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Eltayeb A, Al-Sarraj F, Alharbi M, Albiheyri R, Mattar EH, Abu Zeid IM, Bouback TA, Bamagoos A, Uversky VN, Rubio-Casillas A, Redwan EM. Intrinsic factors behind long COVID: IV. Hypothetical roles of the SARS-CoV-2 nucleocapsid protein and its liquid-liquid phase separation. J Cell Biochem 2024; 125:e30530. [PMID: 38349116 DOI: 10.1002/jcb.30530] [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: 09/09/2023] [Revised: 01/10/2024] [Accepted: 01/24/2024] [Indexed: 03/12/2024]
Abstract
When the SARS-CoV-2 virus infects humans, it leads to a condition called COVID-19 that has a wide spectrum of clinical manifestations, from no symptoms to acute respiratory distress syndrome. The virus initiates damage by attaching to the ACE-2 protein on the surface of endothelial cells that line the blood vessels and using these cells as hosts for replication. Reactive oxygen species levels are increased during viral replication, which leads to oxidative stress. About three-fifths (~60%) of the people who get infected with the virus eradicate it from their body after 28 days and recover their normal activity. However, a large fraction (~40%) of the people who are infected with the virus suffer from various symptoms (anosmia and/or ageusia, fatigue, cough, myalgia, cognitive impairment, insomnia, dyspnea, and tachycardia) beyond 12 weeks and are diagnosed with a syndrome called long COVID. Long-term clinical studies in a group of people who contracted SARS-CoV-2 have been contrasted with a noninfected matched group of people. A subset of infected people can be distinguished by a set of cytokine markers to have persistent, low-grade inflammation and often self-report two or more bothersome symptoms. No medication can alleviate their symptoms efficiently. Coronavirus nucleocapsid proteins have been investigated extensively as potential drug targets due to their key roles in virus replication, among which is their ability to bind their respective genomic RNAs for incorporation into emerging virions. This review highlights basic studies of the nucleocapsid protein and its ability to undergo liquid-liquid phase separation. We hypothesize that this ability of the nucleocapsid protein for phase separation may contribute to long COVID. This hypothesis unlocks new investigation angles and could potentially open novel avenues for a better understanding of long COVID and treating this condition.
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Affiliation(s)
- Ahmed Eltayeb
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Faisal Al-Sarraj
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Raed Albiheyri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ehab H Mattar
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Isam M Abu Zeid
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thamer A Bouback
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Atif Bamagoos
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Moscow Region, Russia
| | - Alberto Rubio-Casillas
- Autlan Regional Hospital, Health Secretariat, Autlan, Jalisco, Mexico
- Biology Laboratory, Autlan Regional Preparatory School, University of Guadalajara, Autlan, Jalisco, Mexico
| | - Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
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2
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El-Baky NA, Amara AA, Uversky VN, Redwan EM. Intrinsic factors behind long COVID: III. Persistence of SARS-CoV-2 and its components. J Cell Biochem 2024; 125:22-44. [PMID: 38098317 DOI: 10.1002/jcb.30514] [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: 09/04/2023] [Revised: 11/27/2023] [Accepted: 12/07/2023] [Indexed: 01/16/2024]
Abstract
Considerable research has been done in investigating SARS-CoV-2 infection, its characteristics, and host immune response. However, debate is still ongoing over the emergence of post-acute sequelae of SARS-CoV-2 infection (PASC). A multitude of long-lasting symptoms have been reported several weeks after the primary acute SARS-CoV-2 infection that resemble several other viral infections. Thousands of research articles have described various post-COVID-19 conditions. Yet, the evidence around these ongoing health problems, the reasons behind them, and their molecular underpinnings are scarce. These persistent symptoms are also known as long COVID-19. The persistence of SARS-CoV-2 and/or its components in host tissues can lead to long COVID. For example, the presence of viral nucleocapsid protein and RNA was detected in the skin, appendix, and breast tissues of some long COVID patients. The persistence of viral RNA was reported in multiple anatomic sites, including non-respiratory tissues such as the adrenal gland, ocular tissue, small intestine, lymph nodes, myocardium, and sciatic nerve. Distinctive viral spike sequence variants were also found in non-respiratory tissues. Interestingly, prolonged detection of viral subgenomic RNA was observed across all tissues, sometimes in multiple tissues of the same patient, which likely reflects recent but defective viral replication. Moreover, the persistence of SARS-CoV-2 RNA was noticed throughout the brain at autopsy, as late as 230 days following symptom onset among unvaccinated patients who died of severe infection. Here, we review the persistence of SARS-CoV-2 and its components as an intrinsic factor behind long COVID. We also highlight the immunological consequences of this viral persistence.
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Affiliation(s)
- Nawal Abd El-Baky
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Egypt
| | - Amro A Amara
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Egypt
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Elrashdy M Redwan
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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3
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Deng Y, Ou YY, Mo CJ, Huang L, Qin X. Characteristics and clustering analysis of peripheral blood lymphocyte subsets in children with systemic lupus erythematosus complicated with clinical infection. Clin Rheumatol 2023; 42:3299-3309. [PMID: 37537315 DOI: 10.1007/s10067-023-06716-3] [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: 05/06/2023] [Revised: 07/14/2023] [Accepted: 07/22/2023] [Indexed: 08/05/2023]
Abstract
OBJECTIVES Clinical infection is a common complication in children with systemic lupus erythematosus (SLE). However, few studies have investigated immune alterations in children with SLE complicated with clinical infection. We assessed lymphocyte subsets in children with SLE to explore the possibility of clinical infection. METHODS We retrospectively analyzed the proportion of peripheral lymphocyte subsets in 140 children with SLE. Children with SLE were classified into different clusters according to the proportion of peripheral blood lymphocyte subsets: (CD3 + /CD4 + T cell, CD3 + /CD8 + T cell, CD3 + /CD4 + /CD8 + T cell, CD3 + /CD4-/CD8- T cell, CD19 + B cell, and CD3-/CD16 + /CD56 + NK cell). Differences in the proportion of lymphoid subsets, infection rates, and systemic lupus erythematosus disease activity index (SLEDAI) scores were compared between clusters. In addition, we grouped the subjects according to the presence or absence of infection. Proportions of lymphoid subsets, demographic variables, clinical presentation, and other laboratory variables were compared between the infected and uninfected groups. Finally, the diagnostic ability of lymphocyte subset ratios to distinguish secondary infection in children with SLE was predicted using an ROC curve. RESULTS Cluster C2 had a higher proportion of B cells than Cluster C1, while Cluster C1 had a lower proportion of NK cells, CD3 + T cells, CD3 + /CD4 + T cells, CD3 + /CD8 + T cells, and CD3 + /CD4-/CD8- T cells. Infection rates and SLEDAI scores were higher in Cluster C2 than in Cluster C1. The infected children had a higher proportion of B cells and a lower proportion of CD3 + T cells, CD3 + /CD4 + T cells, CD3 + /CD8 + T cells, and CD3 + /CD4-/CD8- T cells. There were no significant differences in lymphoid subsets between children in Cluster C2 and the infected groups. The area under the ROC curve of B lymphocytes in predicting SLE children with infection was 0.842. The area under the ROC curve was 0.855 when a combination of B cells, NK cells, CD4 + T cells, and CD8 + T cells was used to predict the outcome of coinfection. CONCLUSIONS A high percentage of B cells and a low percentage of CD3 + T cells, CD3 + /CD4 + T cells, CD3 + /CD8 + T cells, CD3 + /CD4 + /CD8 + T cells, and CD3 + /CD4-/CD8- T cells may be associated with infection in children with SLE. B cells was used to predict the outcome of coinfection in children with SLE. Key Points • A high percentage of B cells and a low percentage of CD3 + T cells, CD3 + /CD4 + T cells, CD3 + /CD8 + T cells, CD3 + /CD4 + /CD8 + T cells, and CD3 + /CD4-/CD8- T cells may be associated with infection in children with SLE • B cells was used to predict the outcome of coinfection in children with SLE.
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Affiliation(s)
- Yan Deng
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Medicine of Guangxi, Department of Education, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Ying-Ying Ou
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Medicine of Guangxi, Department of Education, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Cui-Ju Mo
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Medicine of Guangxi, Department of Education, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Li Huang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Medicine of Guangxi, Department of Education, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Xue Qin
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Medicine of Guangxi, Department of Education, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
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Yousaf I, Hannon WW, Donohue RC, Pfaller CK, Yadav K, Dikdan RJ, Tyagi S, Schroeder DC, Shieh WJ, Rota PA, Feder AF, Cattaneo R. Brain tropism acquisition: The spatial dynamics and evolution of a measles virus collective infectious unit that drove lethal subacute sclerosing panencephalitis. PLoS Pathog 2023; 19:e1011817. [PMID: 38127684 PMCID: PMC10735034 DOI: 10.1371/journal.ppat.1011817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023] Open
Abstract
It is increasingly appreciated that pathogens can spread as infectious units constituted by multiple, genetically diverse genomes, also called collective infectious units or genome collectives. However, genetic characterization of the spatial dynamics of collective infectious units in animal hosts is demanding, and it is rarely feasible in humans. Measles virus (MeV), whose spread in lymphatic tissues and airway epithelia relies on collective infectious units, can, in rare cases, cause subacute sclerosing panencephalitis (SSPE), a lethal human brain disease. In different SSPE cases, MeV acquisition of brain tropism has been attributed to mutations affecting either the fusion or the matrix protein, or both, but the overarching mechanism driving brain adaptation is not understood. Here we analyzed MeV RNA from several spatially distinct brain regions of an individual who succumbed to SSPE. Surprisingly, we identified two major MeV genome subpopulations present at variable frequencies in all 15 brain specimens examined. Both genome types accumulated mutations like those shown to favor receptor-independent cell-cell spread in other SSPE cases. Most infected cells carried both genome types, suggesting the possibility of genetic complementation. We cannot definitively chart the history of the spread of this virus in the brain, but several observations suggest that mutant genomes generated in the frontal cortex moved outwards as a collective and diversified. During diversification, mutations affecting the cytoplasmic tails of both viral envelope proteins emerged and fluctuated in frequency across genetic backgrounds, suggesting convergent and potentially frequency-dependent evolution for modulation of fusogenicity. We propose that a collective infectious unit drove MeV pathogenesis in this brain. Re-examination of published data suggests that similar processes may have occurred in other SSPE cases. Our studies provide a primer for analyses of the evolution of collective infectious units of other pathogens that cause lethal disease in humans.
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Affiliation(s)
- Iris Yousaf
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, Minnesota, United States of America
| | - William W. Hannon
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America
| | - Ryan C. Donohue
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, Minnesota, United States of America
| | - Christian K. Pfaller
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, Minnesota, United States of America
| | - Kalpana Yadav
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Ryan J. Dikdan
- Public Health Research Institute, Rutgers University, Newark, New Jersey, United States of America
| | - Sanjay Tyagi
- Public Health Research Institute, Rutgers University, Newark, New Jersey, United States of America
| | - Declan C. Schroeder
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, Minnesota, United States of America
| | - Wun-Ju Shieh
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Center for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Paul A. Rota
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Center for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Alison F. Feder
- Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Public Health Sciences and Computational Biology, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Roberto Cattaneo
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, Minnesota, United States of America
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Züst R, Ackermann-Gäumann R, Liechti N, Siegrist D, Ryter S, Portmann J, Lenz N, Beuret C, Koller R, Staehelin C, Kuenzli AB, Marschall J, Rothenberger S, Engler O. Presence and Persistence of Andes Virus RNA in Human Semen. Viruses 2023; 15:2266. [PMID: 38005942 PMCID: PMC10675069 DOI: 10.3390/v15112266] [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: 10/20/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
When infecting humans, Andes orthohantavirus (ANDV) may cause a severe disease called hantavirus cardiopulmonary syndrome (HCPS). Following non-specific symptoms, the infection may progress to a syndrome of hemorrhagic fever combined with hyper-acute cardiopulmonary failure. The case fatality rate ranges between 25-40%, depending on the outbreak. In this study, we present the follow-up of a male patient who recovered from HCPS six years ago. We demonstrate that the ANDV genome persists within the reproductive tract for at least 71 months. Genome sequence analysis early and late after infection reveals a low number of mutations (two single nucleotide variants and one deletion), suggesting limited replication activity. We can exclude the integration of the viral genome into the host genome, since the treatment of the specimen with RNAse led to a loss of signal. We demonstrate a long-lasting, strong neutralizing antibody response using pseudovirions expressing the ANDV glycoprotein. Taken together, our results show that ANDV has the potential for sexual transmission.
