1
|
Kaushik R, Kumar N, Yadav P, Sircar S, Shete-Aich A, Singh A, Tomar S, Launey T, Malik YS. Comprehensive Genomics Investigation of Neboviruses Reveals Distinct Codon Usage Patterns and Host Specificity. Microorganisms 2024; 12:696. [PMID: 38674640 PMCID: PMC11052288 DOI: 10.3390/microorganisms12040696] [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: 03/06/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Neboviruses (NeVs) from the Caliciviridae family have been linked to enteric diseases in bovines and have been detected worldwide. As viruses rely entirely on the cellular machinery of the host for replication, their ability to thrive in a specific host is greatly impacted by the specific codon usage preferences. Here, we systematically analyzed the codon usage bias in NeVs to explore the genetic and evolutionary patterns. Relative Synonymous Codon Usage and Effective Number of Codon analyses indicated a marginally lower codon usage bias in NeVs, predominantly influenced by the nucleotide compositional constraints. Nonetheless, NeVs showed a higher codon usage bias for codons containing G/C at the third codon position. The neutrality plot analysis revealed natural selection as the primary factor that shaped the codon usage bias in both the VP1 (82%) and VP2 (57%) genes of NeVs. Furthermore, the NeVs showed a highly comparable codon usage pattern to bovines, as reflected through Codon Adaptation Index and Relative Codon Deoptimization Index analyses. Notably, yak NeVs showed considerably different nucleotide compositional constraints and mutational pressure compared to bovine NeVs, which appear to be predominantly host-driven. This study sheds light on the genetic mechanism driving NeVs' adaptability, evolution, and fitness to their host species.
Collapse
Affiliation(s)
- Rahul Kaushik
- Biotechnology Research Center, Technology Innovation Institute, Masdar City, Abu Dhabi P.O. Box 9639, United Arab Emirates;
| | - Naveen Kumar
- Diagnostics and Vaccines Group, ICAR—National Institute of High Security Animal Diseases, Bhopal 462021, Madhya Pradesh, India;
| | - Pragya Yadav
- Maximum Containment Facility, ICMR—National Institute of Virology, Pune 411001, Maharashtra, India; (P.Y.); (A.S.-A.)
| | - Shubhankar Sircar
- Department of Animal Sciences, Washington State University, Pullman, WA 99163, USA;
| | - Anita Shete-Aich
- Maximum Containment Facility, ICMR—National Institute of Virology, Pune 411001, Maharashtra, India; (P.Y.); (A.S.-A.)
| | - Ankur Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India; (A.S.); (S.T.)
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India; (A.S.); (S.T.)
| | - Thomas Launey
- Biotechnology Research Center, Technology Innovation Institute, Masdar City, Abu Dhabi P.O. Box 9639, United Arab Emirates;
| | - Yashpal Singh Malik
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana 141004, Punjab, India
| |
Collapse
|
2
|
Negi G, Sharma A, Chaudhary M, Parveen N. Disruption Mechanisms of Enveloped Viruses by Ionic and Nonionic Surfactants. J Phys Chem B 2024; 128:768-780. [PMID: 38228291 DOI: 10.1021/acs.jpcb.3c05531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The world has witnessed multiple pandemics and endemics caused by enveloped viruses in the past century. To name a few, the ongoing COVID-19 pandemic and other pandemics/endemics caused by coronaviruses, influenza viruses, HIV-1, etc. The external and topical applications of surfactants have been effective in limiting the spread of viruses. While it is well-known that surfactants inactivate virus particles (virions), the mechanism of action of surfactants against enveloped virions has not yet been established. In this work, we have evaluated the surfactant-induced disruption mechanism of a cocktail of enveloped viruses containing particles of mumps, measles, and rubella viruses. We applied the total internal reflection fluorescence microscopy technique to trace the temporal changes in the fluorescence signal from single virions upon the addition of a surfactant solution. We report that surfactants solubilize either the viral lipid membrane, proteins, or both. Ionic surfactants, depending on their charge and interaction type with the viral lipids and proteins, can cause bursting or perforation of the viral envelope, whereas a nonionic surfactant can cause either symmetric expansion or perforation of the viral envelope depending on the surfactant concentration.
Collapse
Affiliation(s)
- Geetanjali Negi
- Department of Chemistry, Indian Institute of Technology Kanpur, 208016 Kanpur, India
| | - Anurag Sharma
- Department of Chemistry, Indian Institute of Technology Kanpur, 208016 Kanpur, India
| | - Monika Chaudhary
- Department of Chemistry, Indian Institute of Technology Kanpur, 208016 Kanpur, India
| | - Nagma Parveen
- Department of Chemistry, Indian Institute of Technology Kanpur, 208016 Kanpur, India
| |
Collapse
|
3
|
Stelfox AJ, Oguntuyo KY, Rissanen I, Harlos K, Rambo R, Lee B, Bowden TA. Crystal structure and solution state of the C-terminal head region of the narmovirus receptor binding protein. mBio 2023; 14:e0139123. [PMID: 37737607 PMCID: PMC10653815 DOI: 10.1128/mbio.01391-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/05/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Genetically diverse paramyxoviruses are united in their presentation of a receptor-binding protein (RBP), which works in concert with the fusion protein to facilitate host-cell entry. The C-terminal head region of the paramyxoviral RBP, a primary determinant of host-cell tropism and inter-species transmission potential, forms structurally distinct classes dependent upon protein and glycan receptor specificity. Here, we reveal the architecture of the C-terminal head region of the RBPs from Nariva virus (NarV) and Mossman virus (MosV), two archetypal rodent-borne paramyxoviruses within the recently established genus Narmovirus, family Paramyxoviridae. Our analysis reveals that while narmoviruses retain the general architectural features associated with paramyxoviral RBPs, namely, a six-bladed β-propeller fold, they lack the structural motifs associated with known receptor-mediated host-cell entry pathways. This investigation indicates that the RBPs of narmoviruses exhibit pathobiological features that are distinct from those of other paramyxoviruses.
Collapse
Affiliation(s)
- Alice J. Stelfox
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- European Molecular Biology Laboratory, Grenoble, France
| | | | - Ilona Rissanen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Robert Rambo
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Oxford, United Kingdom
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
4
|
Mollentze N, Streicker DG. Predicting zoonotic potential of viruses: where are we? Curr Opin Virol 2023; 61:101346. [PMID: 37515983 DOI: 10.1016/j.coviro.2023.101346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/31/2023]
Abstract
The prospect of identifying high-risk viruses and designing interventions to pre-empt their emergence into human populations is enticing, but controversial, particularly when used to justify large-scale virus discovery initiatives. We review the current state of these efforts, identifying three broad classes of predictive models that have differences in data inputs that define their potential utility for triaging newly discovered viruses for further investigation. Prospects for model predictions of public health risk to guide preparedness depend not only on computational improvements to algorithms, but also on more efficient data generation in laboratory, field and clinical settings. Beyond public health applications, efforts to predict zoonoses provide unique research value by creating generalisable understanding of the ecological and evolutionary factors that promote viral emergence.
Collapse
Affiliation(s)
- Nardus Mollentze
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G12 8QQ, United Kingdom; MRC-University of Glasgow Centre for Virus Research, G61 1QH, United Kingdom
| | - Daniel G Streicker
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G12 8QQ, United Kingdom; MRC-University of Glasgow Centre for Virus Research, G61 1QH, United Kingdom.
| |
Collapse
|
5
|
Kartashov MY, Gladysheva AV, Naidenova EV, Zakharov KS, Shvalov АN, Krivosheina EI, Senichkina AM, Bah MB, Ternovoi VA, Boumbaly S, Loktev VB. [Molecular and genetic characteristics of the multicomponent flavi-like Kindia tick virus (Flaviviridae) found in ixodes ticks on the territory of the Republic of Guinea]. Vopr Virusol 2023; 67:487-495. [PMID: 37264838 DOI: 10.36233/0507-4088-145] [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: 12/26/2022] [Indexed: 06/03/2023]
Abstract
INTRODUCTION Ixodes ticks are vectors for pathogens of many infectious diseases. Recently, during the study of Rhipicephalus geigyi ticks collected from livestock in the Republic of Guinea, a new multicomponent flavi-like RNA virus, called Kindia tick virus (KITV), was discovered with an unusual mechanism for the implementation of genetic information. The aim of the work is to detect and study the genetic diversity of KITV in ixodes ticks collected in the territory of the Kindia province of the Republic of Guinea. MATERIAL AND METHODS In 2021, 324 specimens of ticks of the species Amblyomma variegatum, Rh. geigyi, Rh. annulatus, Rh. decoloratus, Rh. senegalensis were collected from cattle. The detection of viral RNA was carried out in individual samples of ticks by RT-PCR, followed by the determination of the nucleotide sequence and phylogenetic analysis. RESULTS AND DISCUSSION KITV detection rates in ticks of the species Rh. geigyi was 12.2%, Rh. annulatus 4.4%, Rh. decoloratus 3.3%. However, the KITV genetic material has not been identified in Am. variegatum ticks, which are one of the dominant species in West Africa. For all virus isolates, a partial nucleotide sequences of each of the four viral segments (GenBank, OK345271OK345306) were determined. The phylogenetic analysis showed a high level of identity (98.599.8%) for each of the four segments of the viral genome with those previously found in the Republic of Guinea. The obtained KITV isolates are most genetically close to Mogiana tick virus, which was previously detected in South America in Rh. microplus ticks and significantly differed from other multicomponent viruses circulating in Europe and Asia, including the Russian Federation. CONCLUSION KITV genetic material was found in three species of ixodid ticks collected from livestock in a number of prefectures of the Republic of Guinea. The infection rate in ticks was 3.312.2%. The continuation of research in this direction remains relevant.
Collapse
Affiliation(s)
- M Y Kartashov
- State Research Center of Virology and Biotechnology «Vector»
| | - A V Gladysheva
- State Research Center of Virology and Biotechnology «Vector»
| | | | - K S Zakharov
- Russian Research Anti-Plague Institute «Microbe»
| | - А N Shvalov
- State Research Center of Virology and Biotechnology «Vector»
| | - E I Krivosheina
- State Research Center of Virology and Biotechnology «Vector»
| | | | - M B Bah
- Research Institute of Applied Biology of Guinea
| | - V A Ternovoi
- State Research Center of Virology and Biotechnology «Vector»
| | - S Boumbaly
- Research Institute of Applied Biology of Guinea
| | - V B Loktev
- State Research Center of Virology and Biotechnology «Vector»
| |
Collapse
|
6
|
Roberts KE, Longdon B. Heterogeneities in infection outcomes across species: sex and tissue differences in virus susceptibility. PEER COMMUNITY JOURNAL 2023; 3:pcjournal.242. [PMID: 36811030 PMCID: PMC7614206 DOI: 10.24072/pcjournal.242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Species vary in their susceptibility to pathogens, and this can alter the ability of a pathogen to infect a novel host. However, many factors can generate heterogeneity in infection outcomes, obscuring our ability to understand pathogen emergence. Such heterogeneities can alter the consistency of responses across individuals and host species. For example, sexual dimorphism in susceptibility means males are often intrinsically more susceptible than females (although this can vary by host and pathogen). Further, we know little about whether the tissues infected by a pathogen in one host are the same in another species, and how this relates to the harm a pathogen does to its host. Here, we first take a comparative approach to examine sex differences in susceptibility across 31 species of Drosophilidae infected with Drosophila C Virus (DCV). We found a strong positive inter-specific correlation in viral load between males and females, with a close to 1:1 relationship, suggesting that susceptibility to DCV across species is not sex specific. Next, we made comparisons of the tissue tropism of DCV across seven species of fly. We found differences in viral load between the tissues of the seven host species, but no evidence of tissues showing different patterns of susceptibility in different host species. We conclude that, in this system, patterns of viral infectivity across host species are robust between males and females, and susceptibility in a given host is general across tissue types.
