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Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
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Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
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2
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Köndgen S, Oh DY, Thürmer A, Sedaghatjoo S, Patrono LV, Calvignac-Spencer S, Biere B, Wolff T, Dürrwald R, Fuchs S, Reiche J. A robust, scalable, and cost-efficient approach to whole genome sequencing of RSV directly from clinical samples. J Clin Microbiol 2024; 62:e0111123. [PMID: 38407068 PMCID: PMC10935636 DOI: 10.1128/jcm.01111-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/01/2024] [Indexed: 02/27/2024] Open
Abstract
Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infections causing significant morbidity and mortality among children and the elderly; two RSV vaccines and a monoclonal antibody have recently been approved. Thus, there is an increasing need for a detailed and continuous genomic surveillance of RSV circulating in resource-rich and resource-limited settings worldwide. However, robust, cost-effective methods for whole genome sequencing of RSV from clinical samples that are amenable to high-throughput are still scarce. We developed Next-RSV-SEQ, an experimental and computational pipeline to generate whole genome sequences of historic and current RSV genotypes by in-solution hybridization capture-based next generation sequencing. We optimized this workflow by automating library preparation and pooling libraries prior to enrichment in order to reduce hands-on time and cost, thereby augmenting scalability. Next-RSV-SEQ yielded near-complete to complete genome sequences for 98% of specimens with Cp values ≤31, at median on-target reads >93%, and mean coverage depths between ~1,000 and >5,000, depending on viral load. Whole genomes were successfully recovered from samples with viral loads as low as 230 copies per microliter RNA. We demonstrate that the method can be expanded to other respiratory viruses like parainfluenza virus and human metapneumovirus. Next-RSV-SEQ produces high-quality RSV genomes directly from culture isolates and, more importantly, clinical specimens of all genotypes in circulation. It is cost-efficient, scalable, and can be extended to other respiratory viruses, thereby opening new perspectives for a future effective and broad genomic surveillance of respiratory viruses. IMPORTANCE Respiratory syncytial virus (RSV) is a leading cause of severe acute respiratory tract infections in children and the elderly, and its prevention has become an increasing priority. Recently, vaccines and a long-acting monoclonal antibody to protect effectively against severe disease have been approved for the first time. Hence, there is an urgent need for genomic surveillance of RSV at the global scale to monitor virus evolution, especially with an eye toward immune evasion. However, robust, cost-effective methods for RSV whole genome sequencing that are suitable for high-throughput of clinical samples are currently scarce. Therefore, we have developed Next-RSV-SEQ, an experimental and computational pipeline that produces reliably high-quality RSV genomes directly from clinical specimens and isolates.
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Affiliation(s)
- Sophie Köndgen
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
| | - Djin-Ye Oh
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
| | - Andrea Thürmer
- Genome Competence Center, Robert Koch-Institute, Berlin, Germany
| | | | - Livia V. Patrono
- Epidemiology of highly pathogenic microorganisms, Robert Koch-Institute, Berlin, Germany
| | | | - Barbara Biere
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
| | - Thorsten Wolff
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
| | - Ralf Dürrwald
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
| | - Stephan Fuchs
- Genome Competence Center, Robert Koch-Institute, Berlin, Germany
| | - Janine Reiche
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
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3
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Glasgow HL, Zhu H, Xie H, Kenkel EJ, Lee C, Huang ML, Greninger AL. Genotypic testing improves detection of antiviral resistance in human herpes simplex virus. J Clin Virol 2023; 167:105554. [PMID: 37586184 DOI: 10.1016/j.jcv.2023.105554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/28/2023] [Accepted: 07/28/2023] [Indexed: 08/18/2023]
Abstract
BACKGROUND Antiviral resistance in human herpes simplex viruses (HSV) remains a significant clinical challenge in immunocompromised populations. Although molecular tests have largely replaced viral culture for HSV diagnosis and molecular antiviral resistance testing is available for many viruses, HSV resistance testing continues to rely on phenotypic, viral culture-based methods, requiring weeks for results. Consequently, treatment of suspected HSV resistance remains largely empiric. METHODS We used HSV whole genome sequencing and a database of previously characterized HSV acyclovir and foscarnet resistance mutations to evaluate the performance of genotypic antiviral resistance testing among 19 control strains compared to in-house plaque reduction assay (PRA) and 25 clinical isolates sent for reference lab PRA antiviral resistance testing. RESULTS Among control strains, 23/29 (79.3%) results were concordant, 5 (17.2%) were indeterminate, and 1 (3.4%) was discordant. Indeterminate results were caused by variants of uncertain significance (VUS), including mutations without published phenotypes and mutations with contradictory results. Among clinical isolates, 14/40 (35%) results were concordant, 17 (42.5%) were indeterminate, and 9 (22.5%) were discordant. All discordant results were in reportedly phenotypically-susceptible HSV-1 strains yet possessed resistance mutations. Three contained resistant subpopulations. 6/8 (75%) discordant phenotypes were concordant with resistant genotypes upon repeat PRA. CONCLUSIONS These data support the combination of genotypic and phenotypic testing to diagnose HSV resistance more accurately and likely more rapidly than phenotypic testing alone. Genotypic context of resistance mutations and the ability of viral strains to form plaques in culture may affect phenotypic resistance results, highlighting the limitations of PRA alone as a gold standard method.
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Affiliation(s)
- Heather L Glasgow
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, United States.
| | - Haiying Zhu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, United States
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, United States
| | - Elizabeth J Kenkel
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, United States
| | - Carrie Lee
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, United States
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, United States
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, United States
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Baumeier C, Harms D, Aleshcheva G, Gross U, Escher F, Schultheiss HP. Advancing Precision Medicine in Myocarditis: Current Status and Future Perspectives in Endomyocardial Biopsy-Based Diagnostics and Therapeutic Approaches. J Clin Med 2023; 12:5050. [PMID: 37568452 PMCID: PMC10419903 DOI: 10.3390/jcm12155050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
The diagnosis and specific and causal treatment of myocarditis and inflammatory cardiomyopathy remain a major clinical challenge. Despite the rapid development of new imaging techniques, endomyocardial biopsies remain the gold standard for accurate diagnosis of inflammatory myocardial disease. With the introduction and continued development of immunohistochemical inflammation diagnostics in combination with viral nucleic acid testing, myocarditis diagnostics have improved significantly since their introduction. Together with new technologies such as miRNA and gene expression profiling, quantification of specific immune cell markers, and determination of viral activity, diagnostic accuracy and patient prognosis will continue to improve in the future. In this review, we summarize the current knowledge on the pathogenesis and diagnosis of myocarditis and inflammatory cardiomyopathies and highlight future perspectives for more in-depth and specialized biopsy diagnostics and precision, personalized medicine approaches.
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Affiliation(s)
- Christian Baumeier
- Institute of Cardiac Diagnostics and Therapy, IKDT GmbH, 12203 Berlin, Germany; (D.H.); (G.A.); (U.G.); (H.-P.S.)
| | - Dominik Harms
- Institute of Cardiac Diagnostics and Therapy, IKDT GmbH, 12203 Berlin, Germany; (D.H.); (G.A.); (U.G.); (H.-P.S.)
- Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| | - Ganna Aleshcheva
- Institute of Cardiac Diagnostics and Therapy, IKDT GmbH, 12203 Berlin, Germany; (D.H.); (G.A.); (U.G.); (H.-P.S.)
| | - Ulrich Gross
- Institute of Cardiac Diagnostics and Therapy, IKDT GmbH, 12203 Berlin, Germany; (D.H.); (G.A.); (U.G.); (H.-P.S.)
| | - Felicitas Escher
- Department of Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum der Charité, Campus Virchow Klinikum, 13353 Berlin, Germany;
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, 10785 Berlin, Germany
| | - Heinz-Peter Schultheiss
- Institute of Cardiac Diagnostics and Therapy, IKDT GmbH, 12203 Berlin, Germany; (D.H.); (G.A.); (U.G.); (H.-P.S.)
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Colón-Thillet R, Stone D, Loprieno MA, Klouser L, Roychoudhury P, Santo TK, Xie H, Stensland L, Upham SL, Pepper G, Huang ML, Aubert M, Jerome KR. Liver-Humanized NSG-PiZ Mice Support the Study of Chronic Hepatitis B Virus Infection and Antiviral Therapies. Microbiol Spectr 2023; 11:e0517622. [PMID: 37199630 PMCID: PMC10269919 DOI: 10.1128/spectrum.05176-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/27/2023] [Indexed: 05/19/2023] Open
Abstract
Hepatitis B virus (HBV) is a pathogen of major public health importance that is largely incurable once a chronic infection is established. Only humans and great apes are fully permissive to HBV infection, and this species restriction has impacted HBV research by limiting the utility of small animal models. To combat HBV species restrictions and enable more in vivo studies, liver-humanized mouse models have been developed that are permissive to HBV infection and replication. Unfortunately, these models can be difficult to establish and are expensive commercially, which has limited their academic use. As an alternative mouse model to study HBV, we evaluated liver-humanized NSG-PiZ mice and showed that they are fully permissive to HBV. HBV selectively replicates in human hepatocytes within chimeric livers, and HBV-positive (HBV+) mice secrete infectious virions and hepatitis B surface antigen (HBsAg) into blood while also harboring covalently closed circular DNA (cccDNA). HBV+ mice develop chronic infections lasting at least 169 days, which should enable the study of new curative therapies targeting chronic HBV, and respond to entecavir therapy. Furthermore, HBV+ human hepatocytes in NSG-PiZ mice can be transduced by AAV3b and AAV.LK03 vectors, which should enable the study of gene therapies that target HBV. In summary, our data demonstrate that liver-humanized NSG-PiZ mice can be used as a robust and cost-effective alternative to existing chronic hepatitis B (CHB) models and may enable more academic research labs to study HBV disease pathogenesis and antiviral therapy. IMPORTANCE Liver-humanized mouse models have become the gold standard for the in vivo study of hepatitis B virus (HBV), yet their complexity and cost have prohibited widespread use of existing models in research. Here, we show that the NSG-PiZ liver-humanized mouse model, which is relatively inexpensive and simple to establish, can support chronic HBV infection. Infected mice are fully permissive to hepatitis B, supporting both active replication and spread, and can be used to study novel antiviral therapies. This model is a viable and cost-effective alternative to other liver-humanized mouse models that are used to study HBV.
