, Julian C, Blondin L, Lett JM, Roumagnac P, Lefeuvre P. Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses. Microorganisms 2021; 9:903. [PMID: 33922452 PMCID: PMC8147096 DOI: 10.3390/microorganisms9050903] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 01/23/2023] Open
Abstract
Next-generation sequencing (NGS), through the implementation of metagenomic protocols, has led to the discovery of thousands of new viruses in the last decade. Nevertheless, these protocols are still laborious and costly to implement, and the technique has not yet become routine for everyday virus characterization. Within the context of CRESS DNA virus studies, we implemented two alternative long-read NGS protocols, one that is agnostic to the sequence (without a priori knowledge of the viral genome) and the other that use specific primers to target a virus (with a priori). Agnostic and specific long read NGS-based assembled genomes of two capulavirus strains were compared to those obtained using the gold standard technique of Sanger sequencing. Both protocols allowed the detection and accurate full genome characterization of both strains. Globally, the assembled genomes were very similar (99.5-99.7% identity) to the Sanger sequences consensus, but differences in the homopolymeric tracks of these sequences indicated a specific lack of accuracy of the long reads NGS approach that has yet to be improved. Nevertheless, the use of the bench-top sequencer has proven to be a credible alternative in the context of CRESS DNA virus study and could offer a new range of applications not previously accessible.
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Affiliation(s)
- Selim Ben Chehida
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France; (S.B.C.); (M.H.); (J.-M.L.)
| | - Denis Filloux
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Oumaima Moubset
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Murielle Hoareau
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France; (S.B.C.); (M.H.); (J.-M.L.)
| | - Charlotte Julian
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Laurence Blondin
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Jean-Michel Lett
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France; (S.B.C.); (M.H.); (J.-M.L.)
| | - Philippe Roumagnac
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France; (S.B.C.); (M.H.); (J.-M.L.)
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12
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Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review. Viruses 2021; 13:v13030412. [PMID: 33807625 PMCID: PMC7999175 DOI: 10.3390/v13030412] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 12/24/2022] Open
Abstract
Plant viral diseases are the foremost threat to sustainable agriculture, leading to several billion dollars in losses every year. Many viruses infecting several crops have been described in the literature; however, new infectious viruses are emerging frequently through outbreaks. For the effective treatment and prevention of viral diseases, there is great demand for new techniques that can provide accurate identification on the causative agents. With the advancements in biochemical and molecular biology techniques, several diagnostic methods with improved sensitivity and specificity for the detection of prevalent and/or unknown plant viruses are being continuously developed. Currently, serological and nucleic acid methods are the most widely used for plant viral diagnosis. Nucleic acid-based techniques that amplify target DNA/RNA have been evolved with many variants. However, there is growing interest in developing techniques that can be based in real-time and thus facilitate in-field diagnosis. Next-generation sequencing (NGS)-based innovative methods have shown great potential to detect multiple viruses simultaneously; however, such techniques are in the preliminary stages in plant viral disease diagnostics. This review discusses the recent progress in the use of NGS-based techniques for the detection, diagnosis, and identification of plant viral diseases. New portable devices and technologies that could provide real-time analyses in a relatively short period of time are prime important for in-field diagnostics. Current development and application of such tools and techniques along with their potential limitations in plant virology are likewise discussed in detail.
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13
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Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. mSphere 2021; 6:6/1/e01043-20. [PMID: 33408229 PMCID: PMC7845592 DOI: 10.1128/msphere.01043-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The D222G/N substitution in the hemagglutinin (HA) protein of influenza A(H1N1)pdm09 virus has been reported to be associated with disease severity and mortality in numerous previous studies. In the present study, 75% of lower respiratory samples contained heterogeneous influenza populations that carried different amino acids at position 222 of the HA protein, whereas all upper respiratory samples only contained the wild-type 222D. The influenza A(H1N1)pdm09 virus emerged in April 2009 with an unusual incidence of severe disease and mortality, and currently circulates as a seasonal influenza virus. Previous studies using consensus viral genome sequencing data have overlooked the viral genomic and phenotypic diversity. Next-generation sequencing (NGS) may instead be used to characterize viral populations in an unbiased manner and to measure within-host genetic diversity. In this study, we used NGS analysis to investigate the within-host genetic diversity of influenza A(H1N1)pdm09 virus in the upper and lower respiratory samples from nine patients who were admitted to the intensive care unit (ICU). A total of 47 amino acid substitution positions were found to differ between the upper and lower respiratory tract samples from all patients. However, the D222G/N substitution in hemagglutinin (HA) protein was the only amino acid substitution common to multiple patients. Furthermore, the substitution was detected only in the six samples from the lower respiratory tract. Therefore, it is important to investigate influenza A(H1N1)pdm09 virus populations using multiple paired samples from the upper and lower respiratory tract to avoid overlooking potentially important substitutions, especially in patients with severe disease. IMPORTANCE The D222G/N substitution in the hemagglutinin (HA) protein of influenza A(H1N1)pdm09 virus has been reported to be associated with disease severity and mortality in numerous previous studies. In the present study, 75% of lower respiratory samples contained heterogeneous influenza populations that carried different amino acids at position 222 of the HA protein, whereas all upper respiratory samples only contained the wild-type 222D. These results suggest the influenza A(H1N1)pdm09 virus has diversified inside the host owing to differences in tissue specificity. In this study, the within-host genetic diversity of influenza A(H1N1)pdm09 virus was investigated for the first time using next-generation sequencing analysis of the viral whole-genome in samples extracted from the upper and lower respiratory tracts of patients with severe disease.
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14
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A New Method for Next-Generation Sequencing of the Full Hepatitis B Virus Genome from A Clinical Specimen: Impact for Virus Genotyping. Microorganisms 2020; 8:microorganisms8091391. [PMID: 32932752 PMCID: PMC7564258 DOI: 10.3390/microorganisms8091391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/28/2020] [Accepted: 09/07/2020] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) is an enveloped virus that induces chronic liver disease. HBV has been classified into eight genotypes (A–H) according to its genome sequence by using Sanger sequencing or reverse hybridization. Sanger sequencing is often restricted to analyzing the S gene and is inaccurate for detecting minority genetic variants, whereas reverse hybridization detects only known mutations. Next-generation sequencing (NGS) is a robust tool for clinical virology with different protocols available. The objective of this study was to develop a new method for the study of viral genetic polymorphisms or more accurate genotyping using genome amplification followed by NGS. Plasma obtained from five chronically infected HBV individuals was used for viral DNA isolation. HBV full-genome PCR amplification was the enrichment method for NGS. Primers were used to amplify all HBV genotypes in three overlapping amplicons, following a tagmentation step and Illumina NGS. For phylogenetic analysis, sequences were extracted from the HBVdb database. We were able to amplify a full HBV genome; further, NGS was shown to be a robust method and allowed better genotyping, mainly in patients carrying mixed genotypes, classified according to other techniques. This new method may be significant for whole genome analyses, including other viruses.
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15
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Hepatitis C Reinfection in People Who Inject Drugs in Resource-Limited Countries: A Systematic Review and Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17144951. [PMID: 32659974 PMCID: PMC7400365 DOI: 10.3390/ijerph17144951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/01/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
Hepatitis C (HCV) is a global pandemic. The World Health Organization has developed a strategic plan for HCV elimination that focuses on low- and middle-income countries (LMICs) and high-risk populations, including people who inject drugs (PWID). While direct-acting antiviral (DAA) therapies are highly effective at eliminating HCV infections and have few side effects, medical professionals and policymakers remain concerned about the risk of reinfection among PWID. This study is a systematic review of research measuring the rate of HCV reinfection among PWID in LMICs and identifies additional areas for further research. A systematic search strategy was used to identify studies documenting HCV reinfection after sustained virologic response in PWID in LMICs. We refined results to include studies where at least 50% of participants had DAA treatment for primary HCV infection. Pooled reinfection rate was calculated across all studies. Seven studies met eligibility criteria. Most studies were conducted in six upper middle-income countries (Mexico, Romania, Russia, Taiwan, Georgi, and Brazil) and one lower middle-income country (Bangladesh) with a total of 7665 participants. No study included information from PWID in low-income countries. Sample sizes ranged from 200 to 3004 individuals, with demographic data missing for most participants. Four studies used deep gene sequencing, and reflex genotyping procedures to differentiate reinfection (infection by a different HCV genotype/subtype) from virologic relapse (infection by the same strain). The follow-up time of people cured from primary chronic HCV infection ranged from 12 weeks to 6.6 years. The pooled reinfection rate of all seven studies was 2.8 (range: 0.02 to 10.5) cases per 100 person-years (PY). In the five studies that differentiated relapse from reinfection, the incidence of reinfection was 1.0 per 100 PY. To date, research on reinfection rates among PWID in LMICs remains limited. Research focused on PWID in low-income countries is particularly needed to inform clinical decision making and evidence-based programs. While rates of reinfection among PWID who complete DAA treatment in upper and lower middle-income countries were similar or lower than rates observed in PWID in high-income countries, the rates were highly variable and factors may influence the accuracy of these measurements. This systematic review identifies several areas for continued research. Policies concerning access to HCV testing and treatment should be comprehensive and not place restrictions on PWID in these settings.
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16
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Lu R, Niu P, Zhao L, Wang H, Wang W, Tan W. Sequencing the Complete Genome of COVID-19 Virus from Clinical Samples Using the Sanger Method. China CDC Wkly 2020; 2:447-452. [PMID: 34594676 PMCID: PMC8393061 DOI: 10.46234/ccdcw2020.088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 12/13/2022] Open
Abstract
What is already known on this topic? Coronavirus disease 2019 (COVID-19), a disease caused by a novel human coronavirus named the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or COVID-19 virus, was reported in December 2019. Complete genomes of the COVID-19 virus from clinical samples using next generation sequencing (NGS) have been reported. What is added by this report? Here we provide the technical data for sequencing complete genome of COVID-19 virus from clinical samples using the Sanger method. Two complete COVID-19 virus genome sequences (named WH19004-S and GX0002) were obtained from clinical samples of COVID-19 patients, and two single nucleotide polymorphisms (SNPs) in ORF7a (T/C, nt 27,493) and ORF8 (T/C, nt 28,253) of WH19004-S were identified by Sanger sequencing. What are the implications for public health practice? The COVID-19 virus genome sequencing by Sanger method reported here could be used to generate data of high enough quality without requirement for expensive NGS equipment, which support sequencing complete genomes from clinical samples and monitoring of viral genetic variations of COVID-19 infections.