Collapse
Affiliation(s)
- Katherine E Roberts
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, TR10 9FE, UK
| | - Ben Longdon
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, TR10 9FE, UK,corresponding author
| |
Collapse
|
7
|
Haas GD, Lee B. Paramyxoviruses from bats: changes in receptor specificity and their role in host adaptation. Curr Opin Virol 2023; 58:101292. [PMID: 36508860 PMCID: PMC9974588 DOI: 10.1016/j.coviro.2022.101292] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022]
Abstract
Global metagenomic surveys have revealed that bats host a diverse array of paramyxoviruses, including species from at least five major genera. An essential determinant of successful spillover is the entry of a virus into a new host. We evaluate the role of receptor usage in the zoonotic potential of bat-borne henipaviruses, morbilliviruses, pararubulaviruses, orthorubulaviruses, and jeilongviruses; successful spillover into humans depends upon compatibility of a respective viral attachment protein with its cognate receptor. We also emphasize the importance of postentry restrictions in preventing spillover. Metagenomics and characterization of newly identified paramyxoviruses have greatly improved our understanding of spillover determinants, allowing for better forecasts of which bat-borne viruses may pose the greatest risk for cross-species transmission into humans.
Collapse
Affiliation(s)
- Griffin D Haas
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA.
| |
Collapse
|
8
|
Valente MC, Prakoso D, Vittor AY, Blosser EM, Abid N, Pu R, Beachboard SE, Long MT, Burkett-Cadena ND, Mavian CN. Everglades virus evolution: Genome sequence analysis of the envelope 1 protein reveals recent mutation and divergence in South Florida wetlands. Virus Evol 2022; 8:veac111. [PMID: 36582503 PMCID: PMC9795574 DOI: 10.1093/ve/veac111] [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: 07/29/2022] [Revised: 10/16/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022] Open
Abstract
Everglades virus (EVEV) is a subtype (II) of Venezuelan equine encephalitis virus (VEEV), endemic in southern Florida, USA. EVEV has caused clinical encephalitis in humans, and antibodies have been found in a variety of wild and domesticated mammals. Over 29,000 Culex cedecei females, the main vector of EVEV, were collected in 2017 from Big Cypress and Fakahatchee Strand Preserves in Florida and pool-screened for the presence of EVEV using reverse transcription real-time polymerase chain reaction. The entire 1 E1 protein gene was successfully sequenced from fifteen positive pools. Phylogenetic analysis showed that isolates clustered, based on the location of sampling, into two monophyletic clades that diverged in 2009. Structural analyses revealed two mutations of interest, A116V and H441R, which were shared among all isolates obtained after its first isolation of EVEV in 1963, possibly reflecting adaptation to a new host. Alterations of the Everglades ecosystem may have contributed to the evolution of EVEV and its geographic compartmentalization. This is the first report that shows in detail the evolution of EVEV in South Florida. This zoonotic pathogen warrants inclusion into routine surveillance given the high natural infection rate in the vectors. Invasive species, increasing urbanization, the Everglades restoration, and modifications to the ecosystem due to climate change and habitat fragmentation in South Florida may increase rates of EVEV spillover to the human population.
Collapse
Affiliation(s)
| | | | - Amy Y Vittor
- Department of Pathology, Emerging Pathogens Institute, College of Medicine, University of Florida, Gainesville, FL 32601, USA,Division of Infectious Diseases and Global Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL 32601, USA
| | | | | | - Ruiyu Pu
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32601, USA
| | - Sarah E Beachboard
- Department of Pathology, Emerging Pathogens Institute, College of Medicine, University of Florida, Gainesville, FL 32601, USA
| | | | | | | |
Collapse
|
9
|
Contrasting the Practices of Virus Isolation and Characterization between the Early Period in History and Modern Times: The Case of Japanese Encephalitis Virus. Viruses 2022; 14:v14122640. [PMID: 36560644 PMCID: PMC9781737 DOI: 10.3390/v14122640] [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: 10/10/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Japanese encephalitis is a serious disease transmitted by mosquitoes. With its recent spread beyond the traditional territory of endemicity in Asia, the magnitude of global threat has increased sharply. While much of the current research are largely focused on changing epidemiology, molecular genetics of virus, and vaccination, little attention has been paid to the early history of virus isolation and phenotypic characterization of this virus. In this review, using this piece of history as an example, I review the transition of the concept and practice of virus isolation and characterization from the early period of history to modern times. The spectacular development of molecular techniques in modern times has brought many changes in practices as well as enormous amount of new knowledge. However, many aspects of virus characterization, in particular, transmission mechanism and host relationship, remain unsolved. As molecular techniques are not perfect in all respects, beneficial accommodation of molecular and biologic data is critically important in many branches of research. Accordingly, I emphasize exercising caution in applying only these modern techniques, point out unrecognized communication problems, and stress that JE research history is a rich source of interesting works still valuable even today and waiting to be discovered.
Collapse
|
10
|
Ibrahim YM, Zhang W, Werid GM, Zhang H, Pan Y, Zhang L, Xu Y, Li C, Chen H, Wang Y. Characterization of parainfluenza virus 5 from diarrheic piglet highlights its zoonotic potential. Transbound Emerg Dis 2022; 69:e1510-e1525. [PMID: 35179303 DOI: 10.1111/tbed.14482] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/25/2022] [Accepted: 02/16/2022] [Indexed: 11/28/2022]
Abstract
Parainfluenza virus 5 (PIV5), a member of paramyxoviruses, causes respiratory and neurological infection in several animal species. Whereas information on PIV5 infection in digestive system is very scarce. Here, we successfully isolated one PIV5 strain from diarrhetic piglets. After four times plaque purification and ultracentrifugation, the paramyxovirus-like particles were observed by electron microscopy. The genome-wide phylogenetic analysis showed that the isolated strain was closely related to the PIV5 strain from a lesser panda and pigs in China. Therefore, we characterized this isolated PIV5 and found that this virus could hemagglutinate red blood cells from both guinea pigs and chickens. Further, we observed that this PIV5 could infect cell lines from various host species including pig, human, monkey, bovine, dog, cat, rabbit, hamster, and mouse, which was confirmed with the immunofluorescent assay. To evaluate the distribution of PIV5 in the field, we developed an indirect ELISA (iELISA) for the first time to detect the specific antibodies based on recombinant nucleocapsid protein. A total of 530 porcine serum samples were tested and the PIV5-positive rate was 75.7%. To our knowledge, this is the first report describing the full characterization of PIV5 strain isolated from a diarrheic piglet. The ability of this PIV5 strain to infect a wide range of mammalian cell types indicates that PIV5 can transmit across different species, providing a remarkable insight into potential zoonosis. The virus strain and iELISA developed in this study can be used to investigate the pathogenesis, epidemiology, and zoonotic potential of PIV5. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Yassein M Ibrahim
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wenli Zhang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Gebremeskel Mamu Werid
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - He Zhang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yu Pan
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lin Zhang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yunfei Xu
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Changwen Li
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hongyan Chen
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yue Wang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| |
Collapse
|
11
|
Imrie RM, Roberts KE, Longdon B. Between virus correlations in the outcome of infection across host species: Evidence of virus by host species interactions. Evol Lett 2021; 5:472-483. [PMID: 34621534 PMCID: PMC8484721 DOI: 10.1002/evl3.247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/15/2021] [Accepted: 06/28/2021] [Indexed: 12/24/2022] Open
Abstract
Virus host shifts are a major source of outbreaks and emerging infectious diseases, and predicting the outcome of novel host and virus interactions remains a key challenge for virus research. The evolutionary relationships between host species can explain variation in transmission rates, virulence, and virus community composition between hosts, but it is unclear if correlations exist between related viruses in infection traits across novel hosts. Here, we measure correlations in viral load of four Cripavirus isolates across experimental infections of 45 Drosophilidae host species. We find positive correlations between every pair of viruses tested, suggesting that some host clades show broad susceptibility and could act as reservoirs and donors for certain types of viruses. Additionally, we find evidence of virus by host species interactions, highlighting the importance of both host and virus traits in determining the outcome of virus host shifts. Of the four viruses tested here, those that were more closely related tended to be more strongly correlated, providing tentative evidence that virus evolutionary relatedness may be a useful proxy for determining the likelihood of novel virus emergence, which warrants further research.
Collapse
Affiliation(s)
- Ryan M. Imrie
- Centre for Ecology and Conservation, Biosciences, College of Life and Environmental SciencesUniversity of ExeterPenrynTR10 9FEUnited Kingdom
| | - Katherine E. Roberts
- Centre for Ecology and Conservation, Biosciences, College of Life and Environmental SciencesUniversity of ExeterPenrynTR10 9FEUnited Kingdom
| | - Ben Longdon
- Centre for Ecology and Conservation, Biosciences, College of Life and Environmental SciencesUniversity of ExeterPenrynTR10 9FEUnited Kingdom
| |
Collapse
|
12
|
Piewbang C, Wardhani SW, Dankaona W, Yostawonkul J, Boonrungsiman S, Surachetpong W, Kasantikul T, Techangamsuwan S. Feline morbillivirus-1 in dogs with respiratory diseases. Transbound Emerg Dis 2021; 69:e175-e184. [PMID: 34355534 DOI: 10.1111/tbed.14278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/29/2021] [Accepted: 08/04/2021] [Indexed: 01/04/2023]
Abstract
Feline morbillivirus-1 (FeMV-1) is a viral pathogen associated with kidney disease in domestic cats and wild felids. We initially identified the FeMV-1 from the lung of a necropsied dog with severe pulmonary disease by the reverse transcription polymerase chain reaction (RT-PCR). Thereafter, we investigated FeMV-1 in nasal and oral swab samples from 73 healthy and 113 dogs with respiratory illnesses. We found polymerase chain reaction (PCR)-positive FeMV-1 from only 14/113 (12.39%) dogs with respiratory disease (p = .001). Of these 14 dogs, six were co-infected with other canine respiratory viruses (6/14; 42.86%). Two independent immunohistochemistry procedures, using antibodies against matrix and phosphoprotein of FeMV-1, confirmed the presence of FeMV-1 in lung tissues of two necropsied dogs (out of a total of 22 dogs, 9.09%) that died from respiratory disease. This finding corresponded to transmission electron microscopy findings that paramyxoviral particles exist in lung epithelia. FeMV-1 antigen localization was also evident in the kidney, lymphoid and brain tissues of two deceased dogs. FeMV-1 was successfully isolated from a necropsied dog and from two living dogs, all with respiratory illnesses, which supports FeMV infection in dogs. The detection of FeMV-1 in dog tissues expands the known tropism of this virus to a non-felid host. Our findings indicate that FeMV-1, alone or in co-infection with other viral pathogens, might contribute to respiratory illness and death in dogs.
Collapse
Affiliation(s)
- Chutchai Piewbang
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Animal Virome and Diagnostic Development Research Group, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Sabrina Wahyu Wardhani
- Animal Virome and Diagnostic Development Research Group, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Wichan Dankaona
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Animal Virome and Diagnostic Development Research Group, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Jakarwan Yostawonkul
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Suwimon Boonrungsiman
- National Nanotechnology Center, National Science and Technology Development Agency, Thailand Science Park, Pathumthani, Thailand
| | - Win Surachetpong
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Tanit Kasantikul
- Clemson Veterinary Diagnostic Center, Clemson University, Columbia, South Carolina, USA
| | - Somporn Techangamsuwan
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Animal Virome and Diagnostic Development Research Group, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| |
Collapse
|
13
|
Vale FF, Vítor JMB, Marques AT, Azevedo-Pereira JM, Anes E, Goncalves J. Origin, phylogeny, variability and epitope conservation of SARS-CoV-2 worldwide. Virus Res 2021; 304:198526. [PMID: 34339772 PMCID: PMC8323504 DOI: 10.1016/j.virusres.2021.198526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/30/2021] [Accepted: 07/26/2021] [Indexed: 12/23/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses innumerous challenges, like understanding what triggered the emergence of this new human virus, how this RNA virus is evolving or how the variability of viral genome may impact the primary structure of proteins that are targets for vaccine. We analyzed 19471 SARS-CoV-2 genomes available at the GISAID database from all over the world and 3335 genomes of other Coronoviridae family members available at GenBank, collecting SARS-CoV-2 high-quality genomes and distinct Coronoviridae family genomes. Additionally, we analyzed 199,984 spike glycoprotein sequences. Here, we identify a SARS-CoV-2 emerging cluster containing 13 closely related genomes isolated from bat and pangolin that showed evidence of recombination, which may have contributed to the emergence of SARS-CoV-2. The analyzed SARS-CoV-2 genomes presented 9632 single nucleotide variants (SNVs) corresponding to a variant density of 0.3 over the genome, and a clear geographic distribution. SNVs are unevenly distributed throughout the genome and hotspots for mutations were found for the spike gene and ORF 1ab. We describe a set of predicted spike protein epitopes whose variability is negligible. Additionally, all predicted epitopes for the structural E, M and N proteins are highly conserved. The amino acid changes present in the spike glycoprotein of variables of concern (VOCs) comprise between 3.4% and 20.7% of the predicted epitopes of this protein. These results favors the continuous efficacy of the available vaccines targeting the spike protein, and other structural proteins. Multiple epitopes vaccines should sustain vaccine efficacy since at least some of the epitopes present in variability regions of VOCs are conserved and thus recognizable by antibodies.