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Affiliation(s)
- Rossana Colón-Thillet
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Michelle A. Loprieno
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lindsay Klouser
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Tracy K. Santo
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Laurence Stensland
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Sarah L. Upham
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Gregory Pepper
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Martine Aubert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
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Roychoudhury P, Sereewit J, Xie H, Nunley E, Bakhash SM, Lieberman NA, Greninger AL. Genomic Analysis of Early Monkeypox Virus Outbreak Strains, Washington, USA. Emerg Infect Dis 2023; 29:644-646. [PMID: 36732066 PMCID: PMC9973680 DOI: 10.3201/eid2903.221446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We conducted a genomic analysis of monkeypox virus sequences collected early in the 2022 outbreak, during July-August , in Washington, USA. Using 109 viral genomes, we found low overall genetic diversity, multiple introductions into the state, ongoing community transmission, and potential for co-infections by multiple strains.
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Chang A, Sholukh AM, Wieland A, Jaye DL, Carrington M, Huang ML, Xie H, Jerome KR, Roychoudhury P, Greninger AL, Koff JL, Cohen JB, Koelle DM, Corey L, Flowers CR, Ahmed R. Herpes simplex virus lymphadenitis is associated with tumor reduction in a patient with chronic lymphocytic leukemia. J Clin Invest 2022; 132:e161109. [PMID: 35862190 PMCID: PMC9479599 DOI: 10.1172/jci161109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
BackgroundHerpes simplex virus lymphadenitis (HSVL) is an unusual presentation of HSV reactivation in patients with chronic lymphocytic leukemia (CLL) and is characterized by systemic symptoms and no herpetic lesions. The immune responses during HSVL have not, to our knowledge, been studied.MethodsPeripheral blood and lymph node (LN) samples were obtained from a patient with HSVL. HSV-2 viral load, antibody levels, B and T cell responses, cytokine levels, and tumor burden were measured.ResultsThe patient showed HSV-2 viremia for at least 6 weeks. During this period, she had a robust HSV-specific antibody response with neutralizing and antibody-dependent cellular phagocytotic activity. Activated (HLA-DR+, CD38+) CD4+ and CD8+ T cells increased 18-fold, and HSV-specific CD8+ T cells in the blood were detected at higher numbers. HSV-specific B and T cell responses were also detected in the LN. Markedly elevated levels of proinflammatory cytokines in the blood were also observed. Surprisingly, a sustained decrease in CLL tumor burden without CLL-directed therapy was observed with this and also a prior episode of HSVL.ConclusionHSVL should be considered part of the differential diagnosis in patients with CLL who present with signs and symptoms of aggressive lymphoma transformation. An interesting finding was the sustained tumor control after 2 episodes of HSVL in this patient. A possible explanation for the reduction in tumor burden may be that the HSV-specific response served as an adjuvant for the activation of tumor-specific or bystander T cells. Studies in additional patients with CLL are needed to confirm and extend these findings.FundingNIH grants 4T32CA160040, UL1TR002378, and 5U19AI057266 and NIH contracts 75N93019C00063 and HHSN261200800001E. Neil W. and William S. Elkin Fellowship (Winship Cancer Institute).
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Affiliation(s)
- Andres Chang
- Department of Hematology and Medical Oncology, Winship Cancer Institute and
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine Atlanta, Georgia, USA
| | - Anton M. Sholukh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Andreas Wieland
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine Atlanta, Georgia, USA
| | - David L. Jaye
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | - Meei-Li Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Hong Xie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Alexander L. Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Jean L. Koff
- Department of Hematology and Medical Oncology, Winship Cancer Institute and
| | - Jonathon B. Cohen
- Department of Hematology and Medical Oncology, Winship Cancer Institute and
| | - David M. Koelle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department Medicine and
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Translational Immunology, Benaroya Research Institute, Seattle, Washington, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department Medicine and
| | | | - Rafi Ahmed
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine Atlanta, Georgia, USA
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Guellil M, van Dorp L, Inskip SA, Dittmar JM, Saag L, Tambets K, Hui R, Rose A, D’Atanasio E, Kriiska A, Varul L, Koekkelkoren AMHC, Goldina RD, Cessford C, Solnik A, Metspalu M, Krause J, Herbig A, Robb JE, Houldcroft CJ, Scheib CL. Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia. SCIENCE ADVANCES 2022; 8:eabo4435. [PMID: 35895820 PMCID: PMC9328674 DOI: 10.1126/sciadv.abo4435] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/10/2022] [Indexed: 05/05/2023]
Abstract
Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, infects a majority of adults globally. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups has suggested the virus codiverged with human migrations out of Africa, although a much younger origin has also been proposed. We present three full ancient European HSV-1 genomes and one partial genome, dating from the 3rd to 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. Considering a dataset of modern and ancient genomes, we apply phylogenetic methods to estimate the age of sampled modern Eurasian HSV-1 diversity to 4.68 (3.87 to 5.65) ka. Extrapolation of estimated rates to a global dataset points to the age of extant sampled HSV-1 as 5.29 (4.60 to 6.12) ka, suggesting HSV-1 lineage replacement coinciding with the late Neolithic period and following Bronze Age migrations.
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Affiliation(s)
- Meriam Guellil
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Lucy van Dorp
- UCL Genetics Institute, Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
| | - Sarah A. Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of Archaeology and Ancient History, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Jenna M. Dittmar
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of Archaeology, University of Aberdeen, UK
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
- UCL Genetics Institute, Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Ruoyun Hui
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Alan Turing Institute, 2QR, John Dodson House, 96 Euston Rd., London NW1 2DB, UK
| | - Alice Rose
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | | | - Aivar Kriiska
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia
| | - Liivi Varul
- Archaeological Research Collection, School of Humanities, Tallinn University, Tallinn 10130, Estonia
| | | | - Rimma D. Goldina
- Department History of Udmurtia, Archaeology and Ethnology, Udmurt State University, 1, Universitetskaya St. 1, 426034 Izhevsk, Russia
| | - Craig Cessford
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010 Estonia
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - John E. Robb
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | | | - Christiana L. Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
- St. John’s College, University of Cambridge, Cambridge, CB2 1TP, UK
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Rathbun MM, Shipley MM, Bowen CD, Selke S, Wald A, Johnston C, Szpara ML. Comparison of herpes simplex virus 1 genomic diversity between adult sexual transmission partners with genital infection. PLoS Pathog 2022; 18:e1010437. [PMID: 35587470 PMCID: PMC9119503 DOI: 10.1371/journal.ppat.1010437] [Citation(s) in RCA: 3] [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: 11/16/2021] [Accepted: 03/11/2022] [Indexed: 01/15/2023] Open
Abstract
Herpes simplex virus (HSV) causes chronic infection in the human host, characterized by self-limited episodes of mucosal shedding and lesional disease, with latent infection of neuronal ganglia. The epidemiology of genital herpes has undergone a significant transformation over the past two decades, with the emergence of HSV-1 as a leading cause of first-episode genital herpes in many countries. Though dsDNA viruses are not expected to mutate quickly, it is not yet known to what degree the HSV-1 viral population in a natural host adapts over time, or how often viral population variants are transmitted between hosts. This study provides a comparative genomics analysis for 33 temporally-sampled oral and genital HSV-1 genomes derived from five adult sexual transmission pairs. We found that transmission pairs harbored consensus-level viral genomes with near-complete conservation of nucleotide identity. Examination of within-host minor variants in the viral population revealed both shared and unique patterns of genetic diversity between partners, and between anatomical niches. Additionally, genetic drift was detected from spatiotemporally separated samples in as little as three days. These data expand our prior understanding of the complex interaction between HSV-1 genomics and population dynamics after transmission to new infected persons.
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Affiliation(s)
- Molly M. Rathbun
- Department of Biochemistry and Molecular Biology, Department of Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Mackenzie M. Shipley
- Department of Biochemistry and Molecular Biology, Department of Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Christopher D. Bowen
- Department of Biochemistry and Molecular Biology, Department of Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Anna Wald
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Christine Johnston
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Moriah L. Szpara
- Department of Biochemistry and Molecular Biology, Department of Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
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10
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Lin MJ, Rachleff VM, Xie H, Shrestha L, Lieberman NAP, Peddu V, Addetia A, Casto AM, Breit N, Mathias PC, Huang ML, Jerome KR, Greninger AL, Roychoudhury P. Host-pathogen dynamics in longitudinal clinical specimens from patients with COVID-19. Sci Rep 2022; 12:5856. [PMID: 35393464 PMCID: PMC8987511 DOI: 10.1038/s41598-022-09752-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/16/2022] [Indexed: 12/30/2022] Open
Abstract
Rapid dissemination of SARS-CoV-2 sequencing data to public repositories has enabled widespread study of viral genomes, but studies of longitudinal specimens from infected persons are relatively limited. Analysis of longitudinal specimens enables understanding of how host immune pressures drive viral evolution in vivo. Here we performed sequencing of 49 longitudinal SARS-CoV-2-positive samples from 20 patients in Washington State collected between March and September of 2020. Viral loads declined over time with an average increase in RT-QPCR cycle threshold of 0.87 per day. We found that there was negligible change in SARS-CoV-2 consensus sequences over time, but identified a number of nonsynonymous variants at low frequencies across the genome. We observed enrichment for a relatively small number of these variants, all of which are now seen in consensus genomes across the globe at low prevalence. In one patient, we saw rapid emergence of various low-level deletion variants at the N-terminal domain of the spike glycoprotein, some of which have previously been shown to be associated with reduced neutralization potency from sera. In a subset of samples that were sequenced using metagenomic methods, differential gene expression analysis showed a downregulation of cytoskeletal genes that was consistent with a loss of ciliated epithelium during infection and recovery. We also identified co-occurrence of bacterial species in samples from multiple hospitalized individuals. These results demonstrate that the intrahost genetic composition of SARS-CoV-2 is dynamic during the course of COVID-19, and highlight the need for continued surveillance and deep sequencing of minor variants.