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Affiliation(s)
- Roland Züst
- Spiez Laboratory, Swiss Federal Office for Civil Protection, 3700 Spiez, Switzerland (O.E.)
| | | | - Nicole Liechti
- Spiez Laboratory, Swiss Federal Office for Civil Protection, 3700 Spiez, Switzerland (O.E.)
| | - Denise Siegrist
- Spiez Laboratory, Swiss Federal Office for Civil Protection, 3700 Spiez, Switzerland (O.E.)
| | - Sarah Ryter
- Spiez Laboratory, Swiss Federal Office for Civil Protection, 3700 Spiez, Switzerland (O.E.)
| | - Jasmine Portmann
- Spiez Laboratory, Swiss Federal Office for Civil Protection, 3700 Spiez, Switzerland (O.E.)
| | - Nicole Lenz
- Food Microbial Systems, Risk Assessment and Mitigation Group, Agroscope, 3097 Bern, Switzerland
| | - Christian Beuret
- Spiez Laboratory, Swiss Federal Office for Civil Protection, 3700 Spiez, Switzerland (O.E.)
| | - Roger Koller
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Cornelia Staehelin
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Andrea B. Kuenzli
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Jonas Marschall
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Sylvia Rothenberger
- Spiez Laboratory, Swiss Federal Office for Civil Protection, 3700 Spiez, Switzerland (O.E.)
- Institute of Microbiology, University Hospital Center and University of Lausanne, 1005 Lausanne, Switzerland
| | - Olivier Engler
- Spiez Laboratory, Swiss Federal Office for Civil Protection, 3700 Spiez, Switzerland (O.E.)
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Randall RE, Young DF, Hughes DJ, Goodbourn S. Persistent paramyxovirus infections: in co-infections the parainfluenza virus type 5 persistent phenotype is dominant over the lytic phenotype. J Gen Virol 2023; 104:001916. [PMID: 37962188 PMCID: PMC10768688 DOI: 10.1099/jgv.0.001916] [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: 09/19/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Parainfluenza virus type 5 (PIV5) can either have a persistent or a lytic phenotype in cultured cells. We have previously shown that the phenotype is determined by the phosphorylation status of the phosphoprotein (P). Single amino acid substitutions at critical residues, including a serine-to-phenylalanine substitution at position 157 on P, result in a switch between persistent and lytic phenotypes. Here, using PIV5 vectors expressing either mCherry or GFP with persistent or lytic phenotypes, we show that in co-infections the persistent phenotype is dominant. Thus, in contrast to the cell death observed with cells infected solely with the lytic variant, in co-infected cells persistence is immediately established and both lytic and persistent genotypes persist. Furthermore, 10-20 % of virus released from dually infected cells contains both genotypes, indicating that PIV5 particles can package more than one genome. Co-infected cells continue to maintain both genotypes/phenotypes during cell passage, as do individual colonies of cells derived from a culture of persistently infected cells. A refinement of our model on how the dynamics of virus selection may occur in vivo is presented.
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Affiliation(s)
- Richard E. Randall
- School of Biology, Centre for Biomolecular Sciences, BMS Building, North Haugh, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - Dan F. Young
- School of Biology, Centre for Biomolecular Sciences, BMS Building, North Haugh, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - David J. Hughes
- School of Biology, Centre for Biomolecular Sciences, BMS Building, North Haugh, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - Steve Goodbourn
- Section for Pathogen Research, Institute for Infection and Immunity, St George’s, University of London, London SW17 0RE, UK
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7
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Chaimongkol N, Dábilla N, Tohma K, Matsushima Y, Yardley AB, Levenson EA, Johnson JA, Ahorrio C, Oler AJ, Kim DY, Souza M, Sosnovtsev SV, Parra GI, Green KY. Norovirus evolves as one or more distinct clonal populations in immunocompromised hosts. mBio 2023; 14:e0217723. [PMID: 37905910 PMCID: PMC10746188 DOI: 10.1128/mbio.02177-23] [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: 08/16/2023] [Accepted: 08/30/2023] [Indexed: 11/02/2023] Open
Abstract
Noroviruses are a major cause of acute gastroenteritis worldwide and can establish chronic infection in immunocompromised individuals. To investigate the mechanisms of norovirus evolution during chronic infection, we selected seven representative patients from a National Institutes of Health study cohort who sustained norovirus infection for periods ranging from 73 to 1,492 days. Six patients shed viruses belonging to a single genotype (GII.2[PNA], GII.4 New Orleans[P4], GII.4 Den Haag[P4], GII.3[P21], GII.6[P7], or GII.14[P7]) over the period examined, while one patient sequentially shed two genotypes (GII.6[P7] followed by GII.4 Sydney[P31]). Norovirus genomes from consecutive stool samples were sequenced at high resolution (>3,300 reads/nucleotide position) using the Illumina platform and subjected to bioinformatics analysis. Norovirus sequences could be resolved into one or more discrete clonal RNA genomes that persisted within these patients over time. Phylogenetic analyses inferred that clonal populations originated from a single founder virus and not by reinfection with community strains. Estimated evolutionary rates of clonal populations during persistent infection were similar to those of noroviruses from acute infection in the global database, suggesting that inherently higher RNA-dependent polymerase error rates were not associated with the ability to persist. The high-resolution analysis of norovirus diversity and evolution at the population level described here should allow a better understanding of adaptive mutations sustained during chronic infection. IMPORTANCE Noroviruses are an important cause of chronic diarrhea in patients with compromised immune systems. Presently, there are no effective therapies to clear the virus, which can persist for years in the intestinal tract. The goal of our study was to develop a better understanding of the norovirus strains that are associated with these long-term infections. With the remarkable diversity of norovirus strains detected in the immunocompromised patient cohort we studied, it appears that most, if not all, noroviruses circulating in nature may have the capacity to establish a chronic infection when a person is unable to mount an effective immune response. Our work is the most comprehensive genetic data set generated to date in which near full-length genomes from noroviruses associated with chronic infection were analyzed by high-resolution next-generation sequencing. Analysis of this data set led to our discovery that certain patients in our cohort were shedding noroviruses that could be subdivided into distinct haplotypes or populations of viruses that were co-evolving independently. The ability to track haplotypes of noroviruses during chronic infection will allow us to fine-tune our understanding of how the virus adapts and maintains itself in the human host, and how selective pressures such as antiviral drugs can affect these distinct populations.
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Affiliation(s)
- Natthawan Chaimongkol
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nathânia Dábilla
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Virology and Cell Culture, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Kentaro Tohma
- Division of Viral Products, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Yuki Matsushima
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Allison Behrle Yardley
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Eric A. Levenson
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jordan A. Johnson
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Courtney Ahorrio
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew J. Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Daniel Y. Kim
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Menira Souza
- Laboratory of Virology and Cell Culture, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Stanislav V. Sosnovtsev
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Gabriel I. Parra
- Division of Viral Products, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Kim Y. Green
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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8
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Ocanto A, Mielgo-Rubio X, Luna Tirado J, Linares Mesa N, López Valcárcel M, Pedraza S, Barragan VV, Nieto PV, Martín JZ, Couñago F. Coronavirus disease 2019 and lung cancer: where are we? EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:1082-1094. [PMID: 38023992 PMCID: PMC10651354 DOI: 10.37349/etat.2023.00182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/26/2023] [Indexed: 12/01/2023] Open
Abstract
Oncology patients are more susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection due to hospital contact and an immunological system that can be compromised by antineoplastic therapy and supportive treatments. Certain similarities have been described in the physiopathology of coronavirus disease 2019 (COVID-19) and lung cancer (LC) that may explain the higher probability of these patients of developing a more serious disease with more frequent hospitalizations and even death, especially with the addition of smoking, cardiovascular and respiratory comorbidities, old age and corticosteroids use. Pre-existing lesions and cancer therapies change the normal architecture of the lungs, so diagnostic scales such as COVID-19 Reporting and Data System (CO-RADS) are of vital importance for a correct diagnosis and patient homogenization, with a high inter-observer correlation. Moreover, anticancer treatments have required an adaptation to reduce the number of visits to the hospital [hypofractionated radiotherapy (RT), larger intervals between chemotherapy cycles, delay in follow-up tests, among others]. In a way, this has also caused a delay in the diagnosis of new cancers. On the other hand, vaccination has had a positive impact on the mortality of these patients, who maintain a similar seroprevalence to the rest of the population, with a similar impact in mortality.
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Affiliation(s)
- Abrahams Ocanto
- Department of Radiation Oncology, Hospital Universitario San Francisco de Asís, GenesiCare Madrid, 28002 Madrid, Spain
- Department of Radiation Oncology, Hospital Universitario Vithas La Milagrosa, GenesiCare Madrid, 28002 Madrid, Spain
| | - Xabier Mielgo-Rubio
- Department of Medical Oncology, Hospital Universitario Fundación Alcorcón, 28922 Madrid, Spain
| | - Javier Luna Tirado
- Department of Radiation Oncology, Hospital Universitario Fundación Jiménez Díaz, 28040 Madrid, Spain
| | - Nuria Linares Mesa
- Department of Radiation Oncology, Hospital Universitario Juan Ramón Jiménez, 21005 Huelva, Spain
| | - Marta López Valcárcel
- Department of Radiation Oncology, Hospital Universitario Puerta de Hierro, 28222 Madrid, Spain
| | - Sara Pedraza
- Department of Radiation Oncology, Hospital Universitario 12 de Octubre Madrid, 28041 Madrid, Spain
| | - Victoria Vera Barragan
- Department of Radiation Oncology, Hospital Universitario de Badajoz, 06080 Badajoz, Spain
| | - Patricia Valencia Nieto
- Department of Radiation Oncology, Hospital Clínico Universitario de Valladolid, 47003 Valladolid, Spain
| | - Juan Zafra Martín
- Group of Translational Research in Cancer Immunotherapy, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga (UMA), Instituto de Investigación Biomédica de Málaga (IBIMA), 29010 Málaga, Spain
- Department of Radiation Oncology, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
| | - Felipe Couñago
- Department of Radiation Oncology, Hospital Universitario San Francisco de Asís, GenesiCare Madrid, 28002 Madrid, Spain
- Department of Radiation Oncology, Hospital Universitario Vithas La Milagrosa, GenesiCare Madrid, 28002 Madrid, Spain
- Department of Radiation Oncology, Emilio Vargas, GenesisCare Madrid, 28002 Madrid, Spain
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9
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Mitrofanova L, Makarov I, Goncharova E, Makarova T, Starshinova A, Kudlay D, Shlaykhto E. High Risk of Heart Tumors after COVID-19. Life (Basel) 2023; 13:2087. [PMID: 37895467 PMCID: PMC10608002 DOI: 10.3390/life13102087] [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: 09/17/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
An emergence of evidence suggests that severe COVID-19 is associated with an increased risk of developing breast and gastrointestinal cancers. The aim of this research was to assess the risk of heart tumors development in patients who have had COVID-19. METHODS A comparative analysis of 173 heart tumors was conducted between 2016 and 2023. Immunohistochemical examination with antibodies against spike SARS-CoV-2 was performed on 21 heart tumors: 10 myxomas operated before 2020 (the control group), four cardiac myxomas, one proliferating myxoma, three papillary fibroelastomas, two myxofibrosarcomas, one chondrosarcoma resected in 2022-2023. Immunohistochemical analysis with antibodies against CD34 and CD68 was also conducted on the same 11 Post-COVID period heart tumors. Immunofluorescent examination with a cocktail of antibodies against spike SARS-CoV-2/CD34 and spike SARS-CoV-2/CD68 was performed in 2 cases out of 11 (proliferating myxoma and classic myxoma). RESULTS A 1.5-fold increase in the number of heart tumors by 2023 was observed, with a statistically significant increase in the number of myxomas. There was no correlation with vaccination, and no significant differences were found between patients from 2016-2019 and 2021-2023 in terms of gender, age, and cardiac rhythm dis-orders. Morphological examination revealed the expression of spike SARS-CoV-2 in tumor cells, endothelial cells, and macrophages in 10 out of 11 heart tumors. CONCLUSION The detection of SARS-CoV-2 persistence in endothelium and macrophages as well as in tumor cells of benign and malignant cardiac neoplasms, the increase in the number of these tumors, especially cardiac myxomas, after the pandemic by 2023 may indicate a trend toward an increased risk of cardiac neoplasms in COVID-19 patients, which re-quires further research on this issue and a search for new evidence.
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Affiliation(s)
- Lubov Mitrofanova
- Almazov National Medical Research Centre, 197341 St. Petersburg, Russia; (L.M.); (I.M.); (E.G.); (T.M.); (E.S.)
| | - Igor Makarov
- Almazov National Medical Research Centre, 197341 St. Petersburg, Russia; (L.M.); (I.M.); (E.G.); (T.M.); (E.S.)
| | - Ekaterina Goncharova
- Almazov National Medical Research Centre, 197341 St. Petersburg, Russia; (L.M.); (I.M.); (E.G.); (T.M.); (E.S.)
| | - Taiana Makarova
- Almazov National Medical Research Centre, 197341 St. Petersburg, Russia; (L.M.); (I.M.); (E.G.); (T.M.); (E.S.)
| | - Anna Starshinova
- Almazov National Medical Research Centre, 197341 St. Petersburg, Russia; (L.M.); (I.M.); (E.G.); (T.M.); (E.S.)
| | - Dmitry Kudlay
- Department of Pharmacology, I.M. Sechenov First Moscow State Medical University, 119992 Moscow, Russia;
- Institute of Immunology, 115478 Moscow, Russia
| | - Evgeny Shlaykhto
- Almazov National Medical Research Centre, 197341 St. Petersburg, Russia; (L.M.); (I.M.); (E.G.); (T.M.); (E.S.)