Collapse
Affiliation(s)
- Filipa F Vale
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa 1649-003, Portugal.
| | - Jorge M B Vítor
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa 1649-003, Portugal; Pharmacy, Pharmacology and Health Technologies Department, Faculty of Pharmacy, Universidade de Lisboa, Lisbon 1649-003, Portugal
| | - Andreia T Marques
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - José Miguel Azevedo-Pereira
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - Elsa Anes
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - Joao Goncalves
- Molecular Microbiology and Biotechnology Department, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, Lisbon 1649-003, Portugal
| |
Collapse
|
14
|
Samanta B. Structural evolution of SLA promoter in mosquito-borne flaviviruses: A sequence-structure based phylogenetic framework. Virology 2021; 562:110-120. [PMID: 34311294 DOI: 10.1016/j.virol.2021.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/05/2021] [Accepted: 07/15/2021] [Indexed: 11/18/2022]
Abstract
All the flaviviruses have a Y-shaped stem-loop secondary structure known as the SLA element, and the structural features of this element are crucial to initiating the infection cycle. The present study particularly investigated how flaviviruses retained the common core SLA element secondary structure during the species evolution by selecting mosquito-borne flaviviruses (MBFVs) as a case study. The detailed search of nucleotide substitutions in species-wise consensus SLA secondary structure models suggested that the compensatory and hemi-compensatory base changes in the helices are crucial to preserving the common core secondary structure. In contrast to the coding region-based phylogeny, the SLA sequence-structure-based phylogenetic tree revealed an intriguing evolutionary relationship among MBFVs. Overall, this paper demonstrated for the first time the efficacy of RNA secondary structures as a phylogenetic marker to study the RNA virus evolution.
Collapse
Affiliation(s)
- Brajogopal Samanta
- Department of Microbiology and FST, GITAM Institute of Science, GITAM (Deemed to be University), Rushikonda, Visakhapatnam, 530045, Andhra Pradesh, India.
| |
Collapse
|
15
|
Agrawal AA, Zhang X. The evolution of coevolution in the study of species interactions. Evolution 2021; 75:1594-1606. [PMID: 34166533 DOI: 10.1111/evo.14293] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/31/2021] [Accepted: 06/06/2021] [Indexed: 01/05/2023]
Abstract
The study of reciprocal adaptation in interacting species has been an active and inspiring area of evolutionary research for nearly 60 years. Perhaps owing to its great natural history and potential consequences spanning population divergence to species diversification, coevolution continues to capture the imagination of biologists. Here we trace developments following Ehrlich and Raven's classic paper, with a particular focus on the modern influence of two studies by Dr. May Berenbaum in the 1980s. This series of classic work presented a compelling example exhibiting the macroevolutionary patterns predicted by Ehrlich and Raven and also formalized a microevolutionary approach to measuring selection, functional traits, and understanding reciprocal adaptation between plants and their herbivores. Following this breakthrough was a wave of research focusing on diversifying macroevolutionary patterns, mechanistic chemical ecology, and natural selection on populations within and across community types. Accordingly, we breakdown coevolutionary theory into specific hypotheses at different scales: reciprocal adaptation between populations within a community, differential coevolution among communities, lineage divergence, and phylogenetic patterns. We highlight progress as well as persistent gaps, especially the link between reciprocal adaptation and diversification.
Collapse
Affiliation(s)
- Anurag A Agrawal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Xuening Zhang
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| |
Collapse
|
16
|
Viral footprints across Gulfs of Kathiawar Peninsula and Arabian Sea: Unraveled from pelagic sediment metagenomic data. Virus Res 2021; 302:198485. [PMID: 34146609 DOI: 10.1016/j.virusres.2021.198485] [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: 11/19/2020] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 11/21/2022]
Abstract
Marine biosphere is one of the largest, diverse and dynamic system hosting numerous of microorganisms. Viruses being the most abundant under explored lifeforms in ocean, represent a reservoir of great genetic diversity. We report the metagenomic insights on the viral communities in the deep sediments of the two Gulfs of Gujarat i.e. Gulf of Khambhat and Gulf of Kutch, with one sample from Arabian Sea, treated as open sea control. The viral reads were filtered from the whole dataset, assembled and studied for viral diversity, which was visualized by Pavian. The sequences were checked for the viral abundance, diversity and functionality. The resulting viral taxonomic classification contained 6 orders, 8 families and 47 genera. The results revealed that the phages infecting Cyanobacterium, Bacillus and Vibrio dominated the sediments. Further, it was observed that majority of viral sequences belonged to double-stranded DNA phages. The present study attempts to provide a primary insight of the viral signals and potential genetic content in the Gulfs of Kathiawar.
Collapse
|
17
|
Niner MD, Stepien CA, Gorgoglione B, Leaman DW. Genomic and immunogenic changes of Piscine novirhabdovirus (Viral Hemorrhagic Septicemia Virus) over its evolutionary history in the Laurentian Great Lakes. PLoS One 2021; 16:e0232923. [PMID: 34048438 PMCID: PMC8162641 DOI: 10.1371/journal.pone.0232923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 04/22/2021] [Indexed: 01/21/2023] Open
Abstract
A unique and highly virulent subgenogroup (-IVb) of Piscine novirhabdovirus, also known as Viral Hemorrhagic Septicemia Virus (VHSV), suddenly appeared in the Laurentian Great Lakes, causing large mortality outbreaks in 2005 and 2006, and affecting >32 freshwater fish species. Periods of apparent dormancy have punctuated smaller and more geographically-restricted outbreaks in 2007, 2008, and 2017. In this study, we conduct the largest whole genome sequencing analysis of VHSV-IVb to date, evaluating its evolutionary changes from 48 isolates in relation to immunogenicity in cell culture. Our investigation compares genomic and genetic variation, selection, and rates of sequence changes in VHSV-IVb, in relation to other VHSV genogroups (VHSV-I, VHSV-II, VHSV-III, and VHSV-IVa) and with other Novirhabdoviruses. Results show that the VHSV-IVb isolates we sequenced contain 253 SNPs (2.3% of the total 11,158 nucleotides) across their entire genomes, with 85 (33.6%) of them being non-synonymous. The most substitutions occurred in the non-coding region (NCDS; 4.3%), followed by the Nv- (3.8%), and M- (2.8%) genes. Proportionally more M-gene substitutions encoded amino acid changes (52.9%), followed by the Nv- (50.0%), G- (48.6%), N- (35.7%) and L- (23.1%) genes. Among VHSV genogroups and subgenogroups, VHSV-IVa from the northeastern Pacific Ocean has shown the fastest substitution rate (2.01x10-3), followed by VHSV-IVb (6.64x10-5) and by the VHSV-I, -II and-III genogroups from Europe (4.09x10-5). A 2016 gizzard shad (Dorosoma cepedianum) from Lake Erie possessed the most divergent VHSV-IVb sequence. The in vitro immunogenicity analysis of that sample displayed reduced virulence (as did the other samples from 2016), in comparison to the original VHSV-IVb isolate (which had been traced back to 2003, as an origin date). The 2016 isolates that we tested induced milder impacts on fish host cell innate antiviral responses, suggesting altered phenotypic effects. In conclusion, our overall findings indicate that VHSV-IVb has undergone continued sequence change and a trend to lower virulence over its evolutionary history (2003 through present-day), which may facilitate its long-term persistence in fish host populations.
Collapse
Affiliation(s)
- Megan D. Niner
- Department of Environmental Sciences, University of Toledo, Toledo, Ohio, United States of America
| | - Carol A. Stepien
- School of Oceanography, University of Washington, Seattle, WA, United States of America
- Genetics and Genomics Group, NOAA Pacific Marine Environmental Laboratory, Seattle, Washington, United States of America
- * E-mail: ,
| | - Bartolomeo Gorgoglione
- Department of Biological Sciences, University of Toledo, Toledo, Ohio, United States of America
| | - Douglas W. Leaman
- Department of Biological Sciences, University of Toledo, Toledo, Ohio, United States of America
- Department of Biological Sciences, Wright State University, Dayton, Ohio, United States of America
| |
Collapse
|
18
|
Khan FM, Ahmad T, Gulistan M, Chammam W, Khan M, Hui J. Epidemiology of coronaviruses, genetics, vaccines, and scenario of current pandemic of coronavirus diseases 2019 (COVID-19): a fuzzy set approach. Hum Vaccin Immunother 2021; 17:1296-1303. [PMID: 33720797 DOI: 10.1080/21645515.2020.1798697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Human coronaviruses (HCoVs) are associated with a range of respiratory complications. In the last two decades, three major outbreaks have been reported due to HCoVs including the current pandemic. In December 2019, a newly emerged virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan city, China. This paper presents a detailed review of the literature and discusses the uncertain spread of coronavirus disease 2019 (COVID-19) using fuzzy set as classical set theory logic to measure uncertainty and vagueness of COVID-19 in China. Our findings show that both infection and death rate touched the peak (normal fuzzy sets) and have shown a decline. The graphs are not convex, which shows that there remains much uncertainty in the spread of COVID-19. Effective vaccines are clearly needed to control and prevent the COVID-19 pandemic.
Collapse
Affiliation(s)
- Fazal Mehmood Khan
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China
| | - Tauseef Ahmad
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China.,Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Muhammad Gulistan
- Department of Mathematics and Statistics, Hazara University, Mansehra, Khyber Pakhtunkhwa, Islamic Republic of Pakistan
| | - Wathek Chammam
- Department of Mathematics, College of Science Al-Zulfi, Majmaah University, Al-Majmaah, Saudi Arabia
| | - Muhammad Khan
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Khyber Pakhtunkhwa, Islamic Republic of Pakistan
| | - Jin Hui
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China.,Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| |
Collapse
|
19
|
Shohael AM, Moin AT, Chowdhury MAB, Riana SH, Ullah MA, Araf Y, Sarkar B. An Updated Overview of Herpes Simplex Virus-1 Infection: Insights from Origin to Mitigation Measures. ELECTRONIC JOURNAL OF GENERAL MEDICINE 2021. [DOI: 10.29333/ejgm/10869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
20
|
Using Data Mining and Network Analysis to Infer Arboviral Dynamics: The Case of Mosquito-Borne Flaviviruses Reported in Mexico. INSECTS 2021; 12:insects12050398. [PMID: 33946977 PMCID: PMC8146811 DOI: 10.3390/insects12050398] [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: 03/17/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 11/17/2022]
Abstract
Given the significant impact of mosquito-borne flaviviruses (MBFVs) on both human and animal health, predicting their dynamics and understanding their transmission cycle is of the utmost importance. Usually, predictions about the distribution of priority pathogens, such as Dengue, Yellow fever, West Nile Virus and St. Louis encephalitis, relate abiotic elements to simple biotic components, such as a single causal agent. Furthermore, focusing on single pathogens neglects the possibility of interactions and the existence of common elements in the transmission cycles of multiple pathogens. A necessary, but not sufficient, condition that a mosquito be a vector of a MBFV is that it co-occurs with hosts of the pathogen. We therefore use a recently developed modeling framework, based on co-occurrence data, to infer potential biotic interactions between those mosquito and mammal species which have previously been identified as vectors or confirmed positives of at least one of the considered MBFVs. We thus create models for predicting the relative importance of mosquito species as potential vectors for each pathogen, and also for all pathogens together, using the known vectors to validate the models. We infer that various mosquito species are likely to be significant vectors, even though they have not currently been identified as such, and are likely to harbor multiple pathogens, again validating the predictions with known results. Besides the above "niche-based" viewpoint we also consider an assemblage-based analysis, wherein we use a community-identification algorithm to identify those mosquito and/or mammal species that form assemblages by dint of their significant degree of co-occurrence. The most cohesive assemblage includes important primary vectors, such as A. aegypti, A. albopictus, C. quinquefasciatus, C. pipiens and mammals with abundant populations that are well-adapted to human environments, such as the white-tailed deer (Odocoileus virginianus), peccary (Tayassu pecari), opossum (Didelphis marsupialis) and bats (Artibeus lituratus and Sturnira lilium). Our results suggest that this assemblage has an important role in the transmission dynamics of this viral group viewed as a complex multi-pathogen-vector-host system. By including biotic risk factors our approach also modifies the geographical risk profiles of the spatial distribution of MBFVs in Mexico relative to a consideration of only abiotic niche variables.