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Affiliation(s)
- Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Victoria M Rachleff
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Program in Molecular and Cellular Biology, University of Washington School of Medicine, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Nicole A P Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Vikas Peddu
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Amin Addetia
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Amanda M Casto
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA, USA
| | - Nathan Breit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Patrick C Mathias
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA. .,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA. .,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98102, USA. .,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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11
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Lieberman NAP, Lin MJ, Xie H, Shrestha L, Nguyen T, Huang ML, Haynes AM, Romeis E, Wang QQ, Zhang RL, Kou CX, Ciccarese G, Dal Conte I, Cusini M, Drago F, Nakayama SI, Lee K, Ohnishi M, Konda KA, Vargas SK, Eguiluz M, Caceres CF, Klausner JD, Mitjà O, Rompalo A, Mulcahy F, Hook EW, Lukehart SA, Casto AM, Roychoudhury P, DiMaio F, Giacani L, Greninger AL. Treponema pallidum genome sequencing from six continents reveals variability in vaccine candidate genes and dominance of Nichols clade strains in Madagascar. PLoS Negl Trop Dis 2021; 15:e0010063. [PMID: 34936652 PMCID: PMC8735616 DOI: 10.1371/journal.pntd.0010063] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/06/2022] [Accepted: 12/06/2021] [Indexed: 11/19/2022] Open
Abstract
In spite of its immutable susceptibility to penicillin, Treponema pallidum (T. pallidum) subsp. pallidum continues to cause millions of cases of syphilis each year worldwide, resulting in significant morbidity and mortality and underscoring the urgency of developing an effective vaccine to curtail the spread of the infection. Several technical challenges, including absence of an in vitro culture system until very recently, have hampered efforts to catalog the diversity of strains collected worldwide. Here, we provide near-complete genomes from 196 T. pallidum strains-including 191 T. pallidum subsp. pallidum-sequenced directly from patient samples collected from 8 countries and 6 continents. Maximum likelihood phylogeny revealed that samples from most sites were predominantly SS14 clade. However, 99% (84/85) of the samples from Madagascar formed two of the five distinct Nichols subclades. Although recombination was uncommon in the evolution of modern circulating strains, we found multiple putative recombination events between T. pallidum subsp. pallidum and subsp. endemicum, shaping the genomes of several subclades. Temporal analysis dated the most recent common ancestor of Nichols and SS14 clades to 1717 (95% HPD: 1543-1869), in agreement with other recent studies. Rates of SNP accumulation varied significantly among subclades, particularly among different Nichols subclades, and was associated in the Nichols A subclade with a C394F substitution in TP0380, a ERCC3-like DNA repair helicase. Our data highlight the role played by variation in genes encoding putative surface-exposed outer membrane proteins in defining separate lineages, and provide a critical resource for the design of broadly protective syphilis vaccines targeting surface antigens.
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Affiliation(s)
- Nicole A. P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Michelle J. Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Tien Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Austin M. Haynes
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Emily Romeis
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Qian-Qiu Wang
- Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- National Center for STD Control, China Centers for Disease Control and Prevention, Nanjing, China
| | - Rui-Li Zhang
- Department of Dermatology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Cai-Xia Kou
- Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- National Center for STD Control, China Centers for Disease Control and Prevention, Nanjing, China
| | - Giulia Ciccarese
- Health Sciences Department, Section of Dermatology, San Martino University Hospital, Genoa, Italy
| | - Ivano Dal Conte
- STI Clinic, Infectious Diseases Unit, University of Turin, Turin, Italy
| | - Marco Cusini
- Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Drago
- Health Sciences Department, Section of Dermatology, San Martino University Hospital, Genoa, Italy
| | - Shu-ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kelika A. Konda
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Silver K. Vargas
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Maria Eguiluz
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Carlos F. Caceres
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Jeffrey D. Klausner
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Oriol Mitjà
- Fight Aids and Infectious Diseases Foundation, Hospital Germans Trias i Pujol, Barcelona, Spain
- Lihir Medical Centre-International SOS, Newcrest Mining, Lihir Island, Papua New Guinea
| | - Anne Rompalo
- Department of Infectious Diseases, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Fiona Mulcahy
- Department of Genito Urinary Medicine and Infectious Diseases, St James’s Hospital, Dublin, Ireland
| | - Edward W. Hook
- Department of Medicine, University of Alabama, Birmingham, Birmingham, Alabama, United States of America
| | - Sheila A. Lukehart
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Amanda M. Casto
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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12
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Assessing the potential correlation of polymorphisms in the IL6R with relative IL6 elevation in severely ill COVID-19 patients'. Cytokine 2021; 148:155662. [PMID: 34353696 PMCID: PMC8318728 DOI: 10.1016/j.cyto.2021.155662] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 01/18/2023]
Abstract
Background Elevated Interleukin-6 (IL-6) may play an important role in the pathophysiology of COVID-19 yet attenuated response is not seen across all severe patients. We aimed to determine the effect of IL-6 baseline levels and other clinical variables on mortality and outcomes in hospitalized COVID-19 patients as well as to explore genetic variants associated with attenuated IL-6 response. Methods Baseline IL-6 cytokine levels were measured in hospitalized patients participating in ongoing ODYSSEY phase 3 randomized study of tradipitant and placebo in hospitalized patients with severe COVID-19 who are receiving supplemental oxygen support. Furthermore blood samples for whole genome sequencing analysis were collected from 150 participants. Results We report significantly elevated IL-6 in COVID-19 infected hospitalized patients, n = 100 (p-value < 0.0001) when compared to controls n = 324. We also report a significantly increased level of IL-6 (p-value < 0.01) between the severe and mild COVID-19 patients with severity defined on a WHO scale. Excessive IL-6 plasma levels correlate with higher mortality (p-value 0.001). Additionally, based on our classification analysis, combination of IL-6 elevation and high levels of serum glucose can identify highest risk-group of COVID19 patients. Furthermore, we explore the role of genetic regulatory variants affecting baseline IL-6 levels specifically in COVID-19 patients. We have directly tested the association between variants in the IL6 and IL6R gene region and IL6 plasma levels. We provide results for a common IL-6 variant previously associated with pneumonia, rs1800795, and rs2228145 that was previously shown to affect IL-6 plasma levels, as well as report on novel variants associated with IL-6 plasma levels detected in our study patients. Conclusions While it is unlikely that “cytokine storm” is the norm in severe COVID19, baseline elevations above 150 pg/ml may be associated with worst outcomes and as such may warrant treatment considerations. So far no clinical studies used IL-6 baseline assessment to stratify the patient population participating in clinical studies. We believe that careful examination and interpretation of the IL-6 levels and genetic variants can help to determine a patient population with a potentially very robust clinical response to IL-6 inhibition. Trial Registration: Clinicaltrials.gov: NCT04326426.
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13
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Abstract
Herpes simplex viruses (HSV) cause chronic infection in humans that are characterized by periodic episodes of mucosal shedding and ulcerative disease. HSV causes millions of infections world-wide, with lifelong bouts of viral reactivation from latency in neuronal ganglia. Infected individuals experience different levels of disease severity and frequency of reactivation. There are two distantly related HSV species, with HSV-1 infections historically found most often in the oral niche and HSV-2 infections in the genital niche. Over the last two decades, HSV-1 has emerged as the leading cause of first-episode genital herpes in multiple countries. While HSV-1 has the highest level of genetic diversity among human alpha-herpesviruses, it is not yet known how quickly the HSV-1 viral population in a human host adapts over time, or if there are population bottlenecks associated with viral reactivation and/or transmission. It is also unknown how the ecological environments in which HSV infections occur influence their evolutionary trajectory, or that of co-occurring viruses and microbes. In this review, we explore how HSV accrues genetic diversity within each new infection, and yet maintains its ability to successfully infect most of the human population. A holistic examination of the ecological context of natural human infections can expand our awareness of how HSV adapts as it moves within and between human hosts, and reveal the complexity of these lifelong human-virus interactions. These insights may in turn suggest new areas of exploration for other chronic pathogens that successfully evolve and persist among their hosts.
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14
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Aswad A, Aimola G, Wight D, Roychoudhury P, Zimmermann C, Hill J, Lassner D, Xie H, Huang ML, Parrish NF, Schultheiss HP, Venturini C, Lager S, Smith GCS, Charnock-Jones DS, Breuer J, Greninger AL, Kaufer BB. Evolutionary History of Endogenous Human Herpesvirus 6 Reflects Human Migration out of Africa. Mol Biol Evol 2021; 38:96-107. [PMID: 32722766 PMCID: PMC7782865 DOI: 10.1093/molbev/msaa190] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Human herpesvirus 6A and 6B (HHV-6) can integrate into the germline, and as a result, ∼70 million people harbor the genome of one of these viruses in every cell of their body. Until now, it has been largely unknown if 1) these integrations are ancient, 2) if they still occur, and 3) whether circulating virus strains differ from integrated ones. Here, we used next-generation sequencing and mining of public human genome data sets to generate the largest and most diverse collection of circulating and integrated HHV-6 genomes studied to date. In genomes of geographically dispersed, only distantly related people, we identified clades of integrated viruses that originated from a single ancestral event, confirming this with fluorescent in situ hybridization to directly observe the integration locus. In contrast to HHV-6B, circulating and integrated HHV-6A sequences form distinct clades, arguing against ongoing integration of circulating HHV-6A or “reactivation” of integrated HHV-6A. Taken together, our study provides the first comprehensive picture of the evolution of HHV-6, and reveals that integration of heritable HHV-6 has occurred since the time of, if not before, human migrations out of Africa.
