1
|
Wu LY, Wijesekara Y, Piedade GJ, Pappas N, Brussaard CPD, Dutilh BE. Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes. Genome Biol 2024; 25:97. [PMID: 38622738 PMCID: PMC11020464 DOI: 10.1186/s13059-024-03236-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training and reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance. RESULTS We compare the performance of nine state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools have highly variable true positive rates (0-97%) and false positive rates (0-30%). PPR-Meta best distinguishes viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identify different subsets of the benchmarking data and all tools, except for Sourmash, find unique viral contigs. Performance of tools improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered. CONCLUSIONS Together, our independent benchmarking facilitates selecting choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments to viromics researchers.
Collapse
Affiliation(s)
- Ling-Yi Wu
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Yasas Wijesekara
- Institute of Bioinformatics, University Medicine Greifswald, Felix Hausdorff Str. 8, 17475, Greifswald, Germany
| | - Gonçalo J Piedade
- Department Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, PO Box 59, Texel, 1790 AB, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Nikolaos Pappas
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Corina P D Brussaard
- Department Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, PO Box 59, Texel, 1790 AB, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743, Jena, Germany.
| |
Collapse
|
2
|
Forni D, Pozzoli U, Cagliani R, Sironi M. Dinucleotide biases in the genomes of prokaryotic and eukaryotic dsDNA viruses and their hosts. Mol Ecol 2024; 33:e17287. [PMID: 38263702 DOI: 10.1111/mec.17287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/21/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
The genomes of cellular organisms display CpG and TpA dinucleotide composition biases. Such biases have been poorly investigated in dsDNA viruses. Here, we show that in dsDNA virus, bacterial, and eukaryotic genomes, the representation of TpA and CpG dinucleotides is strongly dependent on genomic G + C content. Thus, the classical observed/expected ratios do not fully capture dinucleotide biases across genomes. Because a larger portion of the variance in TpA frequency was explained by G + C content, we explored which additional factors drive the distribution of CpG dinucleotides. Using the residuals of the linear regressions as a measure of dinucleotide abundance and ancestral state reconstruction across eukaryotic and prokaryotic virus trees, we identified an important role for phylogeny in driving CpG representation. Nonetheless, phylogenetic ANOVA analyses showed that few host associations also account for significant variations. Among eukaryotic viruses, most significant differences were observed between arthropod-infecting viruses and viruses that infect vertebrates or unicellular organisms. However, an effect of viral DNA methylation status (either driven by the host or by viral-encoded methyltransferases) is also likely. Among prokaryotic viruses, cyanobacteria-infecting phages resulted to be significantly CpG-depleted, whereas phages that infect bacteria in the genera Burkolderia and Staphylococcus were CpG-rich. Comparison with bacterial genomes indicated that this effect is largely driven by the general tendency for phages to resemble the host's genomic CpG content. Notably, such tendency is stronger for temperate than for lytic phages. Our data shed light into the processes that shape virus genome composition and inform manipulation strategies for biotechnological applications.
Collapse
Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| |
Collapse
|
3
|
Lucia-Sanz A, Peng S, Leung CY(J, Gupta A, Meyer JR, Weitz JS. Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes. bioRxiv 2024:2024.01.08.574707. [PMID: 38260415 PMCID: PMC10802490 DOI: 10.1101/2024.01.08.574707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The enormous diversity of bacteriophages and their bacterial hosts presents a significant challenge to predict which phages infect a focal set of bacteria. Infection is largely determined by complementary -and largely uncharacterized- genetics of adsorption, injection, and cell take-over. Here we present a machine learning (ML) approach to predict phage-bacteria interactions trained on genome sequences of and phenotypic interactions amongst 51 Escherichia coli strains and 45 phage λ strains that coevolved in laboratory conditions for 37 days. Leveraging multiple inference strategies and without a priori knowledge of driver mutations, this framework predicts both who infects whom and the quantitative levels of infections across a suite of 2,295 potential interactions. The most effective ML approach inferred interaction phenotypes from independent contributions from phage and bacteria mutations, predicting phage host range with 86% mean classification accuracy while reducing the relative error in the estimated strength of the infection phenotype by 40%. Further, transparent feature selection in the predictive model revealed 18 of 176 phage λ and 6 of 18 E. coli mutations that have a significant influence on the outcome of phage-bacteria interactions, corroborating sites previously known to affect phage λ infections, as well as identifying mutations in genes of unknown function not previously shown to influence bacterial resistance. While the genetic variation studied was limited to a focal, coevolved phage-bacteria system, the method's success at recapitulating strain-level infection outcomes provides a path forward towards developing strategies for inferring interactions in non-model systems, including those of therapeutic significance.
Collapse
Affiliation(s)
- Adriana Lucia-Sanz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | | | | | - Animesh Gupta
- Department of Physics, University of California San Diego, La Jolla, California, USA
| | - Justin R. Meyer
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, California, USA
| | - Joshua S. Weitz
- Department of Biology, University of Maryland, College Park, MD, USA
- Department of Physics, University of Maryland, College Park, MD, USA
- Institut d’Biologie, École Normale Supérieure, Paris, France
| |
Collapse
|
4
|
Wang Y, Chi C, Zhang J, Zhang K, Deng D, Zheng W, Chen N, Meurens F, Zhu J. Systematic analysis of the codon usage patterns of African swine fever virus genome coding sequences reveals its host adaptation phenotype. Microb Genom 2024; 10:001186. [PMID: 38270515 PMCID: PMC10868601 DOI: 10.1099/mgen.0.001186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
African swine fever (ASF) is a severe haemorrhagic disease caused by the African swine fever virus (ASFV), transmitted by ticks, resulting in high mortality among domestic pigs and wild boars. The global spread of ASFV poses significant economic threats to the swine industry. This study employs diverse analytical methods to explore ASFV's evolution and host adaptation, focusing on codon usage patterns and associated factors. Utilizing phylogenetic analysis methods including neighbour-joining and maximum-likelihood, 64 ASFV strains were categorized into four clades. Codon usage bias (CUB) is modest in ASFV coding sequences. This research identifies multiple factors - such as nucleotide composition, mutational pressures, natural selection and geographical diversity - contributing to the formation of CUB in ASFV. Analysis of relative synonymous codon usage reveals CUB variations within clades and among ASFVs and their hosts. Both Codon Adaptation Index and Similarity Index analyses confirm that ASFV strains are highly adapted to soft ticks (Ornithodoros moubata) but less so to domestic pigs, which could be a result of the long-term co-evolution of ASFV with ticks. This study sheds light on the factors influencing ASFV's codon usage and fitness dynamics, enriching our understanding of its evolution, adaptation and host interactions.
Collapse
Affiliation(s)
- Yuening Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Chenglin Chi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Jiajia Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Kaili Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Dafu Deng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Wanglong Zheng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Nanhua Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - François Meurens
- Swine and Poultry Infectious Diseases Research Center, Faculty of Veterinary Medicine, University of Montreal, St. Hyacinthe, QC, J2S 2M2, Canada
- Department of Veterinary Microbiology and Immunology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada
| | - Jianzhong Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, PR China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| |
Collapse
|
5
|
Forni D, Pozzoli U, Cagliani R, Clerici M, Sironi M. Dinucleotide biases in RNA viruses that infect vertebrates or invertebrates. Microbiol Spectr 2023; 11:e0252923. [PMID: 37800906 PMCID: PMC10714974 DOI: 10.1128/spectrum.02529-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/12/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Akin to a molecular signature, dinucleotide composition can be exploited by the zinc-finger antiviral protein (ZAP) to restrict CpG-rich (and UpA-rich) RNA viruses. ZAP evolved in tetrapods, and it is not encoded by invertebrates and fish. Because a systematic analysis is missing, we analyzed the genomes of RNA viruses that infect vertebrates or invertebrates. We show that vertebrate single-stranded (ss) RNA(+) viruses and, to a lesser extent, double-stranded RNA viruses tend to have stronger CpG bias than invertebrate viruses. Conversely, ssRNA(-) viruses have similar dinucleotide composition whether they infect vertebrates or invertebrates. Analysis of ssRNA(+) viruses that infect mammals, reptiles, and fish indicated that ZAP is unlikely to be a major driver of CpG depletion. We also show that, compared to other coronaviruses, the genome of SARS-CoV-2 is not homogeneously CpG-depleted. Our study provides new insights into virus evolution and strategies for recoding RNA virus genomes.