Collapse
|
21
|
Halabowski D, Rzymski P. Taking a lesson from the COVID-19 pandemic: Preventing the future outbreaks of viral zoonoses through a multi-faceted approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143723. [PMID: 33213901 PMCID: PMC7666614 DOI: 10.1016/j.scitotenv.2020.143723] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 05/22/2023]
Abstract
The pandemic of the novel coronavirus disease 2019 (COVID-19) has caused a significant burden to healthcare systems, economic crisis, and public fears. It is also a lesson to be learned and a call-to-action to minimize the risk of future viral pandemics and their associated challenges. The present paper outlines selected measures (i.e., monitoring and identification of novel viral agents in animals, limitations to wildlife trade, decreasing hunting activities, changes to mink farming and meat production), the implementation of which would decrease such a risk. The role of viral surveillance systems and research exploring the virus strains associated with different animal hosts is emphasized along with the need for stricter wild trade regulations and changes to hunting activities. Finally, the paper suggests modifications to the meat production system, particularly through the introduction of cultured meat that would not only decrease the risk of exposure to novel human viral pathogens but also strengthen food security and decrease the environmental impacts of food production.
Collapse
Affiliation(s)
- Dariusz Halabowski
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-007 Katowice, Poland.
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland; Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), 60-806 Poznań, Poland.
| |
Collapse
|
22
|
Stepien CA, Niner MD. Evolutionary trajectory of fish Piscine novirhabdovirus (=Viral Hemorrhagic Septicemia Virus) across its Laurentian Great Lakes history: Spatial and temporal diversification. Ecol Evol 2020; 10:9740-9775. [PMID: 33005343 PMCID: PMC7520192 DOI: 10.1002/ece3.6611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/04/2020] [Accepted: 05/10/2020] [Indexed: 02/05/2023] Open
Abstract
Piscine novirhabdovirus = Viral Hemorrhagic Septicemia Virus (VHSV) first appeared in the Laurentian Great Lakes with large outbreaks from 2005 to 2006, as a new and novel RNA rhabdovirus subgenogroup (IVb) that killed >30 fish species. Interlude periods punctuated smaller more localized outbreaks in 2007, 2010, and 2017, although some fishes tested positive in the intervals. There have not been reports of outbreaks or positives from 2018, 2019, or 2020. Here, we employ a combined population genetics and phylogenetic approach to evaluate spatial and temporal evolutionary trajectory on its G-gene sequence variation, in comparison with whole-genome sequences (11,083 bp) from a subset of 44 individual isolates (including 40 newly sequenced ones). Our results show that IVb (N = 184 individual fish isolates) diversified into 36 G-gene haplotypes from 2003 to 2017, stemming from two originals ("a" and "b"). G-gene haplotypes "a" and "b" differed by just one synonymous single-nucleotide polymorphism (SNP) substitution, remained the most abundant until 2011, then disappeared. Group "a" descendants (14 haplotypes) remained most prevalent in the Upper and Central Great Lakes, with eight (51%) having nonsynonymous substitutions. Group "b" descendants primarily have occurred in the Lower Great Lakes, including 22 haplotypes, of which 15 (68%) contained nonsynonymous changes. Evolutionary patterns of the whole-genome sequences (which had 34 haplotypes among 44 isolates) appear congruent with those from the G-gene. Virus populations significantly diverged among the Upper, Central, and Lower Great Lakes, diversifying over time. Spatial divergence was apparent in the overall patterns of nucleotide substitutions, while amino acid changes increased temporally. VHSV-IVb thus significantly differentiated across its less than two decades in the Great Lakes, accompanied by declining outbreaks and virulence. Continuing diversification likely allowed the virus to persist at low levels in resident fish populations, and may facilitate its potential for further and future spread to new habitats and nonacclimated hosts.
Collapse
Affiliation(s)
- Carol A. Stepien
- Genetics and Genomics Group (G3)NOAA Pacific Marine Environmental Laboratory (PMEL)SeattleWAUSA
| | - Megan D. Niner
- Genetics and Genomics Group (G3), Department of Environmental SciencesUniversity of ToledoToledoOHUSA
| |
Collapse
|
23
|
Guo JJ, Lin XD, Chen YM, Hao ZY, Wang ZX, Yu ZM, Lu M, Li K, Qin XC, Wang W, Holmes EC, Hou W, Zhang YZ. Diversity and circulation of Jingmen tick virus in ticks and mammals. Virus Evol 2020; 6:veaa051. [PMID: 33976906 PMCID: PMC8097133 DOI: 10.1093/ve/veaa051] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Since its initial identification in ticks in 2010, Jingmen tick virus (JMTV) has been described in cattle, rodents, and primates. To better understand the diversity, evolution, and transmission of JMTV, we sampled 215 ticks, 104 cattle bloods, 216 bats, and 119 rodents in Wenzhou city, Zhejiang Province, China as well as 240 bats from Guizhou and Henan Provinces. JMTV was identified in 107 ticks (from two species), 54 bats (eleven species), 8 rodents (three species), and 10 cattle, with prevalence levels of 49.8, 11.8, 6.7, and 9.6 per cent, respectively, suggesting that bats may be a natural reservoir of JMTV. Phylogenetic analyses revealed that all the newly identified JMTVs were closely related to each other and to previously described viruses. Additionally, all tick and mammalian JMTV sampled in Wenzhou shared a consistent genomic structure, suggesting that the virus can cocirculate between ticks and mammals without observable variation in genome organization. All JMTVs sampled globally could be divided into two phylogenetic groups, Mantel tests suggested that geographic isolation, rather than host species, may be the main driver of JMTV diversity. However, the exact geographical origin of JMTV was difficult to determine, suggesting that this virus has a complex evolutionary history.
Collapse
Affiliation(s)
- Jing-Jing Guo
- State Key Laboratory of Virology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.,Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xian-Dan Lin
- Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang, 325001,China
| | - Yan-Mei Chen
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Shanghai Public Health Clinical Center and School of Life Science, Fudan University, Shanghai, 201052, China
| | - Zong-Yu Hao
- Henan Center for Disease Control and Prevention, Zhengzhou, Henan Province, 450000, China
| | - Zhao-Xiao Wang
- GGuizhou Center for Disease Control and Prevention, Guiyang, Guizhou Province, 550000, China and
| | - Zhu-Mei Yu
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Miao Lu
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Kun Li
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xin-Cheng Qin
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Wen Wang
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Edward C Holmes
- Shanghai Public Health Clinical Center and School of Life Science, Fudan University, Shanghai, 201052, China.,Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Wei Hou
- State Key Laboratory of Virology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yong-Zhen Zhang
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Shanghai Public Health Clinical Center and School of Life Science, Fudan University, Shanghai, 201052, China
| |
Collapse
|
24
|
Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts. Proc Natl Acad Sci U S A 2020; 117:9423-9430. [PMID: 32284401 PMCID: PMC7196766 DOI: 10.1073/pnas.1919176117] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Identifying whether novel human viruses disproportionately originate from certain animal groups could inform risk-based allocations of research and surveillance effort. Whether such “special reservoirs” exist remains controversial. We show that the proportion of viruses that infect humans varies minimally across reservoir taxonomic orders. Instead, the number of human-infecting viruses increases proportionately to the total number of viruses maintained by each reservoir group, which is in turn explained by the number of animal species within each group. This supports a host-neutral explanation for observed variation in the number of zoonoses among animal groups, such that traits of animal orders are unlikely to produce viruses that disproportionately threaten humans. These findings refine strategies to identify high-risk viruses prior to their emergence. The notion that certain animal groups disproportionately maintain and transmit viruses to humans due to broad-scale differences in ecology, life history, and physiology currently influences global health surveillance and research in disease ecology, virology, and immunology. To directly test whether such “special reservoirs” of zoonoses exist, we used literature searches to construct the largest existing dataset of virus–reservoir relationships, consisting of the avian and mammalian reservoir hosts of 415 RNA and DNA viruses along with their histories of human infection. Reservoir host effects on the propensity of viruses to have been reported as infecting humans were rare and when present were restricted to one or two viral families. The data instead support a largely host-neutral explanation for the distribution of human-infecting viruses across the animal orders studied. After controlling for higher baseline viral richness in mammals versus birds, the observed number of zoonoses per animal order increased as a function of their species richness. Animal orders of established importance as zoonotic reservoirs including bats and rodents were unexceptional, maintaining numbers of zoonoses that closely matched expectations for mammalian groups of their size. Our findings show that variation in the frequency of zoonoses among animal orders can be explained without invoking special ecological or immunological relationships between hosts and viruses, pointing to a need to reconsider current approaches aimed at finding and predicting novel zoonoses.
Collapse
|
25
|
Ng WM, Stelfox AJ, Bowden TA. Unraveling virus relationships by structure-based phylogenetic classification. Virus Evol 2020; 6:veaa003. [PMID: 32064119 PMCID: PMC7015158 DOI: 10.1093/ve/veaa003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Delineation of the intricacies of protein function from macromolecular structure constitutes a continual obstacle in the study of cell and pathogen biology. Structure-based phylogenetic analysis has emerged as a powerful tool for addressing this challenge, allowing the detection and quantification of conserved architectural properties between proteins, including those with low or no detectable sequence homology. With a focus on viral protein structure, we highlight how a number of investigations have utilized this powerful method to infer common functionality and ancestry.
Collapse
Affiliation(s)
- Weng M Ng
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Alice J Stelfox
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| |
Collapse
|
26
|
Rodríguez-Nevado C, G Gavilán R, Pagán I. Host Abundance and Identity Determine the Epidemiology and Evolution of a Generalist Plant Virus in a Wild Ecosystem. PHYTOPATHOLOGY 2020; 110:94-105. [PMID: 31589103 DOI: 10.1094/phyto-07-19-0271-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Increasing evidence indicates that in wild ecosystems plant viruses are important ecological agents, and with potential to jump into crops, but only recently have the diversity and population dynamics of wild plant viruses begun to be explored. Theory proposes that biotic factors (e.g., ecosystem biodiversity, host abundance, and host density) and climatic conditions would determine the epidemiology and evolution of wild plant viruses. However, these predictions seldom have been empirically tested. For 3 years, we analyzed the prevalence and genetic diversity of Potyvirus species in preserved riparian forests of Spain. Results indicated that potyviruses were always present in riparian forests, with a novel generalist potyvirus species provisionally named Iberian hop mosaic virus (IbHMV), explaining the largest fraction of infected plants. Focusing on this potyvirus, we analyzed the biotic and climatic factors affecting virus infection risk and population genetic diversity in its native ecosystem. The main predictors of IbHMV infection risk were host relative abundance and species richness. Virus prevalence and host relative abundance were the major factors determining the genetic diversity and selection pressures in the virus population. These observations support theoretical predictions assigning these ecological factors a key role in parasite epidemiology and evolution. Finally, our phylogenetic analysis indicated that the viral population was genetically structured according to host and location of origin, as expected if speciation is largely sympatric. Thus, this work contributes to characterizing viral diversity and provides novel information on the determinants of plant virus epidemiology and evolution in wild ecosystems.