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Affiliation(s)
- Amr Aswad
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Giulia Aimola
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Darren Wight
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, WA
| | | | - Joshua Hill
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, WA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Dirk Lassner
- HighTech Center, Vinmec Hospital, Hanoi, Vietnam.,Institut Kardiale Diagnostik und Therapie, Berlin, Germany
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, WA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, WA
| | - Nicholas F Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Cristina Venturini
- Division of Infection and Immunity, UCL Research Department of Infection, UCL, London, United Kingdom
| | - Susanne Lager
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden.,Department of Obstetrics and Gynaecology, Cambridge University, United Kingdom
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, Cambridge University, United Kingdom
| | | | - Judith Breuer
- Division of Infection and Immunity, UCL Research Department of Infection, UCL, London, United Kingdom
| | - Alexander L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, WA
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15
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Müller NF, Wagner C, Frazar CD, Roychoudhury P, Lee J, Moncla LH, Pelle B, Richardson M, Ryke E, Xie H, Shrestha L, Addetia A, Rachleff VM, Lieberman NAP, Huang ML, Gautom R, Melly G, Hiatt B, Dykema P, Adler A, Brandstetter E, Han PD, Fay K, Ilcisin M, Lacombe K, Sibley TR, Truong M, Wolf CR, Boeckh M, Englund JA, Famulare M, Lutz BR, Rieder MJ, Thompson M, Duchin JS, Starita LM, Chu HY, Shendure J, Jerome KR, Lindquist S, Greninger AL, Nickerson DA, Bedford T. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. Sci Transl Med 2021; 13:eabf0202. [PMID: 33941621 PMCID: PMC8158963 DOI: 10.1126/scitranslmed.abf0202] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/23/2021] [Accepted: 04/25/2021] [Indexed: 12/16/2022]
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has gravely affected societies around the world. Outbreaks in different parts of the globe have been shaped by repeated introductions of new viral lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State (USA) to characterize how the spread of SARS-CoV-2 in Washington State in early 2020 was shaped by differences in timing of mitigation strategies across counties and by repeated introductions of viral lineages into the state. In addition, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G but not the other variant (614D) into the state. At an individual level, we observed evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we did not find any evidence that the 614G variant affects clinical severity or patient outcomes. Overall, this suggests that with regard to D614G, the behavior of individuals has been more important in shaping the course of the pandemic in Washington State than this variant of the virus.
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Affiliation(s)
- Nicola F Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Cassia Wagner
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Chris D Frazar
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Louise H Moncla
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Benjamin Pelle
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Matthew Richardson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Erica Ryke
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Victoria M Rachleff
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Nicole A P Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Romesh Gautom
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Geoff Melly
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Brian Hiatt
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Philip Dykema
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Amanda Adler
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Elisabeth Brandstetter
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Peter D Han
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kirsten Lacombe
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Thomas R Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Melissa Truong
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Caitlin R Wolf
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Janet A Englund
- Seattle Children's Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | | | - Barry R Lutz
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Matthew Thompson
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Jeffrey S Duchin
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Public Health - Seattle & King County, Seattle, WA98121, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Helen Y Chu
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Scott Lindquist
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
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16
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Shapiro M, Krug LT, MacCarthy T. Mutational pressure by host APOBEC3s more strongly affects genes expressed early in the lytic phase of herpes simplex virus-1 (HSV-1) and human polyomavirus (HPyV) infection. PLoS Pathog 2021; 17:e1009560. [PMID: 33930088 PMCID: PMC8115780 DOI: 10.1371/journal.ppat.1009560] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 05/12/2021] [Accepted: 04/14/2021] [Indexed: 01/22/2023] Open
Abstract
Herpes-Simplex Virus 1 (HSV-1) infects most humans when they are young, sometimes with fatal consequences. Gene expression occurs in a temporal order upon lytic HSV-1 infection: immediate early (IE) genes are expressed, then early (E) genes, followed by late (L) genes. During this infection cycle, the HSV-1 genome has the potential for exposure to APOBEC3 (A3) proteins, a family of cytidine deaminases that cause C>U mutations on single-stranded DNA (ssDNA), often resulting in a C>T transition. We developed a computational model for the mutational pressure of A3 on the lytic cycle of HSV-1 to determine which viral kinetic gene class is most vulnerable to A3 mutations. Using in silico stochastic methods, we simulated the infectious cycle under varying intensities of A3 mutational pressure. We found that the IE and E genes are more vulnerable to A3 than L genes. We validated this model by analyzing the A3 evolutionary footprints in 25 HSV-1 isolates. We find that IE and E genes have evolved to underrepresent A3 hotspot motifs more so than L genes, consistent with greater selection pressure on IE and E genes. We extend this model to two-step infections, such as those of polyomavirus, and find that the same pattern holds for over 25 human Polyomavirus (HPyVs) genomes. Genes expressed earlier during infection are more vulnerable to mutations than those expressed later.
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Affiliation(s)
- Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America
| | - Laurie T. Krug
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, United States of America
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17
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Casto AM, Stout SC, Selvarangan R, Freeman AF, Newell BD, Stahl ED, Ahmed AA, Greninger AL, Yin DE. Evaluation of Genotypic Antiviral Resistance Testing as an Alternative to Phenotypic Testing in a Patient with DOCK8 Deficiency and Severe HSV-1 Disease. J Infect Dis 2021; 221:2035-2042. [PMID: 31970398 DOI: 10.1093/infdis/jiaa020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/21/2020] [Indexed: 11/14/2022] Open
Abstract
Antiviral resistance frequently complicates the treatment of herpes simplex virus (HSV) infections in immunocompromised patients. Here we present the case of an adolescent boy with dedicator of cytokinesis 8 (DOCK8) deficiency, who experienced recurrent infections with resistant HSV-1. We used both phenotypic and genotypic methodologies to characterize the resistance profile of HSV-1 in the patient and conclude that genotypic testing outperformed phenotypic testing. We also present the first analysis of intrahost HSV-1 evolution in an immunocompromised patient. While HSV-1 can remain static in an immunocompetent individual for decades, the virus from this patient rapidly acquired genetic changes throughout its genome. Finally, we document a likely case of transmitted resistance in HSV-1 between the patient and his brother, who also has DOCK8 deficiency. This event demonstrates that resistant HSV-1 is transmissible among immunocompromised persons.
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Affiliation(s)
- Amanda M Casto
- Department of Medicine, University of Washington, Seattle, Washington, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Sean C Stout
- Department of Pediatrics, Children's Mercy, Kansas City, Missouri, USA
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA.,Division of Infectious Diseases, Department of Pediatrics, Children's Mercy, Kansas City, Missouri, USA
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Brandon D Newell
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA.,Division of Dermatology, Department of Pediatrics, Children's Mercy, Kansas City, Missouri, USA
| | - Erin D Stahl
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA.,Section of Ophthalmology, Department of Surgery, Children's Mercy, Kansas City, Missouri, USA
| | - Atif A Ahmed
- Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, Missouri, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Dwight E Yin
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA.,Division of Infectious Diseases, Department of Pediatrics, Children's Mercy, Kansas City, Missouri, USA.,Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Department of Pediatrics, Children's Mercy, Kansas City, Missouri, USA
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18
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Obisesan OS, Sithebe NP, Mufhandu HT. Seroprevalence and characterisation of herpes simplex virus from human immunodeficiency virus in samples collected from two provinces in South Africa: a retrospective study. F1000Res 2021; 10:105. [PMID: 34853674 PMCID: PMC8591517 DOI: 10.12688/f1000research.28105.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/16/2021] [Indexed: 04/05/2024] Open
Abstract
Background: Herpes simplex virus (HSV) is a widely distributed human pathogen that is known for its ulcerative lesions at the infection site. HSV can cause persistent infection in the host that is often followed by a period of latency within the neurons. Considering the high rate of HIV infection in South Africa, it is important to assess the seroprevalence of HSV with a focus to determine the epidemiological association between HSV-DNA and HIV-1 in the population. Methods: A total of 44 sera samples were screened for HSV and HIV-1 using the highly sensitive enzyme-linked immunosorbent assay (ELISA). The ELISA positive samples were characterized using polymerase chain reaction (PCR) to confirm the positivity of both viruses and to further differentiate HSV into HSV-1 and -2. Thereafter, the samples were analysed for relatedness using phylogenetic analysis. Results: Of the 44 samples, 36 (81.8%) were positive for HIV-1, while 35 (79.5%) were positive for HSV when screened with ELISA kits. The PCR results, with the use of type specific primers, showed that 4/35 (11.4%) samples were specific for HSV-1 while 30/35 (85.7%) were specific for HSV-2. Statistical analysis performed using the chi-squared goodness-of-fit test showed that there is a significant relationship between HSV-2 and HIV-1 transmission. Conclusions: The prevalence of HSV in the population is high with an increased HSV-2 infection in women. Our study shows that some of the HSV-2 isolates are not related to the clinical isolate SD90e from South Africa, suggesting diversity in HSV-2 viral transmission.