Collapse
Affiliation(s)
- Diego Forni
- Bioinformatics Lab, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Uberto Pozzoli
- Bioinformatics Lab, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Rachele Cagliani
- Bioinformatics Lab, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy
- Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Bioinformatics Lab, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| |
Collapse
|
6
|
Parry RH, Slonchak A, Campbell LJ, Newton ND, Debat HJ, Gifford RJ, Khromykh AA. A novel tamanavirus ( Flaviviridae) of the European common frog ( Rana temporaria) from the UK. J Gen Virol 2023; 104:001927. [PMID: 38059479 PMCID: PMC10770923 DOI: 10.1099/jgv.0.001927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/19/2023] [Indexed: 12/08/2023] Open
Abstract
Flavivirids are small, enveloped, positive-sense RNA viruses from the family Flaviviridae with genomes of ~9-13 kb. Metatranscriptomic analyses of metazoan organisms have revealed a diversity of flavivirus-like or flavivirid viral sequences in fish and marine invertebrate groups. However, no flavivirus-like virus has been identified in amphibians. To remedy this, we investigated the virome of the European common frog (Rana temporaria) in the UK, utilizing high-throughput sequencing at six catch locations. De novo assembly revealed a coding-complete virus contig of a novel flavivirid ~11.2 kb in length. The virus encodes a single ORF of 3456 aa and 5' and 3' untranslated regions (UTRs) of 227 and 666 nt, respectively. We named this virus Rana tamanavirus (RaTV), as BLASTp analysis of the polyprotein showed the closest relationships to Tamana bat virus (TABV) and Cyclopterus lumpus virus from Pteronotus parnellii and Cyclopterus lumpus, respectively. Phylogenetic analysis of the RaTV polyprotein compared to Flavivirus and Flavivirus-like members indicated that RaTV was sufficiently divergent and basal to the vertebrate Tamanavirus clade. In addition to the Mitcham strain, partial but divergent RaTV, sharing 95.64-97.39 % pairwise nucleotide identity, were also obtained from the Poole and Deal samples, indicating that RaTV is widespread in UK frog samples. Bioinformatic analyses of predicted secondary structures in the 3'UTR of RaTV showed the presence of an exoribonuclease-resistant RNA (xrRNA) structure standard in flaviviruses and TABV. To examine this biochemically, we conducted an in vitro Xrn1 digestion assay showing that RaTV probably forms a functional Xrn1-resistant xrRNA.
Collapse
Affiliation(s)
- Rhys H. Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Andrii Slonchak
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
| | - Lewis J. Campbell
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Institute of Zoology, Zoological Society of London, London, UK
- Environment and Sustainability Institute, University of Exeter, Penryn, UK
| | - Natalee D. Newton
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
| | - Humberto J. Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola (UFYMA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5020ICA, Argentina
| | | | - Alexander A. Khromykh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
- AIDRC Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| |
Collapse
|
7
|
Aktürk Dizman Y. Codon usage bias analysis of the gene encoding NAD +-dependent DNA ligase protein of Invertebrate iridescent virus 6. Arch Microbiol 2023; 205:352. [PMID: 37812231 DOI: 10.1007/s00203-023-03688-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 09/18/2023] [Indexed: 10/10/2023]
Abstract
The genome of Invertebrate iridescent virus 6 (IIV6) contains a sequence that shows similarity to eubacterial NAD+-dependent DNA ligases. The 615-amino acid open reading frame (ORF 205R) consists of several domains, including an N-terminal domain Ia, followed by an adenylation domain, an OB-fold domain, a helix-hairpin-helix (HhH) domain, and a BRCT domain. Notably, the zinc finger domain, typically present in NAD+-dependent DNA ligases, is absent in ORF 205R. Since the protein encoded by ORF 205R (IIV6 DNA ligase gene) is involved in critical functions such as DNA replication, modification, and repair, it is crucial to comprehend the codon usage associated with this gene. In this paper, the codon usage bias (CUB) in DNA ligase gene of IIV6 and 11 reference iridoviruses was analyzed by comparing the nucleotide contents, relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), relative abundance of dinucleotides and other indices. Both the base content and the RCSU analysis indicated that the A- and T-ending codons were mostly favored in the DNA ligase gene of IIV6. The ENC value of 35.64 implied a high CUB in the IIV6 DNA ligase gene. The ENC plot, neutrality plot, parity rule 2 plot, correspondence analysis revealed that mutation pressure and natural selection had an impact on the CUB of the IIVs DNA ligase genes. Additionally, the analysis of codon adaptation index demonstrated that the IIV6 DNA ligase gene is strongly adapted to its host. These findings will improve our comprehension of the CUB of IIV6 DNA ligase and reference genes, which may provide the required information for a fundamental evolutionary analysis of these genes.
Collapse
Affiliation(s)
- Yeşim Aktürk Dizman
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, 53100, Rize, Turkey.
| |
Collapse
|
8
|
Fonseca PLC, Gaur RK, Aguiar ERGR. Editorial: Using virus specific-signatures during infection to characterize host-pathogen interactions. Front Genet 2023; 14:1290714. [PMID: 37811151 PMCID: PMC10556736 DOI: 10.3389/fgene.2023.1290714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023] Open
Affiliation(s)
- Paula Luize Camargos Fonseca
- Genetics Department, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rajarshi Kumar Gaur
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, India
| | | |
Collapse
|
9
|
Rajput M, Thakur N. Editorial: Advances in host-pathogen interactions for diseases in animals and birds. Front Vet Sci 2023; 10:1282110. [PMID: 37766859 PMCID: PMC10520279 DOI: 10.3389/fvets.2023.1282110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Affiliation(s)
- Mrigendra Rajput
- Department of Biology, University of Dayton, Dayton, OH, United States
| | | |
Collapse
|
10
|
Wang L, Zhao H, Wang Z, Ding S, Qin L, Jiang R, Deng X, He Z, Li L. An Evolutionary Perspective of Codon Usage Pattern, Dinucleotide Composition and Codon Pair Bias in Prunus Necrotic Ringspot Virus. Genes (Basel) 2023; 14:1712. [PMID: 37761852 PMCID: PMC10530913 DOI: 10.3390/genes14091712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Prunus necrotic ringspot virus (PNRSV) is a significant virus of ornamental plants and fruit trees. It is essential to study this virus due to its impact on the horticultural industry. Several studies on PNRSV diversity and phytosanitary detection technology were reported, but the content on the codon usage bias (CUB), dinucleotide preference and codon pair bias (CPB) of PNRSV is still uncertain. We performed comprehensive analyses on a dataset consisting of 359 coat protein (CP) gene sequences in PNRSV to examine the characteristics of CUB, dinucleotide composition, and CPB. The CUB analysis of PNRSV CP sequences showed that it was not only affected by natural selection, but also affected by mutations, and natural selection played a more significant role compared to mutations as the driving force. The dinucleotide composition analysis showed an over-expression of the CpC/GpA dinucleotides and an under-expression of the UpA/GpC dinucleotides. The dinucleotide composition of the PNRSV CP gene showed a weak association with the viral lineages and hosts, but a strong association with viral codon positions. Furthermore, the CPB of PNRSV CP gene is low and is related to dinucleotide preference and codon usage patterns. This research provides reference for future research on PNRSV genetic diversity and gene evolution mechanism.