Collapse
Affiliation(s)
- Cristina Rodríguez-Nevado
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Departamento de Biotecnología-Biología Vegetal, Universidad Politécnica de Madrid, Madrid, Spain
| | - Rosario G Gavilán
- Facultad de Farmacia, Departamento de Farmacología, Farmacognosia y Botánica, unidad de Botánica, Universidad Complutense de Madrid, Madrid, Spain
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Departamento de Biotecnología-Biología Vegetal, Universidad Politécnica de Madrid, Madrid, Spain
| |
Collapse
|
27
|
In Vivo Dynamics of Reporter Flaviviridae Viruses. J Virol 2019; 93:JVI.01191-19. [PMID: 31462560 DOI: 10.1128/jvi.01191-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/15/2019] [Indexed: 11/20/2022] Open
Abstract
Recombinant viruses possessing reporter proteins have been generated for virus research. In the case of the family Flaviviridae, we recently generated recombinant viruses, including the hepatitis C virus of the genus Hepacivirus, Japanese encephalitis virus (JEV) of the genus Flavivirus, and bovine viral diarrhea virus of the genus Pestivirus; all three viruses possess an 11-amino-acid subunit derived from NanoLuc luciferase (HiBiT). Here, we further developed the recombinant viruses and investigated their utility in vivo Recombinant viruses harboring HiBiT in the E, NS1, or NS3 protein constructed based on the predicted secondary structure, solvent-accessible surface area, and root mean square fluctuation of the proteins exhibited comparable replication to that of the wild-type virus in vitro The recombinant JEV carrying HiBiT in the NS1 protein exhibited propagation in mice comparable to that of the parental virus, and propagation of the recombinant was monitored by the luciferase activity. In addition, the recombinants of classical swine fever virus (CSFV) possessing HiBiT in the Erns or E2 protein also showed propagation comparable to that of the wild-type virus. The recombinant CSFV carrying HiBiT in Erns exhibited similar replication to the parental CSFV in pigs, and detection of viral propagation of this recombinant by luciferase activity was higher than that by quantitative PCR (qPCR). Taken together, these results demonstrated that the reporter Flaviviridae viruses generated herein are powerful tools for elucidating the viral life cycle and pathogeneses and provide a robust platform for the development of novel antivirals.IMPORTANCE In vivo applications of reporter viruses are necessary to understand viral pathogenesis and provide a robust platform for antiviral development. In developing such applications, determination of an ideal locus to accommodate foreign genes is important, because insertion of foreign genes into irrelevant loci can disrupt the protein functions required for viral replication. Here, we investigated the criteria to determine ideal insertion sites of foreign genes from the protein structure of viral proteins. The recombinant viruses generated by our criteria exhibited propagation comparable to that of parental viruses in vivo Our proteomic approach based on the flexibility profile of viral proteins may provide a useful tool for constructing reporter viruses, including Flaviviridae viruses.
Collapse
|
28
|
Feng H, Sander AL, Moreira-Soto A, Yamane D, Drexler JF, Lemon SM. Hepatovirus 3ABC proteases and evolution of mitochondrial antiviral signaling protein (MAVS). J Hepatol 2019; 71:25-34. [PMID: 30876947 PMCID: PMC6581616 DOI: 10.1016/j.jhep.2019.02.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/31/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Unlike other hepatitis viruses that have infected primates for millions of years, hepatitis A virus (HAV) likely entered human populations only 10-12 thousand years ago after jumping from a rodent host. The phylogeny of modern hepatoviruses that infect rodents and bats suggest that multiple similar host shifts have occurred in the past. The factors determining such shifts are unknown, but the capacity to overcome innate antiviral responses in a foreign species is likely key. METHODS We assessed the capacity of diverse hepatovirus 3ABC proteases to cleave mitochondrial antiviral signaling protein (MAVS) and disrupt antiviral signaling in HEK293 and human hepatocyte-derived cell lines. We also applied maximum-likelihood and Bayesian algorithms to identify sites of diversifying selection in MAVS orthologs from 75 chiropteran, rodent and primate species. RESULTS 3ABC proteases from bat, but not rodent hepatoviruses efficiently cleaved human MAVS at Glu463/Gly464, disrupting virus activation of the interferon-β promoter, whereas human HAV 3ABC cleaved at Gln427/Val428. In contrast, MAVS orthologs from rodents and bats were resistant to cleavage by 3ABC proteases of cognate hepatoviruses and in several cases human HAV. A search for diversifying selection among MAVS orthologs from all 3 orders revealed 90 of ∼540 residues to be under positive selection, including residues in chiropteran MAVS that align with the site of cleavage of human MAVS by bat 3ABC proteases. CONCLUSIONS 3ABC protease cleavage of MAVS is a conserved attribute of hepatoviruses, acting broadly across different mammalian species and associated with evidence of diversifying selection at cleavage sites in rodent and bat MAVS orthologs. The capacity of hepatoviruses to disrupt MAVS-mediated innate immune responses has shaped evolution of both hepatoviruses and their hosts, and facilitates cross-species transmission of hepatitis A. LAY SUMMARY Hepatitis A virus, a common cause of acute hepatitis globally, is likely to have evolved from a virus that jumped from a rodent species to humans within the last 10-12 thousand years. Here we show that distantly related hepatoviruses, that infect bats and rodents today, express proteases that disrupt innate antiviral responses in human cells. This conserved attribute of hepatoviruses may have contributed to that ancient host species shift.
Collapse
Affiliation(s)
- Hui Feng
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anna-Lena Sander
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany
| | - Andrés Moreira-Soto
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany
| | - Daisuke Yamane
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany; German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin, Germany
| | - Stanley M Lemon
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology & Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
29
|
Maeki T, Tajima S, Ikeda M, Kato F, Taniguchi S, Nakayama E, Takasaki T, Lim CK, Saijo M. Analysis of cross-reactivity between flaviviruses with sera of patients with Japanese encephalitis showed the importance of neutralization tests for the diagnosis of Japanese encephalitis. J Infect Chemother 2019; 25:786-790. [PMID: 31105002 DOI: 10.1016/j.jiac.2019.04.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/23/2019] [Accepted: 04/09/2019] [Indexed: 12/21/2022]
Abstract
Japanese encephalitis (JE) is one of the most important viral encephalitis in Asia. JE is caused by the Japanese encephalitis virus (JEV), which belongs to the genus Flavivirus, family Flaviviridae. The diagnosis of JE is usually based on serological assays, and it has been reported that cross-reactivity between flaviviruses has complicated the interpretations of results from serological assays. Therefore, analysis of the cross-reactivity is an important subject for serological diagnosis of JE and other diseases caused by flaviviruses. In the present study, the cross-reactivity of the sera of patients with JE to other flaviviruses was analyzed using enzyme-linked immunosorbent assay (ELISA) and neutralization tests. Sixteen serum samples were collected from patients with JE and were tested for: i) IgM antibody against West Nile virus (WNV), dengue virus (DENV), zika virus (ZIKV), and tick-borne encephalitis virus (TBEV) using IgM-ELISA, ii) IgG antibody against DENV and TBEV using IgG-ELISA, and iii) neutralization tests with DENV 1-4, ZIKV, TBEV, and WNV. Out of the 16 samples tested using ELISA, 11 and 14 samples were positive for IgM and IgG, respectively, against at least one of the other flaviviruses. In neutralization tests, neutralizing potency against DENV, ZIKV, or TBEV was not detected in any samples. Although 13 samples showed neutralizing potency against WNV, their neutralizing antibody titers were equal to or less than one-eighth of those against JEV. These results show that neutralization tests are more specific than ELISA, indicating the importance of the neutralization tests in the diagnosis of JE.
Collapse
Affiliation(s)
- Takahiro Maeki
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan.
| | - Shigeru Tajima
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Makiko Ikeda
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Fumihiro Kato
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Satoshi Taniguchi
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Eri Nakayama
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Tomohiko Takasaki
- Kanagawa Prefectural Institute of Public Health, 1-3-1 Shimomachiya, Chigasaki, Kanagawa 253-0087, Japan
| | - Chang-Kweng Lim
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Masayuki Saijo
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| |
Collapse
|
30
|
Saxenhofer M, Schmidt S, Ulrich RG, Heckel G. Secondary contact between diverged host lineages entails ecological speciation in a European hantavirus. PLoS Biol 2019; 17:e3000142. [PMID: 30785873 PMCID: PMC6382107 DOI: 10.1371/journal.pbio.3000142] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/22/2019] [Indexed: 11/19/2022] Open
Abstract
The diversity of viruses probably exceeds biodiversity of eukaryotes, but little is known about the origin and emergence of novel virus species. Experimentation and disease outbreak investigations have allowed the characterization of rapid molecular virus adaptation. However, the processes leading to the establishment of functionally distinct virus taxa in nature remain obscure. Here, we demonstrate that incipient speciation in a natural host species has generated distinct ecological niches leading to adaptive isolation in an RNA virus. We found a very strong association between the distributions of two major phylogenetic clades in Tula orthohantavirus (TULV) and the rodent host lineages in a natural hybrid zone of the European common vole (Microtus arvalis). The spatial transition between the virus clades in replicated geographic clines is at least eight times narrower than between the hybridizing host lineages. This suggests a strong barrier for effective virus transmission despite frequent dispersal and gene flow among local host populations, and translates to a complete turnover of the adaptive background of TULV within a few hundred meters in the open, unobstructed landscape. Genetic differences between TULV clades are homogenously distributed in the genomes and mostly synonymous (93.1%), except for a cluster of nonsynonymous changes in the 5' region of the viral envelope glycoprotein gene, potentially involved in host-driven isolation. Evolutionary relationships between TULV clades indicate an emergence of these viruses through rapid differential adaptation to the previously diverged host lineages that resulted in levels of ecological isolation exceeding the progress of speciation in their vertebrate hosts.
Collapse
Affiliation(s)
- Moritz Saxenhofer
- Institute of Ecology and Evolution, University of Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, Lausanne, Switzerland
| | - Sabrina Schmidt
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Rainer G. Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel-Insel Riems, Germany
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, Lausanne, Switzerland
| |
Collapse
|
31
|
Chakraborty AK, Mukherjee P, Karam A, Das S, Barkalita L, Puro K, Sanjukta R, Ghatak S, Sakuntala I, Laha RG, Borah P, Ngachan SV, Sharma I, Sen A. Evidence of BVDV in Pigs from North Eastern Part of India- Genetic Profiling and Characterisation. Open Virol J 2018; 12:110-120. [PMID: 30288199 PMCID: PMC6142659 DOI: 10.2174/1874357901812010110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 07/06/2018] [Accepted: 07/16/2018] [Indexed: 01/27/2023] Open
Abstract
Introduction: The work has been attempted to detect and genetically characterise the nature of Bovine Viral Diarrhea Virus (BVDV) isolates from the porcine population of the north east. Methods and Material: The samples have been collected over a two year period and are from areas where there is a mixed and integrated rearing of livestock in close proximity. The isolates were identified, cloned and sequenced using BVD specific genomic primers for two important domains viz., E-2 and 5’ UTR. Results: Porcine BVD Sequences were analysed phylogenetically. Divergence in 3 sequences is noted in the 5’ UTR region that are forming a clear outlier group while E-2 sequences are coming close to BVDV group but forming a separate cluster.
Collapse
Affiliation(s)
- Amit Kr Chakraborty
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India.,Department of Microbiology, Assam University, Silchar - 788011, India
| | - Priyanka Mukherjee
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India.,Department of Microbiology, Assam University, Silchar - 788011, India
| | - Amarjit Karam
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Samir Das
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Luit Barkalita
- Department of Biotechnology, C.V.Sc, AAU, Khanapara, Assam, India
| | - Kekungo Puro
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Rajkumari Sanjukta
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Sandeep Ghatak
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Ingudam Sakuntala
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Ram Gopal Laha
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Prabodh Borah
- Department of Biotechnology, C.V.Sc, AAU, Khanapara, Assam, India
| | - S V Ngachan
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Indu Sharma
- Department of Microbiology, Assam University, Silchar - 788011, India
| | - Arnab Sen
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| |
Collapse
|
32
|
Pagán I. The diversity, evolution and epidemiology of plant viruses: A phylogenetic view. INFECTION GENETICS AND EVOLUTION 2018; 65:187-199. [PMID: 30055330 DOI: 10.1016/j.meegid.2018.07.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/24/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
During the past four decades, the scientific community has seen an exponential advance in the number, sophistication, and quality of molecular techniques and bioinformatics tools for the genetic characterization of plant virus populations. Predating these advances, the field of Phylogenetics has significantly contributed to understand important aspects of plant virus evolution. This review aims at summarizing the impact of Phylogenetics in the current knowledge on three major aspects of plant virus evolution that have benefited from the development of phylogenetic inference: (1) The identification and classification of plant virus diversity. (2) The mechanisms and forces shaping the evolution of plant virus populations. (3) The understanding of the interaction between plant virus evolution, epidemiology and ecology. The work discussed here highlights the important role of phylogenetic approaches in the study of the dynamics of plant virus populations.