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19
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Obisesan OS, Sithebe NP, Mufhandu HT. Seroprevalence and characterisation of herpes simplex virus from human immunodeficiency virus in samples collected from two provinces in South Africa: a retrospective study. F1000Res 2021; 10:105. [PMID: 34853674 PMCID: PMC8591517 DOI: 10.12688/f1000research.28105.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Herpes simplex virus (HSV) is a widely distributed human pathogen that is known for its ulcerative lesions at the infection site. HSV can cause persistent infection in the host that is often followed by a period of latency within the neurons. Considering the high rate of HIV infection in South Africa, it is important to assess the seroprevalence of HSV with a focus to determine the epidemiological association between HSV-DNA and HIV-1 in the population. Methods: A total of 44 sera samples were screened for HSV and HIV-1 using the highly sensitive enzyme-linked immunosorbent assay (ELISA). The ELISA positive samples were characterized using polymerase chain reaction (PCR) to confirm the positivity of both viruses and to further differentiate HSV into HSV-1 and -2. Thereafter, the samples were analysed for relatedness using phylogenetic analysis. Results: Of the 44 samples, 36 (81.8%) were positive for HIV-1, while 35 (79.5%) were positive for HSV when screened with ELISA kits. The PCR results, with the use of type specific primers, showed that 4/35 (11.4%) samples were specific for HSV-1 while 30/35 (85.7%) were specific for HSV-2. Statistical analysis performed using the chi-squared goodness-of-fit test showed that there is a significant relationship between HSV-2 and HIV-1 transmission. Conclusions: There is a significant positive association between HSV-2 and HIV-1 in the study population. Our study shows that some of the HSV-2 isolates are not related to the clinical isolate SD90e from South Africa, suggesting diversity in HSV-2 viral transmission.
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20
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Obisesan OS, Sithebe NP, Mufhandu HT. Seroprevalence and characterisation of herpes simplex virus from human immunodeficiency virus in samples collected from the North-West and KwaZulu-Natal Provinces: a retrospective study. F1000Res 2021; 10:105. [PMID: 34853674 PMCID: PMC8591517 DOI: 10.12688/f1000research.28105.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/22/2020] [Indexed: 04/05/2024] Open
Abstract
Background: Herpes simplex viruses (HSVs) are highly pervasive and show a strong synergistic interaction with human immunodeficiency virus (HIV). High prevalence of HSV type 1 (HSV-1) has been reported in Africa with a prevalence rate of 20-80% in women and 10-50% in men. Studies on the prevalence of HSV in South Africa are few considering the rate of HIV infection in the country. Our focus was to determine the molecular prevalence of HSV-DNA in HIV-1 sera. Methods: In total, 44 convenience samples were screened for HSV and HIV-1 using the highly sensitive enzyme-linked immunosorbent assay (ELISA). The ELISA positive samples were characterized using polymerase chain reaction (PCR) to confirm the positivity of both viruses and to further differentiate HSV into HSV-1 and -2. Thereafter, the samples were analysed for relatedness using phylogenetic analysis. Results: Of 44 samples, 36 (81.8%) were positive for HIV-1, while 35 (79.5%) were positive for HSV when screened with ELISA kits. The results of PCR with type specific primers showed that 4/35 (11.4%) samples were specific for HSV-1 while 30/35 (85.7%) were specific for HSV-2. Statistical analysis performed using chi-squared goodness-of-fit test showed that there is a significant relationship between HSV-2 and HIV-1 transmission. Conclusions: High prevalence of HSV-2 recorded in HIV-1 sera corroborate with similar studies conducted within different cohorts in the continent. SPSS Pearson's chi-squared test established that there is a significant relationship between HSV-2 and HIV-1 transmission.
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21
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Obisesan OS, Sithebe NP, Mufhandu HT. Seroprevalence and characterisation of herpes simplex virus from human immunodeficiency virus in samples collected from two provinces in South Africa: a retrospective study. F1000Res 2021; 10:105. [PMID: 34853674 PMCID: PMC8591517 DOI: 10.12688/f1000research.28105.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/13/2021] [Indexed: 04/05/2024] Open
Abstract
Background: Herpes simplex virus (HSV) is a widely distributed human pathogen that is known for its ulcerative lesions at the infection site. HSV can cause persistent infection in the host that is often followed by a period of latency within the neurons. Considering the high rate of HIV infection in South Africa, it is important to assess the seroprevalence of HSV with a focus to determine the epidemiological association between HSV-DNA and HIV-1 in the population. Methods: A total of 44 sera samples were screened for HSV and HIV-1 using the highly sensitive enzyme-linked immunosorbent assay (ELISA). The ELISA positive samples were characterized using polymerase chain reaction (PCR) to confirm the positivity of both viruses and to further differentiate HSV into HSV-1 and -2. Thereafter, the samples were analysed for relatedness using phylogenetic analysis. Results: Of the 44 samples, 36 (81.8%) were positive for HIV-1, while 35 (79.5%) were positive for HSV when screened with ELISA kits. The PCR results, with the use of type specific primers, showed that 4/35 (11.4%) samples were specific for HSV-1 while 30/35 (85.7%) were specific for HSV-2. Statistical analysis performed using the chi-squared goodness-of-fit test showed that there is a significant relationship between HSV-2 and HIV-1 transmission. Conclusions:There is a significant relationship between HSV-2 and HIV-1 in the study population. Our study shows that some of the HSV-2 isolates are not related to the clinical isolate SD90e from South Africa, suggesting diversity in HSV-2 viral transmission.
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22
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Casto AM, Roychoudhury P, Xie H, Selke S, Perchetti GA, Wofford H, Huang ML, Verjans GMGM, Gottlieb GS, Wald A, Jerome KR, Koelle DM, Johnston C, Greninger AL. Large, Stable, Contemporary Interspecies Recombination Events in Circulating Human Herpes Simplex Viruses. J Infect Dis 2021; 221:1271-1279. [PMID: 31016321 DOI: 10.1093/infdis/jiz199] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/20/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The ubiquitous human pathogens, herpes simplex virus (HSV)-1 and HSV-2, are distinct viral species that diverged approximately 6 million years ago. At least 4 small, ancient HSV-1 × HSV-2 interspecies recombination events have affected the HSV-2 genome, with recombinants and nonrecombinants at each locus circulating today. However, it is unknown whether interspecies recombination can affect other loci and whether new recombinants continue to be generated. METHODS Using 255 newly sequenced and 230 existing HSV genome sequences, we comprehensively assessed interspecies recombination in HSV. RESULTS Our findings show that the sizes and locations of interspecies recombination events in HSV-2 are significantly more variable than previously appreciated and that they can impact species-specific T-cell recognition of HSV. CONCLUSIONS We describe 2 large (>5 kb) recombination events, one of which arose in its current host, demonstrating that interspecies recombination continues to occur today. These results raise concerns about the use of live-attenuated HSV-2 vaccines in high HSV-1 prevalence areas.
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Affiliation(s)
- Amanda M Casto
- Departments of Medicine, University of Washington, Seattle
| | | | - Hong Xie
- Laboratory Medicine, University of Washington, Seattle
| | - Stacy Selke
- Departments of Medicine, University of Washington, Seattle
| | | | - Haley Wofford
- Departments of Medicine, University of Washington, Seattle
| | - Meei-Li Huang
- Laboratory Medicine, University of Washington, Seattle
| | - Georges M G M Verjans
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands.,Research Center for Emerging Infectious and Zoonoses, University of Veterinary Medicine Hannover, Germany
| | - Geoffrey S Gottlieb
- Departments of Medicine, University of Washington, Seattle.,Global Health, University of Washington, Seattle.,Center for Emerging and Re-Emerging Infectious Diseases, University of Washington, Seattle
| | - Anna Wald
- Departments of Medicine, University of Washington, Seattle
| | - Keith R Jerome
- Laboratory Medicine, University of Washington, Seattle.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - David M Koelle
- Departments of Medicine, University of Washington, Seattle.,Laboratory Medicine, University of Washington, Seattle.,Global Health, University of Washington, Seattle.,Center for Emerging and Re-Emerging Infectious Diseases, University of Washington, Seattle.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Benaroya Research Institute, Seattle, Washington
| | - Christine Johnston
- Departments of Medicine, University of Washington, Seattle.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
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23
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Abstract
Alphaherpesviruses, as large double-stranded DNA viruses, were long considered to be genetically stable and to exist in a homogeneous state. Recently, the proliferation of high-throughput sequencing (HTS) and bioinformatics analysis has expanded our understanding of herpesvirus genomes and the variations found therein. Recent data indicate that herpesviruses exist as diverse populations, both in culture and in vivo, in a manner reminiscent of RNA viruses. In this review, we discuss the past, present, and potential future of alphaherpesvirus genomics, including the technical challenges that face the field. We also review how recent data has enabled genome-wide comparisons of sequence diversity, recombination, allele frequency, and selective pressures, including those introduced by cell culture. While we focus on the human alphaherpesviruses, we draw key insights from related veterinary species and from the beta- and gamma-subfamilies of herpesviruses. Promising technologies and potential future directions for herpesvirus genomics are highlighted as well, including the potential to link viral genetic differences to phenotypic and disease outcomes.
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Affiliation(s)
- Chad V. Kuny
- Departments of Biology, and Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Moriah L. Szpara
- Departments of Biology, and Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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24
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Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Han PD, Fay K, Frazar CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ, Englund JA, Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Müller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin JS, Gautom R, Melly G, Hiatt B, Dykema P, Lindquist S, Queen K, Tao Y, Uehara A, Tong S, MacCannell D, Armstrong GL, Baird GS, Chu HY, Shendure J, Jerome KR. Cryptic transmission of SARS-CoV-2 in Washington state. Science 2020; 370:571-575. [PMID: 32913002 PMCID: PMC7810035 DOI: 10.1126/science.abc0523] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/08/2020] [Indexed: 01/08/2023]
Abstract
After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington state in the United States. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subsequently spread locally before active community surveillance was implemented.