Collapse
Affiliation(s)
- Lingqi Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China;
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Haiting Zhao
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Zhilei Wang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Shiwen Ding
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Lang Qin
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Runzhou Jiang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Xiaolong Deng
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Zhen He
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Liangjun Li
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China;
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
11
|
Silva KCP, Messias TS, Soares S. Investigation of Flaviviruses Emerging in Brazil as Etiology Factor in Nonsyndromic Orofacial Cleft. J Craniofac Surg 2023. [PMID: 36935399 DOI: 10.1097/SCS.0000000000009262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 03/21/2023] Open
Abstract
Brazil has one of the largest forest areas on the planet and the potential for the emergence of new diseases. In turn, orofacial clefts, especially cleft lip and or palate (CL/P), are characterized as congenital malformations and may be associated with genetic and environmental factors. The present study aimed to investigate in silico the flavivirus's potential to emerge in Brazil as an etiology of CL/P. A scoring method was created based on literature and nucleotide similarity analysis. An integrative analysis of the literature was performed to answer the questions through the databases PubMed/MEDLINE, SciELO, LILACS, and Google Scholar to have a more significant number of results. The software Basic Local Alignment Search Tool-BLAST 2.12.0, through the Genomic + Transcript Databases (Human Genomic plus Transcript Human G+T), was selected to find similarities with human sequences associated with CL/P. The viral sequences used were obtained from the National Center for Biotechnology Information Virus-NCBI Virus, in which only complete and referential genomes were selected. The flavivirus that emerged in Brazil and presented a high potential to cause CL/P was the Iguape virus strain (species Aroa virus), followed by the Cacipacore virus and the Rocio virus strain (species Ilheus virus) with medium potential to cause CL/P. In conclusion, we suggest among the virus evaluated that the Iguape virus presented a high potential of causing CL/P. As prevention, the control of arthropods and the hospital diffusion on viral dynamics, mainly in the CL/P context and other congenital malformations, are indicated.
Collapse
|
12
|
Khandia R, Khan AA, Karuvantevida N, Gurjar P, Rzhepakovsky IV, Legaz I. Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts. Pathogens 2023; 12:pathogens12020325. [PMID: 36839597 PMCID: PMC9961758 DOI: 10.3390/pathogens12020325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Hepatitis C virus (HCV) is enveloped RNA virus, encoding for a polyprotein that is processed by cellular proteases. The virus is responsible for liver cirrhosis, allograft rejection, and human hepatocellular carcinoma. Based on studies including compositional analysis, odds ratio analysis, parity analysis, skew analysis, relative synonymous codon usage, codon bias, and protein properties, it was evident that codon usage bias in HCV is dependent upon the nucleotide composition. Codon context analysis revealed CTC-CTG as a preferred codon pair. While CGA and CGT codons were rare, none of the codons were rare in HCV-like viruses envisaged in the present study. Many of the preferred codon pairs were valine amino acid-initiated, which possibly infers viral infectivity; hence the role of selection forces appears to act on the HCV genome, which was further validated by neutrality analysis where selection accounted for 87.28%, while mutation accounted for 12.72% force shaping codon usage. Furthermore, codon usage was correlated with the length of the genome. HCV viruses prefer valine-initiated codon pairs, while HCV-like viruses prefer alanine-initiated codon pairs. The HCV host range is very narrow and is confined to only humans and chimpanzees. Based on indices including codon usage correlation analysis, similarity index, and relative codon deoptimization index, it is evident in the study that the chimpanzee is the primary host of the virus. The present study helped elucidate the preferred host for HCV. The information presented in the study paved the way for generating an attenuated vaccine candidate through viral recoding, with finely tuned nucleotide composition and a perfect balance of preferred and rare codons.
Collapse
Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal 462026, India
- Correspondence: (R.K.); (I.L.)
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai P.O. Box 505055, United Arab Emirates
| | - Pankaj Gurjar
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
| | | | - Isabel Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, 30120 Murcia, Spain
- Correspondence: (R.K.); (I.L.)
| |
Collapse
|
13
|
Zhou J, Xing Y, Zhou Z, Wang S. A comprehensive analysis of Usutu virus (USUV) genomes revealed lineage-specific codon usage patterns and host adaptations. Front Microbiol 2023; 13:967999. [PMID: 36713228 PMCID: PMC9878346 DOI: 10.3389/fmicb.2022.967999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/19/2022] [Indexed: 01/15/2023] Open
Abstract
The Usutu virus (USUV) is an emerging arbovirus virus maintained in the environment of Afro-Eurasia via a bird-mosquito-bird enzootic cycle and sporadically infected other vertebrates. Despite primarily asymptomatic or mild symptoms, humans infected by USUV can develop severe neurological diseases such as meningoencephalitis. However, no detailed study has yet been conducted to investigate its evolution from the perspective of codon usage patterns. Codon usage choice of viruses reflects the genetic variations that enable them to reconcile their viability and fitness toward the external environment and new hosts. This study performed a comprehensive evolution and codon usage analysis of USUVs. Our reconstructed phylogenetic tree confirmed that the circulation viruses belong to eight distinct lineages, reaffirmed by principal component analysis based on codon usage patterns. We also found a relatively small codon usage bias and that natural selection, mutation pressure, dinucleotide abundance, and evolutionary processes collectively shaped the codon usage of the USUV, with natural selection predominating over the others. Additionally, a complex interaction of codon usage between the USUV and its host was observed. This process could have enabled USUV to adapt to various hosts and vectors, including humans. Therefore, the USUV may possess a potential risk of cross-species transmission and subsequent outbreaks. In this respect, further epidemiologic surveys, diversity monitoring, and pathogenetic research are warranted.
Collapse
|
14
|
Jiang L, Zhang Q, Xiao S, Si F. Deep decoding of codon usage strategies and host adaption preferences of soybean mosaic virus. Int J Biol Macromol 2022; 222:803-817. [PMID: 36167098 DOI: 10.1016/j.ijbiomac.2022.09.179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/13/2022] [Accepted: 09/17/2022] [Indexed: 11/05/2022]
Abstract
Soybean mosaic virus (SMV) has threatened the global yield of Leguminosae crops, but the mechanism of its infection, spread, and evolution remains unknown. A systemic analysis of 107 SMV strains was performed to explore the genome-wide codon usage profile and the various factors influencing the codon usage patterns of SMV, which provides insight into its molecular evolution and elucidates its unknown host adaptation pattern. The overall nucleotide composition and correlation analysis revealed that the preferred synonymous codons mostly end with A/U. Clustering by RSCU value of each strain and phylogenetic tree analysis showed that the SMV isolates studied were divided into four clades, with a low overall extent of codon usage bias (CUB) in SMV. According to the ENC, PR2, neutrality plot, and correspondence analysis, natural selection of geographical diversity may play a critical role in the CUB. Higher adaptability was shown in Glycine with SMV and more pressure was received by clade III. These findings could not only provide valuable information about the overall codon usage pattern of the SMV genome, but could also aid in the clarification of the involved mechanisms that dominate the codon usage patterns and genetic evolution of the SMV genome.