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10
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Chetta M, Cammarota AL, De Marco M, Bukvic N, Marzullo L, Rosati A. The Continuous Adaptive Challenge Played by Arboviruses: An In Silico Approach to Identify a Possible Interplay between Conserved Viral RNA Sequences and Host RNA Binding Proteins (RBPs). Int J Mol Sci 2023; 24:11051. [PMID: 37446229 DOI: 10.3390/ijms241311051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Climate change and globalization have raised the risk of vector-borne disease (VBD) introduction and spread in various European nations in recent years. In Italy, viruses carried by tropical vectors have been shown to cause viral encephalitis, one of the symptoms of arboviruses, a spectrum of viral disorders spread by arthropods such as mosquitoes and ticks. Arboviruses are currently causing alarm and attention, and the World Health Organization (WHO) has released recommendations to adopt essential measures, particularly during the hot season, to restrict the spreading of the infectious agents among breeding stocks. In this scenario, rapid analysis systems are required, because they can quickly provide information on potential virus-host interactions, the evolution of the infection, and the onset of disabling clinical symptoms, or serious illnesses. Such systems include bioinformatics approaches integrated with molecular evaluation. Viruses have co-evolved different strategies to transcribe their own genetic material, by changing the host's transcriptional machinery, even in short periods of time. The introduction of genetic alterations, particularly in RNA viruses, results in a continuous adaptive fight against the host's immune system. We propose an in silico pipeline method for performing a comprehensive motif analysis (including motif discovery) on entire genome sequences to uncover viral sequences that may interact with host RNA binding proteins (RBPs) by interrogating the database of known RNA binding proteins, which play important roles in RNA metabolism and biological processes. Indeed, viral RNA sequences, able to bind host RBPs, may compete with cellular RNAs, altering important metabolic processes. Our findings suggest that the proposed in silico approach could be a useful and promising tool to investigate the complex and multiform clinical manifestations of viral encephalitis, and possibly identify altered metabolic pathways as targets of pharmacological treatments and innovative therapeutic protocols.
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Affiliation(s)
- Massimiliano Chetta
- U.O.C. Medical and Laboratory Genetics, A.O.R.N., Cardarelli, 80131 Naples, Italy
| | - Anna Lisa Cammarota
- Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, 84084 Baronissi, SA, Italy
| | - Margot De Marco
- Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, 84084 Baronissi, SA, Italy
- FIBROSYS s.r.l. Academic Spin-Off, University of Salerno, 84084 Baronissi, Italy
| | - Nenad Bukvic
- Medical Genetics Section, University Hospital Consortium Corporation Polyclinics of Bari, 70124 Bari, Italy
| | - Liberato Marzullo
- Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, 84084 Baronissi, SA, Italy
- FIBROSYS s.r.l. Academic Spin-Off, University of Salerno, 84084 Baronissi, Italy
| | - Alessandra Rosati
- Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, 84084 Baronissi, SA, Italy
- FIBROSYS s.r.l. Academic Spin-Off, University of Salerno, 84084 Baronissi, Italy
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11
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Ruivinho C, Gama-Carvalho M. Small non-coding RNAs encoded by RNA viruses: old controversies and new lessons from the COVID-19 pandemic. Front Genet 2023; 14:1216890. [PMID: 37415603 PMCID: PMC10322155 DOI: 10.3389/fgene.2023.1216890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
The recurring outbreaks caused by emerging RNA viruses have fostered an increased interest in the research of the mechanisms that regulate viral life cycles and the pathological outcomes associated with infections. Although interactions at the protein level are well-studied, interactions mediated by RNA molecules are less explored. RNA viruses can encode small non-coding RNAs molecules (sncRNAs), including viral miRNAs (v-miRNAs), that play important roles in modulating host immune responses and viral replication by targeting viral or host transcripts. Starting from the analysis of public databases compiling the known repertoire of viral ncRNA molecules and the evolution of publications and research interests on this topic in the wake of the COVID-19 pandemic, we provide an updated view on the current knowledge on viral sncRNAs, with a focus on v-miRNAs encoded by RNA viruses, and their mechanisms of action. We also discuss the potential of these molecules as diagnostic and prognostic biomarkers for viral infections and the development of antiviral therapies targeting v-miRNAs. This review emphasizes the importance of continued research efforts to characterize sncRNAs encoded by RNA viruses, identifies the most relevant pitfalls in the study of these molecules, and highlights the paradigm changes that have occurred in the last few years regarding their biogenesis, prevalence and functional relevance in the context of host-pathogen interactions.
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12
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Megremis S, Constantinides B, Xepapadaki P, Yap CF, Sotiropoulos AG, Bachert C, Finotto S, Jartti T, Tapinos A, Vuorinen T, Andreakos E, Robertson DL, Papadopoulos NG. Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma. Sci Rep 2023; 13:8319. [PMID: 37221274 PMCID: PMC10205716 DOI: 10.1038/s41598-023-34730-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/06/2023] [Indexed: 05/25/2023] Open
Abstract
Asthma development and exacerbation is linked to respiratory virus infections. There is limited information regarding the presence of viruses during non-exacerbation/infection periods. We investigated the nasopharyngeal/nasal virome during a period of asymptomatic state, in a subset of 21 healthy and 35 asthmatic preschool children from the Predicta cohort. Using metagenomics, we described the virome ecology and the cross-species interactions within the microbiome. The virome was dominated by eukaryotic viruses, while prokaryotic viruses (bacteriophages) were independently observed with low abundance. Rhinovirus B species consistently dominated the virome in asthma. Anelloviridae were the most abundant and rich family in both health and asthma. However, their richness and alpha diversity were increased in asthma, along with the co-occurrence of different Anellovirus genera. Bacteriophages were richer and more diverse in healthy individuals. Unsupervised clustering identified three virome profiles that were correlated to asthma severity and control and were independent of treatment, suggesting a link between the respiratory virome and asthma. Finally, we observed different cross-species ecological associations in the healthy versus the asthmatic virus-bacterial interactome, and an expanded interactome of eukaryotic viruses in asthma. Upper respiratory virome "dysbiosis" appears to be a novel feature of pre-school asthma during asymptomatic/non-infectious states and merits further investigation.
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Affiliation(s)
- Spyridon Megremis
- University of Manchester, Manchester, UK.
- University of Leicester, Leicester, UK.
| | | | | | | | | | | | - Susetta Finotto
- Friedrich Alexander University Erlangen-Nurnberg, Erlangen, Germany
| | - Tuomas Jartti
- University of Turku, Turku, Finland
- University of Oulu, Oulu, Finland
| | | | | | | | | | - Nikolaos G Papadopoulos
- University of Manchester, Manchester, UK.
- National and Kapodistrian University of Athens, Athens, Greece.
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13
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Should We Expect an Increase in the Number of Cancer Cases in People with Long COVID? Microorganisms 2023; 11:microorganisms11030713. [PMID: 36985286 PMCID: PMC10051562 DOI: 10.3390/microorganisms11030713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
The relationship between viral infections and the risk of developing cancer is well known. Multiple mechanisms participate in and determine this process. The COVID-19 pandemic caused by the SARS-CoV-2 virus has resulted in the deaths of millions of people worldwide. Although the effects of COVID-19 are limited for most people, a large number of people continue to show symptoms for a long period of time (long COVID). Several studies have suggested that cancer could also be a potential long-term complication of the virus; however, the causes of this risk are not yet well understood. In this review, we investigated arguments that could support or reject this possibility.
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14
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Kumar R, Aktay-Cetin Ö, Craddock V, Morales-Cano D, Kosanovic D, Cogolludo A, Perez-Vizcaino F, Avdeev S, Kumar A, Ram AK, Agarwal S, Chakraborty A, Savai R, de Jesus Perez V, Graham BB, Butrous G, Dhillon NK. Potential long-term effects of SARS-CoV-2 infection on the pulmonary vasculature: Multilayered cross-talks in the setting of coinfections and comorbidities. PLoS Pathog 2023; 19:e1011063. [PMID: 36634048 PMCID: PMC9836319 DOI: 10.1371/journal.ppat.1011063] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The Coronavirus Disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and its sublineages pose a new challenge to healthcare systems worldwide due to its ability to efficiently spread in immunized populations and its resistance to currently available therapies. COVID-19, although targeting primarily the respiratory system, is also now well established that later affects every organ in the body. Most importantly, despite the available therapy and vaccine-elicited protection, the long-term consequences of viral infection in breakthrough and asymptomatic individuals are areas of concern. In the past two years, investigators accumulated evidence on how the virus triggers our immune system and the molecular signals involved in the cross-talk between immune cells and structural cells in the pulmonary vasculature to drive pathological lung complications such as endothelial dysfunction and thrombosis. In the review, we emphasize recent updates on the pathophysiological inflammatory and immune responses associated with SARS-CoV-2 infection and their potential long-term consequences that may consequently lead to the development of pulmonary vascular diseases.
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Affiliation(s)
- Rahul Kumar
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Lung Biology Center, Zuckerberg San Francisco General Hospital, San Francisco, California, United States of America
| | - Öznur Aktay-Cetin
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
| | - Vaughn Craddock
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Daniel Morales-Cano
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Djuro Kosanovic
- Department of Pulmonology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Angel Cogolludo
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
- Ciber Enfermedades Respiratorias (Ciberes), Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IISGM), Madrid, Spain
| | - Francisco Perez-Vizcaino
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
- Ciber Enfermedades Respiratorias (Ciberes), Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IISGM), Madrid, Spain
| | - Sergey Avdeev
- Department of Pulmonology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Ashok Kumar
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Anil Kumar Ram
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Stuti Agarwal
- Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University Medical Center, California, United States of America
| | - Ananya Chakraborty
- Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University Medical Center, California, United States of America
| | - Rajkumar Savai
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
- Department of Internal Medicine, Justus Liebig University Giessen, Member of the DZL, Member of CPI, Giessen, Germany
- Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany
| | - Vinicio de Jesus Perez
- Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University Medical Center, California, United States of America
| | - Brian B. Graham
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Lung Biology Center, Zuckerberg San Francisco General Hospital, San Francisco, California, United States of America
| | - Ghazwan Butrous
- Cardiopulmonary Sciences, University of Kent, Canterbury, United Kingdom
| | - Navneet K. Dhillon
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
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15
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Loop-Mediated Isothermal Amplification-Based Microfluidic Platforms for the Detection of Viral Infections. Curr Infect Dis Rep 2022; 24:205-215. [PMID: 36341307 PMCID: PMC9628606 DOI: 10.1007/s11908-022-00790-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2022] [Indexed: 11/09/2022]
Abstract
Purpose of Review Easy-to-use, fast, and accurate virus detection method is essential for patient management and epidemic surveillance, especially during severe pandemics. Loop-mediated isothermal amplification (LAMP) on a microfluidic platform is suitable for detecting infectious viruses, regardless of the availability of medical resources. The purpose of this review is to introduce LAMP-based microfluidic devices for virus detection, including their detection principles, methods, and application. Recent Findings Facing the uncontrolled spread of viruses, the large-scale deployment of LAMP-based microfluidic platforms at the grassroots level can help expand the coverage of nucleic acid testing and shorten the time to obtain test reports. Microfluidic chip technology is highly integrated and miniaturized, enabling precise fluid control for effective virus detection. Performing LAMP on miniaturized systems can reduce analysis time, reagent consumption and risk of sample contamination, and improve analytical performance. Summary Compared to traditional benchtop protocols, LAMP-based microfluidic devices reduce the testing time, reagent consumption, and the risk of sample contamination. In addition to simultaneous detection of multiple target genes by special channel design, microfluidic chips can also integrate digital LAMP to achieve absolute quantification of target genes.
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16
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Wu C, Holehouse AS, Leung DW, Amarasinghe GK, Dutch RE. Liquid Phase Partitioning in Virus Replication: Observations and Opportunities. Annu Rev Virol 2022; 9:285-306. [PMID: 35709511 DOI: 10.1146/annurev-virology-093020-013659] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses frequently carry out replication in specialized compartments within cells. The effect of these structures on virus replication is poorly understood. Recent research supports phase separation as a foundational principle for organization of cellular components with the potential to influence viral replication. In this review, phase separation is described in the context of formation of viral replication centers, with an emphasis on the nonsegmented negative-strand RNA viruses. Consideration is given to the interplay between phase separation and the critical processes of viral transcription and genome replication, and the role of these regions in pathogen-host interactions is discussed. Finally, critical questions that must be addressed to fully understand how phase separation influences viral replication and the viral life cycle are presented, along with information about new approaches that could be used to make important breakthroughs in this emerging field.