Collapse
Affiliation(s)
- Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28223, Spain.
| |
Collapse
|
33
|
Abstract
Due to their dependence on cellular organisms for metabolism and replication, viruses are typically named and assigned to species according to their genome structure and the original host that they infect. But because viruses often infect multiple hosts and the numbers of distinct lineages within a host can be vast, their delineation into species is often dictated by arbitrary sequence thresholds, which are highly inconsistent across lineages. Here we apply an approach to determine the boundaries of viral species based on the detection of gene flow within populations, thereby defining viral species according to the biological species concept (BSC). Despite the potential for gene transfer between highly divergent genomes, viruses, like the cellular organisms they infect, assort into reproductively isolated groups and can be organized into biological species. This approach revealed that BSC-defined viral species are often congruent with the taxonomic partitioning based on shared gene contents and host tropism, and that bacteriophages can similarly be classified in biological species. These results open the possibility to use a single, universal definition of species that is applicable across cellular and acellular lifeforms.
Collapse
|
34
|
Broad receptor engagement of an emerging global coronavirus may potentiate its diverse cross-species transmissibility. Proc Natl Acad Sci U S A 2018; 115:E5135-E5143. [PMID: 29760102 DOI: 10.1073/pnas.1802879115] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Porcine deltacoronavirus (PDCoV), identified in 2012, is a common enteropathogen of swine with worldwide distribution. The source and evolutionary history of this virus is, however, unknown. PDCoV belongs to the Deltacoronavirus genus that comprises predominantly avian CoV. Phylogenetic analysis suggests that PDCoV originated relatively recently from a host-switching event between birds and mammals. Insight into receptor engagement by PDCoV may shed light into such an exceptional phenomenon. Here we report that PDCoV employs host aminopeptidase N (APN) as an entry receptor and interacts with APN via domain B of its spike (S) protein. Infection of porcine cells with PDCoV was drastically reduced by APN knockout and rescued after reconstitution of APN expression. In addition, we observed that PDCoV efficiently infects cells of unusual broad species range, including human and chicken. Accordingly, PDCoV S was found to target the phylogenetically conserved catalytic domain of APN. Moreover, transient expression of porcine, feline, human, and chicken APN renders cells susceptible to PDCoV infection. Binding of PDCoV to an interspecies conserved site on APN may facilitate direct transmission of PDCoV to nonreservoir species, including humans, potentially reflecting the mechanism that enabled a virus, ancestral to PDCoV, to breach the species barrier between birds and mammals. The APN cell surface protein is also used by several members of the Alphacoronavirus genus. Hence, our data constitute the second identification of CoVs from different genera that use the same receptor, implying that CoV receptor selection is subjected to specific restrictions that are still poorly understood.
Collapse
|
35
|
Full-Genome Characterization and Genetic Evolution of West African Isolates of Bagaza Virus. Viruses 2018; 10:v10040193. [PMID: 29652824 PMCID: PMC5923487 DOI: 10.3390/v10040193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/12/2018] [Accepted: 03/30/2018] [Indexed: 01/26/2023] Open
Abstract
Bagaza virus is a mosquito-borne flavivirus, first isolated in 1966 in Central African Republic. It has currently been identified in mosquito pools collected in the field in West and Central Africa. Emergence in wild birds in Europe and serological evidence in encephalitis patients in India raise questions on its genetic evolution and the diversity of isolates circulating in Africa. To better understand genetic diversity and evolution of Bagaza virus, we describe the full-genome characterization of 11 West African isolates, sampled from 1988 to 2014. Parameters such as genetic distances, N-glycosylation patterns, recombination events, selective pressures, and its codon adaptation to human genes are assessed. Our study is noteworthy for the observation of N-glycosylation and recombination in Bagaza virus and provides insight into its Indian origin from the 13th century. Interestingly, evidence of Bagaza virus codon adaptation to human house-keeping genes is also observed to be higher than those of other flaviviruses well known in human infections. Genetic variations on genome of West African Bagaza virus could play an important role in generating diversity and may promote Bagaza virus adaptation to other vertebrates and become an important threat in human health.
Collapse
|
36
|
Woolhouse MEJ, Brierley L. Epidemiological characteristics of human-infective RNA viruses. Sci Data 2018; 5:180017. [PMID: 29461515 PMCID: PMC5819479 DOI: 10.1038/sdata.2018.17] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/08/2017] [Indexed: 01/27/2023] Open
Abstract
RNA viruses are a major threat to human health. Here, based on extensive literature searches carried out over a period of 18 years, we provide a catalogue of all 214 known human-infective RNA virus species. We link these viruses to metadata for a number of traits that influence their epidemiology, including the date of the first report of human infection, transmissibility in human populations, transmission route(s) and host range. This database can be used in comparative studies of human-infective RNA viruses to identify the characteristics of viruses most likely to pose the greatest public health threat, both now and in the future.
Collapse
Affiliation(s)
- Mark E. J. Woolhouse
- Centre for Immunology, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Liam Brierley
- Centre for Immunology, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| |
Collapse
|
37
|
Chakraborty AK, Karam A, Mukherjee P, Barkalita L, Borah P, Das S, Sanjukta R, Puro K, Ghatak S, Shakuntala I, Sharma I, Laha RG, Sen A. Detection of classical swine fever virus E2 gene in cattle serum samples from cattle herds of Meghalaya. Virusdisease 2018; 29:89-95. [PMID: 29607364 DOI: 10.1007/s13337-018-0433-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/20/2018] [Indexed: 10/18/2022] Open
Abstract
The present study focused on the detection and genetic characterisation of 5' untranslated region (5'UTR) and E2 gene of classical swine fever virus (CSFV, family Flaviviridae, genus Pestivirus) from bovine population of the northeastern region of India. A total of 134 cattle serum samples were collected from organised cattle farms and were screened for CSFV antigen with a commercial antigen capture enzyme linked immunosorbent assay (Ag-ELISA) and reverse transcription-polymerase chain reaction (RT-PCR). A total of 10 samples were positive for CSFV antigen by ELISA, while all of them were positive in PCR for 5'UTR region. Full length E2 region of CSFV were successfully amplified from two positive samples and used for subsequent phylogenetic analysis and determination of protein 3D structure which showed similarity with reported CSFV isolate from Assam of sub-genogroup 2.1, with minor variations in protein structure.
Collapse
Affiliation(s)
- A K Chakraborty
- Division of Animal Health, ICAR RC for NEH Region, Umiam, Meghalaya India.,2Department of Microbiology, Assam University, Silchar, Assam India
| | - A Karam
- Division of Animal Health, ICAR RC for NEH Region, Umiam, Meghalaya India
| | - P Mukherjee
- Division of Animal Health, ICAR RC for NEH Region, Umiam, Meghalaya India.,2Department of Microbiology, Assam University, Silchar, Assam India
| | - L Barkalita
- Department of Biotechnology, C.V.Sc, AAU, Khanapara, Assam India
| | - P Borah
- Department of Biotechnology, C.V.Sc, AAU, Khanapara, Assam India
| | - S Das
- Division of Animal Health, ICAR RC for NEH Region, Umiam, Meghalaya India
| | - R Sanjukta
- Division of Animal Health, ICAR RC for NEH Region, Umiam, Meghalaya India
| | - K Puro
- Division of Animal Health, ICAR RC for NEH Region, Umiam, Meghalaya India
| | - S Ghatak
- Division of Animal Health, ICAR RC for NEH Region, Umiam, Meghalaya India
| | - I Shakuntala
- Division of Animal Health, ICAR RC for NEH Region, Umiam, Meghalaya India
| | - I Sharma
- 2Department of Microbiology, Assam University, Silchar, Assam India
| | - R G Laha
- Division of Animal Health, ICAR RC for NEH Region, Umiam, Meghalaya India
| | - A Sen
- Division of Animal Health, ICAR RC for NEH Region, Umiam, Meghalaya India
| |
Collapse
|
38
|
Corman VM, Rasche A, Baronti C, Aldabbagh S, Cadar D, Reusken CB, Pas SD, Goorhuis A, Schinkel J, Molenkamp R, Kümmerer BM, Bleicker T, Brünink S, Eschbach-Bludau M, Eis-Hübinger AM, Koopmans MP, Schmidt-Chanasit J, Grobusch MP, de Lamballerie X, Drosten C, Drexler JF. Assay optimization for molecular detection of Zika virus. Bull World Health Organ 2018; 94:880-892. [PMID: 27994281 PMCID: PMC5153932 DOI: 10.2471/blt.16.175950] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Objective To examine the diagnostic performance of real-time reverse transcription (RT)-polymerase chain reaction (PCR) assays for Zika virus detection. Methods We compared seven published real-time RT–PCR assays and two new assays that we have developed. To determine the analytical sensitivity of each assay, we constructed a synthetic universal control ribonucleic acid (uncRNA) containing all of the assays’ target regions on one RNA strand and spiked human blood or urine with known quantities of African or Asian Zika virus strains. Viral loads in 33 samples from Zika virus-infected patients were determined by using one of the new assays. Findings Oligonucleotides of the published real-time RT–PCR assays, showed up to 10 potential mismatches with the Asian lineage causing the current outbreak, compared with 0 to 4 mismatches for the new assays. The 95% lower detection limit of the seven most sensitive assays ranged from 2.1 to 12.1 uncRNA copies/reaction. Two assays had lower sensitivities of 17.0 and 1373.3 uncRNA copies/reaction and showed a similar sensitivity when using spiked samples. The mean viral loads in samples from Zika virus-infected patients were 5 × 104 RNA copies/mL of blood and 2 × 104 RNA copies/mL of urine. Conclusion We provide reagents and updated protocols for Zika virus detection suitable for the current outbreak strains. Some published assays might be unsuitable for Zika virus detection, due to the limited sensitivity and potential incompatibility with some strains. Viral concentrations in the clinical samples were close to the technical detection limit, suggesting that the use of insensitive assays will cause false-negative results.
Collapse
Affiliation(s)
- Victor M Corman
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Andrea Rasche
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Cecile Baronti
- UMR EPV Emergence des Pathologies Virales, Aix Marseille Université, Marseille, France
| | - Souhaib Aldabbagh
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Daniel Cadar
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | | | - Suzan D Pas
- Erasmus MC, Department of Viroscience, Rotterdam, Netherlands
| | - Abraham Goorhuis
- Department of Infectious Diseases, University of Amsterdam, Amsterdam, Netherlands
| | - Janke Schinkel
- Clinical Virology Laboratory, University of Amsterdam, Amsterdam, Netherlands
| | - Richard Molenkamp
- Clinical Virology Laboratory, University of Amsterdam, Amsterdam, Netherlands
| | - Beate M Kümmerer
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Tobias Bleicker
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Sebastian Brünink
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Monika Eschbach-Bludau
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Anna M Eis-Hübinger
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | | | - Jonas Schmidt-Chanasit
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Martin P Grobusch
- Department of Infectious Diseases, University of Amsterdam, Amsterdam, Netherlands
| | - Xavier de Lamballerie
- UMR EPV Emergence des Pathologies Virales, Aix Marseille Université, Marseille, France
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| |
Collapse
|
39
|
Characterization of Recombinant Flaviviridae Viruses Possessing a Small Reporter Tag. J Virol 2018; 92:JVI.01582-17. [PMID: 29093094 DOI: 10.1128/jvi.01582-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/19/2017] [Indexed: 01/13/2023] Open
Abstract
The family Flaviviridae consists of four genera, Flavivirus, Pestivirus, Pegivirus, and Hepacivirus, and comprises important pathogens of human and animals. Although the construction of recombinant viruses carrying reporter genes encoding fluorescent and bioluminescent proteins has been reported, the stable insertion of foreign genes into viral genomes retaining infectivity remains difficult. Here, we applied the 11-amino-acid subunit derived from NanoLuc luciferase to the engineering of the Flaviviridae viruses and then examined the biological characteristics of the viruses. We successfully generated recombinant viruses carrying the split-luciferase gene, including dengue virus, Japanese encephalitis virus, hepatitis C virus (HCV), and bovine viral diarrhea virus. The stability of the viruses was confirmed by five rounds of serial passages in the respective susceptible cell lines. The propagation of the recombinant luciferase viruses in each cell line was comparable to that of the parental viruses. By using a purified counterpart luciferase protein, this split-luciferase assay can be applicable in various cell lines, even when it is difficult to transduce the counterpart gene. The efficacy of antiviral reagents against the recombinant viruses could be monitored by the reduction of luciferase expression, which was correlated with that of viral RNA, and the recombinant HCV was also useful to examine viral dynamics in vivo Taken together, our findings indicate that the recombinant Flaviviridae viruses possessing the split NanoLuc luciferase gene generated here provide powerful tools to understand viral life cycle and pathogenesis and a robust platform to develop novel antivirals against Flaviviridae viruses.IMPORTANCE The construction of reporter viruses possessing a stable transgene capable of expressing specific signals is crucial to investigations of viral life cycle and pathogenesis and the development of antivirals. However, it is difficult to maintain the stability of a large foreign gene, such as those for fluorescence and bioluminescence, after insertion into a viral genome. Here, we successfully generated recombinant Flaviviridae viruses carrying the 11-amino-acid subunit derived from NanoLuc luciferase and demonstrated that these viruses are applicable to in vitro and in vivo experiments, suggesting that these recombinant Flaviviridae viruses are powerful tools for increasing our understanding of viral life cycle and pathogenesis and that these recombinant viruses will provide a robust platform to develop antivirals against Flaviviridae viruses.