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Affiliation(s)
- Roujian Lu
- Key Laboratory of Biosafety, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Peihua Niu
- Key Laboratory of Biosafety, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Li Zhao
- Key Laboratory of Biosafety, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Huijuan Wang
- Key Laboratory of Biosafety, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Wenling Wang
- Key Laboratory of Biosafety, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Wenjie Tan
- Key Laboratory of Biosafety, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
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17
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Howison M, Coetzer M, Kantor R. Measurement error and variant-calling in deep Illumina sequencing of HIV. Bioinformatics 2020; 35:2029-2035. [PMID: 30407489 DOI: 10.1093/bioinformatics/bty919] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 09/21/2018] [Accepted: 11/06/2018] [Indexed: 01/23/2023] Open
Abstract
MOTIVATION Next-generation deep sequencing of viral genomes, particularly on the Illumina platform, is increasingly applied in HIV research. Yet, there is no standard protocol or method used by the research community to account for measurement errors that arise during sample preparation and sequencing. Correctly calling high and low-frequency variants while controlling for erroneous variants is an important precursor to downstream interpretation, such as studying the emergence of HIV drug-resistance mutations, which in turn has clinical applications and can improve patient care. RESULTS We developed a new variant-calling pipeline, hivmmer, for Illumina sequences from HIV viral genomes. First, we validated hivmmer by comparing it to other variant-calling pipelines on real HIV plasmid datasets. We found that hivmmer achieves a lower rate of erroneous variants, and that all methods agree on the frequency of correctly called variants. Next, we compared the methods on an HIV plasmid dataset that was sequenced using Primer ID, an amplicon-tagging protocol, which is designed to reduce errors and amplification bias during library preparation. We show that the Primer ID consensus exhibits fewer erroneous variants compared to the variant-calling pipelines, and that hivmmer more closely approaches this low error rate compared to the other pipelines. The frequency estimates from the Primer ID consensus do not differ significantly from those of the variant-calling pipelines. AVAILABILITY AND IMPLEMENTATION hivmmer is freely available for non-commercial use from https://github.com/kantorlab/hivmmer. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mark Howison
- Watson Institute for International and Public Affairs
| | - Mia Coetzer
- Division of Infectious Diseases, The Alpert Medical School, Brown University, Providence, RI, USA
| | - Rami Kantor
- Division of Infectious Diseases, The Alpert Medical School, Brown University, Providence, RI, USA
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18
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Batista FM, Stapleton T, Lowther JA, Fonseca VG, Shaw R, Pond C, Walker DI, van Aerle R, Martinez-Urtaza J. Whole Genome Sequencing of Hepatitis A Virus Using a PCR-Free Single-Molecule Nanopore Sequencing Approach. Front Microbiol 2020; 11:874. [PMID: 32523561 PMCID: PMC7261825 DOI: 10.3389/fmicb.2020.00874] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/14/2020] [Indexed: 12/18/2022] Open
Abstract
Hepatitis A virus (HAV) is one of the most common causes of acute viral hepatitis in humans. Although HAV has a relatively small genome, there are several factors limiting whole genome sequencing such as PCR amplification artefacts and ambiguities in de novo assembly. The recently developed Oxford Nanopore technologies (ONT) allows single-molecule sequencing of long-size fragments of DNA or RNA using PCR-free strategies. We have sequenced the whole genome of HAV using a PCR-free approach by direct reverse-transcribed sequencing. We were able to sequence HAV cDNA and obtain reads over 7 kilobases in length containing almost the whole genome of the virus. The comparison of these raw long nanopore reads with the HAV reference wild type revealed a nucleotide sequence identity between 81.1 and 96.6%. By de novo assembly of all HAV reads we obtained a consensus sequence of 7362 bases, with a nucleotide sequence identity of 99.0% with the genome of the HAV strain pHM175/18f. When the assembly was performed using as reference the HAV strain pHM175/18f a consensus with a sequence similarity of 99.8 % was obtained. We have also used an ONT amplicon-based assay to sequence two fragments of the VP3 and VP1 regions which showed a sequence similarity of 100% with matching regions of the consensus sequence obtained using the direct cDNA sequencing approach. This study showed the applicability of ONT sequencing technologies to obtain the whole genome of HAV by direct cDNA nanopore sequencing, highlighting the utility of this PCR-free approach for HAV characterization and potentially other viruses of the Picornaviridae family.
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Affiliation(s)
- Frederico M Batista
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Tina Stapleton
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - James A Lowther
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Vera G Fonseca
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Rebecca Shaw
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Christopher Pond
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - David I Walker
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Jaime Martinez-Urtaza
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom.,Department of Genetics and Microbiology, Facultat de Biociències - Edifici C, Campus Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
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19
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Hahn A, Podbielski A, Meyer T, Zautner AE, Loderstädt U, Schwarz NG, Krüger A, Cadar D, Frickmann H. On detection thresholds-a review on diagnostic approaches in the infectious disease laboratory and the interpretation of their results. Acta Trop 2020; 205:105377. [PMID: 32007448 DOI: 10.1016/j.actatropica.2020.105377] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/18/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023]
Abstract
Diagnostic testing in the infectious disease laboratory facilitates decision-making by physicians at the bedside as well as epidemiological assessments and surveillance at study level. Problems may arise if test results are uncritically considered as being the same as the unknown true value. To allow a better understanding, the influence of external factors on the interpretation of test results is introduced with the example of prevalence, followed by the presentation of strengths and weaknesses of important techniques in the infectious disease laboratory like microscopy, cultural diagnostics, serology, mass spectrometry, nucleic acid amplification and hypothesis-free metagenomic sequencing with focus on basic, high-technology and potential future approaches. Special problems like multiplex testing as well as uncertainty of test evaluations, if no gold standard is available, are also stressed with a final glimpse on emerging future technologies for the infectious disease laboratory. In the conclusions, suitability for point-of-care-testing and field laboratory applications is summarized. The aim is to illustrate the limitations of diagnostic accuracy to both clinicians and study planners and to stress the importance of close cooperation with experts in laboratory disciplines so as to avoid potentially critical misunderstandings due to inappropriate interpretation of diagnostic test results.
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Affiliation(s)
- Andreas Hahn
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Andreas Podbielski
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Thomas Meyer
- Department of Dermatology, St. Josef Hospital, Bochum, Germany
| | - Andreas Erich Zautner
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Ulrike Loderstädt
- Bernhard Nocht Institute for Tropical Medicine Hamburg, Hamburg, Germany
| | | | - Andreas Krüger
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany
| | - Daniel Cadar
- Bernhard Nocht Institute for Tropical Medicine Hamburg, Hamburg, Germany
| | - Hagen Frickmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany; Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany.
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Single-molecular real-time deep sequencing reveals the dynamics of multi-drug resistant haplotypes and structural variations in the hepatitis C virus genome. Sci Rep 2020; 10:2651. [PMID: 32060395 PMCID: PMC7021670 DOI: 10.1038/s41598-020-59397-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/24/2020] [Indexed: 12/25/2022] Open
Abstract
While direct-acting antivirals (DAAs) for hepatitis C virus (HCV) have dramatically progressed, patients still suffer from treatment failures. For the radical eradication of HCV, a deeper understanding of multiple resistance-associated substitutions (RASs) at the single-clone level is essential. To understand HCV quasispecies and their dynamics during DAA treatment, we applied single-molecule real-time (SMRT) deep sequencing on sera from 12 patients with genotype-1b HCV infections with DAA treatment failures, both pre- and post-treatment. We identified >3.2 kbp sequences between NS3 and NS5A genes of 187,539 clones in total, classifying into haplotype codes based on the linkage of seven RAS loci. The number of haplotype codes during the treatment, per sample, significantly decreased from 14.67 ± 9.12 to 6.58 ± 7.1, while the number of nonsynonymous codons on the seven RAS loci, per clone, significantly increased from 1.50 ± 0.92 to 3.64 ± 0.75. In five cases, the minority multi-drug resistant haplotypes at pre-treatment were identical to the major haplotypes at relapse. Moreover, various structural variations (SVs) were detected and their dynamics analysed. These results suggest that SMRT deep sequencing is useful for detecting minority haplotypes and SVs, and to evaluate the dynamics of viral genomes at the single-clone level.
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21
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Dailey PJ, Elbeik T, Holodniy M. Companion and complementary diagnostics for infectious diseases. Expert Rev Mol Diagn 2020; 20:619-636. [PMID: 32031431 DOI: 10.1080/14737159.2020.1724784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Companion diagnostics (CDx) are important in oncology therapeutic decision-making, but specific regulatory-approved CDx for infectious disease treatment are officially lacking. While not approved as CDx, several ID diagnostics are used as CDx. The diagnostics community, manufacturers, and regulatory agencies have made major efforts to ensure that diagnostics for new antimicrobials are available at or near release of new agents. AREAS COVERED This review highlights the status of Complementary and companion diagnostic (c/CDx) in the infectious disease literature, with a focus on genotypic antimicrobial resistance testing against pathogens as a class of diagnostic tests. EXPERT OPINION CRISPR, sepsis markers, and narrow spectrum antimicrobials, in addition to current and emerging technologies, present opportunities for infectious disease c/CDx. Challenges include slow guideline revision, high costs for regulatory approval, lengthy buy in by agencies, discordant pharmaceutical/diagnostic partnerships, and higher treatment costs. The number of patients and available medications used to treat different infectious diseases is well suited to support competing diagnostic tests. However, newer approaches to treatment (for example, narrow spectrum antibiotics), may be well suited for a small number of patients, i.e. a niche market in support of a CDx. The current emphasis is rapid and point-of-care (POC) diagnostic platforms as well as changes in treatment.
