#Systems analysis of #subjects acutely infected with the #Chikungunya virus (PLoS Pathog., abstract)

[Source: PLoS Pathogens, full page: (LINK). Abstract, edited.]

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

Systems analysis of subjects acutely infected with the Chikungunya virus

Alessandra Soares-Schanoski, Natália Baptista Cruz, Luíza Antunes de Castro-Jorge, Renan Villanova Homem de Carvalho, Cliomar Alves dos Santos, Nancy da Rós, Úrsula Oliveira, Danuza Duarte Costa, Cecília Luíza Simões dos Santos, Marielton dos Passos Cunha, Maria Leonor Sarno Oliveira, Juliana Cardoso Alves, Regina Adalva de Lucena Couto Océa,  [ … ], Helder I. Nakaya

Published: June 18, 2019 / DOI: https://doi.org/10.1371/journal.ppat.1007880 / This is an uncorrected proof.

 

Abstract

The largest ever recorded epidemic of the Chikungunya virus (CHIKV) broke out in 2004 and affected four continents. Acute symptomatic infections are typically associated with the onset of fever and often debilitating polyarthralgia/polyarthritis. In this study, a systems biology approach was adopted to analyze the blood transcriptomes of adults acutely infected with the CHIKV. Gene signatures that were associated with viral RNA levels and the onset of symptoms were identified. Among these genes, the putative role of the Eukaryotic Initiation Factor (eIF) family genes and apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC3A) in the CHIKV replication process were displayed. We further compared these signatures with signatures induced by the Dengue virus infection and rheumatoid arthritis. Finally, we demonstrated that the CHIKV in vitro infection of murine bone marrow-derived macrophages induced IL-1 beta production in a mechanism that is significantly dependent on the inflammasome NLRP3 activation. The observations provided valuable insights into virus-host interactions during the acute phase and can be instrumental in the investigation of new and effective therapeutic interventions.

 

Author summary

The Chikungunya virus (CHIKV) has infected millions of people worldwide and presents a serious public health issue. Acute symptomatic infections caused by contracting this mosquito-transmitted arbovirus are typically associated with an abrupt onset of fever and often debilitating polyarthralgia/ polyarthritis, as well as prolonged periods of disability in some patients. These dramatic effects call for a careful evaluation of the molecular mechanisms involved in this puzzling infection. By analyzing the blood transcriptome of adults acutely infected with CHIKV, we were able to provide a detailed picture of the early molecular events induced by the infection. Additionally, the systems biology approach revealed genes that can be investigated extensively as probable therapeutic targets for the disease.

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Citation: Soares-Schanoski A, Baptista Cruz N, de Castro-Jorge LA, de Carvalho RVH, Santos CAd, Rós Nd, et al. (2019) Systems analysis of subjects acutely infected with the Chikungunya virus. PLoS Pathog 15(6): e1007880. https://doi.org/10.1371/journal.ppat.1007880

Editor: David H. O’Connor, University of Wisconsin, UNITED STATES

Received: February 1, 2019; Accepted: May 30, 2019; Published: June 18, 2019

Copyright: © 2019 Soares-Schanoski et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All RNA-seq raw data is available at the NCBI in BioProject: PRJNA507472 and the BioSample Range from SAMN10847030 to SAMN10847088

Funding: H.I.N. is supported by the São Paulo Research Foundation (FAPESP; grants 2017/50137-3, 2012/19278-6, and 2013/08216-2). A.S.S. is supported by Butantan Foundation, CNPq (Grant 443371/2016-4) and Brazilian Health Ministry. R.A. is supported by FINEP Grant 0116005600. D.R.R. has a postdoctoral fellowship from CNPq. J.C.A. has a postdoctoral fellowship from CAPES – Finance Code 001. M.P.C. has a PhD fellowship from FAPESP – 2016/08204-2. I.J.A is supported by São Paulo Research Foundation (FAPESP; grant: CEPID 2013/07467-1). P.L.H is supported by Butantan Foundation, CNPq 306992/2014-0 and Fapesp 2015/25055-8. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Chikungunya fever, Viral pathogenesis.

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SNX11 Identified as an Essential #Host Factor for #SFTS Virus #Infection by #CRISPR Knockout Screening (Virol Sin., abstract)

[Source: Virologica Sinica, full page: (LINK). Abstract, edited.]