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Affiliation(s)
- Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Meei-Li Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Arun Nalla
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Gregory Pepper
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Adam Reinhardt
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Truong N Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Amanda Adler
- Division of Infectious Disease, Seattle Children's Hospital, Seattle, WA, USA
| | - Elisabeth Brandstetter
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Shari Cho
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Danielle Giroux
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Peter D Han
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chris D Frazar
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kirsten Lacombe
- Division of Infectious Disease, Seattle Children's Hospital, Seattle, WA, USA
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Anahita Kiavand
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Matthew Richardson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Thomas R Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Melissa Truong
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Caitlin R Wolf
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Deborah A Nickerson
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Janet A Englund
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Division of Infectious Disease, Seattle Children's Hospital, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Louise H Moncla
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nicola F Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey S Duchin
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
- Public Health - Seattle & King County, Seattle, WA, USA
| | - Romesh Gautom
- Washington State Department of Health, Shoreline, WA, USA
| | - Geoff Melly
- Washington State Department of Health, Shoreline, WA, USA
| | - Brian Hiatt
- Washington State Department of Health, Shoreline, WA, USA
| | - Philip Dykema
- Washington State Department of Health, Shoreline, WA, USA
| | | | - Krista Queen
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ying Tao
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anna Uehara
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suxiang Tong
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Duncan MacCannell
- Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Gregory L Armstrong
- Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Geoffrey S Baird
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Helen Y Chu
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
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25
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Müller NF, Wagner C, Frazar CD, Roychoudhury P, Lee J, Moncla LH, Pelle B, Richardson M, Ryke E, Xie H, Shrestha L, Addetia A, Rachleff VM, Lieberman NAP, Huang ML, Gautom R, Melly G, Hiatt B, Dykema P, Adler A, Brandstetter E, Han PD, Fay K, Llcisin M, Lacombe K, Sibley TR, Truong M, Wolf CR, Boeckh M, Englund JA, Famulare M, Lutz BR, Rieder MJ, Thompson M, Duchin JS, Starita LM, Chu HY, Shendure J, Jerome KR, Lindquist S, Greninger AL, Nickerson DA, Bedford T. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.09.30.20204230. [PMID: 33024981 PMCID: PMC7536883 DOI: 10.1101/2020.09.30.20204230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The rapid spread of SARS-CoV-2 has gravely impacted societies around the world. Outbreaks in different parts of the globe are shaped by repeated introductions of new lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State to characterize how the spread of SARS-CoV-2 in Washington State (USA) was shaped by differences in timing of mitigation strategies across counties, as well as by repeated introductions of viral lineages into the state. Additionally, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G, but not the other variant (614D) into the state. At an individual level, we see evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we do not find any evidence that the 614G variant impacts clinical severity or patient outcomes. Overall, this suggests that at least to date, the behavior of individuals has been more important in shaping the course of the pandemic than changes in the virus.
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Affiliation(s)
| | - Cassia Wagner
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | | | - Pavitra Roychoudhury
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | - Jover Lee
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | | | - Erica Ryke
- University of Washington, Seattle, WA, USA
| | - Hong Xie
- University of Washington, Seattle, WA, USA
| | | | | | - Victoria M Rachleff
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | | | | | - Romesh Gautom
- Washington State Department of Health, Shoreline, WA, USA
| | - Geoff Melly
- Washington State Department of Health, Shoreline, WA, USA
| | - Brian Hiatt
- Washington State Department of Health, Shoreline, WA, USA
| | - Philip Dykema
- Washington State Department of Health, Shoreline, WA, USA
| | - Amanda Adler
- Seattle Children's Research Institute, Seattle, WA, USA
| | | | | | - Kairsten Fay
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Misja Llcisin
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | | | | | - Michael Boeckh
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Janet A Englund
- University of Washington, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Barry R Lutz
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Jeffrey S Duchin
- University of Washington, Seattle, WA, USA
- Public Health - Seattle & King County, Seattle, WA, USA
| | - Lea M Starita
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Helen Y Chu
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Jay Shendure
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Keith R Jerome
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | | | - Alexander L Greninger
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | - Deborah A Nickerson
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Trevor Bedford
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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26
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Casto AM, Huang MLW, Xie H, Jerome KR, Wald A, Johnston CM, Greninger AL. Herpes Simplex Virus Mistyping due to HSV-1 × HSV-2 Interspecies Recombination in Viral Gene Encoding Glycoprotein B. Viruses 2020; 12:E860. [PMID: 32781734 PMCID: PMC7472045 DOI: 10.3390/v12080860] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 12/26/2022] Open
Abstract
Human herpes simplex viruses (HSV) 1 and 2 are extremely common human pathogens with overlapping disease spectra. Infections due to HSV-1 and HSV-2 are distinguished in clinical settings using sequence-based "typing" assays. Here we describe a case of HSV mistyping caused by a previously undescribed HSV-1 × HSV-2 recombination event in UL27, the HSV gene that encodes glycoprotein B. This is the first documented case of HSV mistyping caused by an HSV-1 × HSV-2 recombination event and the first description of an HSV interspecies recombination event in UL27, which is frequently used as a target for diagnostics and experimental therapeutics. We also review the primer and probe target sequences for a commonly used HSV typing assay from nearly 700 HSV-1 and HSV-2 samples and find that about 4% of HSV-1 samples have a single nucleotide change in at least one of these loci, which could impact assay performance. Our findings illustrate how knowledge of naturally occurring genomic variation in HSV-1 and HSV-2 is essential for the design and interpretation of molecular diagnostics for these viruses.
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Affiliation(s)
- Amanda M. Casto
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA 98195, USA; (A.W.); (C.M.J.)
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
| | - Meei-Li W. Huang
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; (M.-L.W.H.); (H.X.); (A.L.G.)
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; (M.-L.W.H.); (H.X.); (A.L.G.)
| | - Keith R. Jerome
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; (M.-L.W.H.); (H.X.); (A.L.G.)
| | - Anna Wald
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA 98195, USA; (A.W.); (C.M.J.)
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; (M.-L.W.H.); (H.X.); (A.L.G.)
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Christine M. Johnston
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA 98195, USA; (A.W.); (C.M.J.)
| | - Alexander L. Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; (M.-L.W.H.); (H.X.); (A.L.G.)
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27
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Sergeyev OV, Bosh'ian RE, Barinsky IF. [RETRACTED: High-throughput sequencing in diagnostics and prevention of herpes simplex virus infection (Herpesviridae, Alphaherpesvirinae, Simplexvirus, Human alphaherpesvirus 1)]. Vopr Virusol 2020; 65:126-131. [PMID: 33533214 DOI: 10.36233/0507-4088-2020-65-3-126-131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 12/13/2022]
Abstract
RETRACTEDHerpes simplex viruses types 1 (HSV-1) and 2 (HSV-2) are among the most common viruses in the human population. The clinical manifestations of HSV infection vary widely, which necessitates reliable molecular methods for the timely diagnosis of herpes virus infection, as well as for detection of mutations in the genes responsible for drug resistance. PCR is often unable to detect HSV isolates with nucleotide substitutions at the primer binding site. Sanger sequencing of the whole genome reveals mutations mainly at the consensus level, which accumulate at advanced stages of viral infection. High-throughput sequencing (HTS, next generation sequencing) offers an obvious advantage both in early diagnosis of herpes virus infection and identification of HSV variants.
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Affiliation(s)
- O V Sergeyev
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - R E Bosh'ian
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - I F Barinsky
- National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya
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28
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Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Han PD, Fay K, Frazar CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ, Englund JA, Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Müller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin J, Gautom R, Melly G, Hiatt B, Dykema P, Lindquist S, Queen K, Tao Y, Uehara A, Tong S, MacCannell D, Armstrong GL, Baird GS, Chu HY, Shendure J, Jerome KR. Cryptic transmission of SARS-CoV-2 in Washington State. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.04.02.20051417. [PMID: 32511596 PMCID: PMC7276023 DOI: 10.1101/2020.04.02.20051417] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. On March 11, 2020, the World Health Organization declared Coronavirus Disease 2019 (COVID-19) a pandemic. Genome sequencing of SARS-CoV-2 strains allows for the reconstruction of transmission history connecting these infections. Here, we analyze 346 SARS-CoV-2 genomes from samples collected between 20 February and 15 March 2020 from infected patients in Washington State, USA. We found that the large majority of SARS-CoV-2 infections sampled during this time frame appeared to have derived from a single introduction event into the state in late January or early February 2020 and subsequent local spread, strongly suggesting cryptic spread of COVID-19 during the months of January and February 2020, before active community surveillance was implemented. We estimate a common ancestor of this outbreak clade as occurring between 18 January and 9 February 2020. From genomic data, we estimate an exponential doubling between 2.4 and 5.1 days. These results highlight the need for large-scale community surveillance for SARS-CoV-2 introductions and spread and the power of pathogen genomics to inform epidemiological understanding.
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Affiliation(s)
- Trevor Bedford
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | - Alexander L Greninger
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | - Pavitra Roychoudhury
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | | | | | - Arun Nalla
- University of Washington, Seattle, WA USA
| | | | | | - Hong Xie
- University of Washington, Seattle, WA USA
| | | | | | - Amanda Adler
- Seattle Children's Research Institute, Seattle, WA USA
| | | | - Shari Cho
- University of Washington, Seattle, WA USA
| | | | | | - Kairsten Fay
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | | | - Misja Ilcisin
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | | | - Jover Lee
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | | | | | | | | | | | - Deborah A Nickerson
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | - Janet A Englund
- University of Washington, Seattle, WA USA
- Seattle Children's Research Institute, Seattle, WA USA
| | | | - Emma B Hodcroft
- University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - John Huddleston
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | | | | | - Richard A Neher
- University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Xianding Deng
- University of California San Francisco, San Francisco, CA USA
| | - Wei Gu
- University of California San Francisco, San Francisco, CA USA
| | - Scot Federman
- University of California San Francisco, San Francisco, CA USA
| | - Charles Chiu
- University of California San Francisco, San Francisco, CA USA
| | - Jeff Duchin
- University of Washington, Seattle, WA USA
- Public Health - Seattle & King County, Seattle, WA USA
| | - Romesh Gautom
- Washington State Department of Health, Shoreline, WA USA
| | - Geoff Melly
- Washington State Department of Health, Shoreline, WA USA
| | - Brian Hiatt
- Washington State Department of Health, Shoreline, WA USA
| | - Philip Dykema
- Washington State Department of Health, Shoreline, WA USA
| | | | - Krista Queen
- Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Ying Tao
- Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Anna Uehara
- Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Suxiang Tong
- Centers for Disease Control and Prevention, Atlanta, GA USA
| | | | | | | | - Helen Y Chu
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
- University of Washington, Seattle, WA USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
- University of Washington, Seattle, WA USA
- Howard Hughes Medical Institute, Seattle, WA USA
| | - Keith R Jerome
- Fred Hutchinson Cancer Research Center, Seattle, WA USA
- University of Washington, Seattle, WA USA
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29
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Marshak JO, Dong L, Koelle DM. The Murine Intravaginal HSV-2 Challenge Model for Investigation of DNA Vaccines. Methods Mol Biol 2020; 2060:429-454. [PMID: 31617196 DOI: 10.1007/978-1-4939-9814-2_27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
DNA vaccines have been licensed in veterinary medicine and have promise for humans. This format is relatively immunogenic in mice and guinea pigs, the two principle HSV-2 animal models, permitting rapid assessment of vectors, antigens, adjuvants, and delivery systems. Limitations include the relatively poor immunogenicity of naked DNA in humans and the profound differences in HSV-2 pathogenesis between host species. Herein, we detail lessons learned investigating candidate DNA vaccines in the progesterone-primed female mouse vaginal model of HSV-2 infection as a guide to investigators in the field.