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Affiliation(s)
- Peter J Dailey
- School of Public Health, University of California, Berkeley , Berkeley, CA, USA.,The Foundation for Innovative New Diagnostics (FIND) , Geneva, Switzerland
| | - Tarek Elbeik
- VA Palo Alto Health Care System, Department of Veterans Affairs , Palo Alto, CA, USA
| | - Mark Holodniy
- VA Palo Alto Health Care System, Department of Veterans Affairs , Palo Alto, CA, USA.,Division of Infectious Diseases and Geographic Medicine, Stanford University , Stanford, CA, USA
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22
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Chen Q, Perales C, Soria ME, García-Cehic D, Gregori J, Rodríguez-Frías F, Buti M, Crespo J, Calleja JL, Tabernero D, Vila M, Lázaro F, Rando-Segura A, Nieto-Aponte L, Llorens-Revull M, Cortese MF, Fernandez-Alonso I, Castellote J, Niubó J, Imaz A, Xiol X, Castells L, Riveiro-Barciela M, Llaneras J, Navarro J, Vargas-Blasco V, Augustin S, Conde I, Rubín Á, Prieto M, Torras X, Margall N, Forns X, Mariño Z, Lens S, Bonacci M, Pérez-Del-Pulgar S, Londoño MC, García-Buey ML, Sanz-Cameno P, Morillas R, Martró E, Saludes V, Masnou-Ridaura H, Salmerón J, Quíles R, Carrión JA, Forné M, Rosinach M, Fernández I, García-Samaniego J, Madejón A, Castillo-Grau P, López-Núñez C, Ferri MJ, Durández R, Sáez-Royuela F, Diago M, Gimeno C, Medina R, Buenestado J, Bernet A, Turnes J, Trigo-Daporta M, Hernández-Guerra M, Delgado-Blanco M, Cañizares A, Arenas JI, Gomez-Alonso MJ, Rodríguez M, Deig E, Olivé G, Río OD, Cabezas J, Quiñones I, Roget M, Montoliu S, García-Costa J, Force L, Blanch S, Miralbés M, López-de-Goicoechea MJ, García-Flores A, Saumoy M, Casanovas T, Baliellas C, Gilabert P, Martin-Cardona A, Roca R, Barenys M, Villaverde J, Salord S, Camps B, Silvan di Yacovo M, Ocaña I, Sauleda S, Bes M, Carbonell J, Vargas-Accarino E, Ruzo SP, Guerrero-Murillo M, Von Massow G, Costafreda MI, López RM, González-Moreno L, Real Y, Acero-Fernández D, Viroles S, Pamplona X, Cairó M, Ocete MD, Macías-Sánchez JF, Estébanez A, Quer JC, Mena-de-Cea Á, Otero A, Castro-Iglesias Á, Suárez F, Vázquez Á, Vieito D, López-Calvo S, Vázquez-Rodríguez P, Martínez-Cerezo FJ, Rodríguez R, Macenlle R, Cachero A, Mereish G, Mora-Moruny C, Fábregas S, Sacristán B, Albillos A, Sánchez-Ruano JJ, Baluja-Pino R, Fernández-Fernández J, González-Portela C, García-Martin C, Sánchez-Antolín G, Andrade RJ, Simón MA, Pascasio JM, Romero-Gómez M, Antonio Del-Campo J, Domingo E, Esteban R, Esteban JI, Quer J. Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure. Antiviral Res 2020; 174:104694. [PMID: 31857134 DOI: 10.1016/j.antiviral.2019.104694] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 10/24/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
A percentage of hepatitis C virus (HCV)-infected patients fail direct acting antiviral (DAA)-based treatment regimens, often because of drug resistance-associated substitutions (RAS). The aim of this study was to characterize the resistance profile of a large cohort of patients failing DAA-based treatments, and investigate the relationship between HCV subtype and failure, as an aid to optimizing management of these patients. A new, standardized HCV-RAS testing protocol based on deep sequencing was designed and applied to 220 previously subtyped samples from patients failing DAA treatment, collected in 39 Spanish hospitals. The majority had received DAA-based interferon (IFN) α-free regimens; 79% had failed sofosbuvir-containing therapy. Genomic regions encoding the nonstructural protein (NS) 3, NS5A, and NS5B (DAA target regions) were analyzed using subtype-specific primers. Viral subtype distribution was as follows: genotype (G) 1, 62.7%; G3a, 21.4%; G4d, 12.3%; G2, 1.8%; and mixed infections 1.8%. Overall, 88.6% of patients carried at least 1 RAS, and 19% carried RAS at frequencies below 20% in the mutant spectrum. There were no differences in RAS selection between treatments with and without ribavirin. Regardless of the treatment received, each HCV subtype showed specific types of RAS. Of note, no RAS were detected in the target proteins of 18.6% of patients failing treatment, and 30.4% of patients had RAS in proteins that were not targets of the inhibitors they received. HCV patients failing DAA therapy showed a high diversity of RAS. Ribavirin use did not influence the type or number of RAS at failure. The subtype-specific pattern of RAS emergence underscores the importance of accurate HCV subtyping. The frequency of "extra-target" RAS suggests the need for RAS screening in all three DAA target regions.
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Affiliation(s)
- Qian Chen
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Celia Perales
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - María Eugenia Soria
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Damir García-Cehic
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Gregori
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Roche Diagnostics SL, Sant Cugat del Valles, Barcelona, Spain
| | - Francisco Rodríguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | - María Buti
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Crespo
- Gastroenterology and Hepatology Department, Instituto de Investigación (IDIVAL), Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | | | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | - Marta Vila
- Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | - Fernando Lázaro
- Microbiology Department, Hospital Universitario La Paz, Madrid, Spain
| | | | | | - Meritxell Llorens-Revull
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Irati Fernandez-Alonso
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - José Castellote
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Jordi Niubó
- Microbiology Department, Hospital Universitari de Bellvitge, Barcelona
| | - Arkaitz Imaz
- HIV and STI Unit, Infectious Diseases Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Xavier Xiol
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Lluís Castells
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Mar Riveiro-Barciela
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Llaneras
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Víctor Vargas-Blasco
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Salvador Augustin
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Conde
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario La Fe, Valencia, Spain
| | - Ángel Rubín
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario La Fe, Valencia, Spain
| | - Martín Prieto
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario La Fe, Valencia, Spain
| | - Xavier Torras
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Microbiology Department, Hospital Universitari Santa Creu i Sant Pau, Barcelona, Spain
| | - Nuria Margall
- Digestive Pathology Unit, Hospital Universitari Santa Creu i Sant Pau, Barcelona, Spain
| | - Xavier Forns
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Zoe Mariño
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Sabela Lens
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Martin Bonacci
- Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Sofía Pérez-Del-Pulgar
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Maria Carlota Londoño
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | | | | | - Rosa Morillas
- Liver Unit, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Elisa Martró
- Microbiology Department, Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Institut de Recerca Germans Trias i Pujol (IGTP), Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Verónica Saludes
- Microbiology Department, Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Institut de Recerca Germans Trias i Pujol (IGTP), Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | | | - Javier Salmerón
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Complejo Hospitalario de Granada, Granada, Spain
| | - Rosa Quíles
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Complejo Hospitalario de Granada, Granada, Spain
| | - José Antonio Carrión
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Parc de Salut Mar - Hospital del Mar, Barcelona, Spain
| | - Montserrat Forné
- Gastroenterology Unit, Hospital Universitari Mútua Terrassa, Spain
| | - Mercè Rosinach
- Gastroenterology Unit, Hospital Universitari Mútua Terrassa, Spain
| | | | - Javier García-Samaniego
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ) - Hospital Universitario La Paz, Madrid, Spain
| | - Antonio Madejón
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ) - Hospital Universitario La Paz, Madrid, Spain
| | - Pilar Castillo-Grau
- Liver Unit, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ) - Hospital Universitario La Paz, Madrid, Spain
| | - Carme López-Núñez
- Gastroenterology Department, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - María José Ferri
- Clinical Laboratory, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - Rosa Durández
- Laboratori Territorial - Hospital Santa Caterina, Girona, Spain
| | - Federico Sáez-Royuela
- Gastroenterology and Hepatology Depart., Hospital Universitario de Burgos, Burgos, Spain
| | - Moisés Diago
- Liver Unit, Hospital General de Valencia, Valencia, Spain
| | | | - Rafael Medina
- Microbiology Unit, Hospital General de Valencia, Valencia, Spain
| | - Juan Buenestado
- Medicine Department-Medical School, Hospital Univ. Arnau de Vilanova, Lleida, Spain
| | - Albert Bernet
- Microbiology Department, Hospital Universitari Arnau de Vilanova, Lleida, Spain
| | - Juan Turnes
- Gastroenterology and Hepatology Department, Instituto de Investigación Sanitaria Galicia Sur (IISGS) - Complejo Hospitalario de Pontevedra, Pontevedra, Spain
| | - Matilde Trigo-Daporta
- Microbiology and Parasitology Department, Complejo Hospitalario de Pontevedra, Pontevedra, Spain
| | | | | | - Angelina Cañizares
- Microbiology Department, Institut de Investigación Biomédica de a Coruña (INIBIC) - Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | | | | | - Manuel Rodríguez
- Gastroenterology Depart., Central University Hospital of Asturias (HUCA), Oviedo, Spain
| | | | - Gemma Olivé
- Sant Jaume de Calella County Hospital, Barcelona, Spain
| | - Oscar Del Río
- Sant Jaume de Calella County Hospital, Barcelona, Spain
| | - Joaquín Cabezas
- Gastroenterology and Hepatology Department, Instituto de Investigación (IDIVAL), Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Ildefonso Quiñones
- Gastroenterology Department, Dr Negrin University Hospital of Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Mercè Roget
- Liver Unit, Consorci Sanitari de Terrassa - Hospital de Terrassa, Terrassa, Spain
| | - Silvia Montoliu
- Gastroenterology Unit, Joan XXIII University Hospital, Tarragona, Spain
| | - Juan García-Costa
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | | | - Silvia Blanch
- Hospital Universitari Sant Pau i Santa Tecla, Tarragona, Spain
| | - Miguel Miralbés
- Gastroenterology Department, Hospital Universitari Santa Maria de Lleida, Lleida, Spain
| | | | | | - María Saumoy
- HIV and STI Unit, Infectious Diseases Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Teresa Casanovas
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Carme Baliellas
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Pau Gilabert
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | | | - Rosa Roca
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Mercè Barenys
- Liver Unit, Hospital de Viladecans, Barcelona, Spain
| | - Joana Villaverde
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Silvia Salord
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Blau Camps
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | | | - Imma Ocaña
- Infectious Disease Unit, HUVH, Barcelona, Spain
| | - Silvia Sauleda
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Marta Bes
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Judit Carbonell
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Elena Vargas-Accarino
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Sofía P Ruzo
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Mercedes Guerrero-Murillo
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Georg Von Massow
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - María Isabel Costafreda
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Rosa Maria López
- Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | | | - Yolanda Real
- Liver Unit, Hospital Universitario La Princesa, Madrid, Spain
| | | | - Silvia Viroles
- Gastroenterology Department, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - Xavier Pamplona
- Gastroenterology Department, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - Mireia Cairó
- Gastroenterology Unit, Hospital Universitari Mútua Terrassa, Spain
| | | | | | - Angel Estébanez
- Gastroenterology and Hepatology Department, Instituto de Investigación (IDIVAL), Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Joan Carles Quer
- Gastroenterology Unit, Joan XXIII University Hospital, Tarragona, Spain
| | - Álvaro Mena-de-Cea
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - Alejandra Otero
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | | | - Francisco Suárez
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - Ángeles Vázquez
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - David Vieito
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - Soledad López-Calvo
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | | | | | - Raúl Rodríguez
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | - Ramiro Macenlle
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | - Alba Cachero
- Liver Unit, Hospital d'Igualada, Barcelona, Spain
| | | | | | - Silvia Fábregas
- Fundació Salut Empordà - Hospital de Figueres, Girona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | - Manolo Romero-Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario Virgen de Valme, Seville, Spain
| | - José Antonio Del-Campo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario Virgen de Valme, Seville, Spain
| | - Esteban Domingo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Centro de Biología Molecular "Severo Ochoa" (CBMSO), Universidad Autónoma de Madrid, Madrid, Spain
| | - Rafael Esteban
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
| | - Josep Quer
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
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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.