SNX11 Identified as an Essential Host Factor for SFTS Virus Infection by CRISPR Knockout Screening

Authors: Tiezhu Liu, Jiajia Li, Yang Liu, Yuanyuan Qu, Aqian Li, Chuan Li, Quanfu Zhang,Wei Wu, Jiandong Li, Yan Liu, Dexin Li, Shiwen Wang, Mifang Liang

Research Article / First Online: 18 June 2019

 

Abstract

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a highly pathogenic tick-borne bunyavirus that causes lethal infectious disease and severe fever with thrombocytopenia syndrome (SFTS) in humans. The molecular mechanisms and host cellular factors required for SFTSV infection remain uncharacterized. Using a genome-wide CRISPR-based screening strategy, we identified a host cellular protein, sorting nexin 11 (SNX11) which is involved in the intracellular endosomal trafficking pathway, as an essential cell factor for SFTSV infection. An SNX11-KO HeLa cell line was established, and SFTSV replication was significantly reduced. The glycoproteins of SFTSV were detected and remained in later endosomal compartments but were not detectable in the endoplasmic reticulum (ER) or Golgi apparatus. pH values in the endosomal compartments of the SNX11-KO cells increased compared with the pH of normal HeLa cells, and lysosomal-associated membrane protein 1 (LAMP1) expression was significantly elevated in the SNX11-KO cells. Overall, these results indicated that penetration of SFTSV from the endolysosomes into the cytoplasm of host cells was blocked in the cells lacking SNX11. Our study for the first time provides insight into the important role of the SNX11 as an essential host factor in the intracellular trafficking and penetrating process of SFTSV infection via potential regulation of viral protein sorting, membrane fusion, and other endocytic machinery.

Keywords: CRISPR – screen – Severe fever with thrombocytopenia syndrome virus (SFTSV) – Host factor – Sorting nexin 11 (SNX11)

Electronic supplementary material

The online version of this article ( https://doi.org/10.1007/s12250-019-00141-0) contains supplementary material, which is available to authorized users.

 

Notes

Acknowledgements

This work was supported by the National Key Project for Infectious Disease from the Ministry of Science and Technology (Grant No. 2018ZX10711-001).

Author Contributions

TL performed the experiments and wrote the paper; Jiajia Li, YL, and YQ performed the experiments; AL, QZ, CL, WW, YL, and Jiandong Li contributed reagents/materials/analysis tools. Jiajia Li, TL, ML, YL, Jiandong Li, and DL analyzed and discussed the data. ML and SW designed the project and edited the manuscript. All authors read and approved the final manuscript.

 

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Animal and Human Rights Statement

This article does not contain any studies with human or animal subjects performed by any of the authors.

Keywords: SFTS virus; Bunyavirus; CRISPR; Viral pathogenesis.

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Low #Polymerase #Activity Attributed to PA Drives the Acquisition of the #PB2 E627K #Mutation of #H7N9 #Avian #Influenza Virus in Mammals (mBio, abstract)

[Source: mBio, full page: (LINK). Abstract, edited.]

Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals

Libin Liang, Li Jiang, Junping Li, Qingqing Zhao, Jinguang Wang, Xijun He, Shanyu Huang, Qian Wang, Yuhui Zhao, Guangwen Wang, Nan Sun, Guohua Deng, Jianzhong Shi, Guobin Tian,Xianying Zeng, Yongping Jiang, Liling Liu, Jinxiong Liu, Pucheng Chen, Zhigao Bu, Yoshihiro Kawaoka, Hualan Chen, Chengjun Li

Terence S. Dermody, Editor

DOI: 10.1128/mBio.01162-19

 