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Affiliation(s)
- Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Science and Engineering Living Systems, Washington University, St. Louis, Missouri, USA
| | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rebecca Ellis Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA;
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17
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Loh D, Reiter RJ. Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19. Int J Mol Sci 2022; 23:8122. [PMID: 35897696 PMCID: PMC9368024 DOI: 10.3390/ijms23158122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA;
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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18
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AuNP-based biosensors for the diagnosis of pathogenic human coronaviruses: COVID-19 pandemic developments. Anal Bioanal Chem 2022; 414:7069-7084. [PMID: 35781591 PMCID: PMC9251037 DOI: 10.1007/s00216-022-04193-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022]
Abstract
The outbreak rate of human coronaviruses (CoVs) especially highly pathogenic CoVs is increasing alarmingly. Early detection of these viruses allows treatment interventions to be provided more quickly to people at higher risk, as well as helping to identify asymptomatic carriers and isolate them as quickly as possible, thus preventing the disease transmission chain. The current diagnostic methods such as RT-PCR are not ideal due to high cost, low accuracy, low speed, and probability of false results. Therefore, a reliable and accurate method for the detection of CoVs in biofluids can become a front-line tool in order to deal with the spread of these deadly viruses. Currently, the nanomaterial-based sensing devices for detection of human coronaviruses from laboratory diagnosis to point-of-care (PoC) diagnosis are progressing rapidly. Gold nanoparticles (AuNPs) have revolutionized the field of biosensors because of the outstanding optical and electrochemical properties. In this review paper, a detailed overview of AuNP-based biosensing strategies with the varied transducers (electrochemical, optical, etc.) and also different biomarkers (protein antigens and nucleic acids) was presented for the detection of human coronaviruses including SARS-CoV-2, SARS-CoV-1, and MERS-CoV and lowly pathogenic CoVs. The present review highlights the newest trends in the SARS-CoV-2 nanobiosensors from the beginning of the COVID-19 epidemic until 2022. We hope that the presented examples in this review paper convince readers that AuNPs are a suitable platform for the designing of biosensors.
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19
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Sumi T, Harada K. Immune response to SARS-CoV-2 in severe disease and long COVID-19. iScience 2022; 25:104723. [PMID: 35813874 PMCID: PMC9251893 DOI: 10.1016/j.isci.2022.104723] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/23/2022] [Accepted: 06/29/2022] [Indexed: 01/10/2023] Open
Abstract
COVID-19 is mild to moderate in otherwise healthy individuals but may nonetheless cause life-threatening disease and/or a wide range of persistent symptoms. The general determinant of disease severity is age mainly because the immune response declines in aging patients. Here, we developed a mathematical model of the immune response to SARS-CoV-2 and revealed that typical age-related risk factors such as only a several 10% decrease in innate immune cell activity and inhibition of type-I interferon signaling by autoantibodies drastically increased the viral load. It was reported that the numbers of certain dendritic cell subsets remained less than half those in healthy donors even seven months after infection. Hence, the inflammatory response was ongoing. Our model predicted the persistent DC reduction and showed that certain patients with severe and even mild symptoms could not effectively eliminate the virus and could potentially develop long COVID. Systemic SARS-CoV-2 infection owing to ACE2 expression on a wide range of cell types Persistent viral infection can be ongoing within the host even if it is not severe Long-term dendritic cell deficiency is owing to viruses that cannot be removed by the host Ongoing persistent viral infection within the host potentially causes long COVID or PASC
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Affiliation(s)
- Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
- Department of Chemistry, Faculty of Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
- Corresponding author
| | - Kouji Harada
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
- Center for IT-Based Education, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
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20
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Schultheiß C, Willscher E, Paschold L, Gottschick C, Klee B, Henkes SS, Bosurgi L, Dutzmann J, Sedding D, Frese T, Girndt M, Höll JI, Gekle M, Mikolajczyk R, Binder M. The IL-1β, IL-6, and TNF cytokine triad is associated with post-acute sequelae of COVID-19. Cell Rep Med 2022; 3:100663. [PMID: 35732153 PMCID: PMC9214726 DOI: 10.1016/j.xcrm.2022.100663] [Citation(s) in RCA: 155] [Impact Index Per Article: 77.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/28/2022] [Accepted: 05/25/2022] [Indexed: 02/07/2023]
Abstract
Post-acute sequelae of COVID-19 (PASC) is emerging as global problem with unknown molecular drivers. Using a digital epidemiology approach, we recruited 8,077 individuals to the cohort study for digital health research in Germany (DigiHero) to respond to a basic questionnaire followed by a PASC-focused survey and blood sampling. We report the first 318 participants, the majority thereof after mild infections. Of those, 67.8% report PASC, predominantly consisting of fatigue, dyspnea, and concentration deficit, which persists in 60% over the mean 8-month follow-up period and resolves independently of post-infection vaccination. PASC is not associated with autoantibodies, but with elevated IL-1β, IL-6, and TNF plasma levels, which we confirm in a validation cohort with 333 additional participants and a longer time from infection of 10 months. Blood profiling and single-cell data from early infection suggest the induction of these cytokines in COVID-19 lung pro-inflammatory macrophages creating a self-sustaining feedback loop. We report a post-COVID-19 digital epidemiology study with biomarker analysis (n = 651) PASC persists in 60% of participants up to 24 months after mild COVID-19 PASC is associated with high IL-1β, IL-6, and TNF levels but not autoantibodies Overactivated monocytes/macrophages are likely the source of cytokine production
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Affiliation(s)
- Christoph Schultheiß
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany
| | - Edith Willscher
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany
| | - Lisa Paschold
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany
| | - Cornelia Gottschick
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06097 Halle (Saale), Germany
| | - Bianca Klee
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06097 Halle (Saale), Germany
| | - Svenja-Sibylla Henkes
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany
| | - Lidia Bosurgi
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20251 Hamburg, Germany; Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Strasse 74, 20359 Hamburg, Germany
| | - Jochen Dutzmann
- Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany
| | - Daniel Sedding
- Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany
| | - Thomas Frese
- Institute of General Practice and Family Medicine, Martin-Luther-University Halle-Wittenberg, Magdeburger Str. 8, 06112 Halle (Saale), Germany
| | - Matthias Girndt
- Department of Internal Medicine II, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany
| | - Jessica I Höll
- Pediatric Hematology and Oncology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany
| | - Michael Gekle
- Julius Bernstein-Institute of Physiology, Faculty of Medicine, Martin-Luther-University Halle-Wittenberg, Magdeburger Str. 6, 06110 Halle (Saale), Germany
| | - Rafael Mikolajczyk
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther University Halle-Wittenberg, Magdeburger Strasse 8, 06097 Halle (Saale), Germany
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany.
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Abstract
DNA viruses often persist in the body of their host, becoming latent and recurring many months or years later. By contrast, most RNA viruses cause acute infections that are cleared from the host as they lack the mechanisms to persist. However, it is becoming clear that viral RNA can persist after clinical recovery and elimination of detectable infectious virus. This persistence can either be asymptomatic or associated with late progressive disease or nonspecific lingering symptoms, such as may be the case following infection with Ebola or Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Why does viral RNA sometimes persist after recovery from an acute infection? Where does the RNA come from? And what are the consequences?
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22
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Grupstra CGB, Howe-Kerr LI, Veglia AJ, Bryant RL, Coy SR, Blackwelder PL, Correa AMS. Thermal stress triggers productive viral infection of a key coral reef symbiont. THE ISME JOURNAL 2022; 16:1430-1441. [PMID: 35046559 PMCID: PMC9038915 DOI: 10.1038/s41396-022-01194-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 01/03/2022] [Accepted: 01/07/2022] [Indexed: 04/27/2023]
Abstract
Climate change-driven ocean warming is increasing the frequency and severity of bleaching events, in which corals appear whitened after losing their dinoflagellate endosymbionts (family Symbiodiniaceae). Viral infections of Symbiodiniaceae may contribute to some bleaching signs, but little empirical evidence exists to support this hypothesis. We present the first temporal analysis of a lineage of Symbiodiniaceae-infecting positive-sense single-stranded RNA viruses ("dinoRNAVs") in coral colonies, which were exposed to a 5-day heat treatment (+2.1 °C). A total of 124 dinoRNAV major capsid protein gene "aminotypes" (unique amino acid sequences) were detected from five colonies of two closely related Pocillopora-Cladocopium (coral-symbiont) combinations in the experiment; most dinoRNAV aminotypes were shared between the two coral-symbiont combinations (64%) and among multiple colonies (82%). Throughout the experiment, seventeen dinoRNAV aminotypes were found only in heat-treated fragments, and 22 aminotypes were detected at higher relative abundances in heat-treated fragments. DinoRNAVs in fragments of some colonies exhibited higher alpha diversity and dispersion under heat stress. Together, these findings provide the first empirical evidence that exposure to high temperatures triggers some dinoRNAVs to switch from a persistent to a productive infection mode within heat-stressed corals. Over extended time frames, we hypothesize that cumulative dinoRNAV production in the Pocillopora-Cladocopium system could affect colony symbiotic status, for example, by decreasing Symbiodiniaceae densities within corals. This study sets the stage for reef-scale investigations of dinoRNAV dynamics during bleaching events.
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Affiliation(s)
| | | | - Alex J Veglia
- BioSciences at Rice, Rice University, Houston, TX, USA
| | - Reb L Bryant
- BioSciences at Rice, Rice University, Houston, TX, USA
- Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS, USA
| | | | - Patricia L Blackwelder
- Department of Chemistry, University of Miami Center for Advanced Microscopy (UMCAM), 1301 Memorial Dr, Coral Gables, FL, 33146-0630, USA
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23
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Kheshtchin N, Bakhshi P, Arab S, Nourizadeh M. Immunoediting in SARS-CoV-2: Mutual relationship between the virus and the host. Int Immunopharmacol 2022; 105:108531. [PMID: 35074569 PMCID: PMC8743495 DOI: 10.1016/j.intimp.2022.108531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 11/05/2022]
Abstract
Immunoediting is a well-known concept that occurs in cancer through three steps of elimination, equilibrium, and escape (3Es), where the immune system first suppresses the growth of tumor cells and then promotes them towards the malignancy. This phenomenon has been conceptualized in some chronic viral infections such as HTLV-1 and HIV by obtaining the resistance to elimination and making a persistent form of infected cells especially in untreated patients. Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a heterogeneous disease characterizing from mild/asymptomatic to severe/critical courses with some behavioral aspects in an immunoediting setting. In this context, a coordinated effort between innate and adaptive immune system leads to detection and destruction of early infection followed by equilibrium between virus-specific responses and infected cells, which eventually ends up with an uncontrolled inflammatory response in severe/critical patients. Although the SARS-CoV-2 applies several escape strategies such as mutations in viral epitopes, modulating the interferon response and inhibiting the MHC I molecules similar to the cancer cells, the 3Es hallmark may not occur in all clinical conditions. Here, we discuss how the lesson learnt from cancer immunoediting and accurate understanding of these pathophysiological mechanisms helps to develop more effective therapeutic strategies for COVID-19.
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24
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Mehandru S, Merad M. Pathological sequelae of long-haul COVID. Nat Immunol 2022; 23:194-202. [PMID: 35105985 PMCID: PMC9127978 DOI: 10.1038/s41590-021-01104-y] [Citation(s) in RCA: 342] [Impact Index Per Article: 171.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/30/2021] [Indexed: 02/08/2023]
Abstract
The world continues to contend with successive waves of coronavirus disease 2019 (COVID-19), fueled by the emergence of viral variants. At the same time, persistent, prolonged and often debilitating sequelae are increasingly recognized in convalescent individuals, named 'post-COVID-19 syndrome' or 'long-haul COVID'. Clinical symptomatology includes fatigue, malaise, dyspnea, defects in memory and concentration and a variety of neuropsychiatric syndromes as the major manifestations, and several organ systems can be involved. The underlying pathophysiological mechanisms are poorly understood at present. This Review details organ-specific sequelae of post-COVID-19 syndromes and examines the underlying pathophysiological mechanisms available so far, elaborating on persistent inflammation, induced autoimmunity and putative viral reservoirs. Finally, we propose diagnostic strategies to better understand this heterogeneous disorder that continues to afflict millions of people worldwide.