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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.
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24
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Phan T, Nagaro K. Cutavirus: A newly discovered parvovirus on the rise. INFECTION GENETICS AND EVOLUTION 2020; 80:104175. [PMID: 31917360 DOI: 10.1016/j.meegid.2020.104175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/03/2020] [Accepted: 01/05/2020] [Indexed: 12/11/2022]
Abstract
Cutavirus is a new member of the Parvoviridae family. It was first discovered in 2016 through unbiased metagenomics performed on fecal samples collected from patients with diarrhea, and also in skin biopsies collected from patients with cutaneous T-cell lymphoma (CTCL, also known as mycosis fungoides). We have systematically reviewed the literature to describe the discovery, genomic organization, prevalence, and geographic distribution of cutavirus.
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Affiliation(s)
- Tung Phan
- Division of Clinical Microbiology, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
| | - Kristin Nagaro
- Division of Clinical Microbiology, Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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25
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Zamperin G, Lucas P, Cano I, Ryder D, Abbadi M, Stone D, Cuenca A, Vigouroux E, Blanchard Y, Panzarin V. Sequencing of animal viruses: quality data assurance for NGS bioinformatics. Virol J 2019; 16:140. [PMID: 31752912 PMCID: PMC6868765 DOI: 10.1186/s12985-019-1223-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/16/2019] [Indexed: 12/30/2022] Open
Abstract
Background Next generation sequencing (NGS) is becoming widely used among diagnostics and research laboratories, and nowadays it is applied to a variety of disciplines, including veterinary virology. The NGS workflow comprises several steps, namely sample processing, library preparation, sequencing and primary/secondary/tertiary bioinformatics (BI) analyses. The latter is constituted by a complex process extremely difficult to standardize, due to the variety of tools and metrics available. Thus, it is of the utmost importance to assess the comparability of results obtained through different methods and in different laboratories. To achieve this goal, we have organized a proficiency test focused on the bioinformatics components for the generation of complete genome sequences of salmonid rhabdoviruses. Methods Three partners, that performed virus sequencing using different commercial library preparation kits and NGS platforms, gathered together and shared with each other 75 raw datasets which were analyzed separately by the participants to produce a consensus sequence according to their own bioinformatics pipeline. Results were then compared to highlight discrepancies, and a subset of inconsistencies were investigated more in detail. Results In total, we observed 526 discrepancies, of which 39.5% were located at genome termini, 14.1% at intergenic regions and 46.4% at coding regions. Among these, 10 SNPs and 99 indels caused changes in the protein products. Overall reproducibility was 99.94%. Based on the analysis of a subset of inconsistencies investigated more in-depth, manual curation appeared the most critical step affecting sequence comparability, suggesting that the harmonization of this phase is crucial to obtain comparable results. The analysis of a calibrator sample allowed assessing BI accuracy, being 99.983%. Conclusions We demonstrated the applicability and the usefulness of BI proficiency testing to assure the quality of NGS data, and recommend a wider implementation of such exercises to guarantee sequence data uniformity among different virology laboratories.
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Affiliation(s)
- Gianpiero Zamperin
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), viale dell'Università 10, 35120, Legnaro (PD), Italy
| | - Pierrick Lucas
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan-Plouzané-Niort Laboratory, Viral Genetics and Biosecurity Unit, 22440, Ploufragan, France.,Bretagne Loire University, place Paul Ricoeur CS 54417, 35044, Rennes, France
| | - Irene Cano
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, The Nothe Weymouth, Dorset, DT4 8UB, UK
| | - David Ryder
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, The Nothe Weymouth, Dorset, DT4 8UB, UK
| | - Miriam Abbadi
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), viale dell'Università 10, 35120, Legnaro (PD), Italy
| | - David Stone
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, The Nothe Weymouth, Dorset, DT4 8UB, UK
| | - Argelia Cuenca
- European Union Reference Laboratory for Fish and Crustacean Diseases, DTU aqua, Kemitorvet 202, 2800, Kgs. Lyngby, Denmark
| | - Estelle Vigouroux
- Bretagne Loire University, place Paul Ricoeur CS 54417, 35044, Rennes, France.,French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan-Plouzané-Niort Laboratory, Viral Diseases in Fish Unit, 29280, Plouzané, France
| | - Yannick Blanchard
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan-Plouzané-Niort Laboratory, Viral Genetics and Biosecurity Unit, 22440, Ploufragan, France. .,Bretagne Loire University, place Paul Ricoeur CS 54417, 35044, Rennes, France.
| | - Valentina Panzarin
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), viale dell'Università 10, 35120, Legnaro (PD), Italy.
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26
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Clinique et diagnostic de la grippe saisonnière. ACTUALITES PHARMACEUTIQUES 2019. [DOI: 10.1016/j.actpha.2019.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Matsushima Y, Mizukoshi F, Sakon N, Doan YH, Ueki Y, Ogawa Y, Motoya T, Tsukagoshi H, Nakamura N, Shigemoto N, Yoshitomi H, Okamoto-Nakagawa R, Suzuki R, Tsutsui R, Terasoma F, Takahashi T, Sadamasu K, Shimizu H, Okabe N, Nagasawa K, Aso J, Ishii H, Kuroda M, Ryo A, Katayama K, Kimura H. Evolutionary Analysis of the VP1 and RNA-Dependent RNA Polymerase Regions of Human Norovirus GII.P17-GII.17 in 2013-2017. Front Microbiol 2019; 10:2189. [PMID: 31611853 PMCID: PMC6777354 DOI: 10.3389/fmicb.2019.02189] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/05/2019] [Indexed: 01/05/2023] Open
Abstract
Human norovirus (HuNoV) GII.P17-GII.17 (Kawasaki2014 variant) reportedly emerged in 2014 and caused gastroenteritis outbreaks worldwide. To clarify the evolution of both VP1 and RNA-dependent RNA polymerase (RdRp) regions of GII.P17-GII.17, we analyzed both global and novel Japanese strains detected during 2013–2017. Time-scaled phylogenetic trees revealed that the ancestral GII.17 VP1 region diverged around 1949, while the ancestral GII.P17 RdRp region diverged around 2010. The evolutionary rates of the VP1 and RdRp regions were estimated at ~2.7 × 10−3 and ~2.3 × 10−3 substitutions/site/year, respectively. The phylogenetic distances of the VP1 region exhibited no overlaps between intra-cluster and inter-cluster peaks in the GII.17 strains, whereas those of the RdRp region exhibited a unimodal distribution in the GII.P17 strains. Conformational epitope positions in the VP1 protein of the GII.P17-GII.17 strains were similar, although some substitutions, insertions and deletions had occurred. Strains belonging to the same cluster also harbored substitutions around the binding sites for the histo-blood group antigens of the VP1 protein. Moreover, some amino acid substitutions were estimated to be near the interface between monomers and the active site of the RdRp protein. These results suggest that the GII.P17-GII.17 virus has produced variants with the potential to alter viral antigenicity, host-binding capability, and replication property over the past 10 years.
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Affiliation(s)
- Yuki Matsushima
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | - Fuminori Mizukoshi
- Department of Microbiology, Tochigi Prefectural Institute of Public Health and Environmental Science, Utsunomiya, Japan
| | - Naomi Sakon
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Yen Hai Doan
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Yo Ueki
- Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, Sendai, Japan
| | - Yasutaka Ogawa
- Division of Virology, Saitama Institute of Public Health, Saitama, Japan
| | - Takumi Motoya
- Ibaraki Prefectural Institute of Public Health, Mito, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi, Japan
| | | | - Naoki Shigemoto
- Hiroshima Prefectural Technology Research Institute Public Health and Environment Center, Hiroshima, Japan
| | - Hideaki Yoshitomi
- Fukuoka Institute of Health and Environmental Sciences, Dazaifu, Japan
| | | | - Rieko Suzuki
- Kanagawa Prefectural Institute of Public Health, Chigasaki, Japan
| | - Rika Tsutsui
- Aomori Prefecture Public Health and Environment Center, Aomori, Japan
| | - Fumio Terasoma
- Wakayama Prefectural Research Center of Environment and Public Health, Wakayama, Japan
| | - Tomoko Takahashi
- Iwate Prefectural Research Institute for Environmental Sciences and Public Health, Morioka, Japan
| | - Kenji Sadamasu
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku, Japan
| | - Hideaki Shimizu
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | - Nobuhiko Okabe
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | | | - Jumpei Aso
- Graduate School of Health Sciences, Gunma Paz University, Takasaki, Japan.,Department of Respiratory Medicine, Kyorin University School of Medicine, Mitaka, Japan
| | - Haruyuki Ishii
- Department of Respiratory Medicine, Kyorin University School of Medicine, Mitaka, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Kitasato University, Minato, Japan
| | - Hirokazu Kimura
- Graduate School of Health Sciences, Gunma Paz University, Takasaki, Japan.,Department of Microbiology, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
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Comparison of nucleic acid extraction methods for next-generation sequencing of avian influenza A virus from ferret respiratory samples. J Virol Methods 2019; 270:95-105. [DOI: 10.1016/j.jviromet.2019.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/13/2019] [Accepted: 04/15/2019] [Indexed: 11/13/2022]
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Cuypers L, Thijssen M, Shakibzadeh A, Sabahi F, Ravanshad M, Pourkarim MR. Next-generation sequencing for the clinical management of hepatitis C virus infections: does one test fits all purposes? Crit Rev Clin Lab Sci 2019; 56:420-434. [PMID: 31317801 DOI: 10.1080/10408363.2019.1637394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
While the prospect of viral cure is higher than ever for individuals infected with the hepatitis C virus (HCV) due to ground-breaking progress in antiviral treatment, success rates are still negatively influenced by HCV's high genetic variability. This genetic diversity is represented in the circulation of various genotypes and subtypes, mixed infections, recombinant forms and the presence of numerous drug resistant variants among infected individuals. Common misclassifications by commercial genotyping assays in combination with the limitations of currently used targeted population sequencing approaches have encouraged researchers to exploit alternative methods for the clinical management of HCV infections. Next-generation sequencing (NGS), a revolutionary and powerful tool with a variety of applications in clinical virology, can characterize viral diversity and depict viral dynamics in an ultra-wide and ultra-deep manner. The level of detail it provides makes it the method of choice for the diagnosis and clinical assessment of HCV infections. The sequence library provided by NGS is of a higher magnitude and sensitivity than data generated by conventional methods. Therefore, these technologies are helpful to guide clinical practice and at the same time highly valuable for epidemiological studies. The decreasing costs of NGS to determine genotypes, mixed infections, recombinant strains and drug resistant variants will soon make it feasible to employ NGS in clinical laboratories, to assist in the daily care of patients with HCV.