ABSTRACT

Avian influenza viruses (AIVs) must acquire mammalian-adaptive mutations before they can efficiently replicate in and transmit among humans. The PB2 E627K mutation is known to play a prominent role in the mammalian adaptation of AIVs. The H7N9 AIVs that emerged in 2013 in China easily acquired the PB2 E627K mutation upon replication in humans. Here, we generate a series of reassortant or mutant H7N9 AIVs and test them in mice. We show that the low polymerase activity attributed to the viral PA protein is the intrinsic driving force behind the emergence of PB2 E627K during H7N9 AIV replication in mice. Four residues in the N-terminal region of PA are critical in mediating the PB2 E627K acquisition. Notably, due to the identity of viral PA protein, the polymerase activity and growth of H7N9 AIV are highly sensitive to changes in expression levels of human ANP32A protein. Furthermore, the impaired viral polymerase activity of H7N9 AIV caused by the depletion of ANP32A led to reduced virus replication in Anp32a−/− mice, abolishing the acquisition of the PB2 E627K mutation and instead driving the virus to acquire the alternative PB2 D701N mutation. Taken together, our findings show that the emergence of the PB2 E627K mutation of H7N9 AIV is driven by the intrinsic low polymerase activity conferred by the viral PA protein, which also involves the engagement of mammalian ANP32A.

 

IMPORTANCE

The emergence of the PB2 E627K substitution is critical in the mammalian adaptation and pathogenesis of AIV. H7N9 AIVs that emerged in 2013 possess a prominent ability in gaining the PB2 E627K mutation in humans. Here, we demonstrate that the acquisition of the H7N9 PB2 E627K mutation is driven by the low polymerase activity conferred by the viral PA protein in human cells, and four PA residues are collectively involved in this process. Notably, the H7N9 PA protein leads to significant dependence of viral polymerase function on human ANP32A protein, and Anp32a knockout abolishes PB2 E627K acquisition in mice. These findings reveal that viral PA and host ANP32A are crucial for the emergence of PB2 E627K during adaptation of H7N9 AIVs to humans.

Keywords: Avian Influenza; H7N9; Viral pathogenesis.

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PD1+CCR2+CD8+ T Cells Infiltrate the #CNS during Acute #JEV #Infection (Virol Sin., abstract)

[Source: Virologica Sinica, full page: (LINK). Abstract, edited.]

PD1+CCR2+CD8+ T Cells Infiltrate the Central Nervous System during Acute Japanese Encephalitis Virus Infection

Authors: Fang Zhang, Linlin Qi, Tong Li, Xiaojing Li, Dan Yang, Shengbo Cao, Jing Ye, Bin Wei

Research Article / First Online: 18 June 2019

 

Abstract

Japanese encephalitis (JE) is a viral encephalitis disease caused by Japanese encephalitis virus (JEV) infection. Uncontrolled inflammatory responses in the central nervous system (CNS) are a hallmark of severe JE. Although the CCR2–CCL2 axis is important for monocytes trafficking during JEV infection, little is known about its role in CNS trafficking of CD8+ T cells. Here, we characterized a mouse model of JEV infection, induced via intravenous injection (i.v.) and delineated the chemokines and infiltrating peripheral immune cells in the brains of infected mice. The CNS expression of chemokines, Ccl2, Ccl3, and Ccl5, and their receptors, Ccr2 or Ccr5, was significantly up-regulated after JEV infection and was associated with the degree of JE pathogenesis. Moreover, JEV infection resulted in the migration of a large number of CD8+T cells into the CNS. In the brains of JEV-infected mice, infiltrating CD8+ T cells expressed CCR2 and CCR5 and were found to comprise mainly effector T cells (CD44+CD62L−). JEV infection dramatically enhanced the expression of programmed death 1 (PD-1) on infiltrating CD8+ T cells in the brain, as compared to that on peripheral CD8+ T cells in the spleen. This effect was more pronounced on infiltrating CCR2+CD8+ T cells than on CCR2−CD8+ T cells. In conclusion, we identified a new subset of CD8+ T cells (PD1+CCR2+CD8+ T cells) present in the CNS of mice during acute JEV infection. These CD8+ T cells might play a role in JE pathogenesis.

Keywords: Japanese encephalitis virus (JEV) – CD8+ T cell – CCL2 – CCR2 – PD-1

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Fang Zhang and Linlin Qi have contributed equally to this work.

Electronic supplementary material

The online version of this article ( https://doi.org/10.1007/s12250-019-00134-z) contains supplementary material, which is available to authorized users.

 

Notes

Acknowledgements

This work was supported by grants from the Key Research and Development Program of the Ministry of Science and Technology of China (2016YFD500407), Precision Medicine program of Ministry of Science and Technology of China (2016YFC0905902), and the National Natural Science Foundation of China (81630043, 81571552). We thank the Core Facility and Technical Support in the Wuhan Investigate of Virology. We are grateful to Ding Gao and Juan Min for technical support for flow cytometry and mass cytometry, as well as Xuefang An and Fan Zhang for valuable assistance in the animal studies.