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Affiliation(s)
- Joshua O Marshak
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lichun Dong
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, WA, USA. .,Department of Laboratory Medicine, University of Washington, Seattle, WA, USA. .,Department of Global Health, University of Washington, Seattle, WA, USA. .,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,Benaroya Research Institute, Seattle, WA, USA.
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30
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Lassalle F, Beale MA, Bharucha T, Williams CA, Williams RJ, Cudini J, Goldstein R, Haque T, Depledge DP, Breuer J. Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses. Virus Evol 2020; 6:veaa012. [PMID: 32099667 PMCID: PMC7031915 DOI: 10.1093/ve/veaa012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Herpes Simplex Virus type 1 (HSV-1) chronically infects over 70 per cent of the global population. Clinical manifestations are largely restricted to recurrent epidermal vesicles. However, HSV-1 also leads to encephalitis, the infection of the brain parenchyma, with high associated rates of mortality and morbidity. In this study, we performed target enrichment followed by direct sequencing of HSV-1 genomes, using target enrichment methods on the cerebrospinal fluid (CSF) of clinical encephalitis patients and from skin swabs of epidermal vesicles on non-encephalopathic patients. Phylogenetic analysis revealed high inter-host diversity and little population structure. In contrast, samples from different lesions in the same patient clustered with similar patterns of allelic variants. Comparison of consensus genome sequences shows HSV-1 has been freely recombining, except for distinct islands of linkage disequilibrium (LD). This suggests functional constraints prevent recombination between certain genes, notably those encoding pairs of interacting proteins. Distinct LD patterns characterised subsets of viruses recovered from CSF and skin lesions, which may reflect different evolutionary constraints in different body compartments. Functions of genes under differential constraint related to immunity or tropism and provide new hypotheses on tissue-specific mechanisms of viral infection and latency.
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Affiliation(s)
- Florent Lassalle
- Department of Infectious Disease Epidemiology, Imperial College London, St-Mary's Hospital campus, Praed Street, London W2 1NY, UK
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, St-Mary's Hospital campus, Praed Street, London W2 1NY, UK
| | - Mathew A Beale
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Saffron Walden CB10 1SA, UK
| | - Tehmina Bharucha
- Department of Virology, Royal Free Hospital, 10 Pond Street, Hampstead, London NW3 2PS, UK
| | - Charlotte A Williams
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Rachel J Williams
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Juliana Cudini
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Saffron Walden CB10 1SA, UK
| | - Richard Goldstein
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Tanzina Haque
- Department of Virology, Royal Free Hospital, 10 Pond Street, Hampstead, London NW3 2PS, UK
| | - Daniel P Depledge
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, London WC1N 3JH
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31
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Shipley MM, Rathbun MM, Szpara ML. Oligonucleotide Enrichment of HSV-1 Genomic DNA from Clinical Specimens for Use in High-Throughput Sequencing. Methods Mol Biol 2020; 2060:199-217. [PMID: 31617180 DOI: 10.1007/978-1-4939-9814-2_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To date more than 400 genomes of herpes simplex virus 1 (HSV-1) and the distantly related HSV-2 have been examined using deep sequencing techniques. This powerful approach has been especially useful for revealing the global genetic diversity that exists within and between strains of each virus species. However, most early methods for high-throughput sequencing required the input of abundant viral genomic DNA to enable the successful production of sequencing libraries, and the generation of sufficient short-read sequencing data for de novo genome assembly and similar applications. Therefore, the majority of sequenced HSV strains have been cultured and expanded in vitro prior to genomic analysis, to facilitate isolation of sufficient viral DNA for sequencing-library preparation. Here, we describe an in-solution targeted enrichment procedure for isolating, enriching, and sequencing HSV genomic DNA directly from clinical specimens. When this enrichment technique is combined with traditional sequencing-library preparation procedures, the need for in vitro culturing, expansion, and purification of viral DNA is eliminated. Furthermore, enrichment reduces the large amount of nonviral DNA that is typically present in specimens obtained directly from natural infections, thereby increasing the likelihood of successful viral genome sequencing and assembly. We have used this approach to prepare viral DNA libraries from clinical specimens derived from skin swabs, saliva, blood, and similar sources. We then use these libraries for deep sequencing and successful de novo assembly of the ~152 kb viral genomes, at coverage depths exceeding 100-1000×, for both HSV-1 and HSV-2.
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Affiliation(s)
- Mackenzie M Shipley
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Molly M Rathbun
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Moriah L Szpara
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
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32
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Kuny CV, Bowen CD, Renner DW, Johnston CM, Szpara ML. In vitro evolution of herpes simplex virus 1 (HSV-1) reveals selection for syncytia and other minor variants in cell culture. Virus Evol 2020; 6:veaa013. [PMID: 32296542 PMCID: PMC7151645 DOI: 10.1093/ve/veaa013] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The large dsDNA virus herpes simplex virus 1 (HSV-1) is considered to be genetically stable, yet it can rapidly evolve in response to strong selective pressures such as antiviral treatment. Deep sequencing has revealed that clinical and laboratory isolates of this virus exist as populations that contain a mixture of minor alleles or variants, similar to many RNA viruses. The classic virology approach of plaque purifying virus creates a genetically homogenous population, but it is not clear how closely this represents the mixed virus populations found in nature. We sought to study the evolution of mixed versus highly purified HSV-1 populations in controlled cell culture conditions, to examine the impact of this genetic diversity on evolution. We found that a mixed population of HSV-1 acquired more genetic diversity and underwent a more dramatic phenotypic shift than a plaque-purified population, producing a viral population that was almost entirely syncytial after just ten passages. At the genomic level, adaptation and genetic diversification occurred at the level of minor alleles or variants in the viral population. Certain genetic variants in the mixed viral population appeared to be positively selected in cell culture, and this shift was also observed in clinical samples during their first passages in vitro. In contrast, the plaque-purified viral population did not appear to change substantially in phenotype or overall quantity of minor allele diversity. These data indicate that HSV-1 is capable of evolving rapidly in a given environment, and that this evolution is facilitated by diversity in the viral population.
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Affiliation(s)
- Chad V Kuny
- Departments of Biology, and Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Christopher D Bowen
- Departments of Biology, and Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Daniel W Renner
- Departments of Biology, and Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Christine M Johnston
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Moriah L Szpara
- Departments of Biology, and Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
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33
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Akhtar LN, Szpara ML. Viral genetic diversity and its potential contributions to the development and progression of neonatal herpes simplex virus (HSV) disease. CURRENT CLINICAL MICROBIOLOGY REPORTS 2019; 6:249-256. [PMID: 32944492 PMCID: PMC7491914 DOI: 10.1007/s40588-019-00131-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
PURPOSE OF REVIEW Neonatal infection by herpes simplex virus (HSV) 1 or 2 presents a devastating burden to new parents, due to the unpredictability of severe clinical outcomes, as well as the potential for lifelong reactivation. While just under half of neonatal HSV infections have mild clinical impacts akin to those observed in adults, the other half experience viral spread throughout the body (disseminated infection) and/or the brain (central nervous system infection). SUMMARY Here we summarize current data on clinical diagnostic measures, antiviral therapy, and known factors of human host biology that contribute to the distinct neonatal outcomes of HSV infection. RECENT FINDINGS We then explore recent new data on how viral genetic diversity between infections may impact clinical outcomes. Further research will be critical to build upon these early findings and to provide statistical power to our ability to discern and/or predict the potential clinical path of a given neonatal infection.
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Affiliation(s)
- Lisa N. Akhtar
- Department of Pediatrics, Division of Infectious Diseases, Children’s Hospital of Philadelphia, and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Moriah L. Szpara
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA
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34
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Ikuta K, Roychoudhury P, Xie H, Mcclurkan CL, Walkiewicz M, Makhsous N, Huang ML, Beru Y, Alam M, Shepherd A, Lamotte ED, Patel K, Morris A, Ҫoruh B, Yu L, Bhattacharya R, Cheng R, Walter RB, Limaye AP, Lockwood CM, Holland SM, Rakita RM, Koelle DM, Greninger AL. Trillions and Trillions: Herpes Simplex Virus-1 Hepatitis in an Immunocompetent Adult. Open Forum Infect Dis 2019; 6:ofz465. [PMID: 31777756 PMCID: PMC6868424 DOI: 10.1093/ofid/ofz465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/23/2019] [Indexed: 11/14/2022] Open
Abstract
We describe a case of acute liver failure and myopericarditis due to herpes simplex virus-1 (HSV-1) in an immunocompetent adult. We estimate that, at the height of viremia, the patient contained a quantity of HSV-1 virions approaching that of human cells. The patient recovered with acyclovir that was dose-adjusted for neurotoxicity and developed a vigorous anti-HSV-1 T-cell response.