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Affiliation(s)
- Lize Cuypers
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven , Leuven , Belgium
| | - Marijn Thijssen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven , Leuven , Belgium
| | - Arash Shakibzadeh
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University , Tehran , Iran
| | - Farzaneh Sabahi
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University , Tehran , Iran
| | - Mehrdad Ravanshad
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University , Tehran , Iran
| | - Mahmoud Reza Pourkarim
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven , Leuven , Belgium.,Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences , Shiraz , Iran.,Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine , Tehran , Iran
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30
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Nucleic acid testing and molecular characterization of HIV infections. Eur J Clin Microbiol Infect Dis 2019; 38:829-842. [PMID: 30798399 DOI: 10.1007/s10096-019-03515-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/14/2019] [Indexed: 01/21/2023]
Abstract
Significant advances have been made in the molecular assays used for the detection of human immunodeficiency virus (HIV), which are crucial in preventing HIV transmission and monitoring disease progression. Molecular assays for HIV diagnosis have now reached a high degree of specificity, sensitivity and reproducibility, and have less operator involvement to minimize risk of contamination. Furthermore, analyses have been developed for the characterization of host gene polymorphisms and host responses to better identify and monitor HIV-1 infections in the clinic. Currently, molecular technologies including HIV quantitative and qualitative assays are mainly based on the polymerase chain reaction (PCR), transcription-mediated amplification (TMA), nucleic acid sequence-based amplification (NASBA), and branched chain (b) DNA methods and widely used for HIV detection and characterization, such as blood screening, point-of-care testing (POCT), pediatric diagnosis, acute HIV infection (AHI), HIV drug resistance testing, antiretroviral (AR) susceptibility testing, host genome polymorphism testing, and host response analysis. This review summarizes the development and the potential utility of molecular assays used to detect and characterize HIV infections.
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Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons. PLoS Comput Biol 2018; 14:e1006498. [PMID: 30543621 PMCID: PMC6314628 DOI: 10.1371/journal.pcbi.1006498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/02/2019] [Accepted: 09/10/2018] [Indexed: 01/07/2023] Open
Abstract
Next generation sequencing of viral populations has advanced our understanding of viral population dynamics, the development of drug resistance, and escape from host immune responses. Many applications require complete gene sequences, which can be impossible to reconstruct from short reads. HIV env, the protein of interest for HIV vaccine studies, is exceptionally challenging for long-read sequencing and analysis due to its length, high substitution rate, and extensive indel variation. While long-read sequencing is attractive in this setting, the analysis of such data is not well handled by existing methods. To address this, we introduce FLEA (Full-Length Envelope Analyzer), which performs end-to-end analysis and visualization of long-read sequencing data. FLEA consists of both a pipeline (optionally run on a high-performance cluster), and a client-side web application that provides interactive results. The pipeline transforms FASTQ reads into high-quality consensus sequences (HQCSs) and uses them to build a codon-aware multiple sequence alignment. The resulting alignment is then used to infer phylogenies, selection pressure, and evolutionary dynamics. The web application provides publication-quality plots and interactive visualizations, including an annotated viral alignment browser, time series plots of evolutionary dynamics, visualizations of gene-wide selective pressures (such as dN/dS) across time and across protein structure, and a phylogenetic tree browser. We demonstrate how FLEA may be used to process Pacific Biosciences HIV env data and describe recent examples of its use. Simulations show how FLEA dramatically reduces the error rate of this sequencing platform, providing an accurate portrait of complex and variable HIV env populations. A public instance of FLEA is hosted at http://flea.datamonkey.org. The Python source code for the FLEA pipeline can be found at https://github.com/veg/flea-pipeline. The client-side application is available at https://github.com/veg/flea-web-app. A live demo of the P018 results can be found at http://flea.murrell.group/view/P018. Viral populations constantly evolve and diversify. In this article we introduce a method, FLEA, for reconstructing and visualizing the details of evolutionary changes. FLEA specifically processes data from sequencing platforms that generate reads that are long, but error-prone. To study the evolutionary dynamics of entire genes during viral infection, data is collected via long-read sequencing at discrete time points, allowing us to understand how the virus changes over time. However, the experimental and sequencing process is imperfect, so the resulting data contain not only real evolutionary changes, but also mutations and other genetic artifacts caused by sequencing errors. Our method corrects most of these errors by combining thousands of erroneous sequences into a much smaller number of unique consensus sequences that represent biologically meaningful variation. The resulting high-quality sequences are used for further analysis, such as building an evolutionary tree that tracks and interprets the genetic changes in the viral population over time. FLEA is open source, and is freely available online.
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Maggi F, Pistello M, Antonelli G. Future management of viral diseases: role of new technologies and new approaches in microbial interactions. Clin Microbiol Infect 2018; 25:136-141. [PMID: 30502490 DOI: 10.1016/j.cmi.2018.11.015] [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: 08/22/2018] [Revised: 11/03/2018] [Accepted: 11/10/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND New technologies allow rapid detecting and counting of virus genomes in clinical specimens, defining susceptibility to specific antivirals, pinpointing molecular sequences correlated to virulence traits, and identifying viral and host factors driving resolution or chronicity of infections. As a result, during the past three decades the diagnostic virology laboratory has become crucial for patient care and an integral component of the multifarious armamentarium for patient management. This change in paradigm has caused obsolescence of methods once considered the reference standard of infectious disease diagnosis that were used to detect whole or specific components of virions in the specimen. OBJECTIVES This review provides an overview of standard and novel technologies applied to molecular diagnosis of viral infections and illustrates some crucial points for correcting interpretation of the laboratory data. SOURCES Peer-reviewed literature of topics pertinent to this review. CONTENT AND IMPLICATIONS New technologies are reinventing the way virologic diagnoses are made, with a conversion to new, simpler-to-use platforms. Although indicated for the same purpose, not all methods are equal and can yield different results. Further, tests identifying multiple analytes at once can detect microorganisms present or activated as a result of pathologic processes triggered by other pathogens or noninfectious causes. Thus, new directions will have to be taken in the way in which the diagnoses of viral diseases are performed. This represents a breakthrough in the clinical virology laboratory.
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Affiliation(s)
- F Maggi
- Department of Translational Research, Retrovirus Center and Virology Section, University of Pisa, Pisa, Italy; Virology Division, Pisa University Hospital, Pisa, Italy
| | - M Pistello
- Department of Translational Research, Retrovirus Center and Virology Section, University of Pisa, Pisa, Italy; Virology Division, Pisa University Hospital, Pisa, Italy
| | - G Antonelli
- Department of Molecular Medicine, Laboratory of Virology and Pasteur Institute-Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy; Microbiology and Virology Unit, Sapienza University Hospital 'Policlinico Umberto I,' Rome, Italy.
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33
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Silver N, Paynter M, McAllister G, Atchley M, Sayir C, Short J, Winner D, Alouani DJ, Sharkey FH, Bergefall K, Templeton K, Carrington D, Quiñones-Mateu ME. Characterization of minority HIV-1 drug resistant variants in the United Kingdom following the verification of a deep sequencing-based HIV-1 genotyping and tropism assay. AIDS Res Ther 2018; 15:18. [PMID: 30409215 PMCID: PMC6223033 DOI: 10.1186/s12981-018-0206-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/30/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The widespread global access to antiretroviral drugs has led to considerable reductions in morbidity and mortality but, unfortunately, the risk of virologic failure increases with the emergence, and potential transmission, of drug resistant viruses. Detecting and quantifying HIV-1 drug resistance has therefore become the standard of care when designing new antiretroviral regimens. The sensitivity of Sanger sequencing-based HIV-1 genotypic assays is limited by its inability to identify minority members of the quasispecies, i.e., it only detects variants present above ~ 20% of the viral population, thus, failing to detect minority variants below this threshold. It is clear that deep sequencing-based HIV-1 genotyping assays are an important step change towards accurately monitoring HIV-infected individuals. METHODS We implemented and verified a clinically validated HIV-1 genotyping assay based on deep sequencing (DEEPGEN™) in two clinical laboratories in the United Kingdom: St. George's University Hospitals Healthcare NHS Foundation Trust (London) and at NHS Lothian (Edinburgh), to characterize minority HIV-1 variants in 109 plasma samples from ART-naïve or -experienced individuals. RESULTS Although subtype B HIV-1 strains were highly prevalent (44%, 48/109), most individuals were infected with non-B subtype viruses (i.e., A1, A2, C, D, F1, G, CRF02_AG, and CRF01_AE). DEEPGEN™ was able to accurately detect drug resistance-associated mutations not identified using standard Sanger sequencing-based tests, which correlated significantly with patient's antiretroviral treatment histories. A higher proportion of minority PI-, NRTI-, and NNRTI-resistance mutations was detected in NHS Lothian patients compared to individuals from St. George's, mainly M46I/L and I50 V (associated with PIs), D67 N, K65R, L74I, M184 V/I, and K219Q (NRTIs), and L100I (NNRTIs). Interestingly, we observed an inverse correlation between intra-patient HIV-1 diversity and CD4+ T cell counts in the NHS Lothian patients. CONCLUSIONS This is the first study evaluating the transition, training, and implementation of DEEPGEN™ between three clinical laboratories in two different countries. More importantly, we were able to characterize the HIV-1 drug resistance profile (including minority variants), coreceptor tropism, subtyping, and intra-patient viral diversity in patients from the United Kingdom, providing a rigorous foundation for basing clinical decisions on highly sensitive and cost-effective deep sequencing-based HIV-1 genotyping assays in the country.