Author Contributions

BW and JY conceptualized and designed the study. LLQ, TL and FZ performed the experiments in this study, and analyzed the data. SBC and JY contributed virus strain and virus infection techniques to this study. DY and XJL participated in part of experimental work. FZ wrote the manuscript. All authors read and approved the final manuscript.

 

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Animal and Human Rights Statement

The study was approved by the Animal Ethics Committee of Wuhan Institute of Virology. All institutional and national guidelines for the care and use of laboratory animals were followed.

Keywords: Japanese encephalitis; Viral pathogenesis; Animal models.

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Therapeutic efficacy of #favipiravir against #Bourbon virus in mice (PLoS One, abstract)

[Source: PLoS One, full page: (LINK). Abstract, edited.]

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

Therapeutic efficacy of favipiravir against Bourbon virus in mice

Traci L. Bricker, Md. Shafiuddin, Anshu P. Gounder, Andrew B. Janowski, Guoyan Zhao, Graham D. Williams, Brett W. Jagger, Michael S. Diamond, Thomas Bailey, Jennie H. Kwon, David Wang, Adrianus C. M. Boon

Published: June 13, 2019 / DOI: https://doi.org/10.1371/journal.ppat.1007790

 

Abstract

Bourbon virus (BRBV) is an emerging tick-borne RNA virus in the orthomyxoviridae family that was discovered in 2014. Although fatal human cases of BRBV have been described, little is known about its pathogenesis, and no antiviral therapies or vaccines exist. We obtained serum from a fatal case in 2017 and successfully recovered the second human infectious isolate of BRBV. Next-generation sequencing of the St. Louis isolate of BRBV (BRBV-STL) showed >99% nucleotide identity to the original reference isolate. Using BRBV-STL, we developed a small animal model to study BRBV-STL tropism in vivo and evaluated the prophylactic and therapeutic efficacy of the experimental antiviral drug favipiravir against BRBV-induced disease. Infection of Ifnar1-/- mice lacking the type I interferon receptor, but not congenic wild-type animals, resulted in uniformly fatal disease 6 to 10 days after infection. RNA in situ hybridization and viral yield assays demonstrated a broad tropism of BRBV-STL with highest levels detected in liver and spleen. In vitro replication and polymerase activity of BRBV-STL were inhibited by favipiravir. Moreover, administration of favipiravir as a prophylaxis or as post-exposure therapy three days after infection prevented BRBV-STL-induced mortality in immunocompromised Ifnar1-/- mice. These results suggest that favipiravir may be a candidate treatment for humans who become infected with BRBV.

 

Author summary

Bourbon virus (BRBV) is a novel tick-borne RNA virus that can cause fatal disease in humans. No approved antiviral treatment is available. We have cultured the second human isolate of BRBV and with it developed a small animal disease model. In this mouse model, BRBV causes severe disease as measured by weight loss after infection and uniform death 6 to 10 days after infection. Virus replication occurred predominantly in the spleen and the liver of the infected animals, with additional organs infected at later time points after infection. This disease model was used to test the efficacy of favipiravir, a viral RNA polymerase inhibitor that was developed for the related Influenza A virus. Prophylactic and therapeutic treatment with favipiravir resulted in complete protection from a lethal BRBV infection. These data suggest that favipiravir and perhaps other RNA polymerase inhibitors could be used to treat BRBV infections in humans.

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Citation: Bricker TL, Shafiuddin M, Gounder AP, Janowski AB, Zhao G, Williams GD, et al. (2019) Therapeutic efficacy of favipiravir against Bourbon virus in mice. PLoS Pathog 15(6): e1007790. https://doi.org/10.1371/journal.ppat.1007790

Editor: Sonja Best, National Institute of Allergy and Infectious Diseases, UNITED STATES

Received: February 6, 2019; Accepted: April 26, 2019; Published: June 13, 2019

Copyright: © 2019 Bricker et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: The genome sequence of Bourbon virus: All sequence files are available from the GenBank database (accession number(s) MK453524-MK453529). All other relevant data are within the manuscript and its supporting information files.