Collapse
Affiliation(s)
- Li Jiang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Qiang Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Shimin Xiao
- Shanwei Marine Industry Institute, Shanwei Institute of Technology, Shanwei 516600, China.
| | - Fusheng Si
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China.
| |
Collapse
|
15
|
Wang X, Sun J, Lu L, Pu FY, Zhang DR, Xie FQ. Evolutionary dynamics of codon usages for peste des petits ruminants virus. Front Vet Sci 2022; 9:968034. [PMID: 36032280 PMCID: PMC9412750 DOI: 10.3389/fvets.2022.968034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Peste des petits ruminants virus (PPRV) is an important agent of contagious, acute and febrile viral diseases in small ruminants, while its evolutionary dynamics related to codon usage are still lacking. Herein, we adopted information entropy, the relative synonymous codon usage values and similarity indexes and codon adaptation index to analyze the viral genetic features for 45 available whole genomes of PPRV. Some universal, lineage-specific, and gene-specific genetic features presented by synonymous codon usages of the six genes of PPRV that encode N, P, M, F, H and L proteins reflected evolutionary plasticity and independence. The high adaptation of PPRV to hosts at codon usages reflected high viral gene expression, but some synonymous codons that are rare in the hosts were selected in high frequencies in the viral genes. Another obvious genetic feature was that the synonymous codons containing CpG dinucleotides had weak tendencies to be selected in viral genes. The synonymous codon usage patterns of PPRV isolated during 2007–2008 and 2013–2014 in China displayed independent evolutionary pathway, although the overall codon usage patterns of these PPRV strains matched the universal codon usage patterns of lineage IV. According to the interplay between nucleotide and synonymous codon usages of the six genes of PPRV, the evolutionary dynamics including mutation pressure and natural selection determined the viral survival and fitness to its host.
Collapse
Affiliation(s)
- Xin Wang
- School of Stomatology, Lanzhou University, Lanzhou, China
| | - Jing Sun
- Geriatrics Department, The Second Hospital of Lanzhou University, Lanzhou, China
| | - Lei Lu
- School of Stomatology, Lanzhou University, Lanzhou, China
| | - Fei-yang Pu
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - De-rong Zhang
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Fu-qiang Xie
- Maxillofacial Surgery Department, The Second Hospital of Lanzhou University, Lanzhou, China
- *Correspondence: Fu-qiang Xie
| |
Collapse
|
16
|
Odon V, Fiddaman SR, Smith AL, Simmonds P. Comparison of CpG- and UpA-mediated restriction of RNA virus replication in mammalian and avian cells and investigation of potential ZAP-mediated shaping of host transcriptome compositions. RNA 2022; 28:1089-1109. [PMID: 35675984 PMCID: PMC9297844 DOI: 10.1261/rna.079102.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
The ability of zinc finger antiviral protein (ZAP) to recognize and respond to RNA virus sequences with elevated frequencies of CpG dinucleotides has been proposed as a functional part of the vertebrate innate immune antiviral response. It has been further proposed that ZAP activity shapes compositions of cytoplasmic mRNA sequences to avoid self-recognition, particularly mRNAs for interferons (IFNs) and IFN-stimulated genes (ISGs) expressed during the antiviral state. We investigated whether restriction of the replication of mutants of influenza A virus (IAV) and the echovirus 7 (E7) replicon with high CpG and UpA frequencies varied in different species of mammals and birds. Cell lines from different bird orders showed substantial variability in restriction of CpG-high mutants of IAV and E7 replicons, whereas none restricted UpA-high mutants, in marked contrast to universal restriction of both mutants in mammalian cells. Dinucleotide representation in ISGs and IFN genes was compared with those of cellular transcriptomes to determine whether potential differences in inferred ZAP activity between species shaped dinucleotide compositions of highly expressed genes during the antiviral state. While mammalian type 1 IFN genes typically showed often profound suppression of CpG and UpA frequencies, there was no oversuppression of either in ISGs in any species, irrespective of their ability to restrict CpG- or UpA-high mutants. Similarly, genome sequences of mammalian and avian RNA viruses were compositionally equivalent, as were IAV strains recovered from ducks, chickens and humans. Overall, we found no evidence for host variability in inferred ZAP function shaping host or viral transcriptome compositions.
Collapse
Affiliation(s)
- Valerie Odon
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Steven R Fiddaman
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Adrian L Smith
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, United Kingdom
| |
Collapse
|
17
|
B HDM, Guru A, Sudhakaran G, Murugan R, Arshad A, Arockiaraj J. Double‐edged sword role of shrimp miRNA explains an evolutionary language between shrimp‐pathogen interactions that unties the knot of shrimp infection. Reviews in Aquaculture 2022; 14:578-593. [DOI: 10.1111/raq.12613] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/21/2021] [Indexed: 10/16/2023]
Abstract
AbstractShrimp production, using a small‐scale enclosed pond system, is a rapidly growing aquaculture sector, which is valued around USD 18.30 billion in 2020. Intensified shrimp culture leads to the outbreak of transmissible diseases to eventually cause a huge loss in the production process and thus the economy. Studies on microRNA (miRNA) reveal that miRNA has an influential role in the host‐pathogen interaction during an infection. Recently, shrimp miRNA has been shown to help pathogen‐like viruses for their replication and infection. Several shrimp miRNAs were reported to be involved in enhancing host immunity against viral infection, especially white spot syndrome virus (WSSV) infection and Vibrio infection caused by bacterial species, whereas some shrimp miRNAs were reported to be hijacked by WSSV and to enhance the viral replication and establish the infection in shrimp. This gives an insight into the double‐edged sword role played by shrimp miRNA during host‐pathogen interaction. In future, this role could be employed against the virus to strengthen the shrimp culture. In this review, we discuss the role of shrimp miRNA and their mechanism(s) associated with the establishment of host‐pathogen interaction during infection, which will reveal the complexity associated with shrimp infection.
Collapse
Affiliation(s)
- Hari Deva Muthu B
- SRM Research Institute SRM Institute of Science and Technology Chennai Tamil Nadu India
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Ajay Guru
- SRM Research Institute SRM Institute of Science and Technology Chennai Tamil Nadu India
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Gokul Sudhakaran
- SRM Research Institute SRM Institute of Science and Technology Chennai Tamil Nadu India
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Raghul Murugan
- SRM Research Institute SRM Institute of Science and Technology Chennai Tamil Nadu India
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Aziz Arshad
- International Institute of Aquaculture and Aquatic Sciences (I‐AQUAS), Universiti Putra Malaysia Negeri Sembilan Malaysia
- Department of Aquaculture, Faculty of Agriculture Universiti Putra Malaysia Serdang Selangor Malaysia
| | - Jesu Arockiaraj
- SRM Research Institute SRM Institute of Science and Technology Chennai Tamil Nadu India
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| |
Collapse
|
18
|
Gaunt ER, Digard P. Compositional biases in RNA viruses: Causes, consequences and applications. Wiley Interdiscip Rev RNA 2022; 13:e1679. [PMID: 34155814 PMCID: PMC8420353 DOI: 10.1002/wrna.1679] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 01/05/2023]
Abstract
If each of the four nucleotides were represented equally in the genomes of viruses and the hosts they infect, each base would occur at a frequency of 25%. However, this is not observed in nature. Similarly, the order of nucleotides is not random (e.g., in the human genome, guanine follows cytosine at a frequency of ~0.0125, or a quarter the number of times predicted by random representation). Codon usage and codon order are also nonrandom. Furthermore, nucleotide and codon biases vary between species. Such biases have various drivers, including cellular proteins that recognize specific patterns in nucleic acids, that once triggered, induce mutations or invoke intrinsic or innate immune responses. In this review we examine the types of compositional biases identified in viral genomes and current understanding of the evolutionary mechanisms underpinning these trends. Finally, we consider the potential for large scale synonymous recoding strategies to engineer RNA virus vaccines, including those with pandemic potential, such as influenza A virus and Severe Acute Respiratory Syndrome Coronavirus Virus 2. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Evolution and Genomics > Computational Analyses of RNA RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