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34
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Barbezange C, Jones L, Blanc H, Isakov O, Celniker G, Enouf V, Shomron N, Vignuzzi M, van der Werf S. Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing. Front Microbiol 2018; 9:2596. [PMID: 30429836 PMCID: PMC6220372 DOI: 10.3389/fmicb.2018.02596] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/11/2018] [Indexed: 01/06/2023] Open
Abstract
After a pandemic wave in 2009 following their introduction in the human population, the H1N1pdm09 viruses replaced the previously circulating, pre-pandemic H1N1 virus and, along with H3N2 viruses, are now responsible for the seasonal influenza type A epidemics. So far, the evolutionary potential of influenza viruses has been mainly documented by consensus sequencing data. However, like other RNA viruses, influenza A viruses exist as a population of diverse, albeit related, viruses, or quasispecies. Interest in this quasispecies nature has increased with the development of next generation sequencing (NGS) technologies that allow a more in-depth study of the genetic variability. NGS deep sequencing methodologies were applied to determine the whole genome genetic heterogeneity of the three categories of influenza A viruses that circulated in humans between 2007 and 2012 in France, directly from clinical respiratory specimens. Mutation frequencies and single nucleotide polymorphisms were used for comparisons to address the level of natural intrinsic heterogeneity of influenza A viruses. Clear differences in single nucleotide polymorphism profiles between seasons for a given subtype also revealed the constant genetic drift that human influenza A virus quasispecies undergo.
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Affiliation(s)
- Cyril Barbezange
- Viral Populations and Pathogenesis, Department of Virology, Institut Pasteur, Paris, France
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
| | - Louis Jones
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
- Bioinformatics and Biostatistics HUB, The Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France
| | - Hervé Blanc
- Viral Populations and Pathogenesis, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Ofer Isakov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gershon Celniker
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Vincent Enouf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
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Yamaguchi J, Olivo A, Laeyendecker O, Forberg K, Ndembi N, Mbanya D, Kaptue L, Quinn TC, Cloherty GA, Rodgers MA, Berg MG. Universal Target Capture of HIV Sequences From NGS Libraries. Front Microbiol 2018; 9:2150. [PMID: 30271393 PMCID: PMC6146096 DOI: 10.3389/fmicb.2018.02150] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/22/2018] [Indexed: 11/13/2022] Open
Abstract
Background: Global surveillance of viral sequence diversity is needed to keep pace with the constant evolution of HIV. Recent next generation sequencing (NGS) methods have realized the goal of sequencing circulating virus directly from patient specimens. Yet, a simple, universal approach that maximizes sensitivity and sequencing capacity remains elusive. Here we present a novel HIV enrichment strategy to yield near complete genomes from low viral load specimens. Methodology: A non-redundant biotin-labeled probe set (HIV-xGen; n = 652) was synthesized to tile all HIV-1 (groups M, N, O, and P) and HIV-2 (A and B) strains. Illumina Nextera barcoded libraries of either gene-specific or randomly primed cDNA derived from infected plasma were hybridized to probes in a single pool and unbound sequences were washed away. Captured viral cDNA was amplified by Illumina adaptor primers, sequenced on a MiSeq, and NGS reads were demultiplexed for alignment with CLC Bio software. Results: HIV-xGen probes selectively captured and amplified reads spanning the entirety of the HIV phylogenetic tree. HIV sequences clearly present in unenriched libraries of specimens but previously not observed due to high host background levels, insufficient sequencing depth or the extent of multiplexing, were now enriched by >1,000-fold. Thus, xGen selection not only substantially increased the depth of existing sequence, but also extended overall genome coverage by an average of 40%. We characterized 50 new, diverse HIV strains from clinical specimens and demonstrated a viral load cutoff of approximately log 3.5 copies/ml for full length coverage. Genome coverage was <20% for 5/10 samples with viral loads <log 3.5 copies/ml and >90% for 35/40 samples with higher viral loads. Conclusions: Characterization of >20 complete genomes at a time is now possible from a single probe hybridization and MiSeq run. With the versatility to capture all HIV strains and the sensitivity to detect low titer specimens, HIV-xGen will serve as an important tool for monitoring HIV sequence diversity.
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Affiliation(s)
- Julie Yamaguchi
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Ana Olivo
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Oliver Laeyendecker
- National Institute of Allergy and Infectious Diseases, NIH, Baltimore, MD, United States
| | - Kenn Forberg
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | | | - Dora Mbanya
- Université de Yaoundé 1, Yaoundé, Cameroon.,University of Bamenda, Bamenda, Cameroon
| | | | - Thomas C Quinn
- National Institute of Allergy and Infectious Diseases, NIH, Baltimore, MD, United States
| | - Gavin A Cloherty
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Mary A Rodgers
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
| | - Michael G Berg
- Infectious Diseases Research, Abbott Diagnostics, Chicago, IL, United States
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Evaluating the accuracy and sensitivity of detecting minority HIV-1 populations by Illumina next-generation sequencing. J Virol Methods 2018; 261:40-45. [PMID: 30086382 DOI: 10.1016/j.jviromet.2018.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/25/2018] [Accepted: 08/03/2018] [Indexed: 01/03/2023]
Abstract
The accuracy and sensitivity of deep sequencing were assessed using viral standards (pNL4-3 and pLAI.2) of both DNA and RNA. The sequencing accuracy did not depend on the type of nucleic acid, but critically depended on the number of reads and threshold of sensitivity to minor viral populations. With coverage of more than 236 reads, the accuracy of viral RNA sequencing was equal to or exceeded 99.9%, with a sensitivity threshold to minor nucleotides of 20%. When the sensitivity threshold was below 1%, reduced accuracy dynamics were clearly visible even when the coverage was massive (more than 9.000 reads). It was found that the floating sensitivity threshold allowed the sequencing accuracy to be maintained at an acceptable level in cases of low coverage (less than 1.500-2.000) of reads. These results indicate the quality that can be expected with a specific number of reads and sensitivity threshold. Deep sequencing is a very powerful tool that can significantly improve the value of study results, but despite its superior performance, it should be used with caution regarding its sensitivity to minor populations below 1%.
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37
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Jester B, Schwerzmann J, Mustaquim D, Aden T, Brammer L, Humes R, Shult P, Shahangian S, Gubareva L, Xu X, Miller J, Jernigan D. Mapping of the US Domestic Influenza Virologic Surveillance Landscape. Emerg Infect Dis 2018; 24. [PMID: 29715078 PMCID: PMC6038762 DOI: 10.3201/eid2407.180028] [Citation(s) in RCA: 18] [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] [Indexed: 11/19/2022] Open
Abstract
Influenza virologic surveillance is critical each season for tracking influenza circulation, following trends in antiviral drug resistance, detecting novel influenza infections in humans, and selecting viruses for use in annual seasonal vaccine production. We developed a framework and process map for characterizing the landscape of US influenza virologic surveillance into 5 tiers of influenza testing: outpatient settings (tier 1), inpatient settings and commercial laboratories (tier 2), state public health laboratories (tier 3), National Influenza Reference Center laboratories (tier 4), and Centers for Disease Control and Prevention laboratories (tier 5). During the 2015–16 season, the numbers of influenza tests directly contributing to virologic surveillance were 804,000 in tiers 1 and 2; 78,000 in tier 3; 2,800 in tier 4; and 3,400 in tier 5. With the release of the 2017 US Pandemic Influenza Plan, the proposed framework will support public health officials in modeling, surveillance, and pandemic planning and response.
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38
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Amarilla AA, Fumagalli MJ, Figueiredo ML, Lima-Junior DS, Santos-Junior NN, Alfonso HL, Lippi V, Trabuco AC, Lauretti F, Muller VD, Colón DF, Luiz JPM, Suhrbier A, Setoh YX, Khromykh AA, Figueiredo LTM, Aquino VH. Ilheus and Saint Louis encephalitis viruses elicit cross-protection against a lethal Rocio virus challenge in mice. PLoS One 2018; 13:e0199071. [PMID: 29897990 PMCID: PMC5999289 DOI: 10.1371/journal.pone.0199071] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/29/2018] [Indexed: 11/30/2022] Open
Abstract
Rocio virus (ROCV) was the causative agent of an unprecedented outbreak of encephalitis during the 1970s in the Vale do Ribeira, Sao Paulo State, in the Southeast region of Brazil. Surprisingly, no further cases of ROCV infection were identified after this outbreak; however, serological surveys have suggested the circulation of ROCV among humans and animals in different regions of Brazil. Cross-protective immunity among flaviviruses is well documented; consequently, immunity induced by infections with other flaviviruses endemic to Brazil could potentially be responsible for the lack of ROCV infections. Herein, we evaluated the cross-protection mediated by other flaviviruses against ROCV infection using an experimental C57BL/6 mouse model. Cross-protection against ROCV infection was observed when animals had prior exposure to Ilheus virus or Saint Louis encephalitis virus, suggesting that cross-reactive anti-flavivirus antibodies may limit ROCV disease outbreaks.