Funding: The work was in part funded by R01-AI118938, and R21-AI137450 and the Children’s Discovery Institute grant PD-II-2018-702. APG and GDW were supported by the Infectious Disease Training Grant (T32 AI007172). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Bourbon virus; Viral pathogenesis; Antivirals; Favipiravir; Animal models.

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#Influenza virus with increased #pH of #HA activation has improved replication in cell culture but at the cost of #infectivity in human #airway #epithelium (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

Influenza virus with increased pH of HA activation has improved replication in cell culture but at the cost of infectivity in human airway epithelium

Anika Singanayagam, Maria Zambon, Wendy Barclay

DOI: 10.1128/JVI.00058-19

 

ABSTRACT

Pandemic H1N1 (pH1N1) influenza virus emerged from swine in 2009 with adequate capability to infect and transmit between people. In subsequent years it has circulated as a seasonal virus and evolved further human-adapting mutations. Mutations in the haemagglutinin (HA) stalk that increase pH stability have been associated with human adaptation and airborne transmission of pH1N1 virus. Yet, our understanding of how pH stability impacts virus/host interactions is incomplete. Here, using recombinant viruses with point mutations that alter the pH stability of pH1N1 HA, we found distinct effects on virus phenotypes in different experimental models. Increased pH sensitivity enabled virus to uncoat in endosomes more efficiently, manifesting as increased replication rate in typical continuous cell cultures under single-cycle conditions. A more acid labile HA also conferred a small reduction in sensitivity to antiviral therapeutics that act at the pH-sensitive HA fusion step. Conversely, in primary human airway epithelium cultured at air-liquid interface, increased pH sensitivity attenuated multicycle viral replication, by compromising virus survival in the extracellular microenvironment. In a mouse model of influenza pathogenicity, there was an optimum HA activation pH and viruses with either more or less pH stable HA were less virulent. Opposing pressures inside and outside the host cell that determine pH stability may influence zoonotic potential. The distinct effects that changes in pH stability exert on viral phenotypes underscore the importance of using the most appropriate systems for assessing virus titre and fitness, which has implications for vaccine manufacture, antiviral drug development and pandemic risk assessment.

 

Importance

The pH stability of the haemagglutinin surface protein varies between different influenza strains and subtypes and can affect the virus’ ability to replicate and transmit. Here, we demonstrate a delicate balance the virus strikes within and without the target cell. We show that a pH-stable haemagglutinin enables a human influenza virus to replicate more effectively in human airway cells and mouse lungs by facilitating virus survival in the extracellular environment of the upper respiratory tract. Conversely after entering target cells, being more pH-stable confers relative disadvantage, resulting in less efficient delivery of the viral genome to the host cell nucleus. Since the balance we describe will be affected differently in different host environments, it may restrict virus’ ability to cross species. In addition, our findings imply that different influenza viruses may show variation in how well they are controlled by antiviral strategies targeting pH-dependent steps in the virus replication cycle.

Copyright © 2019 Singanayagam et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

Keywords: Influenza A; Pandemic Influenza; H1N1pdm09; Viral pathogenesis.

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Essential Role of #Interferon Response in Containing #Human #Pathogenic #Bourbon Virus (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 25, Number 7—July 2019 / Research

Essential Role of Interferon Response in Containing Human Pathogenic Bourbon Virus

Jonas Fuchs, Tobias Straub, Maximilian Seidl, and Georg Kochs

Author affiliations: University of Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany

 

Abstract

Bourbon virus (BRBV) is a recently discovered tick-transmitted viral pathogen that is prevalent in the Midwest and southern United States. Since 2014, zoonotic BRBV infections have been verified in several human cases of severe febrile illness, occasionally with fatal outcomes, indicating a possible public health threat. We analyzed the pathology of BRBV infection in mice and found a high sensitivity of the virus to the host interferon system. Infected standard laboratory mice did not show clinical signs or virus replication. However, in mice carrying defects in the type I and type II interferon system, the virus grew to high titers and caused severe pathology. In cell culture, BRBV was blocked by antiviral agents like ribavirin and favipiravir (T705). Our data suggest that persons having severe BRBV infection might have a deficiency in their innate immunity and could benefit from an already approved antiviral treatment.

Keywords: Arbovirus; Bourbon virus; Tick-borne infections; Viral pathogenesis; Antivirals; Interferons; Ribavirin; Favipiravir.

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