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Affiliation(s)
- Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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25
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SARS-CoV-2 and Variant Diagnostic Testing Approaches in the United States. Viruses 2021; 13:v13122492. [PMID: 34960762 PMCID: PMC8703625 DOI: 10.3390/v13122492] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/29/2021] [Accepted: 12/08/2021] [Indexed: 12/23/2022] Open
Abstract
Purpose of Review Given the rapid development of diagnostic approaches to test for and diagnose infection with SARS-CoV-2 and its associated variants including Omicron (B.1.1.529), many options are available to diagnose infection. Multiple established diagnostic companies are now providing testing platforms whereas initially, testing was being performed with simple PCR-based tests using standard laboratory reagents. Recent Findings Additional testing platforms continue to be developed, including those to detect specific variants, but challenges with testing, including obtaining testing reagents and other related supplies, are frequently encountered. With time, the testing supply chain has improved, and more established companies are providing materials to support these testing efforts. In the United States (U.S.), the need for rapid assay development and subsequent approval through the attainment of emergency use authorization (EUA) has superseded the traditional arduous diagnostic testing approval workflow mandated by the FDA. Through these efforts, the U.S. has been able to continue to significantly increase its testing capabilities to address this pandemic; however, challenges still remain due to the diversity of the performance characteristics of tests being utilized and newly discovered viral variants. Summary This review provides an overview of the current diagnostic testing landscape, with pertinent information related to SARS-CoV-2 virology, variants and antibody responses that are available to diagnose infection in the U.S.
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26
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Bokelmann M, Vogel U, Debeljak F, Düx A, Riesle-Sbarbaro S, Lander A, Wahlbrink A, Kromarek N, Neil S, Couacy-Hymann E, Prescott J, Kurth A. Tolerance and Persistence of Ebola Virus in Primary Cells from Mops condylurus, a Potential Ebola Virus Reservoir. Viruses 2021; 13:v13112186. [PMID: 34834992 PMCID: PMC8622823 DOI: 10.3390/v13112186] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
Although there have been documented Ebola virus disease outbreaks for more than 40 years, the natural reservoir host has not been identified. Recent studies provide evidence that the Angolan free-tailed bat (Mops condylurus), an insectivorous microbat, is a possible ebolavirus reservoir. To investigate the potential role of this bat species in the ecology of ebolaviruses, replication, tolerance, and persistence of Ebola virus (EBOV) were investigated in 10 different primary bat cell isolates from M. condylurus. Varying EBOV replication kinetics corresponded to the expression levels of the integral membrane protein NPC1. All primary cells were highly tolerant to EBOV infection without cytopathic effects. The observed persistent EBOV infection for 150 days in lung primary cells, without resultant selective pressure leading to virus mutation, indicate the intrinsic ability of EBOV to persist in this bat species. These results provide further evidence for this bat species to be a likely reservoir of ebolaviruses.
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Affiliation(s)
- Marcel Bokelmann
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (M.B.); (U.V.); (S.R.-S.); (A.L.); (A.W.); (N.K.); (J.P.)
| | - Uwe Vogel
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (M.B.); (U.V.); (S.R.-S.); (A.L.); (A.W.); (N.K.); (J.P.)
| | - Franka Debeljak
- Department of Infectious Diseases, King’s College London, London WC2R 2LS, UK; (F.D.); (S.N.)
| | - Ariane Düx
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, 13353 Berlin, Germany;
| | - Silke Riesle-Sbarbaro
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (M.B.); (U.V.); (S.R.-S.); (A.L.); (A.W.); (N.K.); (J.P.)
| | - Angelika Lander
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (M.B.); (U.V.); (S.R.-S.); (A.L.); (A.W.); (N.K.); (J.P.)
| | - Annette Wahlbrink
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (M.B.); (U.V.); (S.R.-S.); (A.L.); (A.W.); (N.K.); (J.P.)
| | - Nicole Kromarek
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (M.B.); (U.V.); (S.R.-S.); (A.L.); (A.W.); (N.K.); (J.P.)
| | - Stuart Neil
- Department of Infectious Diseases, King’s College London, London WC2R 2LS, UK; (F.D.); (S.N.)
| | - Emmanuel Couacy-Hymann
- Laboratoire National d’Appui au Développement Agricole, Bingerville BP 206, Côte d’Ivoire;
| | - Joseph Prescott
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (M.B.); (U.V.); (S.R.-S.); (A.L.); (A.W.); (N.K.); (J.P.)
| | - Andreas Kurth
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (M.B.); (U.V.); (S.R.-S.); (A.L.); (A.W.); (N.K.); (J.P.)
- Correspondence:
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27
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Thomas E, Delabat S, Andrews DM. Diagnostic Testing for SARS-CoV-2 Infection. CURRENT HEPATOLOGY REPORTS 2021; 20:166-174. [PMID: 34725630 PMCID: PMC8550867 DOI: 10.1007/s11901-021-00567-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 08/14/2021] [Indexed: 12/22/2022]
Abstract
PURPOSE OF REVIEW Given the rapid development of diagnostic approaches to test for and diagnose infection with SARS-CoV-2, many options are available to assess infection. Multiple established diagnostic companies are now providing testing platforms whereas initially, testing was being performed with simple PCR-based tests using standard laboratory reagents. RECENT FINDINGS Additional testing platforms continue to be developed but challenges with testing, including obtaining testing reagents and other related supplies, are frequently encountered. With time, the testing supply chain will improve and more companies will be providing materials to support these testing efforts. In the USA, the need for rapid assay development and subsequent approval through attainment of emergency use authorization (EUA) has superseded the traditional arduous diagnostic testing approval workflow mandated by the FDA. It is anticipated that the USA will be able to continue to significantly increase its testing capabilities to address this pandemic; however, challenges remain due to the diversity of the performance characteristics of tests being utilized. SUMMARY This review provides an overview of the current diagnostic testing landscape, with pertinent information related to SARS-CoV-2 virology and antibody responses, that is available to diagnose infection.
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Affiliation(s)
- Emmanuel Thomas
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL USA
- Schiff Center for Liver Disease, University of Miami Miller School of Medicine, 1550 NW 10th Ave., Papanicolaou Bldg., RM PAP 514, Miami, FL 33136 USA
| | - Stephanie Delabat
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL USA
| | - David M. Andrews
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL USA
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28
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Gaspar-Rodríguez A, Padilla-González A, Rivera-Toledo E. Coronavirus persistence in human respiratory tract and cell culture: An overview. Braz J Infect Dis 2021; 25:101632. [PMID: 34627782 PMCID: PMC8486621 DOI: 10.1016/j.bjid.2021.101632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/13/2021] [Accepted: 09/13/2021] [Indexed: 01/12/2023] Open
Abstract
Emerging human coronaviruses, including the recently identified SARS-CoV-2, are relevant respiratory pathogens due to their potential to cause epidemics with high case fatality rates, although endemic coronaviruses are also important for immunocompromised patients. Long-term coronavirus infections had been described mainly in experimental models, but it is currently evident that SARS-CoV-2 genomic-RNA can persist for many weeks in the respiratory tract of some individuals clinically recovered from coronavirus infectious disease-19 (COVID-19), despite a lack of isolation of infectious virus. It is still not clear whether persistence of such viral RNA may be pathogenic for the host and related to long-term sequelae. In this review, we summarize evidence of SARS-CoV-2 RNA persistence in respiratory samples besides results obtained from cell culture and histopathology describing long-term coronavirus infection. We also comment on potential mechanisms of coronavirus persistence and relevance for pathogenesis.
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Affiliation(s)
- Adriana Gaspar-Rodríguez
- Universidad Nacional Autonoma de Mexico, Facultad de Medicina, Departamento de Microbiología y Parasitología, Coyoacan, Mexico
| | - Ana Padilla-González
- Universidad Nacional Autonoma de Mexico, Facultad de Medicina, Departamento de Microbiología y Parasitología, Coyoacan, Mexico.
| | - Evelyn Rivera-Toledo
- Universidad Nacional Autonoma de Mexico, Facultad de Medicina, Departamento de Microbiología y Parasitología, Coyoacan, Mexico.
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29
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Greninger AL, Rybkina K, Lin MJ, Drew-Bear J, Marcink TC, Shean RC, Makhsous N, Boeckh M, Harder O, Bovier F, Burstein SR, Niewiesk S, Rima BK, Porotto M, Moscona A. Human parainfluenza virus evolution during lung infection of immunocompromised humans promotes viral persistence. J Clin Invest 2021; 131:150506. [PMID: 34609969 DOI: 10.1172/jci150506] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022] Open
Abstract
The capacity of respiratory viruses to undergo evolution within the respiratory tract raises the possibility of evolution under the selective pressure of the host environment or drug treatment. Long-term infections in immunocompromised hosts are potential drivers of viral evolution and development of infectious variants. We show that intra-host evolution in chronic human parainfluenza virus 3 (HPIV3) infection in immunocompromised individuals elicited mutations that favor viral entry and persistence, suggesting that similar processes may operate across enveloped respiratory viruses. We profiled longitudinal HPIV3 infections from two immunocompromised individuals that persisted for 278 and 98 days. Mutations accrued in the HPIV3 attachment protein hemagglutinin-neuraminidase (HN), including the first in vivo mutation in HN's receptor binding site responsible for activating the viral fusion process. Fixation of this mutation was associated with exposure to a drug that cleaves host cell sialic acid moieties. Longitudinal adaptation of HN was associated with features that promote viral entry and persistence in cells, including greater avidity for sialic acid and more active fusion activity in vitro, but not with antibody escape. Long term infection thus led to mutations promoting viral persistence, suggesting that host-directed therapeutics may support the evolution of viruses that alter their biophysical characteristics to persist in the face of these agents in vivo.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Ksenia Rybkina
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Jennifer Drew-Bear
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Tara C Marcink
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Ryan C Shean
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Negar Makhsous
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Olivia Harder
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, United States of America
| | - Francesca Bovier
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Shana R Burstein
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Stefan Niewiesk
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, United States of America
| | - Bert K Rima
- School of Medicine Dentistry and Biomedical Sceinces, Queen's University of Belfast, Belfast, United Kingdom
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
| | - Anne Moscona
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, United States of America
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30
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Russo AG, Harding EF, Yan GJH, Selechnik D, Ducatez S, DeVore JL, Zhou J, Sarma RR, Lee YP, Richardson MF, Shine R, Rollins LA, White PA. Discovery of Novel Viruses Associated With the Invasive Cane Toad ( Rhinella marina) in Its Native and Introduced Ranges. Front Microbiol 2021; 12:733631. [PMID: 34552575 PMCID: PMC8450580 DOI: 10.3389/fmicb.2021.733631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/05/2021] [Indexed: 11/13/2022] Open
Abstract
Cane toads (Rhinella marina) are notoriously successful invaders: from 101 individuals brought to Australia in 1935, poisonous toads now cover an area >1.2 million km2 with adverse effects on native fauna. Despite extensive research on the role of macroparasites in cane toad invasion, viral research is lagging. We compared viral prevalence and diversity between toads in their native range (French Guiana, n=25) and two introduced ranges: Australia (n=151) and Hawai'i (n=10) with a metatranscriptomic and metagenomic approach combined with PCR screening. Australian toads almost exclusively harbor one of seven viruses detected globally. Rhimavirus-A (Picornaviridae) exhibited low genetic diversity and likely actively infected 9% of sampled Australian toads extending across ~2,000km of Northern Australia and up to the current invasion front. In native range cane toads, we identified multiple phylogenetically distinct viruses (Iridoviridae, Picornaviridae, Papillomaviridae, and Nackedna-like virus). None of the same viruses was detected in both ranges, suggesting that Australian cane toads have largely escaped the viral infection experienced by their native range counterparts. The novel native range viruses described here are potential biocontrol agents, as Australian toads likely lack prior immunological exposure to these viruses. Overall, our evidence suggests that there may be differences between viruses infecting cane toads in their native vs. introduced ranges, which lays the groundwork for further studies on how these viruses have influenced the toads' invasion history.