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Affiliation(s)
- Alberto Anastacio Amarilla
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Marcilio Jorge Fumagalli
- Virology Research Center, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Mario Luis Figueiredo
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Djalma S. Lima-Junior
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Nilton Nascimento Santos-Junior
- Department of Neurosciences and Behavioral Sciences, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - Helda Liz Alfonso
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Veronica Lippi
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Amanda Cristina Trabuco
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Flavio Lauretti
- Virology Research Center, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Vanessa Danielle Muller
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - David F. Colón
- Laboratory of Inflammation and Pain, Department of Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - João P. M. Luiz
- Laboratory of Inflammation and Pain, Department of Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Andreas Suhrbier
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Yin Xiang Setoh
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Alexander A. Khromykh
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Luiz Tadeu Moraes Figueiredo
- Virology Research Center, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Victor Hugo Aquino
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
- * E-mail:
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Charpentier E, Garnaud C, Wintenberger C, Bailly S, Murat JB, Rendu J, Pavese P, Drouet T, Augier C, Malvezzi P, Thiébaut-Bertrand A, Mallaret MR, Epaulard O, Cornet M, Larrat S, Maubon D. Added Value of Next-Generation Sequencing for Multilocus Sequence Typing Analysis of a Pneumocystis jirovecii Pneumonia Outbreak1. Emerg Infect Dis 2018; 23:1237-1245. [PMID: 28726611 PMCID: PMC5547796 DOI: 10.3201/eid2308.161295] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Pneumocystis jirovecii is a major threat for immunocompromised patients, and clusters of pneumocystis pneumonia (PCP) have been increasingly described in transplant units during the past decade. Exploring an outbreak transmission network requires complementary spatiotemporal and strain-typing approaches. We analyzed a PCP outbreak and demonstrated the added value of next-generation sequencing (NGS) for the multilocus sequence typing (MLST) study of P. jirovecii strains. Thirty-two PCP patients were included. Among the 12 solid organ transplant patients, 5 shared a major and unique genotype that was also found as a minor strain in a sixth patient. A transmission map analysis strengthened the suspicion of nosocomial acquisition of this strain for the 6 patients. NGS-MLST enables accurate determination of subpopulation, which allowed excluding other patients from the transmission network. NGS-MLST genotyping approach was essential to deciphering this outbreak. This innovative approach brings new insights for future epidemiologic studies on this uncultivable opportunistic fungus.
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40
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Sauvage V, Boizeau L, Candotti D, Vandenbogaert M, Servant-Delmas A, Caro V, Laperche S. Early MinION™ nanopore single-molecule sequencing technology enables the characterization of hepatitis B virus genetic complexity in clinical samples. PLoS One 2018; 13:e0194366. [PMID: 29566006 PMCID: PMC5864009 DOI: 10.1371/journal.pone.0194366] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/01/2018] [Indexed: 12/14/2022] Open
Abstract
Until recently, the method of choice to characterize viral diversity consisted in cloning PCR amplicons of full-length viral genomes and Sanger-sequencing of multiple clones. However, this is extremely laborious, time-consuming, and low-throughput. Next generation short-read sequencing appears also limited by its inability to directly sequence full-length viral genomes. The MinION™ device recently developed by Oxford Nanopore Technologies can be a promising alternative by applying long-read single-molecule sequencing directly to the overall amplified products generated in a PCR reaction. This new technology was evaluated by using hepatitis B virus (HBV) as a model. Several previously characterized HBV-infected clinical samples were investigated including recombinant virus, variants that harbored deletions and mixed population. Original MinION device was able to generate individual complete 3,200-nt HBV genome sequences and to identify recombinant variants. MinION was particularly efficient in detecting HBV genomes with multiple large in-frame deletions and spliced variants concomitantly with non-deleted parental genomes. However, an average-12% sequencing error rate per individual reads associated to a low throughput challenged single-nucleotide resolution, polymorphism calling and phasing mutations directly from the sequencing reads. Despite this high error rate, the pairwise identity of MinION HBV consensus genome was consistent with Sanger sequencing method. MinION being under continuous development, further studies are needed to evaluate its potential use for viral infection characterization.
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Affiliation(s)
- Virginie Sauvage
- Institut National de la Transfusion Sanguine (INTS), Département D’études des Agents Transmissibles par le Sang, Centre National de Référence Risques Infectieux Transfusionnels, Paris, France
- * E-mail:
| | - Laure Boizeau
- Institut National de la Transfusion Sanguine (INTS), Département D’études des Agents Transmissibles par le Sang, Centre National de Référence Risques Infectieux Transfusionnels, Paris, France
| | - Daniel Candotti
- Institut National de la Transfusion Sanguine (INTS), Département D’études des Agents Transmissibles par le Sang, Centre National de Référence Risques Infectieux Transfusionnels, Paris, France
| | - Mathias Vandenbogaert
- Institut Pasteur, Genotyping of Pathogens Pole, Laboratory for Urgent Response to Biological Threats, Environment and Infectious Risks, Paris, France
| | - Annabelle Servant-Delmas
- Institut National de la Transfusion Sanguine (INTS), Département D’études des Agents Transmissibles par le Sang, Centre National de Référence Risques Infectieux Transfusionnels, Paris, France
| | - Valérie Caro
- Institut Pasteur, Genotyping of Pathogens Pole, Laboratory for Urgent Response to Biological Threats, Environment and Infectious Risks, Paris, France
| | - Syria Laperche
- Institut National de la Transfusion Sanguine (INTS), Département D’études des Agents Transmissibles par le Sang, Centre National de Référence Risques Infectieux Transfusionnels, Paris, France
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41
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Fokam J, Bellocchi MC, Armenia D, Nanfack AJ, Carioti L, Continenza F, Takou D, Temgoua ES, Tangimpundu C, Torimiro JN, Koki PN, Fokunang CN, Cappelli G, Ndjolo A, Colizzi V, Ceccherini-Silberstein F, Perno CF, Santoro MM. Next-generation sequencing provides an added value in determining drug resistance and viral tropism in Cameroonian HIV-1 vertically infected children. Medicine (Baltimore) 2018; 97:e0176. [PMID: 29595649 PMCID: PMC5895385 DOI: 10.1097/md.0000000000010176] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
With limited and low-genetic barrier drugs used for the prevention of mother-to-child transmission (PMTCT) of HIV in sub-Saharan Africa, vertically transmitted HIV-1 drug-resistance (HIVDR) is concerning and might prompt optimal pediatric strategies.The aim of this study was to ascertain HIVDR and viral-tropism in majority and minority populations among Cameroonian vertically infected children.A comparative analysis among 18 HIV-infected children (7 from PMTCT-exposed mothers and 11 from mothers without PMTCT-exposure) was performed. HIVDR and HIV-1 co-receptor usage was evaluated by analyzing sequences obtained by both Sanger sequencing and ultra-deep 454-pyrosequencing (UDPS), set at 1% threshold.Overall, median (interquartile range) age, viremia, and CD4 count were 6 (4-10) years, 5.5 (4.9-6.0) log10 copies/mL, and 526 (282-645) cells/mm, respectively. All children had wild-type viruses through both Sanger sequencing and UDPS, except for 1 PMTCT-exposed infant harboring minority K103N (8.31%), born to a mother exposed to AZT+3TC+NVP. X4-tropic viruses were found in 5 of 15 (33.3%) children (including 2 cases detected only by UDPS). Rate of X4-tropic viruses was 0% (0/6) below 5 years (also as minority species), and became relatively high above 5 years (55.6% [5/9], P = .040. X4-tropic viruses were higher with CD4 ≤15% (4/9 [44.4%]) versus CD4 >15% (1/6 [16.7%], P = .580); similarly for CD4 ≤200 (3/4 [75%]) versus CD4 >200 (2/11 [18.2%] cells/mm, P = .077.NGS has the ability of excluding NRTI- and NNRTI-mutations as minority species in all but 1 children, thus supporting the safe use of these drug-classes in those without such mutations, henceforth sparing ritonavir-boosted protease inhibitors or integrase inhibitors for the few remaining cases. In children under five years, X4-tropic variants would be rare, suggesting vertical-transmission with CCR5-tropic viruses and possible maraviroc usage at younger ages.
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Affiliation(s)
- Joseph Fokam
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- University of Rome Tor Vergata, Rome, Italy
- University of Yaounde I
- National HIV Drug Resistance Prevention and Surveillance Working Group, Yaounde, Cameroon
| | | | | | - Aubin J. Nanfack
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- New York University School of Medicine, New York, NY
| | | | - Fabio Continenza
- National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Desire Takou
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | - Edith S. Temgoua
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | - Charlotte Tangimpundu
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | - Judith N. Torimiro
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- University of Yaounde I
- National HIV Drug Resistance Prevention and Surveillance Working Group, Yaounde, Cameroon
| | - Paul N. Koki
- University of Yaounde I
- Mother-Child Center, Chantal BIYA Foundation, Yaounde
| | | | | | - Alexis Ndjolo
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- University of Yaounde I
| | - Vittorio Colizzi
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- University of Rome Tor Vergata, Rome, Italy
- UNESCO Board of Multidisciplinary Biotechnology, Rome, Italy
| | | | - Carlo-Federico Perno
- Chantal Biya International Reference Centre for research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- University of Rome Tor Vergata, Rome, Italy
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Reeves DB, Magaret AS, Greninger AL, Johnston C, Schiffer JT. Model-based estimation of superinfection prevalence from limited datasets. J R Soc Interface 2018; 15:20170968. [PMID: 29491180 PMCID: PMC5832741 DOI: 10.1098/rsif.2017.0968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/05/2018] [Indexed: 12/24/2022] Open
Abstract
Humans can be infected sequentially by different strains of the same virus. Estimating the prevalence of so-called 'superinfection' for a particular pathogen is vital because superinfection implies a failure of immunologic memory against a given virus despite past exposure, which may signal challenges for future vaccine development. Increasingly, viral deep sequencing and phylogenetic inference can discriminate distinct strains within a host. Yet, a population-level study may misrepresent the true prevalence of superinfection for several reasons. First, certain infections such as herpes simplex virus (HSV-2) only reactivate single strains, making multiple samples necessary to detect superinfection. Second, the number of samples collected in a study may be fewer than the actual number of independently acquired strains within a single person. Third, detecting strains that are relatively less abundant can be difficult, even for other infections such as HIV-1 where deep sequencing may identify multiple strains simultaneously. Here we develop a model of superinfection inspired by ecology. We define an infected individual's richness as the number of infecting strains and use ecological evenness to quantify the relative strain abundances. The model uses an EM methodology to infer the true prevalence of superinfection from limited clinical datasets. Simulation studies with known true prevalence are used to contrast our EM method to a standard (naive) calculation. While varying richness, evenness and sampling we quantify the accuracy and precision of our method. The EM method outperforms in all cases, particularly when sampling is low, and richness or unevenness is high. Here, sensitivity to our assumptions about clinical data is considered. The simulation studies also provide insight into optimal study designs; estimates of prevalence improve equally by enrolling more participants or gathering more samples per person. Finally, we apply our method to data from published studies of HSV-2 and HIV-1 superinfection.