Collapse
Affiliation(s)
- Eleanor R. Gaunt
- Department of Infection and ImmunityThe Roslin Institute, The University of EdinburghEdinburghUK
| | - Paul Digard
- Department of Infection and ImmunityThe Roslin Institute, The University of EdinburghEdinburghUK
| |
Collapse
|
19
|
Etebari K, Gharuka M, Asgari S, Furlong MJ. Diverse Host Immune Responses of Different Geographical Populations of the Coconut Rhinoceros Beetle to Oryctes Rhinoceros Nudivirus (OrNV) Infection. Microbiol Spectr 2021; 9:e0068621. [PMID: 34523987 PMCID: PMC8557903 DOI: 10.1128/spectrum.00686-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/12/2021] [Indexed: 11/20/2022] Open
Abstract
Incursions of the coconut rhinoceros beetle (CRB), Oryctes rhinoceros, into different islands in the South Pacific have been detected in recent years. It has been suggested that this range expansion is related to an O. rhinoceros haplotype reported to show reduced susceptibility to the well-established classical biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). Our understanding of the genetic characteristics which distinguish the population of O. rhinoceros that has recently established in Solomon Islands from other well-established populations across the region is very limited. Here, we hypothesized that the recently established O. rhinoceros population should have greater innate immune responses when challenged by OrNV than those of well-established and native O. rhinoceros populations. We used the RNA sequencing (RNA-Seq) approach to generate gene expression profiles of midgut tissue from OrNV-infected and noninfected individuals collected in the Solomon Islands (recent incursion), Papua New Guinea and Fiji (previously established), and the Philippines (within the native range). The collections included individuals from each of the three major mitochondrial lineages (CRB-G, CRB-PNG, and CRB-S) known to the region, allowing us to explore the specific responses of each haplotype to infection. Although insects from the Philippines and Solomon Islands that were tested belong to the same mitochondrial lineage (CRB-G), their overall responses to infection were different. The number of differentially expressed genes between OrNV-infected and noninfected wild-caught individuals from the four different locations varied from 148 to 252. Persistent OrNV infection caused a high level of induced antimicrobial activity and immune responses in O. rhinoceros, but the direction and magnitude of the responses were population specific. The insects tested from the Solomon Islands displayed extremely high expression of genes which are known to be involved in immune responses (e.g. coleoptericin, cecropin, and serpin). These variations in the host immune system among insects from different geographical regions might be driven by variations in the virulence of OrNV isolates, and this requires further investigation. Overall, our current findings support the importance of immunity in insect pest incursion and an expansion of the pest's geographic range. IMPORTANCE Oryctes rhinoceros nudivirus (OrNV) is a double-stranded DNA (dsDNA) virus which has been used as a biocontrol agent to suppress coconut rhinoceros beetle (CRB) in the Pacific Islands. Recently a new wave of CRB incursions in Oceania is thought to be related to the presence of low-virulence isolates of OrNV or virus-tolerant haplotypes of beetles (CRB-G). Our comparative analysis of OrNV-infected and noninfected CRBs revealed that specific sets of genes were induced by viral infection in the beetles. This induction was much stronger in beetles collected from the Solomon Islands, a newly invaded country, than in individuals collected from within the beetle's native range (the Philippines) or from longer-established populations in its exotic range (Fiji and Papua New Guinea [PNG]). Beetles from the Philippines and the Solomon Islands that were tested in this study all belonged to the CRB-G haplotype, but the country-specific responses of the beetles to OrNV infection were different.
Collapse
Affiliation(s)
- Kayvan Etebari
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Maria Gharuka
- Research Division, Ministry of Agriculture and Livestock, Honiara, Solomon Islands
| | - Sassan Asgari
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael J. Furlong
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
20
|
Tschá MK, Suzukawa AA, Rodrigues-Luiz GF, da Silva AM, Cataneo AHD, Mattoso Coelho G, Ferreira AC, Soares Medeiros LC, Mansur D, Zanluca C, Duarte dos Santos CN. Pirahy virus: Identification of a new and potential emerging arbovirus in South Brazil. Virus Evol 2021; 7:veab105. [PMID: 35310294 PMCID: PMC8928568 DOI: 10.1093/ve/veab105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/07/2021] [Accepted: 12/16/2021] [Indexed: 01/14/2023] Open
Abstract
Genomic and epidemiological surveillance are paramount for the discovery of new viruses with the potential to cross species barriers. Here, we present a new member of the genus Alphavirus found in Trichoprosopon and Wyeomia mosquitoes, tentatively named Pirahy virus (PIRAV). PIRAV was isolated from mosquito pools collected in a rural area of Piraí do Sul, South Brazil. In vitro assays revealed that PIRAV replicates and causes cytopathic effects in vertebrate cell lines such as Vero E6, SH-SY5Y, BHK-21 and UMNSAH/DF-1. Genomic signature analysis supports these results showing a dinucleotide and codon usage balance compatible with several hosts. Phylogenetic analyses placed PIRAV basal to the Venezuelan equine encephalitis complex. Genome analyses, electron microscopy, and biological characterization show findings that may alert for the emergence of a new arbovirus in South America.
Collapse
Affiliation(s)
- Marcel Kruchelski Tschá
- Laboratório de Virologia Molecular, Instituto
Carlos Chagas/Fiocruz-PR, Rua Prof. Algacyr Munhoz Mader 3775, Curitiba,
PR 81350-010, Brazil
| | - Andreia A Suzukawa
- Laboratório de Virologia Molecular, Instituto
Carlos Chagas/Fiocruz-PR, Rua Prof. Algacyr Munhoz Mader 3775, Curitiba,
PR 81350-010, Brazil
| | - Gabriela Flavia Rodrigues-Luiz
- Departamento de Microbiologia, Imunologia e
Parasitologia, Centro de Ciências Biológicas (CCB), Universidade Federal de Santa
Catarina (UFSC), Av. Prof. Henrique da Silva Fontes 2754, Florianópolis,
SC 88040-900, Brazil
| | - Allan Martins da Silva
- Laboratório Central, Secretaria de Estado da
Saúde do Paraná, Rua Sebastiana Santana Fraga 1001, São José dos
Pinhais, PR 83060-500, Brazil
| | - Allan Henrique Depieri Cataneo
- Laboratório de Virologia Molecular, Instituto
Carlos Chagas/Fiocruz-PR, Rua Prof. Algacyr Munhoz Mader 3775, Curitiba,
PR 81350-010, Brazil
| | - Gabriela Mattoso Coelho
- Laboratório de Virologia Molecular, Instituto
Carlos Chagas/Fiocruz-PR, Rua Prof. Algacyr Munhoz Mader 3775, Curitiba,
PR 81350-010, Brazil
| | - Adão Celestino Ferreira
- Núcleo de Entomologia de Foz do Iguaçu,
Secretaria de Estado da Saúde do Paraná, R. Santos Dumont 460, Foz do
Iguaçu, PR 85851-040, Brazil
| | - Lia Carolina Soares Medeiros
- Laboratório de Biologia Celular, Instituto Carlos
Chagas/Fiocruz-PR, Rua Prof. Algacyr Munhoz Mader 3775, Curitiba, PR
81350-010, Brazil
| | - Daniel Mansur
- Departamento de Microbiologia, Imunologia e
Parasitologia, Centro de Ciências Biológicas (CCB), Universidade Federal de Santa
Catarina (UFSC), Av. Prof. Henrique da Silva Fontes 2754, Florianópolis,
SC 88040-900, Brazil
| | - Camila Zanluca
- Laboratório de Virologia Molecular, Instituto
Carlos Chagas/Fiocruz-PR, Rua Prof. Algacyr Munhoz Mader 3775, Curitiba,
PR 81350-010, Brazil
| | - Claudia N Duarte dos Santos
- Laboratório de Virologia Molecular, Instituto
Carlos Chagas/Fiocruz-PR, Rua Prof. Algacyr Munhoz Mader 3775, Curitiba,
PR 81350-010, Brazil
| |
Collapse
|
21
|
Auguste AJ, Langsjoen RM, Porier DL, Erasmus JH, Bergren NA, Bolling BG, Luo H, Singh A, Guzman H, Popov VL, Travassos da Rosa APA, Wang T, Kang L, Allen IC, Carrington CVF, Tesh RB, Weaver SC. Isolation of a novel insect-specific flavivirus with immunomodulatory effects in vertebrate systems. Virology 2021; 562:50-62. [PMID: 34256244 DOI: 10.1016/j.virol.2021.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/13/2022]
Abstract
We describe the isolation and characterization of a novel insect-specific flavivirus (ISFV), tentatively named Aripo virus (ARPV), that was isolated from Psorophora albipes mosquitoes collected in Trinidad. The ARPV genome was determined and phylogenetic analyses showed that it is a dual host associated ISFV, and clusters with the main mosquito-borne flaviviruses. ARPV antigen was significantly cross-reactive with Japanese encephalitis virus serogroup antisera, with significant cross-reactivity to Ilheus and West Nile virus (WNV). Results suggest that ARPV replication is limited to mosquitoes, as it did not replicate in the sandfly, culicoides or vertebrate cell lines tested. We also demonstrated that ARPV is endocytosed into vertebrate cells and is highly immunomodulatory, producing a robust innate immune response despite its inability to replicate in vertebrate systems. We show that prior infection or coinfection with ARPV limits WNV-induced disease in mouse models, likely the result of a robust ARPV-induced type I interferon response.