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Affiliation(s)
- Alice G Russo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Emma F Harding
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Grace J H Yan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel Selechnik
- School of Life and Environmental Sciences (SOLES), University of Sydney, Sydney, NSW, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Simon Ducatez
- School of Life and Environmental Sciences (SOLES), University of Sydney, Sydney, NSW, Australia
| | - Jayna L DeVore
- School of Life and Environmental Sciences (SOLES), University of Sydney, Sydney, NSW, Australia
| | - Jia Zhou
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Roshmi R Sarma
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Yin Peng Lee
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Mark F Richardson
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Richard Shine
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Lee A Rollins
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia.,School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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Kurebayashi Y, Bajimaya S, Watanabe M, Lim N, Lutz M, Dunagan M, Takimoto T. Human parainfluenza virus type 1 regulates cholesterol biosynthesis and establishes quiescent infection in human airway cells. PLoS Pathog 2021; 17:e1009908. [PMID: 34529742 PMCID: PMC8445407 DOI: 10.1371/journal.ppat.1009908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/19/2021] [Indexed: 12/03/2022] Open
Abstract
Human parainfluenza virus type 1 (hPIV1) and 3 (hPIV3) cause seasonal epidemics, but little is known about their interaction with human airway cells. In this study, we determined cytopathology, replication, and progeny virion release from human airway cells during long-term infection in vitro. Both viruses readily established persistent infection without causing significant cytopathic effects. However, assembly and release of hPIV1 rapidly declined in sharp contrast to hPIV3 due to impaired viral ribonucleocapsid (vRNP) trafficking and virus assembly. Transcriptomic analysis revealed that both viruses induced similar levels of type I and III IFNs. However, hPIV1 induced specific ISGs stronger than hPIV3, such as MX2, which bound to hPIV1 vRNPs in infected cells. In addition, hPIV1 but not hPIV3 suppressed genes involved in lipid biogenesis and hPIV1 infection resulted in ubiquitination and degradation of 3-hydroxy-3-methylglutaryl-coenzyme A reductase, a rate limiting enzyme in cholesterol biosynthesis. Consequently, formation of cholesterol-rich lipid rafts was impaired in hPIV1 infected cells. These results indicate that hPIV1 is capable of regulating cholesterol biogenesis, which likely together with ISGs contributes to establishment of a quiescent infection. Seasonal epidemics caused by parainfluenza viruses result in a significant burden of disease in children. These viruses infect airway epithelial cells and cause acute respiratory infection. Humans are the only known hosts for these viruses, but how these viruses are maintained within the population is not known. In this study, we analyzed human airway cells infected with type 1 and 3 parainfluenza viruses. Both viruses readily established persistent infection without causing major cytopathic effects. However, assembly and release of hPIV1 rapidly declined over time in sharp contrast to hPIV3. HPIV1 infected cells formed large aggregates of viral nucleocapsid at late time points, suggesting impaired nucleocapsid trafficking and virus assembly. Transcriptomic analysis of infected cells showed no major difference in IFN induction between the viruses, while hPIV1 induced elevated levels of interferon stimulated genes (ISGs) compared to hPIV3. Interestingly, hPIV1 infection specifically downregulated genes involved in cholesterol biogenesis. We also found that hPIV1 infection induced ubiquitination and degradation of 3-hydroxy-3-methylglutaryl-coenzyme A reductase, a rate limiting enzyme in cholesterol biosynthesis. These results suggest that induction of IFN-independent ISGs and suppression of cholesterol by hPIV1 likely play a role in establishing quiescent infection in human respiratory epithelial cells.
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Affiliation(s)
- Yuki Kurebayashi
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Shringkhala Bajimaya
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Masahiro Watanabe
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Nicholas Lim
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Michael Lutz
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Megan Dunagan
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Toru Takimoto
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail:
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32
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Páez DJ, Powers RL, Jia P, Ballesteros N, Kurath G, Naish KA, Purcell MK. Temperature Variation and Host Immunity Regulate Viral Persistence in a Salmonid Host. Pathogens 2021; 10:855. [PMID: 34358005 PMCID: PMC8308775 DOI: 10.3390/pathogens10070855] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/15/2021] [Accepted: 06/23/2021] [Indexed: 11/17/2022] Open
Abstract
Environmental variation has important effects on host-pathogen interactions, affecting large-scale ecological processes such as the severity and frequency of epidemics. However, less is known about how the environment interacts with host immunity to modulate virus fitness within hosts. Here, we studied the interaction between host immune responses and water temperature on the long-term persistence of a model vertebrate virus, infectious hematopoietic necrosis virus (IHNV) in steelhead trout (Oncorhynchus mykiss). We first used cell culture methods to factor out strong host immune responses, allowing us to test the effect of temperature on viral replication. We found that 15 ∘C water temperature accelerated IHNV replication compared to the colder 10 and 8 ∘C temperatures. We then conducted in vivo experiments to quantify the effect of 6, 10, and 15 ∘C water temperatures on IHNV persistence over 8 months. Fish held at 15 and 10 ∘C were found to have higher prevalence of neutralizing antibodies compared to fish held at 6 ∘C. We found that IHNV persisted for a shorter time at warmer temperatures and resulted in an overall lower fish mortality compared to colder temperatures. These results support the hypothesis that temperature and host immune responses interact to modulate virus persistence within hosts. When immune responses were minimized (i.e., in vitro) virus replication was higher at warmer temperatures. However, with a full potential for host immune responses (i.e., in vivo experiments) longer virus persistence and higher long-term virulence was favored in colder temperatures. We also found that the viral RNA that persisted at later time points (179 and 270 days post-exposure) was mostly localized in the kidney and spleen tissues. These tissues are composed of hematopoietic cells that are favored targets of the virus. By partitioning the effect of temperature on host and pathogen responses, our results help to better understand environmental drivers of host-pathogen interactions within hosts, providing insights into potential host-pathogen responses to climate change.
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Affiliation(s)
- David J. Páez
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195, USA;
| | - Rachel L. Powers
- US Geological Survey, Western Fisheries Research Center, Seattle, WA 98115, USA; (R.L.P.); (P.J.); (N.B.); (G.K.)
| | - Peng Jia
- US Geological Survey, Western Fisheries Research Center, Seattle, WA 98115, USA; (R.L.P.); (P.J.); (N.B.); (G.K.)
- Shenzhen Customs, Animal & Plant Inspection and Quarantine Technology Center, Shenzhen 518045, China
- Quality and Standards Academy, Shenzhen Technology University, Shenzhen 518118, China
| | - Natalia Ballesteros
- US Geological Survey, Western Fisheries Research Center, Seattle, WA 98115, USA; (R.L.P.); (P.J.); (N.B.); (G.K.)
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Gael Kurath
- US Geological Survey, Western Fisheries Research Center, Seattle, WA 98115, USA; (R.L.P.); (P.J.); (N.B.); (G.K.)
| | - Kerry A. Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195, USA;
| | - Maureen K. Purcell
- US Geological Survey, Western Fisheries Research Center, Seattle, WA 98115, USA; (R.L.P.); (P.J.); (N.B.); (G.K.)
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33
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Proal AD, VanElzakker MB. Long COVID or Post-acute Sequelae of COVID-19 (PASC): An Overview of Biological Factors That May Contribute to Persistent Symptoms. Front Microbiol 2021; 12:698169. [PMID: 34248921 PMCID: PMC8260991 DOI: 10.3389/fmicb.2021.698169] [Citation(s) in RCA: 428] [Impact Index Per Article: 142.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/17/2021] [Indexed: 12/23/2022] Open
Abstract
The novel virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic of coronavirus disease 2019 (COVID-19). Across the globe, a subset of patients who sustain an acute SARS-CoV-2 infection are developing a wide range of persistent symptoms that do not resolve over the course of many months. These patients are being given the diagnosis Long COVID or Post-acute sequelae of COVID-19 (PASC). It is likely that individual patients with a PASC diagnosis have different underlying biological factors driving their symptoms, none of which are mutually exclusive. This paper details mechanisms by which RNA viruses beyond just SARS-CoV-2 have be connected to long-term health consequences. It also reviews literature on acute COVID-19 and other virus-initiated chronic syndromes such as post-Ebola syndrome or myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) to discuss different scenarios for PASC symptom development. Potential contributors to PASC symptoms include consequences from acute SARS-CoV-2 injury to one or multiple organs, persistent reservoirs of SARS-CoV-2 in certain tissues, re-activation of neurotrophic pathogens such as herpesviruses under conditions of COVID-19 immune dysregulation, SARS-CoV-2 interactions with host microbiome/virome communities, clotting/coagulation issues, dysfunctional brainstem/vagus nerve signaling, ongoing activity of primed immune cells, and autoimmunity due to molecular mimicry between pathogen and host proteins. The individualized nature of PASC symptoms suggests that different therapeutic approaches may be required to best manage care for specific patients with the diagnosis.
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Affiliation(s)
- Amy D. Proal
- PolyBio Research Foundation, Kenmore, WA, United States
| | - Michael B. VanElzakker
- PolyBio Research Foundation, Kenmore, WA, United States
- Division of Neurotherapeutics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
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Hershberger PK, MacKenzie AH, Gregg JL, Wilmot MD, Powers RL, Purcell MK. Long-term shedding from fully convalesced individuals indicates that Pacific herring are a reservoir for viral hemorrhagic septicemia virus. DISEASES OF AQUATIC ORGANISMS 2021; 144:245-252. [PMID: 34042072 DOI: 10.3354/dao03595] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Processes that allow viral hemorrhagic septicemia (VHS) virus to persist in the marine environment remain enigmatic, owing largely to the presence of covert and cryptic infections in marine fishes during typical sub-epizootic periods. As such, marine host reservoirs for VHS virus have not been fully demonstrated, nor have the mechanism(s) by which infected hosts contribute to virus perpetuation and transmission. Here, we demonstrate that after surviving VHS, convalesced Pacific herring continue to shed virus at a low rate for extended periods. Further, exposure of previously naïve conspecific sentinels to this shed virus can result in infections for at least 6 mo after cessation of overt disease. This transmission mechanism was not necessarily dependent on the magnitude of the disease outbreak, as prolonged transmission occurred from 2 groups of donor herring that experienced cumulative mortalities of 4 and 29%. The results further suggest that the virus persists in association with the gills of fully recovered individuals, and long-term viral shedding or shedding relapses are related to cooler or decreasing water temperatures. These results provide support for a new VHS virus perpetuation paradigm in the marine environment, whereby the virus can be maintained in convalesced survivors and trafficked from these carriers to sympatric susceptible individuals.
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Affiliation(s)
- P K Hershberger
- US Geological Survey, Western Fisheries Research Center, Marrowstone Marine Field Station, Nordland, WA 98328, USA
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Differential miRNA Expression Profiling Reveals Correlation of miR125b-5p with Persistent Infection of Japanese Encephalitis Virus. Int J Mol Sci 2021; 22:ijms22084218. [PMID: 33921710 PMCID: PMC8073291 DOI: 10.3390/ijms22084218] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) play versatile roles in multiple biological processes. However, little is known about miRNA’s involvement in flavivirus persistent infection. Here, we used an miRNA array analysis of Japanese encephalitis virus (JEV)-infected cells to search for persistent infection-associated miRNAs in comparison to acute infection. Among all differentially expressed miRNAs, the miR-125b-5p is the most significantly increased one. The high level of miR-125b-5p in persistently JEV-infected cells was confirmed by Northern analysis and real-time quantitative polymerase chain reaction. As soon as the cells established a persistent infection, a significantly high expression of miR-125b-5p was readily observed. Transfecting excess quantities of a miR-125b-5p mimic into acutely infected cells reduced genome replication and virus titers. Host targets of miR125b-5p were analyzed by target prediction algorithms, and six candidates were confirmed by a dual-luciferase reporter assay. These genes were upregulated in the acutely infected cells and sharply declined in the persistently infected cells. The transfection of the miR125b-5p mimic reduced the expression levels of Stat3, Map2k7, and Triap1. Our studies indicated that miR-125b-5p targets both viral and host sequences, suggesting its role in coordinating viral replication and host antiviral responses. This is the first report to characterize the potential roles of miR-125b-5p in persistent JEV infections.
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36
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Jacobs JJL. Persistent SARS-2 infections contribute to long COVID-19. Med Hypotheses 2021; 149:110538. [PMID: 33621843 PMCID: PMC7884250 DOI: 10.1016/j.mehy.2021.110538] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/11/2021] [Indexed: 01/09/2023]
Abstract
COVID-19 is a serious disease that has infected more than 40 million people. Beside significant mortality, the SARS-CoV-2 infection causes considerable and sustained morbidity, dubbed long COVID. This paper argues that some of this morbidity may be due to a persistent systemic infection. Persistent infection is indicated by continued virus RNA shedding. The virus’ superantigen could overstimulate anti-virus immune responses, and thereby induce negative feedback loops, that paradoxically allow the virus to persist. The superantigen would induce strong immune response to any residual infection. This hypothesis suggests that clearing the virus infection completely would be an appropriate intervention against long COVID.
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Affiliation(s)
- John J L Jacobs
- ORTEC BV, Dept. of Health, Houtsingel 5, Zoetermeer 2719 EA, the Netherlands.
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37
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Viral Infections and Systemic Lupus Erythematosus: New Players in an Old Story. Viruses 2021; 13:v13020277. [PMID: 33670195 PMCID: PMC7916951 DOI: 10.3390/v13020277] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/06/2021] [Accepted: 02/07/2021] [Indexed: 02/07/2023] Open
Abstract
A causal link between viral infections and autoimmunity has been studied for a long time and the role of some viruses in the induction or exacerbation of systemic lupus erythematosus (SLE) in genetically predisposed patients has been proved. The strength of the association between different viral agents and SLE is variable. Epstein-Barr virus (EBV), parvovirus B19 (B19V), and human endogenous retroviruses (HERVs) are involved in SLE pathogenesis, whereas other viruses such as Cytomegalovirus (CMV) probably play a less prominent role. However, the mechanisms of viral-host interactions and the impact of viruses on disease course have yet to be elucidated. In addition to classical mechanisms of viral-triggered autoimmunity, such as molecular mimicry and epitope spreading, there has been a growing appreciation of the role of direct activation of innate response by viral nucleic acids and epigenetic modulation of interferon-related immune response. The latter is especially important for HERVs, which may represent the molecular link between environmental triggers and critical immune genes. Virus-specific proteins modulating interaction with the host immune system have been characterized especially for Epstein-Barr virus and explain immune evasion, persistent infection and self-reactive B-cell "immortalization". Knowledge has also been expanding on key viral proteins of B19-V and CMV and their possible association with specific phenotypes such as antiphospholipid syndrome. This progress may pave the way to new therapeutic perspectives, including the use of known or new antiviral drugs, postviral immune response modulation and innate immunity inhibition. We herein describe the state-of-the-art knowledge on the role of viral infections in SLE, with a focus on their mechanisms of action and potential therapeutic targets.