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Affiliation(s)
- Daniel B Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amalia S Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
- Biostatistics, University of Washington, Seattle, WA, USA
| | - Alex L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Christine Johnston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
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A Bioinformatic Pipeline for Monitoring of the Mutational Stability of Viral Drug Targets with Deep-Sequencing Technology. Viruses 2017; 9:v9120357. [PMID: 29168754 PMCID: PMC5744132 DOI: 10.3390/v9120357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 12/24/2022] Open
Abstract
The efficient development of antiviral drugs, including efficient antiviral small interfering RNAs (siRNAs), requires continuous monitoring of the strict correspondence between a drug and the related highly variable viral DNA/RNA target(s). Deep sequencing is able to provide an assessment of both the general target conservation and the frequency of particular mutations in the different target sites. The aim of this study was to develop a reliable bioinformatic pipeline for the analysis of millions of short, deep sequencing reads corresponding to selected highly variable viral sequences that are drug target(s). The suggested bioinformatic pipeline combines the available programs and the ad hoc scripts based on an original algorithm of the search for the conserved targets in the deep sequencing data. We also present the statistical criteria for the threshold of reliable mutation detection and for the assessment of variations between corresponding data sets. These criteria are robust against the possible sequencing errors in the reads. As an example, the bioinformatic pipeline is applied to the study of the conservation of RNA interference (RNAi) targets in human immunodeficiency virus 1 (HIV-1) subtype A. The developed pipeline is freely available to download at the website http://virmut.eimb.ru/. Brief comments and comparisons between VirMut and other pipelines are also presented.
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Myrmel M, Oma V, Khatri M, Hansen HH, Stokstad M, Berg M, Blomström AL. Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA). PLoS One 2017; 12:e0187780. [PMID: 29112950 PMCID: PMC5675387 DOI: 10.1371/journal.pone.0187780] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/25/2017] [Indexed: 01/07/2023] Open
Abstract
Coronaviruses are of major importance for both animal and human health. With the emergence of novel coronaviruses such as SARS and MERS, the need for fast genome characterisation is ever so important. Further, in order to understand the influence of quasispecies of these viruses in relation to biology, techniques for deep-sequence and full-length viral genome analysis are needed. In the present study, we compared the efficiency of two sequence-independent approaches [sequence-independent single primer amplification (SISPA) and single primer isothermal amplification (SPIA, represented by the Ovation kit)] coupled with high-throughput sequencing to generate the full-length genome of bovine coronavirus (BCoV) from a nasal swab. Both methods achieved high genome coverage (100% for SPIA and 99% for SISPA), however, there was a clear difference in the percentage of reads that mapped to BCoV. While approximately 45% of the Ovation reads mapped to BCoV (sequence depth of 169-284 944), only 0.07% of the SISPA reads (sequence depth of 0-249) mapped to the reference genome. Although BCoV was the focus of the study we also identified a bovine rhinitis B virus (BRBV) in the data sets. The trend for this virus was similar to that observed for BCoV regarding Ovation vs. SISPA, but with fewer sequences mapping to BRBV due to a lower amount of this virus. In summary, the SPIA approach used in this study produced coverage of the entire BCoV (high copy number) and BRBV (low copy number) and a high sequence/genome depth compared to SISPA. Although this is a limited study, the results indicate that the Ovation method could be a preferred approach for full genome sequencing if a low copy number of viral RNA is expected and if high sequence depth is desired.
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Affiliation(s)
- Mette Myrmel
- Department for Food Safety and Infection Biology, Norwegian University of Life Sciences, Oslo, Norway
| | - Veslemøy Oma
- Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
| | - Mamata Khatri
- Department for Food Safety and Infection Biology, Norwegian University of Life Sciences, Oslo, Norway
| | | | - Maria Stokstad
- Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
| | - Mikael Berg
- Department of Biomedical Sciences and Veterinary Public Health, Section of Virology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anne-Lie Blomström
- Department of Biomedical Sciences and Veterinary Public Health, Section of Virology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Zárate S, Taboada B, Yocupicio-Monroy M, Arias CF. Human Virome. Arch Med Res 2017; 48:701-716. [DOI: 10.1016/j.arcmed.2018.01.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/22/2018] [Indexed: 12/16/2022]
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Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Mol Biol Evol 2017; 34:3299-3302. [DOI: 10.1093/molbev/msx248] [Citation(s) in RCA: 2494] [Impact Index Per Article: 356.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Machnowska P, Hauser A, Meixenberger K, Altmann B, Bannert N, Rempis E, Schnack A, Decker S, Braun V, Busingye P, Rubaihayo J, Harms G, Theuring S. Decreased emergence of HIV-1 drug resistance mutations in a cohort of Ugandan women initiating option B+ for PMTCT. PLoS One 2017; 12:e0178297. [PMID: 28562612 PMCID: PMC5451067 DOI: 10.1371/journal.pone.0178297] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/10/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Since 2012, WHO guidelines for the prevention of mother-to-child transmission (PMTCT) of HIV-1 in resource-limited settings recommend the initiation of lifelong antiretroviral combination therapy (cART) for all pregnant HIV-1 positive women independent of CD4 count and WHO clinical stage (Option B+). However, long-term outcomes regarding development of drug resistance are lacking until now. Therefore, we analysed the emergence of drug resistance mutations (DRMs) in women initiating Option B+ in Fort Portal, Uganda, at 12 and 18 months postpartum (ppm). METHODS AND FINDINGS 124 HIV-1 positive pregnant women were enrolled within antenatal care services in Fort Portal, Uganda. Blood samples were collected at the first visit prior starting Option B+ and postpartum at week six, month six, 12 and 18. Viral load was determined by real-time RT-PCR. An RT-PCR covering resistance associated positions in the protease and reverse transcriptase HIV-1 genomic region was performed. PCR-positive samples at 12/18 ppm and respective baseline samples were analysed by next generation sequencing regarding HIV-1 drug resistant variants including low-frequency variants. Furthermore, vertical transmission of HIV-1 was analysed. 49/124 (39.5%) women were included into the DRM analysis. Virological failure, defined as >1000 copies HIV-1 RNA/ml, was observed in three and seven women at 12 and 18 ppm, respectively. Sequences were obtained for three and six of these. In total, DRMs were detected in 3/49 (6.1%) women. Two women displayed dual-class resistance against all recommended first-line regimen drugs. Of 49 mother-infant-pairs no infant was HIV-1 positive at 12 or 18 ppm. CONCLUSION Our findings suggest that the WHO-recommended Option B+ for PMTCT is effective in a cohort of Ugandan HIV-1 positive pregnant women with regard to the low selection rate of DRMs and vertical transmission. Therefore, these results are encouraging for other countries considering the implementation of lifelong cART for all pregnant HIV-1 positive women.
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Affiliation(s)
- Patrycja Machnowska
- Institute of Tropical Medicine and International Health, Charité—Universitätsmedizin Berlin, Berlin, Germany
- Division of HIV and Other Retroviruses, Robert Koch-Institute, Berlin, Germany
| | - Andrea Hauser
- Division of HIV and Other Retroviruses, Robert Koch-Institute, Berlin, Germany
| | | | - Britta Altmann
- Division of HIV and Other Retroviruses, Robert Koch-Institute, Berlin, Germany
| | - Norbert Bannert
- Division of HIV and Other Retroviruses, Robert Koch-Institute, Berlin, Germany
| | - Eva Rempis
- Institute of Tropical Medicine and International Health, Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Alexandra Schnack
- Institute of Tropical Medicine and International Health, Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Sarah Decker
- Institute of Tropical Medicine and International Health, Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Vera Braun
- Institute of Tropical Medicine and International Health, Charité—Universitätsmedizin Berlin, Berlin, Germany
| | | | - John Rubaihayo
- Department of Public Health, Mountains of the Moon University, Fort Portal, Uganda
| | - Gundel Harms
- Institute of Tropical Medicine and International Health, Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Stefanie Theuring
- Institute of Tropical Medicine and International Health, Charité—Universitätsmedizin Berlin, Berlin, Germany
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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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Pitt SJ, Phillips DIM. Diagnostic virology and patient care: from vaguely interesting to vitally important. Br J Biomed Sci 2017; 74:16-23. [PMID: 28206853 DOI: 10.1080/09674845.2016.1264706] [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] [Indexed: 01/16/2023]
Abstract
The existence of pathogenic viruses was inferred by experiments at the turn of the twentieth century. Key developments in detection of viruses, including electron microscopy and monolayer cell culture, were made in the middle of that century. However, in terms of patient care, the results from the virology laboratory often arrived the patient was 'better or dead'. The advent of molecular techniques, particularly polymerase chain reaction and more recently whole genome sequencing made timely and accurate diagnosis of viral infections feasible. A range of approaches have been taken to identify and characterise new viruses. Vaccines against viruses have made it possible to eliminate two pathogenic mammalian viruses altogether, with several others close to eradication. The role of biomedical scientists working in diagnostic virology is more relevant to patient care than ever.
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Affiliation(s)
- Sarah J Pitt
- a School of Pharmacy and Biomolecular Sciences , University of Brighton , Brighton , UK
| | - D Ian M Phillips
- b Public Health Wales Microbiology and Health Protection , Cardiff University Hospital of Wales , Cardiff , UK
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Overlap Extension Barcoding for the Next Generation Sequencing and Genotyping of Plasmodium falciparum in Individual Patients in Western Kenya. Sci Rep 2017; 7:41108. [PMID: 28117350 PMCID: PMC5259759 DOI: 10.1038/srep41108] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/15/2016] [Indexed: 12/23/2022] Open
Abstract
Large-scale molecular epidemiologic studies of Plasmodium falciparum parasites have provided insights into parasite biology and transmission, can identify the spread of drug resistance, and are useful in assessing vaccine targets. The polyclonal nature infections in high transmission settings is problematic for traditional genotyping approaches. Next-generation sequencing (NGS) approaches to parasite genotyping allow sensitive detection of minority variants, disaggregation of complex parasite mixtures, and scalable processing of large samples sets. Therefore, we designed, validated, and applied to field parasites an approach that leverages sequencing of individually barcoded samples in a multiplex manner. We utilize variant barcodes, invariant linker sequences and modular template-specific primers to allow for the simultaneous generation of high-dimensional sequencing data of multiple gene targets. This modularity permits a cost-effective and reproducible way to query many genes at once. In mixtures of reference parasite genomes, we quantitatively detected unique haplotypes comprising as little as 2% of a polyclonal infection. We applied this genotyping approach to field-collected parasites collected in Western Kenya in order to simultaneously obtain parasites genotypes at three unlinked loci. In summary, we present a rapid, scalable, and flexible method for genotyping individual parasites that enables molecular epidemiologic studies of parasite evolution, population structure and transmission.
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