Collapse
Affiliation(s)
- Albert J Auguste
- Department of Entomology, College of Agriculture and Life Sciences, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
| | - Rose M Langsjoen
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Danielle L Porier
- Department of Entomology, College of Agriculture and Life Sciences, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Jesse H Erasmus
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Nicholas A Bergren
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Bethany G Bolling
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Huanle Luo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ankita Singh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Hilda Guzman
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Vsevolod L Popov
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | - Tian Wang
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Lin Kang
- Edward Via College of Osteopathic Medicine, Monroe, LA, 71203, USA; Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, 24060, USA
| | - Irving C Allen
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA; Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, 24060, USA
| | - Christine V F Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Robert B Tesh
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| |
Collapse
|
22
|
Pereira-Gómez M, Carrau L, Fajardo Á, Moreno P, Moratorio G. Altering Compositional Properties of Viral Genomes to Design Live-Attenuated Vaccines. Front Microbiol 2021; 12:676582. [PMID: 34276608 PMCID: PMC8278477 DOI: 10.3389/fmicb.2021.676582] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/01/2021] [Indexed: 12/11/2022] Open
Abstract
Live-attenuated vaccines have been historically used to successfully prevent numerous diseases caused by a broad variety of RNA viruses due to their ability to elicit strong and perdurable immune-protective responses. In recent years, various strategies have been explored to achieve viral attenuation by rational genetic design rather than using classic and empirical approaches, based on successive passages in cell culture. A deeper understanding of evolutionary implications of distinct viral genomic compositional aspects, as well as substantial advances in synthetic biology technologies, have provided a framework to achieve new viral attenuation strategies. Herein, we will discuss different approaches that are currently applied to modify compositional features of viruses in order to develop novel live-attenuated vaccines.
Collapse
Affiliation(s)
- Marianoel Pereira-Gómez
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Lucía Carrau
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Álvaro Fajardo
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pilar Moreno
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Gonzalo Moratorio
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| |
Collapse
|
23
|
Deb B, Uddin A, Chakraborty S. Analysis of codon usage of Horseshoe Bat Hepatitis B virus and its host. Virology 2021; 561:69-79. [PMID: 34171764 DOI: 10.1016/j.virol.2021.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 11/28/2022]
Abstract
In the present analysis, codon usage strategies and base distribution of Horseshoe bat hepatitis B virus (HBHBV) were analyzed and compared with its host Rhinolophus sinicus, as no work was yet reported. The magnitude of synonymous codon usage bias (CUB) in the virus and its host was low with higher proportion of the base C. Notably, 21 more frequently used codons, 19 less frequently used codons and 3 underrepresented codons (TCG, ACG and GCG) were found to be similar in both virus and its host coding sequences. Neutrality plot analysis reported greater role of natural selection in HBHBV (67.84%) and R. sinicus (76.90%) over mutation pressure. Base skewness and protein properties also influenced the CUB of genes. Further, codon usage analysis depicted, HBHBV and R. sinicus had many similarities in codon usage patterns that might reflect viral adaptation to its host.
Collapse
Affiliation(s)
- Bornali Deb
- Department of Biotechnology, Assam University, Silchar, 788150, Assam, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, 788150, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, 788150, Assam, India.
| |
Collapse
|
24
|
Halabi K, Mayrose I. Mechanisms Underlying Host Range Variation in Flavivirus: From Empirical Knowledge to Predictive Models. J Mol Evol 2021; 89:329-40. [PMID: 34059925 DOI: 10.1007/s00239-021-10013-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 05/13/2021] [Indexed: 12/22/2022]
Abstract
Preventing and controlling epidemics caused by vector-borne viruses are particularly challenging due to their diverse pool of hosts and highly adaptive nature. Many vector-borne viruses belong to the Flavivirus genus, whose members vary greatly in host range and specificity. Members of the Flavivirus genus can be categorized to four main groups: insect-specific viruses that are maintained solely in arthropod populations, mosquito-borne viruses and tick-borne viruses that are transmitted to vertebrate hosts by mosquitoes or ticks via blood feeding, and those with no-known vector. The mosquito-borne group encompasses the yellow fever, dengue, and West Nile viruses, all of which are globally spread and cause severe morbidity in humans. The Flavivirus genus is genetically diverse, and its members are subject to different host-specific and vector-specific selective constraints, which do not always align. Thus, understanding the underlying genetic differences that led to the diversity in host range within this genus is an important aspect in deciphering the mechanisms that drive host compatibility and can aid in the constant arms-race against viral threats. Here, we review the phylogenetic relationships between members of the genus, their infection bottlenecks, and phenotypic and genomic differences. We further discuss methods that utilize these differences for prediction of host shifts in flaviviruses and can contribute to viral surveillance efforts.
Collapse
|
25
|
Zarai Y, Zafrir Z, Siridechadilok B, Suphatrakul A, Roopin M, Julander J, Tuller T. Evolutionary selection against short nucleotide sequences in viruses and their related hosts. DNA Res 2021; 27:5825729. [PMID: 32339222 PMCID: PMC7320823 DOI: 10.1093/dnares/dsaa008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/20/2020] [Indexed: 11/13/2022] Open
Abstract
Viruses are under constant evolutionary pressure to effectively interact with the host intracellular factors, while evading its immune system. Understanding how viruses co-evolve with their hosts is a fundamental topic in molecular evolution and may also aid in developing novel viral based applications such as vaccines, oncologic therapies, and anti-bacterial treatments. Here, based on a novel statistical framework and a large-scale genomic analysis of 2,625 viruses from all classes infecting 439 host organisms from all kingdoms of life, we identify short nucleotide sequences that are under-represented in the coding regions of viruses and their hosts. These sequences cannot be explained by the coding regions’ amino acid content, codon, and dinucleotide frequencies. We specifically show that short homooligonucleotide and palindromic sequences tend to be under-represented in many viruses probably due to their effect on gene expression regulation and the interaction with the host immune system. In addition, we show that more sequences tend to be under-represented in dsDNA viruses than in other viral groups. Finally, we demonstrate, based on in vitro and in vivo experiments, how under-represented sequences can be used to attenuated Zika virus strains.