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38
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Dinesh DC, Tamilarasan S, Rajaram K, Bouřa E. Antiviral Drug Targets of Single-Stranded RNA Viruses Causing Chronic Human Diseases. Curr Drug Targets 2021; 21:105-124. [PMID: 31538891 DOI: 10.2174/1389450119666190920153247] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 02/08/2023]
Abstract
Ribonucleic acid (RNA) viruses associated with chronic diseases in humans are major threats to public health causing high mortality globally. The high mutation rate of RNA viruses helps them to escape the immune response and also is responsible for the development of drug resistance. Chronic infections caused by human immunodeficiency virus (HIV) and hepatitis viruses (HBV and HCV) lead to acquired immunodeficiency syndrome (AIDS) and hepatocellular carcinoma respectively, which are one of the major causes of human deaths. Effective preventative measures to limit chronic and re-emerging viral infections are absolutely necessary. Each class of antiviral agents targets a specific stage in the viral life cycle and inhibits them from its development and proliferation. Most often, antiviral drugs target a specific viral protein, therefore only a few broad-spectrum drugs are available. This review will be focused on the selected viral target proteins of pathogenic viruses containing single-stranded (ss) RNA genome that causes chronic infections in humans (e.g. HIV, HCV, Flaviviruses). In the recent past, an exponential increase in the number of available three-dimensional protein structures (>150000 in Protein Data Bank), allowed us to better understand the molecular mechanism of action of protein targets and antivirals. Advancements in the in silico approaches paved the way to design and develop several novels, highly specific small-molecule inhibitors targeting the viral proteins.
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Affiliation(s)
| | - Selvaraj Tamilarasan
- Section of Microbial Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Kaushik Rajaram
- Department of Microbiology, Central University of Tamil Nadu, Thiruvarur, India
| | - Evžen Bouřa
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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39
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Mookhploy W, Krongdang S, Chantawannakul P. Effects of Deformed Wing Virus Infection on Expressions of Immune- and Apoptosis-Related Genes in Western Honeybees ( Apis mellifera). INSECTS 2021; 12:82. [PMID: 33477797 PMCID: PMC7832323 DOI: 10.3390/insects12010082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 01/11/2023]
Abstract
Honeybees are globally threatened by several pathogens, especially deformed wing virus (DWV), as the presence of DWV in western honeybees is indicative of colony loss. The high mortality rate is further exacerbated by the lack of effective treatment, and therefore understanding the immune and apoptosis responses could pave an avenue for the treatment method. In this study, DWV was directly injected into the white-eyed pupae stage of western honeybees (Apis mellifera). The DWV loads and selected gene responses were monitored using the real-time PCR technique. The results showed that honeybee pupae that were injected with the highest concentration of viral loads showed a significantly higher mortality rate than the control groups. Deformed wings could be observed in newly emerged adult bees when the infected bees harbored high levels of viral loads. However, the numbers of viral loads in both normal and crippled wing groups were not significantly different. DWV-injected honeybee pupae with 104 and 107 copy numbers per bee groups showed similar viral loads after 48 h until newly emerged adult bees. Levels of gene expression including immune genes (defensin, abaecin, and hymenoptaecin) and apoptosis genes (buffy, p53, Apaf1, caspase3-like, caspase8-like, and caspase9-like) were analyzed after DWV infection. The expressions of immune and apoptosis genes were significantly different in infected bees compared to those of the control groups. In the pupae stage, the immune genes were activated by injecting DWV (defensin and hymenoptaecin) or Escherichia coli (defensin, abaecin, and hymenoptaecin), a positive control. On the contrary, the expression of apoptosis-related genes (buffy, caspase3-like, caspase8-like, and caspase9-like genes) was suppressed at 96 h post-infection. In DWV-infected newly emerged adult bees, abaecin, hymenoptaecin, Apaf1, and caspase8-like genes were upregulated. However, these genes were not significantly different between the normal and crippled wing bees. Our results suggested that DWV could activate the humoral immunity in honeybees and that honeybee hosts may be able to protect themselves from the virus infection through immune responses. Apoptosis gene expressions were upregulated in newly emerged adult bees by the virus, however, they were downregulated during the initial phase of viral infection.
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Affiliation(s)
- Wannapha Mookhploy
- Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; or
- Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sasiprapa Krongdang
- Faculty of Science and Social Sciences, Burapha University Sa Kaeo Campus, Sa Kaeo 27160, Thailand; or
| | - Panuwan Chantawannakul
- Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; or
- Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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40
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Baang JH, Smith C, Mirabelli C, Valesano AL, Manthei DM, Bachman MA, Wobus CE, Adams M, Washer L, Martin ET, Lauring AS. Prolonged Severe Acute Respiratory Syndrome Coronavirus 2 Replication in an Immunocompromised Patient. J Infect Dis 2021; 223:23-27. [PMID: 33089317 PMCID: PMC7797758 DOI: 10.1093/infdis/jiaa666] [Citation(s) in RCA: 212] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023] Open
Abstract
We describe a case of chronic coronavirus disease 2019 (COVID-19) in a patient with lymphoma and associated B-cell immunodeficiency. Viral cultures and sequence analysis demonstrate ongoing replication of infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for at least 119 days. The patient had 3 admissions related to COVID-19 over a 4-month period and was treated twice with remdesivir and convalescent plasma with resolution of symptoms. The patient’s lack of seroconversion and prolonged course illustrate the importance of humoral immunity in resolving SARS-CoV-2 infection. This case highlights challenges in managing immunocompromised hosts, who may act as persistent shedders and sources of transmission.
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Affiliation(s)
- Ji Hoon Baang
- Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Christopher Smith
- Division of Hospital Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew L Valesano
- Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - David M Manthei
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A Bachman
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael Adams
- Division of Hospital Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Laraine Washer
- Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Emily T Martin
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Adam S Lauring
- Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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Lord JS, Bonsall MB. The evolutionary dynamics of viruses: virion release strategies, time delays and fitness minima. Virus Evol 2021; 7:veab039. [PMID: 34221452 PMCID: PMC8242231 DOI: 10.1093/ve/veab039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Viruses exhibit a diverse array of strategies for infecting host cells and for virion release after replication. Cell exit strategies generally involve either budding from the cell membrane or killing the host cell. The conditions under which either is at a selective advantage is a key question in the evolutionary theory of viruses, with the outcome having potentially important impacts on the course of infection and pathogenicity. Although a plethora of external factors will influence the fitness of either strategy; here, we focus just on the effects of the physical properties of the system. We develop theoretical approaches to assess the effects of the time delays between initial infection and virion release. We show that the length of the delay before apoptosis is an important trait in virus evolutionary dynamics. Our results show that for a fixed time to apoptosis, intermediate delays lead to virus fitness that is lower than short times to apoptosis - leading to an apoptotic strategy - and long times to apoptosis - leading to a budding strategy at the between-cell level. At fitness minima, selection is expected to be disruptive and the potential for adaptive radiation in virus strategies is feasible. Hence, the physical properties of the system are sufficient to explain the existence of both budding and virus-induced apoptosis. The fitness functions presented here provide a formal basis for further work focusing on the evolutionary implications of trade-offs between time delays, intracellular replication and resulting mutation rates.
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Affiliation(s)
- Jennifer S Lord
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Michael B Bonsall
- Mathematical Ecology Research Group, Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
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42
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Singh N, Tandukar S, Zibari G, Naseer MS, Amiri HS, Samaniego-Picota MD. Successful simultaneous pancreas and kidney transplant in a patient post-COVID-19 infection. Kidney Int 2020; 98:1615-1616. [PMID: 32946881 PMCID: PMC7491417 DOI: 10.1016/j.kint.2020.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 09/03/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Neeraj Singh
- John C. McDonald Regional Transplant Center, Willis-Knighton Health System, Shreveport, Louisiana, USA.
| | - Srijan Tandukar
- John C. McDonald Regional Transplant Center, Willis-Knighton Health System, Shreveport, Louisiana, USA
| | - Gazi Zibari
- John C. McDonald Regional Transplant Center, Willis-Knighton Health System, Shreveport, Louisiana, USA
| | - Muhammad Saad Naseer
- John C. McDonald Regional Transplant Center, Willis-Knighton Health System, Shreveport, Louisiana, USA
| | - Hosein S Amiri
- John C. McDonald Regional Transplant Center, Willis-Knighton Health System, Shreveport, Louisiana, USA
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43
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Simmonds P, Cuypers L, Irving WL, McLauchlan J, Cooke GS, Barnes E, Ansari MA. Impact of virus subtype and host IFNL4 genotype on large-scale RNA structure formation in the genome of hepatitis C virus. RNA (NEW YORK, N.Y.) 2020; 26:1541-1556. [PMID: 32747607 PMCID: PMC7566573 DOI: 10.1261/rna.075465.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/29/2020] [Indexed: 05/03/2023]
Abstract
Mechanisms underlying the ability of hepatitis C virus (HCV) to establish persistent infections and induce progressive liver disease remain poorly understood. HCV is one of several positive-stranded RNA viruses capable of establishing persistence in their immunocompetent vertebrate hosts, an attribute previously associated with formation of large-scale RNA structure in their genomic RNA. We developed novel methods to analyze and visualize genome-scale ordered RNA structure (GORS) predicted from the increasingly large data sets of complete genome sequences of HCV. Structurally conserved RNA secondary structure in coding regions of HCV localized exclusively to polyprotein ends (core, NS5B). Coding regions elsewhere were also intensely structured based on elevated minimum folding energy difference (MFED) values, but the actual stem-loop elements involved in genome folding were structurally poorly conserved, even between subtypes 1a and 1b. Dynamic remodeling was further evident from comparison of HCV strains in different host genetic backgrounds. Significantly higher MFED values, greater suppression of UpA dinucleotide frequencies, and restricted diversification were found in subjects with the TT genotype of the rs12979860 SNP in the IFNL4 gene compared to the CC (nonexpressing) allele. These structural and compositional associations with expression of interferon-λ4 were recapitulated on a larger scale by higher MFED values and greater UpA suppression of genotype 1 compared to genotype 3a, associated with previously reported HCV genotype-associated differences in hepatic interferon-stimulated gene induction. Associations between innate cellular responses with HCV structure and further evolutionary constraints represent an important new element in RNA virus evolution and the adaptive interplay between virus and host.
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Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, OX1 3SY, Oxford, United Kingdom
| | - Lize Cuypers
- University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Research, BE 3000, Leuven, Belgium
| | - Will L Irving
- Faculty of Medicine and Health Sciences, University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham, NG7 2UH, United Kingdom
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, United Kingdom
| | | | - Ellie Barnes
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, OX1 3SY, Oxford, United Kingdom
| | - M Azim Ansari
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, OX1 3SY, Oxford, United Kingdom
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44
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Scott P. Long-Lived Skin-Resident Memory T Cells Contribute to Concomitant Immunity in Cutaneous Leishmaniasis. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a038059. [PMID: 32839202 DOI: 10.1101/cshperspect.a038059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Memory T cells, which protect against reinfection in many diseases, have predominantly been characterized in models of acute viral or bacterial infection. In contrast, memory T cells are less well understood in diseases where pathogens persist following disease resolution, such as leishmaniasis, in spite of the fact that these infections often lead to immunity to reinfection, termed concomitant immunity. Defining the T cells that mediate concomitant immunity is an important step in developing vaccines for these diseases. One set of protective T cells are short-lived effector T cells requiring constant stimulation, which would be difficult to maintain by vaccination. However, parasite-independent memory T cells, including central memory T cells (Tcm) and skin-resident T cells (Trm) have recently been described in leishmaniasis. Given their location, Trm cells are particularly suited for protection, and were found to globally seed the skin following Leishmania infection or immunization. Upon challenge, Trm cells rapidly respond to reduce the parasite burden, suggesting that developing strategies to generate parasite-independent Trm cells will be an important step in the quest for a successful leishmaniasis vaccine.
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Affiliation(s)
- Phillip Scott
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-4539, USA
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45
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Ziegler CM, Botten JW. Defective Interfering Particles of Negative-Strand RNA Viruses. Trends Microbiol 2020; 28:554-565. [PMID: 32544442 PMCID: PMC7298151 DOI: 10.1016/j.tim.2020.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/27/2020] [Accepted: 02/25/2020] [Indexed: 12/14/2022]
Abstract
Viral defective interfering particles (DIPs) were intensely studied several decades ago but research waned leaving open many critical questions. New technologies and other advances led to a resurgence in DIP studies for negative-strand RNA viruses. While DIPs have long been recognized, their exact contribution to the outcome of acute or persistent viral infections has remained elusive. Recent studies have identified defective viral genomes (DVGs) in human infections, including respiratory syncytial virus and influenza, and growing evidence indicates that DVGs influence disease severity and may contribute to viral persistence. Further, several studies have advanced our understanding of key viral and host factors that regulate DIP formation and activity. Here we review these discoveries and highlight key questions moving forward.