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Affiliation(s)
- Kevin Ikuta
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Christopher L Mcclurkan
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Magdalena Walkiewicz
- Immunopathogenesis Section, National Institute of Allergy and Infectious Disease, Bethesda, Maryland, USA
| | - Negar Makhsous
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Yodit Beru
- Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Mariam Alam
- Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Amanda Shepherd
- Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Eric D Lamotte
- Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Kevin Patel
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Amy Morris
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Başak Ҫoruh
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Lei Yu
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Renuka Bhattacharya
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Rex Cheng
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Roland B Walter
- Clinical Research Division, Fred Hutchinson Cancer Research Center Seattle, Washington, USA
| | - Ajit P Limaye
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Christina M Lockwood
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Steven M Holland
- Immunopathogenesis Section, National Institute of Allergy and Infectious Disease, Bethesda, Maryland, USA
| | - Robert M Rakita
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - David M Koelle
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA.,Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.,Department of Global Health, University of Washington, Seattle, Washington, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Benaroya Research Institute, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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35
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Houldcroft CJ. Human Herpesvirus Sequencing in the Genomic Era: The Growing Ranks of the Herpetic Legion. Pathogens 2019; 8:E186. [PMID: 31614759 PMCID: PMC6963362 DOI: 10.3390/pathogens8040186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 12/19/2022] Open
Abstract
The nine human herpesviruses are some of the most ubiquitous pathogens worldwide, causing life-long latent infection in a variety of different tissues. Human herpesviruses range from mild childhood infections to known tumour viruses and 'trolls of transplantation'. Epstein-Barr virus was the first human herpesvirus to have its whole genome sequenced; GenBank now includes thousands of herpesvirus genomes. This review will cover some of the recent advances in our understanding of herpesvirus diversity and disease that have come about as a result of new sequencing technologies, such as target enrichment and long-read sequencing. It will also look at the problem of resolving mixed-genotype infections, whether with short or long-read sequencing methods; and conclude with some thoughts on the future of the field as herpesvirus population genomics becomes a reality.
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Affiliation(s)
- Charlotte J Houldcroft
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambs CB2 0QQ UK.
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambs CB10 1SA, UK.
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36
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Comparison of Herpes Simplex Virus 1 Strains Circulating in Finland Demonstrates the Uncoupling of Whole-Genome Relatedness and Phenotypic Outcomes of Viral Infection. J Virol 2019; 93:JVI.01824-18. [PMID: 30760568 PMCID: PMC6450105 DOI: 10.1128/jvi.01824-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/23/2019] [Indexed: 12/14/2022] Open
Abstract
Herpes simplex viruses (HSV) infect a majority of adults. Recent data have highlighted the genetic diversity of HSV-1 strains and demonstrated apparent genomic relatedness between strains from the same geographic regions. We used HSV-1 clinical isolates from Finland to test the relationship between viral genomic and geographic relationships, differences in specific genes, and characteristics of viral infection. We found that viral isolates from Finland separated into two distinct groups of genomic and geographic relatedness, potentially reflecting historical patterns of human and viral migration into Finland. These Finnish HSV-1 isolates had distinct infection characteristics in multiple cell types tested, which were specific to each isolate and did not group according to genomic and geographic relatedness. This demonstrates that HSV-1 strain differences in specific characteristics of infection are set by a combination of host cell type and specific viral gene-level differences. A majority of adults in Finland are seropositive carriers of herpes simplex viruses (HSV). Infection occurs at epithelial or mucosal surfaces, after which virions enter innervating nerve endings, eventually establishing lifelong infection in neurons of the sensory or autonomic nervous system. Recent data have highlighted the genetic diversity of HSV-1 strains and demonstrated apparent geographic patterns in strain similarity. Though multiple HSV-1 genomes have been sequenced from Europe to date, there is a lack of sequenced genomes from the Nordic countries. Finland’s history includes at least two major waves of human migration, suggesting the potential for diverse viruses to persist in the population. Here, we used HSV-1 clinical isolates from Finland to test the relationship between viral phylogeny, genetic variation, and phenotypic characteristics. We found that Finnish HSV-1 isolates separated into two distinct phylogenetic groups, potentially reflecting historical waves of human (and viral) migration into Finland. Each HSV-1 isolate harbored a distinct set of phenotypes in cell culture, including differences in the amount of virus production, extracellular virus release, and cell-type-specific fitness. Importantly, the phylogenetic clusters were not predictive of any detectable pattern in phenotypic differences, demonstrating that whole-genome relatedness is not a proxy for overall viral phenotype. Instead, we highlight specific gene-level differences that may contribute to observed phenotypic differences, and we note that strains from different phylogenetic groups can contain the same genetic variations. IMPORTANCE Herpes simplex viruses (HSV) infect a majority of adults. Recent data have highlighted the genetic diversity of HSV-1 strains and demonstrated apparent genomic relatedness between strains from the same geographic regions. We used HSV-1 clinical isolates from Finland to test the relationship between viral genomic and geographic relationships, differences in specific genes, and characteristics of viral infection. We found that viral isolates from Finland separated into two distinct groups of genomic and geographic relatedness, potentially reflecting historical patterns of human and viral migration into Finland. These Finnish HSV-1 isolates had distinct infection characteristics in multiple cell types tested, which were specific to each isolate and did not group according to genomic and geographic relatedness. This demonstrates that HSV-1 strain differences in specific characteristics of infection are set by a combination of host cell type and specific viral gene-level differences.
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37
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Ramchandani MS, Jing L, Russell RM, Tran T, Laing KJ, Magaret AS, Selke S, Cheng A, Huang ML, Xie H, Strachan E, Greninger AL, Roychoudhury P, Jerome KR, Wald A, Koelle DM. Viral Genetics Modulate Orolabial Herpes Simplex Virus Type 1 Shedding in Humans. J Infect Dis 2019; 219:1058-1066. [PMID: 30383234 PMCID: PMC6420167 DOI: 10.1093/infdis/jiy631] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/30/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Orolabial herpes simplex virus type 1 (HSV-1) infection has a wide spectrum of severity in immunocompetent persons. To study the role of viral genotype and host immunity, we characterized oral HSV-1 shedding rates and host cellular response, and genotyped viral strains, in monozygotic (MZ) and dizygotic (DZ) twins. METHODS A total of 29 MZ and 22 DZ HSV-1-seropositive twin pairs were evaluated for oral HSV-1 shedding for 60 days. HSV-1 strains from twins were genotyped as identical or different. CD4+ T-cell responses to HSV-1 proteins were studied. RESULTS The median per person oral HSV shedding rate was 9% of days that a swab was obtained (mean, 10.2% of days). A positive correlation between shedding rates was observed within all twin pairs, and in the MZ and DZ twins. In twin subsets with sufficient HSV-1 DNA to genotype, 15 had the same strain and 14 had different strains. Viral shedding rates were correlated for those with the same but not different strains. The median number of HSV-1 open reading frames recognized per person was 16. The agreement in the CD4+ T-cell response to specific HSV-1 open reading frames was greater between MZ twins than between unrelated persons (P = .002). CONCLUSION Viral strain characteristics likely contribute to oral HSV-1 shedding rates.
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Affiliation(s)
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, Washington
| | - Ronnie M Russell
- Department of Medicine, University of Washington, Seattle, Washington
| | - Tran Tran
- Department of Medicine, University of Washington, Seattle, Washington
| | - Kerry J Laing
- Department of Medicine, University of Washington, Seattle, Washington
| | - Amalia S Magaret
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle, Washington
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stacy Selke
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Anqi Cheng
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Eric Strachan
- Department of Psychiatry, University of Washington, Seattle, Washington
| | - Alex L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, Washington
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
- Department of Global Health, University of Washington, Seattle, Washington
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Benaroya Research Institute, Seattle, Washington
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38
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Pandey U, Szpara ML. Herpes Simplex Virus Disease Management and Diagnostics in the Era of High-Throughput Sequencing. ACTA ACUST UNITED AC 2019; 41:41-48. [PMID: 34305220 DOI: 10.1016/j.clinmicnews.2019.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Herpes simplex virus (HSV) serotypes 1 and 2 are among the most widespread human viruses. HSV disease has a complex phenotype, with symptoms that can range from mild lesions to encephalitis. In the clinical setting, this diversity of outcomes poses a major challenge, making timely disease diagnosis and treatment challenging. High-throughput sequencing (HTS) has been one of the breakthrough technologies in the modern era of molecular biology, and it is revolutionizing the study of pathogen biology and clinical diagnostics. Here, we review recent studies that have used HTS to answer questions related to the evolution of drug resistance, transmission and spread, virulence marker identification, and the design of better antiviral therapeutics for HSV. We also highlight practical considerations for handling computational analysis of HSV genomes and adoption of HTS as a routine diagnostic procedure in the clinical laboratories.
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Affiliation(s)
- Utsav Pandey
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania.,Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Moriah L Szpara
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
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39
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Gaudin M, Desnues C. Hybrid Capture-Based Next Generation Sequencing and Its Application to Human Infectious Diseases. Front Microbiol 2018; 9:2924. [PMID: 30542340 PMCID: PMC6277869 DOI: 10.3389/fmicb.2018.02924] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 01/12/2023] Open
Abstract
This review describes target-enrichment approaches followed by next generation sequencing and their recent application to the research and diagnostic field of modern and past infectious human diseases caused by viruses, bacteria, parasites and fungi.
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Affiliation(s)
- Maxime Gaudin
- IRD 198, CNRS FRE2013, Assistance-Publique des Hôpitaux de Marseille, UMR Microbes, Evolution, Phylogeny and Infections (MEPHI), IHU Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Christelle Desnues
- IRD 198, CNRS FRE2013, Assistance-Publique des Hôpitaux de Marseille, UMR Microbes, Evolution, Phylogeny and Infections (MEPHI), IHU Méditerranée Infection, Aix-Marseille Université, Marseille, France
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