Collapse
Affiliation(s)
- Yoram Zarai
- Biomedical Engineering Department, Tel Aviv University, Tel Aviv 69978, Israel
| | - Zohar Zafrir
- Biomedical Engineering Department, Tel Aviv University, Tel Aviv 69978, Israel.,SynVaccine Ltd., Ramat Hachayal, Tel Aviv, Israel
| | | | - Amporn Suphatrakul
- National Center for Genetic Engineering and Biotechnology, Pathumthani 12120, Thailand
| | - Modi Roopin
- Biomedical Engineering Department, Tel Aviv University, Tel Aviv 69978, Israel.,SynVaccine Ltd., Ramat Hachayal, Tel Aviv, Israel
| | - Justin Julander
- Institute for Antiviral Research, Utah State University, Logan, UT, USA
| | - Tamir Tuller
- Biomedical Engineering Department, Tel Aviv University, Tel Aviv 69978, Israel.,SynVaccine Ltd., Ramat Hachayal, Tel Aviv, Israel
| |
Collapse
|
26
|
Truong Nguyen P, Garcia-Vallvé S, Puigbò P. An Unsupervised Algorithm for Host Identification in Flaviviruses. Life (Basel) 2021; 11:442. [PMID: 34069049 DOI: 10.3390/life11050442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 12/28/2022] Open
Abstract
Early characterization of emerging viruses is essential to control their spread, such as the Zika Virus outbreak in 2014. Among other non-viral factors, host information is essential for the surveillance and control of virus spread. Flaviviruses (genus Flavivirus), akin to other viruses, are modulated by high mutation rates and selective forces to adapt their codon usage to that of their hosts. However, a major challenge is the identification of potential hosts for novel viruses. Usually, potential hosts of emerging zoonotic viruses are identified after several confirmed cases. This is inefficient for deterring future outbreaks. In this paper, we introduce an algorithm to identify the host range of a virus from its raw genome sequences. The proposed strategy relies on comparing codon usage frequencies across viruses and hosts, by means of a normalized Codon Adaptation Index (CAI). We have tested our algorithm on 94 flaviviruses and 16 potential hosts. This novel method is able to distinguish between arthropod and vertebrate hosts for several flaviviruses with high values of accuracy (virus group 91.9% and host type 86.1%) and specificity (virus group 94.9% and host type 79.6%), in comparison to empirical observations. Overall, this algorithm may be useful as a complementary tool to current phylogenetic methods in monitoring current and future viral outbreaks by understanding host–virus relationships.
Collapse
|
27
|
Kumar N, Kaushik R, Tennakoon C, Uversky VN, Longhi S, Zhang KYJ, Bhatia S. Insights into the evolutionary forces that shape the codon usage in the viral genome segments encoding intrinsically disordered protein regions. Brief Bioinform 2021; 22:6231751. [PMID: 33866372 DOI: 10.1093/bib/bbab145] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/17/2021] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
Intrinsically disordered regions/proteins (IDRs) are abundant across all the domains of life, where they perform important regulatory roles and supplement the biological functions of structured proteins/regions (SRs). Despite the multifunctionality features of IDRs, several interrogations on the evolution of viral genomic regions encoding IDRs in diverse viral proteins remain unreciprocated. To fill this gap, we benchmarked the findings of two most widely used and reliable intrinsic disorder prediction algorithms (IUPred2A and ESpritz) to a dataset of 6108 reference viral proteomes to unravel the multifaceted evolutionary forces that shape the codon usage in the viral genomic regions encoding for IDRs and SRs. We found persuasive evidence that the natural selection predominantly governs the evolution of codon usage in regions encoding IDRs by most of the viruses. In addition, we confirm not only that codon usage in regions encoding IDRs is less optimized for the protein synthesis machinery (transfer RNAs pool) of their host than for those encoding SRs, but also that the selective constraints imposed by codon bias sustain this reduced optimization in IDRs. Our analysis also establishes that IDRs in viruses are likely to tolerate more translational errors than SRs. All these findings hold true, irrespective of the disorder prediction algorithms used to classify IDRs. In conclusion, our study offers a novel perspective on the evolution of viral IDRs and the evolutionary adaptability to multiple taxonomically divergent hosts.
Collapse
Affiliation(s)
- Naveen Kumar
- Diagnostic & Vaccine Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India
| | - Rahul Kaushik
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center 'Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences', Moscow region, Pushchino 142290, Russia
| | - Sonia Longhi
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Sandeep Bhatia
- Diagnostic & Vaccine Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India
| |
Collapse
|
28
|
Fros JJ, Visser I, Tang B, Yan K, Nakayama E, Visser TM, Koenraadt CJM, van Oers MM, Pijlman GP, Suhrbier A, Simmonds P. The dinucleotide composition of the Zika virus genome is shaped by conflicting evolutionary pressures in mammalian hosts and mosquito vectors. PLoS Biol 2021; 19:e3001201. [PMID: 33872300 PMCID: PMC8084339 DOI: 10.1371/journal.pbio.3001201] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 04/29/2021] [Accepted: 03/23/2021] [Indexed: 12/29/2022] Open
Abstract
Most vertebrate RNA viruses show pervasive suppression of CpG and UpA dinucleotides, closely resembling the dinucleotide composition of host cell transcriptomes. In contrast, CpG suppression is absent in both invertebrate mRNA and RNA viruses that exclusively infect arthropods. Arthropod-borne (arbo) viruses are transmitted between vertebrate hosts by invertebrate vectors and thus encounter potentially conflicting evolutionary pressures in the different cytoplasmic environments. Using a newly developed Zika virus (ZIKV) model, we have investigated how demands for CpG suppression in vertebrate cells can be reconciled with potentially quite different compositional requirements in invertebrates and how this affects ZIKV replication and transmission. Mutant viruses with synonymously elevated CpG or UpA dinucleotide frequencies showed attenuated replication in vertebrate cell lines, which was rescued by knockout of the zinc-finger antiviral protein (ZAP). Conversely, in mosquito cells, ZIKV mutants with elevated CpG dinucleotide frequencies showed substantially enhanced replication compared to wild type. Host-driven effects on virus replication attenuation and enhancement were even more apparent in mouse and mosquito models. Infections with CpG- or UpA-high ZIKV mutants in mice did not cause typical ZIKV-induced tissue damage and completely protected mice during subsequent challenge with wild-type virus, which demonstrates their potential as live-attenuated vaccines. In contrast, the CpG-high mutants displayed enhanced replication in Aedes aegypti mosquitoes and a larger proportion of mosquitoes carried infectious virus in their saliva. These findings show that mosquito cells are also capable of discriminating RNA based on dinucleotide composition. However, the evolutionary pressure on the CpG dinucleotides of viral genomes in arthropod vectors directly opposes the pressure present in vertebrate host cells, which provides evidence that an adaptive compromise is required for arbovirus transmission. This suggests that the genome composition of arbo flaviviruses is crucial to maintain the balance between high-level replication in the vertebrate host and persistent replication in the mosquito vector. The genome of the flavivirus Zika virus is stuck in a tug-of-war between two directly opposing evolutionary pressures that are present in the cells of mammalian host organisms and mosquito vectors; this results in an adaptive compromise, as manifested in the virus’s genome dinucleotide composition.
Collapse
Affiliation(s)
- Jelke J. Fros
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
- Laboratory of Virology, Wageningen University and Research, Wageningen, the Netherlands
- * E-mail:
| | - Imke Visser
- Laboratory of Virology, Wageningen University and Research, Wageningen, the Netherlands
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Bing Tang
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kexin Yan
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Eri Nakayama
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tessa M. Visser
- Laboratory of Entomology, Wageningen University and Research, Wageningen, the Netherlands
| | | | - Monique M. van Oers
- Laboratory of Virology, Wageningen University and Research, Wageningen, the Netherlands
| | - Gorben P. Pijlman
- Laboratory of Virology, Wageningen University and Research, Wageningen, the Netherlands
| | - Andreas Suhrbier
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
29
|
Colmant AMG, Hobson-Peters J, Slijkerman TAP, Harrison JJ, Pijlman GP, van Oers MM, Simmonds P, Hall RA, Fros JJ. Insect-Specific Flavivirus Replication in Mammalian Cells Is Inhibited by Physiological Temperature and the Zinc-Finger Antiviral Protein. Viruses 2021; 13:573. [PMID: 33805437 DOI: 10.3390/v13040573] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/16/2022] Open
Abstract
The genus Flavivirus contains pathogenic vertebrate-infecting flaviviruses (VIFs) and insect-specific flaviviruses (ISF). ISF transmission to vertebrates is inhibited at multiple stages of the cellular infection cycle, via yet to be elucidated specific antiviral responses. The zinc-finger antiviral protein (ZAP) in vertebrate cells can bind CpG dinucleotides in viral RNA, limiting virus replication. Interestingly, the genomes of ISFs contain more CpG dinucleotides compared to VIFs. In this study, we investigated whether ZAP prevents two recently discovered lineage II ISFs, Binjari (BinJV) and Hidden Valley viruses (HVV) from replicating in vertebrate cells. BinJV protein and dsRNA replication intermediates were readily observed in human ZAP knockout cells when cultured at 34 °C. In ZAP-expressing cells, inhibition of the interferon response via interferon response factors 3/7 did not improve BinJV protein expression, whereas treatment with kinase inhibitor C16, known to reduce ZAP’s antiviral function, did. Importantly, at 34 °C, both BinJV and HVV successfully completed the infection cycle in human ZAP knockout cells evident from infectious progeny virus in the cell culture supernatant. Therefore, we identify vertebrate ZAP as an important barrier that protects vertebrate cells from ISF infection. This provides new insights into flavivirus evolution and the mechanisms associated with host switching.