Collapse
|
40
|
Larsen BB, Cole KL, Worobey M. Ancient DNA provides evidence of 27,000-year-old papillomavirus infection and long-term codivergence with rodents. Virus Evol 2018; 4:vey014. [PMID: 29977605 PMCID: PMC6007503 DOI: 10.1093/ve/vey014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The long-term evolutionary history of many viral lineages is poorly understood. Novel sources of ancient DNA combined with phylogenetic analyses can provide insight into the time scale of virus evolution. Here we report viral sequences from ancient North American packrat middens. We screened samples up to 27,000-years old and found evidence of papillomavirus (PV) infection in Neotoma cinerea (Bushy-tailed packrat). Phylogenetic analysis placed the PV sequences in a clade with other previously published PV sequences isolated from rodents. Concordance between the host and virus tree topologies along with a correlation in branch lengths suggests a shared evolutionary history between rodents and PVs. Based on host divergence times, PVs have likely been circulating in rodents for at least 17 million years. These results have implications for our understanding of PV evolution and for further research with ancient DNA from Neotoma middens.
Collapse
Affiliation(s)
- Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St., Tucson, 85721 AZ, USA
| | - Kenneth L Cole
- Northern Arizona University, School of Earth Sciences and Environmental Sustainability, 525 S. Beaver St., Flagstaff, 86011 AZ, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St., Tucson, 85721 AZ, USA
| |
Collapse
|
41
|
Antonovics J, Wilson AJ, Forbes MR, Hauffe HC, Kallio ER, Leggett HC, Longdon B, Okamura B, Sait SM, Webster JP. The evolution of transmission mode. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0083. [PMID: 28289251 PMCID: PMC5352810 DOI: 10.1098/rstb.2016.0083] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2016] [Indexed: 12/31/2022] Open
Abstract
This article reviews research on the evolutionary mechanisms leading to different transmission modes. Such modes are often under genetic control of the host or the pathogen, and often in conflict with each other via trade-offs. Transmission modes may vary among pathogen strains and among host populations. Evolutionary changes in transmission mode have been inferred through experimental and phylogenetic studies, including changes in transmission associated with host shifts and with evolution of the unusually complex life cycles of many parasites. Understanding the forces that determine the evolution of particular transmission modes presents a fascinating medley of problems for which there is a lack of good data and often a lack of conceptual understanding or appropriate methodologies. Our best information comes from studies that have been focused on the vertical versus horizontal transmission dichotomy. With other kinds of transitions, theoretical approaches combining epidemiology and population genetics are providing guidelines for determining when and how rapidly new transmission modes may evolve, but these are still in need of empirical investigation and application to particular cases. Obtaining such knowledge is a matter of urgency in relation to extant disease threats.This article is part of the themed issue 'Opening the black box: re-examining the ecology and evolution of parasite transmission'.
Collapse
Affiliation(s)
- Janis Antonovics
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Anthony J Wilson
- Integrative Entomology group, Vector-borne Viral Diseases programme, The Pirbright Institute, Pirbright GU24 0NF, UK
| | - Mark R Forbes
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B7
| | - Heidi C Hauffe
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trentino, Italy
| | - Eva R Kallio
- Department of Biological and Environmental Science, University of Jyvaskyla, PO Box 35, 40014 Jyvaskyla, Finland.,Department of Ecology, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Helen C Leggett
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Ben Longdon
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
| | - Beth Okamura
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW5 7BD, UK
| | - Steven M Sait
- School of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Joanne P Webster
- Department of Pathology and Pathogen Biology, Centre for Emerging, Endemic and Exotic Diseases, Royal Veterinary College, University of London, London AL9 7TA, UK
| |
Collapse
|
42
|
Abstract
Computer-assisted technologies of the genomic structure, biological function, and evolution of viruses remain a largely neglected area of research. The attention of bioinformaticians to this challenging field is currently unsatisfying in respect to its medical and biological importance. The power of new genome sequencing technologies, associated with new tools to handle "big data", provides unprecedented opportunities to address fundamental questions in virology. Here, we present an overview of the current technologies, challenges, and advantages of Next-Generation Sequencing (NGS) in relation to the field of virology. We present how viral sequences can be detected de novo out of current short-read NGS data. Furthermore, we discuss the challenges and applications of viral quasispecies and how secondary structures, commonly shaped by RNA viruses, can be computationally predicted. The phylogenetic analysis of viruses, as another ubiquitous field in virology, forms an essential element of describing viral epidemics and challenges current algorithms. Recently, the first specialized virus-bioinformatic organizations have been established. We need to bring together virologists and bioinformaticians and provide a platform for the implementation of interdisciplinary collaborative projects at local and international scales. Above all, there is an urgent need for dedicated software tools to tackle various challenges in virology.
Collapse
Affiliation(s)
- Martin Hölzer
- RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany; European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Manja Marz
- RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany; European Virus Bioinformatics Center (EVBC), Jena, Germany; FLI Leibniz Institute for Age Research, Jena, Germany.
| |
Collapse
|
43
|
Novel Alphacoronaviruses and Paramyxoviruses Cocirculate with Type 1 and Severe Acute Respiratory System (SARS)-Related Betacoronaviruses in Synanthropic Bats of Luxembourg. Appl Environ Microbiol 2017; 83:AEM.01326-17. [PMID: 28710271 DOI: 10.1128/aem.01326-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 07/05/2017] [Indexed: 01/21/2023] Open
Abstract
Several infectious disease outbreaks with high mortality in humans have been attributed to viruses that are thought to have evolved from bat viruses. In this study from Luxembourg, the genetic diversity and epidemiology of paramyxoviruses and coronaviruses shed by the bat species Rhinolophus ferrumequinum and Myotis emarginatus were evaluated. Feces collection (n = 624) was performed longitudinally in a mixed-species colony in 2015 and 2016. In addition, feces (n = 254) were collected cross-sectionally from six Myotis emarginatus colonies in 2016. By use of degenerate primers in a nested format, overall prevalences of 1.1% (10/878) and 4.9% (43/878) were determined for paramyxoviruses and coronaviruses. Sequences of the partial RNA-dependent RNA polymerase and spike glycoprotein genes of coronaviruses, as well as sequences of the partial L gene of paramyxoviruses, were obtained. Novel paramyxovirus and Alphacoronavirus strains were identified in different Myotis emarginatus colonies, and severe acute respiratory syndrome (SARS)-related Betacoronavirus strains were shed by Rhinolophus ferrumequinum Logistic regression revealed that the level of Alphacoronavirus shedding was highest in July (odds ratio, 2.8; P < 0.01), probably due to periparturient stress. Phylogenetic analyses point to close virus-host coevolution, and the high genetic similarity of the study strains suggests that the Myotis emarginatus colonies in Luxembourg are socially connected. Most interestingly, we show that bats also host Betacoronavirus1 strains. The high similarity of the spike gene sequences of these viruses with mammalian Betacoronavirus 1 strains may be of concern. Both the SARS-related and Betacoronavirus 1 strains detected in bats in Luxembourg may cross the species barrier after a host adaptation process.IMPORTANCE Bats are a natural reservoir of a number of zoonotic pathogens. Several severe outbreaks in humans (e.g., a Nipah virus outbreak in Malaysia in 1998, and the almost global spread of severe acute respiratory syndrome in 2003) have been caused by bat-borne viruses that were transmitted to humans mostly after virus adaptation (e.g., in intermediate animal hosts). Despite the indigenousness of bat species that host viruses with suspected zoonotic potential and despite the zoonotic transmission of European bat 1 lyssavirus in Luxembourg, knowledge about the diversity and epidemiology of bat viruses remains limited in this country. Moreover, in contrast to other European countries, bat viruses are currently not included in the national surveillance activities of this land-locked country. We suggest that this gap in disease surveillance should be addressed, since we show here that synanthropic bats host viruses that may be able to cross the species barrier.
Collapse
|
44
|
Parvez MK, Parveen S. Evolution and Emergence of Pathogenic Viruses: Past, Present, and Future. Intervirology 2017; 60:1-7. [PMID: 28772262 PMCID: PMC7179518 DOI: 10.1159/000478729] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 06/14/2017] [Indexed: 12/14/2022] Open
Abstract
Incidences of emerging/re-emerging deadly viral infections have significantly affected human health despite extraordinary progress in the area of biomedical knowledge. The best examples are the recurring outbreaks of dengue and chikungunya fever in tropical and sub-tropical regions, the recent epidemic of Zika in the Americas and the Caribbean, and the SARS, MERS, and influenza A outbreaks across the globe. The established natural reservoirs of human viruses are mainly farm animals, and, to a lesser extent, wild animals and arthropods. The intricate "host-pathogen-environment" relationship remains the key to understanding the emergence/re-emergence of pathogenic viruses. High population density, rampant constructions, poor sanitation, changing climate, and the introduction of anthropophilic vectors create selective pressure on host-pathogen reservoirs. Nevertheless, the knowledge and understanding of such zoonoses and pathogen diversity in their known non-human reservoirs are very limited. Prevention of arboviral infections using vector control methods has not been very successful. Currently, new approaches to protect against food-borne infections, such as consuming only properly cooked meats and animal products, are the most effective control measures. Though significant progress in controlling human immunodeficiency virus and hepatitis viruses has been achieved, the unpredictable nature of evolving viruses and the rare occasions of outbreaks severely hamper control and preventive modalities.
Collapse
Affiliation(s)
- Mohammad K. Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shama Parveen
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| |
Collapse
|
45
|
Kuno G, Mackenzie JS, Junglen S, Hubálek Z, Plyusnin A, Gubler DJ. Vertebrate Reservoirs of Arboviruses: Myth, Synonym of Amplifier, or Reality? Viruses 2017; 9:E185. [PMID: 28703771 PMCID: PMC5537677 DOI: 10.3390/v9070185] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/10/2017] [Accepted: 07/10/2017] [Indexed: 02/07/2023] Open
Abstract
The rapid succession of the pandemic of arbovirus diseases, such as dengue, West Nile fever, chikungunya, and Zika fever, has intensified research on these and other arbovirus diseases worldwide. Investigating the unique mode of vector-borne transmission requires a clear understanding of the roles of vertebrates. One major obstacle to this understanding is the ambiguity of the arbovirus definition originally established by the World Health Organization. The paucity of pertinent information on arbovirus transmission at the time contributed to the notion that vertebrates played the role of reservoir in the arbovirus transmission cycle. Because this notion is a salient feature of the arbovirus definition, it is important to reexamine its validity. This review addresses controversial issues concerning vertebrate reservoirs and their role in arbovirus persistence in nature, examines the genesis of the problem from a historical perspective, discusses various unresolved issues from multiple points of view, assesses the present status of the notion in light of current knowledge, and provides options for a solution to resolve the issue.
Collapse
Affiliation(s)
- Goro Kuno
- Formerly at the Division of Vector-Borne Infectious Diseases, Centers for Control and Prevention, Fort Collins, CO, USA.
| | - John S Mackenzie
- Faculty of Medical Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
- Division of Microbiology & Infectious Diseases, PathWest, Nedlands, Western Australia 6009.