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Affiliation(s)
- Christopher M Ziegler
- Department of Medicine, Division of Immunobiology, University of Vermont, Burlington, VT 05405, USA
| | - Jason W Botten
- Department of Medicine, Division of Immunobiology, University of Vermont, Burlington, VT 05405, USA; Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; Vaccine Testing Center, University of Vermont, Burlington, VT 05405, USA.
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46
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Alpalhão M, Ferreira JA, Filipe P. Persistent SARS-CoV-2 infection and the risk for cancer. Med Hypotheses 2020; 143:109882. [PMID: 32485314 PMCID: PMC7831646 DOI: 10.1016/j.mehy.2020.109882] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/25/2020] [Indexed: 11/28/2022]
Abstract
The current SARS-CoV-2 has put significant strain on healthcare services worldwide due to acute COVID-19. However, the potential long-term effects of this infection haven’t been extensively discussed. We hypothesize that SARS-CoV-2 may be able to cause persistent infection in some individuals, and should this be the case, that in a few years we may see a rise in cancer incidence due to carcinogenic effects of this coronavirus. Non-retroviral RNA viruses such as Coronaviridae have been shown to cause persistent infection in hosts. Empirical evidence of viral genomic material shedding weeks after apparent clinical and laboratorial resolution of COVID-19 may be an indirect proof for persistent viral infection. Furthermore, tropism towards certain immune-privileged territories may facilitate immune evasion by this virus. Structural homology with SARS-CoV-1 indicates that SARS-CoV-2 may be able to directly impair pRb and p53, which are key gatekeepers with tumor suppressor functions. Additionally, COVID-19 features preeminent inflammatory response with marked oxidative stress, which acts as both as initiator and promotor of carcinogenesis. Should there be a carcinogenic risk associated with SARS-CoV-2, the implications for public health are plenty, as infected patients should be closely watched during long periods of follow-up. Additional investigation to establish or exclude the possibility for persistent infection is paramount to identify and prevent possible complications in the future.
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Affiliation(s)
- Miguel Alpalhão
- Dermatology Department, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte EPE, Lisbon, Portugal; Dermatology Universitary Clinic, Faculty of Medicine, University of Lisbon, Lisbon, Portugal; Dermatology Research Unit, iMM João Lobo Antunes, University of Lisbon, Lisbon, Portugal.
| | - João Augusto Ferreira
- Dermatology Universitary Clinic, Faculty of Medicine, University of Lisbon, Lisbon, Portugal; Dermatology Research Unit, iMM João Lobo Antunes, University of Lisbon, Lisbon, Portugal
| | - Paulo Filipe
- Dermatology Department, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte EPE, Lisbon, Portugal; Dermatology Universitary Clinic, Faculty of Medicine, University of Lisbon, Lisbon, Portugal; Dermatology Research Unit, iMM João Lobo Antunes, University of Lisbon, Lisbon, Portugal
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47
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The UPR sensor IRE1α and the adenovirus E3-19K glycoprotein sustain persistent and lytic infections. Nat Commun 2020; 11:1997. [PMID: 32332742 PMCID: PMC7181865 DOI: 10.1038/s41467-020-15844-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/30/2020] [Indexed: 12/16/2022] Open
Abstract
Persistent viruses cause chronic disease, and threaten the lives of immunosuppressed individuals. Here, we elucidate a mechanism supporting the persistence of human adenovirus (AdV), a virus that can kill immunosuppressed patients. Cell biological analyses, genetics and chemical interference demonstrate that one of five AdV membrane proteins, the E3-19K glycoprotein specifically triggers the unfolded protein response (UPR) sensor IRE1α in the endoplasmic reticulum (ER), but not other UPR sensors, such as protein kinase R-like ER kinase (PERK) and activating transcription factor 6 (ATF6). The E3-19K lumenal domain activates the IRE1α nuclease, which initiates mRNA splicing of X-box binding protein-1 (XBP1). XBP1s binds to the viral E1A-enhancer/promoter sequence, and boosts E1A transcription, E3-19K levels and lytic infection. Inhibition of IRE1α nuclease interrupts the five components feedforward loop, E1A, E3-19K, IRE1α, XBP1s, E1A enhancer/promoter. This loop sustains persistent infection in the presence of the immune activator interferon, and lytic infection in the absence of interferon. Adenovirus (AdV) can cause persistent infections, but underlying mechanisms are poorly understood. Here, Prasad et al. show that the AdV glycoprotein E3-19K activates the unfolded protein response sensor IRE1α, and that this triggers a feedforward loop that sustains persistent infection in the presence of interferon.
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48
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Wei KC, Wei WJ, Liu YS, Yen LC, Chang TH. Assessment of Prolonged Dengue Virus Infection in Dermal Fibroblasts and Hair-Follicle Dermal Papilla Cells. Viruses 2020; 12:v12030267. [PMID: 32121148 PMCID: PMC7150742 DOI: 10.3390/v12030267] [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] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/19/2020] [Accepted: 02/26/2020] [Indexed: 11/16/2022] Open
Abstract
Dengue virus (DENV)-mediated hair loss is one of the post-dengue fatigue syndromes and its pathophysiology remains unknown. Whether long-term or persistent infection with DENV in the scalp results in hair loss is unclear. In this study, we cultured human dermal fibroblasts (WS1 cells) and primary human hair-follicle dermal papilla cells (HFDPCs) in the long term with DENV-2 infection. The production of virion, the expression of inflammatory and anti-virus genes, and their signaling transduction activity in the infected cells were analyzed. DENV-2 NS3 protein and DENV-2 5′ UTR RNA were detected in fibroblasts and HFDPCs that were subjected to long-term infection with DENV-2 for 33 days. A significant amount of DENV-2 virion was produced by both WS1 cells and HFDPCs in the first two days of acute infection. The virion was also detected in WS1 cells that were infected in the long term, but HFDPCs failed to produce DENV-2 after long-term culture. Type I and type III interferons, and inflammatory cytokines were highly expressed in the acute phase of DENV infection in HFPDC and WS1 cells. However, in the long-term cultured cells, modest levels of anti-viral protein genes were expressed and we observed reduced signaling activity, which was correlated with the level of virus production changes. Long-term infection of DENV-2 downregulated the expression of hair growth regulatory factors, such as Rip1, Wnt1, and Wnt4. This in vitro study shows that the long-term infection with DENV-2 in dermal fibroblasts and dermal papilla cells may be involved with the prolonged-DENV-infection-mediated hair loss of post-dengue fatigue syndrome. However, direct evidence for viral replication in the human hair of a dengue victim or animal infection model is required.
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Affiliation(s)
- Kai-Che Wei
- Department of Dermatology, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan; (K.-C.W.); (W.-J.W.)
- Faculty of Yuh-Ing Junior College of Health Care and Management, Kaohsiung 80776, Taiwan
- National Yang Ming University, Taipei 11211, Taiwan
| | - Wan-Ju Wei
- Department of Dermatology, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan; (K.-C.W.); (W.-J.W.)
| | - Yi-Shan Liu
- Department of Dermatology, E-Da Hospital, I-Shou University, Kaohsiung 84001, Taiwan;
- Graduate Institute of Science Education and Environmental Education, National Kaohsiung Normal University, Kaohsiung 82446, Taiwan
| | - Li-Chen Yen
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei 11490, Taiwan;
| | - Tsung-Hsien Chang
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei 11490, Taiwan;
- Correspondence:
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Persistent Infection and Transmission of Senecavirus A from Carrier Sows to Contact Piglets. J Virol 2019; 93:JVI.00819-19. [PMID: 31434730 DOI: 10.1128/jvi.00819-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/22/2019] [Indexed: 01/14/2023] Open
Abstract
Senecavirus A (SVA) is a picornavirus that causes acute vesicular disease (VD), that is clinically indistinguishable from foot-and-mouth disease (FMD), in pigs. Notably, SVA RNA has been detected in lymphoid tissues of infected animals several weeks following resolution of the clinical disease, suggesting that the virus may persist in select host tissues. Here, we investigated the occurrence of persistent SVA infection and the contribution of stressors (transportation, immunosuppression, or parturition) to acute disease and recrudescence from persistent SVA infection. Our results show that transportation stress leads to a slight increase in disease severity following infection. During persistence, transportation, immunosuppression, and parturition stressors did not lead to overt/recrudescent clinical disease, but intermittent viremia and virus shedding were detected up to day 60 postinfection (p.i.) in all treatment groups following stress stimulation. Notably, real-time PCR and in situ hybridization (ISH) assays confirmed that the tonsil harbors SVA RNA during the persistent phase of infection. Immunofluorescence assays (IFA) specific for double-stranded RNA (dsRNA) demonstrated the presence of double-stranded viral RNA in tonsillar cells. Most importantly, infectious SVA was isolated from the tonsil of two animals on day 60 p.i., confirming the occurrence of carrier animals following SVA infection. These findings were supported by the fact that contact piglets (11/44) born to persistently infected sows were infected by SVA, demonstrating successful transmission of the virus from carrier sows to contact piglets. Results here confirm the establishment of persistent infection by SVA and demonstrate successful transmission of the virus from persistently infected animals.IMPORTANCE Persistent viral infections have significant implications for disease control strategies. Previous studies demonstrated the persistence of SVA RNA in the tonsil of experimentally or naturally infected animals long after resolution of the clinical disease. Here, we showed that SVA establishes persistent infection in SVA-infected animals, with the tonsil serving as one of the sites of virus persistence. Importantly, persistently infected carrier animals shedding SVA in oral and nasal secretions or feces can serve as sources of infection to other susceptible animals, as evidenced by successful transmission of SVA from persistently infected sows to contact piglets. These findings unveil an important aspect of SVA infection biology, suggesting that persistently infected pigs may function as reservoirs for SVA.
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50
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Liu J, Swevers L, Kolliopoulou A, Smagghe G. Arboviruses and the Challenge to Establish Systemic and Persistent Infections in Competent Mosquito Vectors: The Interaction With the RNAi Mechanism. Front Physiol 2019; 10:890. [PMID: 31354527 PMCID: PMC6638189 DOI: 10.3389/fphys.2019.00890] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/27/2019] [Indexed: 12/15/2022] Open
Abstract
Arboviruses are capable to establish long-term persistent infections in mosquitoes that do not affect significantly the physiology of the insect vectors. Arbovirus infections are controlled by the RNAi machinery via the production of viral siRNAs and the formation of RISC complexes targeting viral genomes and mRNAs. Engineered arboviruses that contain cellular gene sequences can therefore be transformed to "viral silencing vectors" for studies of gene function in reverse genetics approaches. More specifically, "ideal" viral silencing vectors must be competent to induce robust RNAi effects while other interactions with the host immune system should be kept at a minimum to reduce non-specific effects. Because of their inconspicuous nature, arboviruses may approach the "ideal" viral silencing vectors in insects and it is therefore worthwhile to study the mechanisms by which the interactions with the RNAi machinery occur. In this review, an analysis is presented of the antiviral RNAi response in mosquito vectors with respect to the major types of arboviruses (alphaviruses, flaviviruses, bunyaviruses, and others). With respect to antiviral defense, the exo-RNAi pathway constitutes the major mechanism while the contribution of both miRNAs and viral piRNAs remains a contentious issue. However, additional mechanisms exist in mosquitoes that are capable to enhance or restrict the efficiency of viral silencing vectors such as the amplification of RNAi effects by DNA forms, the existence of incorporated viral elements in the genome and the induction of a non-specific systemic response by Dicer-2. Of significance is the observation that no major "viral suppressors of RNAi" (VSRs) seem to be encoded by arboviral genomes, indicating that relatively tight control of the activity of the RNA-dependent RNA polymerase (RdRp) may be sufficient to maintain the persistent character of arbovirus infections. Major strategies for improvement of viral silencing vectors therefore are proposed to involve engineering of VSRs and modifying of the properties of the RdRp. Because of safety issues (pathogen status), however, arbovirus-based silencing vectors are not well suited for practical applications, such as RNAi-based mosquito control. In that case, related mosquito-specific viruses that also establish persistent infections and may cause similar RNAi responses may represent a valuable alternative solution.
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Affiliation(s)
- Jisheng Liu
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Luc Swevers
- Institute of Biosciences and Applications, National Centre of Scientific Research “Demokritos”, Athens, Greece
| | - Anna Kolliopoulou
- Institute of Biosciences and Applications, National Centre of Scientific Research “Demokritos”, Athens, Greece
| | - Guy Smagghe
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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