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Helmut-Ruska-Haus, Chariteplatz 1, 10117 Berlin, Germany.
| | - Zdeněk Hubálek
- Institute of Vertebrate Biology, Academy of Sciences of Czech Republic, 60365 Brno, Czech Republic.
| | - Alexander Plyusnin
- Department of Virology, University of Helsinki, Haartmaninkatu 3, University of Helsinki, 00014 Helsinki, Finland.
| | - Duane J Gubler
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd., Singapore 169857 Singapore.
| |
Collapse
|
46
|
Geoghegan JL, Duchêne S, Holmes EC. Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families. PLoS Pathog 2017; 13:e1006215. [PMID: 28178344 PMCID: PMC5319820 DOI: 10.1371/journal.ppat.1006215] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/21/2017] [Accepted: 02/02/2017] [Indexed: 01/20/2023] Open
Abstract
The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear whether some virus families have a greater propensity to jump host species than others. If related viruses have an evolutionary history of co-divergence with their hosts there should be evidence of topological similarities between the virus and host phylogenetic trees, whereas host jumping generates incongruent tree topologies. By analyzing co-phylogenetic processes in 19 virus families and their eukaryotic hosts we provide a quantitative and comparative estimate of the relative frequency of virus-host co-divergence versus cross-species transmission among virus families. Notably, our analysis reveals that cross-species transmission is a near universal feature of the viruses analyzed here, with virus-host co-divergence occurring less frequently and always on a subset of viruses. Despite the overall high topological incongruence among virus and host phylogenies, the Hepadnaviridae, Polyomaviridae, Poxviridae, Papillomaviridae and Adenoviridae, all of which possess double-stranded DNA genomes, exhibited more frequent co-divergence than the other virus families studied here. At the other extreme, the virus and host trees for all the RNA viruses studied here, particularly the Rhabdoviridae and the Picornaviridae, displayed high levels of topological incongruence, indicative of frequent host switching. Overall, we show that cross-species transmission plays a major role in virus evolution, with all the virus families studied here having the potential to jump host species, and that increased sampling will likely reveal more instances of host jumping.
Collapse
Affiliation(s)
- Jemma L. Geoghegan
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Sebastián Duchêne
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Centre for Systems Genomics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- * E-mail:
| |
Collapse
|
47
|
Thibault PA, Watkinson RE, Moreira-Soto A, Drexler JF, Lee B. Zoonotic Potential of Emerging Paramyxoviruses: Knowns and Unknowns. Adv Virus Res 2017; 98:1-55. [PMID: 28433050 PMCID: PMC5894875 DOI: 10.1016/bs.aivir.2016.12.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The risk of spillover of enzootic paramyxoviruses and the susceptibility of recipient human and domestic animal populations are defined by a broad collection of ecological and molecular factors that interact in ways that are not yet fully understood. Nipah and Hendra viruses were the first highly lethal zoonotic paramyxoviruses discovered in modern times, but other paramyxoviruses from multiple genera are present in bats and other reservoirs that have unknown potential to spillover into humans. We outline our current understanding of paramyxovirus reservoir hosts and the ecological factors that may drive spillover, and we explore the molecular barriers to spillover that emergent paramyxoviruses may encounter. By outlining what is known about enzootic paramyxovirus receptor usage, mechanisms of innate immune evasion, and other host-specific interactions, we highlight the breadth of unexplored avenues that may be important in understanding paramyxovirus emergence.
Collapse
Affiliation(s)
| | - Ruth E Watkinson
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Jan F Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, NY, United States.
| |
Collapse
|
48
|
Rocha G, Alda F, Pagés A, Merchán T. Experimental transmission of rabbit haemorrhagic disease virus (RHDV) from rabbit to wild mice (Mus spretus and Apodemus sylvaticus) under laboratory conditions. INFECTION GENETICS AND EVOLUTION 2016; 47:94-98. [PMID: 27871816 DOI: 10.1016/j.meegid.2016.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 11/15/2016] [Accepted: 11/16/2016] [Indexed: 12/14/2022]
Abstract
Rabbit haemorrhagic disease (RHD) is a highly lethal and contagious viral disease that produces haemorrhagic lesions in liver and lungs of domestic and wild rabbits (Oryctolagus cuniculus). This study investigates the transmission of RHDV from infected rabbits to mice, based on the detection of viral RNA. Sixteen wild mice (Mus spretus, n=12 and Apodemus sylvaticus, n=4) were put in contact with nine rabbits inoculated with RHDV. No mice died following exposure to RHDV-infected rabbits or developed macroscopic haemorrhagic lesions. On the fourth day of contact, RHDV was detected by RT-PCR in the faeces of three of the four mice killed and in the livers of two of them. Three days after contact period with the inoculated rabbits (7th day of the experiment), RHDV was detected by RT-PCR in 100% (n=4) of the faeces and 50% (n=2) of the livers of euthanized animals. Ten days after contact period (14th day of the experiment), RHDV was not detected in the faeces or liver from any of the mice euthanized. However, 64days after contact period, RHDV was detected in the faeces of one mouse (1 of 4). We demonstrate cross-species transmission of RHDV-RNA from rabbit to rodent and the capability of RHDV-RNA to persist in mice for at least 10days after contact, and potentially up to two months, although viral replication within the rodent and/or infectivity was not evaluated in the present study.
Collapse
Affiliation(s)
- Gregorio Rocha
- Agroforestry Department, University of Extremadura, Avda. Virgen del Puerto 2, 10600 Plasencia, Cáceres, Spain.
| | - Fernando Alda
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13005 Ciudad Real, Spain; Louisiana State University, Museum of Natural Science, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Albert Pagés
- Laboratorios Hipra S.A., La Selva, 135, 17170 Amer, Girona, Spain; Plaza del Mercado, 10, 17853 Tortella, Girona, Spain
| | - Tomás Merchán
- Agroforestry Department, University of Extremadura, Avda. Virgen del Puerto 2, 10600 Plasencia, Cáceres, Spain
| |
Collapse
|
49
|
Klitting R, Gould EA, de Lamballerie X. G+C content differs in conserved and variable amino acid residues of flaviviruses and other evolutionary groups. INFECTION GENETICS AND EVOLUTION 2016; 45:332-340. [PMID: 27663721 DOI: 10.1016/j.meegid.2016.09.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/01/2016] [Accepted: 09/19/2016] [Indexed: 11/25/2022]
Abstract
Flaviviruses are small RNA viruses that exhibit genetic and ecological diversity and a wide range of G+C content (GC%). We discovered that, amongst flaviviruses, the GC% of nucleotides encoding conserved amino acid (AA) residues was consistently higher than that of nucleotides encoding variable AAs. This intriguing phenomenon was also identified for a wide range of other viruses, and some non-viral evolutionary groups. Here, we analyse the possible mechanisms underlying this imbalanced nucleotide content (in particular the role of the specific G content and the AA composition in flaviviral genomes) and discuss its evolutionary implications. Our findings suggest that one of the most simple characteristics of the genetic code (i.e., the G or G+C content of codons) is linked with the evolutionary behavior of the corresponding encoded AAs.
Collapse
Affiliation(s)
- Raphaëlle Klitting
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP), 27 bd Jean Moulin, 13385 Marseille, France.
| | - Ernest Andrew Gould
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP), 27 bd Jean Moulin, 13385 Marseille, France.
| | - Xavier de Lamballerie
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP), 27 bd Jean Moulin, 13385 Marseille, France; Institut Hospitalo-Universitaire Méditerranée-Infection, 27 bd Jean Moulin, 13385 Marseille, France.
| |
Collapse
|
50
|
Mélade J, Wieseke N, Ramasindrazana B, Flores O, Lagadec E, Gomard Y, Goodman SM, Dellagi K, Pascalis H. An eco-epidemiological study of Morbilli-related paramyxovirus infection in Madagascar bats reveals host-switching as the dominant macro-evolutionary mechanism. Sci Rep 2016; 6:23752. [PMID: 27068130 PMCID: PMC4828640 DOI: 10.1038/srep23752] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/08/2016] [Indexed: 11/09/2022] Open
Abstract
An eco-epidemiological investigation was carried out on Madagascar bat communities to better understand the evolutionary mechanisms and environmental factors that affect virus transmission among bat species in closely related members of the genus Morbillivirus, currently referred to as Unclassified Morbilli-related paramyxoviruses (UMRVs). A total of 947 bats were investigated originating from 52 capture sites (22 caves, 18 buildings, and 12 outdoor sites) distributed over different bioclimatic zones of the island. Using RT-PCR targeting the L-polymerase gene of the Paramyxoviridae family, we found that 10.5% of sampled bats were infected, representing six out of seven families and 15 out of 31 species analyzed. Univariate analysis indicates that both abiotic and biotic factors may promote viral infection. Using generalized linear modeling of UMRV infection overlaid on biotic and abiotic variables, we demonstrate that sympatric occurrence of bats is a major factor for virus transmission. Phylogenetic analyses revealed that all paramyxoviruses infecting Malagasy bats are UMRVs and showed little host specificity. Analyses using the maximum parsimony reconciliation tool CoRe-PA, indicate that host-switching, rather than co-speciation, is the dominant macro-evolutionary mechanism of UMRVs among Malagasy bats.
Collapse
Affiliation(s)
- Julien Mélade
- Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien (CRVOI), Plateforme de Recherche CYROI, 2 rue Maxime Rivière, 97490 Sainte Clotilde, La Réunion, France
- Université de La Réunion, UMR PIMIT “Processus Infectieux en Milieu Insulaire Tropical”, INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Denis, La Réunion, France
- Institut de Recherche pour le Développement (IRD), IRD – BP 50172, 97492 Sainte-Clotilde, La Réunion, France
| | - Nicolas Wieseke
- University of Leipzig, Department of Computer Science, Augustusplatz 10, D-04109 Leipzig, Germany
| | - Beza Ramasindrazana
- Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien (CRVOI), Plateforme de Recherche CYROI, 2 rue Maxime Rivière, 97490 Sainte Clotilde, La Réunion, France
- Université de La Réunion, UMR PIMIT “Processus Infectieux en Milieu Insulaire Tropical”, INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Denis, La Réunion, France
- Institut de Recherche pour le Développement (IRD), IRD – BP 50172, 97492 Sainte-Clotilde, La Réunion, France
- Association Vahatra, BP 3972, Antananarivo 101, Madagascar
- Institut Pasteur de Madagascar, BP 1274 Ambohitrakely, Antananarivo 101, Madagascar
| | - Olivier Flores
- UMR C53 CIRAD, Peuplements Végétaux et Bioagresseurs en Milieu Tropical, 7 chemin de l’IRAT, 97410 St Pierre, France
- Université de La Réunion, 15 Avenue René Cassin, 97400 Saint-Denis, France
| | - Erwan Lagadec
- Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien (CRVOI), Plateforme de Recherche CYROI, 2 rue Maxime Rivière, 97490 Sainte Clotilde, La Réunion, France
- Université de La Réunion, UMR PIMIT “Processus Infectieux en Milieu Insulaire Tropical”, INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Denis, La Réunion, France
- Institut de Recherche pour le Développement (IRD), IRD – BP 50172, 97492 Sainte-Clotilde, La Réunion, France
| | - Yann Gomard
- Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien (CRVOI), Plateforme de Recherche CYROI, 2 rue Maxime Rivière, 97490 Sainte Clotilde, La Réunion, France
- Université de La Réunion, UMR PIMIT “Processus Infectieux en Milieu Insulaire Tropical”, INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Denis, La Réunion, France
- Institut de Recherche pour le Développement (IRD), IRD – BP 50172, 97492 Sainte-Clotilde, La Réunion, France
| | - Steven M. Goodman
- Association Vahatra, BP 3972, Antananarivo 101, Madagascar
- Field Museum of Natural History, 1400 S. Lake Shore Dr, Chicago, IL 60605-2496, USA
| | - Koussay Dellagi
- Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien (CRVOI), Plateforme de Recherche CYROI, 2 rue Maxime Rivière, 97490 Sainte Clotilde, La Réunion, France
- Université de La Réunion, UMR PIMIT “Processus Infectieux en Milieu Insulaire Tropical”, INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Denis, La Réunion, France
- Institut de Recherche pour le Développement (IRD), IRD – BP 50172, 97492 Sainte-Clotilde, La Réunion, France
| | - Hervé Pascalis
- Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien (CRVOI), Plateforme de Recherche CYROI, 2 rue Maxime Rivière, 97490 Sainte Clotilde, La Réunion, France
- Université de La Réunion, UMR PIMIT “Processus Infectieux en Milieu Insulaire Tropical”, INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Denis, La Réunion, France
- Institut de Recherche pour le Développement (IRD), IRD – BP 50172, 97492 Sainte-Clotilde, La Réunion, France
| |
Collapse
|