Collapse
|
30
|
Riemersma KK, Jaeger AS, Crooks CM, Braun KM, Weger-Lucarelli J, Ebel GD, Friedrich TC, Aliota MT. Rapid evolution of enhanced Zika virus virulence during direct vertebrate transmission chains. J Virol 2021; 95:JVI. [PMID: 33536175 DOI: 10.1128/JVI.02218-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Zika virus (ZIKV) has the unusual capacity to circumvent natural alternating mosquito-human transmission and be directly transmitted human-to-human via sexual and vertical routes. The impact of direct transmission on ZIKV evolution and adaptation to vertebrate hosts is unknown. Here we show that molecularly barcoded ZIKV rapidly adapted to a mammalian host during direct transmission chains in mice, coincident with the emergence of an amino acid substitution previously shown to enhance virulence. In contrast, little to no adaptation of ZIKV to mice was observed following chains of direct transmission in mosquitoes or alternating host transmission. Detailed genetic analyses revealed that ZIKV evolution in mice was generally more convergent and subjected to more relaxed purifying selection than in mosquitoes or alternate passages. These findings suggest that prevention of direct human transmission chains may be paramount to resist gains in ZIKV virulence.Importance We used experimental evolution to model chains of direct and indirect Zika virus (ZIKV) transmission by serially passaging a synthetic swarm of molecularly barcoded ZIKV within and between mosquitoes and mice. We observed that direct mouse transmission chains facilitated a rapid increase in ZIKV replication and enhanced virulence in mice. These findings demonstrate that ZIKV is capable of rapid adaptation to a vertebrate host and indicate that direct human-to-human transmission could pose a greater threat to public health than currently realized.
Collapse
|
31
|
Harima H, Orba Y, Torii S, Qiu Y, Kajihara M, Eto Y, Matsuta N, Hang'ombe BM, Eshita Y, Uemura K, Matsuno K, Sasaki M, Yoshii K, Nakao R, Hall WW, Takada A, Abe T, Wolfinger MT, Simuunza M, Sawa H. An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3'-untranslated region. Sci Rep 2021; 11:4883. [PMID: 33649491 PMCID: PMC7921595 DOI: 10.1038/s41598-021-84365-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Tick-borne flaviviruses (TBFVs) infect mammalian hosts through tick bites and can cause various serious illnesses, such as encephalitis and hemorrhagic fevers, both in humans and animals. Despite their importance to public health, there is limited epidemiological information on TBFV infection in Africa. Herein, we report that a novel flavivirus, Mpulungu flavivirus (MPFV), was discovered in a Rhipicephalus muhsamae tick in Zambia. MPFV was found to be genetically related to Ngoye virus detected in ticks in Senegal, and these viruses formed a unique lineage in the genus Flavivirus. Analyses of dinucleotide contents of flaviviruses indicated that MPFV was similar to those of other TBFVs with a typical vertebrate genome signature, suggesting that MPFV may infect vertebrate hosts. Bioinformatic analyses of the secondary structures in the 3′-untranslated regions (UTRs) revealed that MPFV exhibited unique exoribonuclease-resistant RNA (xrRNA) structures. Utilizing biochemical approaches, we clarified that two xrRNA structures of MPFV in the 3′-UTR could prevent exoribonuclease activity. In summary, our findings provide new information regarding the geographical distribution of TBFV and xrRNA structures in the 3′-UTR of flaviviruses.
Collapse
Affiliation(s)
- Hayato Harima
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shiho Torii
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yongjin Qiu
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yoshiki Eto
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naoya Matsuta
- Department of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Bernard M Hang'ombe
- Department of Para-Clinical Studies, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia
| | - Yuki Eshita
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kentaro Uemura
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Drug Discovery and Disease Research Laboratory, Shionogi & Co., Ltd., Osaka, Japan
| | - Keita Matsuno
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Unit of Risk Analysis and Management, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kentaro Yoshii
- Laboratory of Public Health, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.,National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - William W Hall
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,National Virus Reference Laboratory, School of Medicine, University College Dublin, Dublin, Ireland.,Centre for Research in Infectious Diseases, School of Medicine, University College Dublin, Dublin, Ireland.,Global Virus Network, Baltimore, MD, USA
| | - Ayato Takada
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia.,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Takashi Abe
- Department of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Martin Simuunza
- Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia.,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan. .,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan. .,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia. .,Global Virus Network, Baltimore, MD, USA. .,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia.
| |
Collapse
|
32
|
Fonseca P, Ferreira F, da Silva F, Oliveira LS, Marques JT, Goes-Neto A, Aguiar E, Gruber A. Characterization of a Novel Mitovirus of the Sand Fly Lutzomyia longipalpis Using Genomic and Virus-Host Interaction Signatures. Viruses 2020; 13:E9. [PMID: 33374584 DOI: 10.3390/v13010009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
Hematophagous insects act as the major reservoirs of infectious agents due to their intimate contact with a large variety of vertebrate hosts. Lutzomyia longipalpis is the main vector of Leishmania chagasi in the New World, but its role as a host of viruses is poorly understood. In this work, Lu. longipalpis RNA libraries were subjected to progressive assembly using viral profile HMMs as seeds. A sequence phylogenetically related to fungal viruses of the genus Mitovirus was identified and this novel virus was named Lul-MV-1. The 2697-base genome presents a single gene coding for an RNA-directed RNA polymerase with an organellar genetic code. To determine the possible host of Lul-MV-1, we analyzed the molecular characteristics of the viral genome. Dinucleotide composition and codon usage showed profiles similar to mitochondrial DNA of invertebrate hosts. Also, the virus-derived small RNA profile was consistent with the activation of the siRNA pathway, with size distribution and 5′ base enrichment analogous to those observed in viruses of sand flies, reinforcing Lu. longipalpis as a putative host. Finally, RT-PCR of different insect pools and sequences of public Lu. longipalpis RNA libraries confirmed the high prevalence of Lul-MV-1. This is the first report of a mitovirus infecting an insect host.
Collapse
|
33
|
Hassert M, Wolf KJ, Rajeh A, Schiebout C, Hoft SG, Ahn TH, DiPaolo RJ, Brien JD, Pinto AK. Diagnostic differentiation of Zika and dengue virus exposure by analyzing T cell receptor sequences from peripheral blood of infected HLA-A2 transgenic mice. PLoS Negl Trop Dis 2020; 14:e0008896. [PMID: 33270635 DOI: 10.1371/journal.pntd.0008896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/15/2020] [Accepted: 10/15/2020] [Indexed: 11/19/2022] Open
Abstract
Zika virus (ZIKV) is a significant global health threat due to its potential for rapid emergence and association with severe congenital malformations during infection in pregnancy. Despite the urgent need, accurate diagnosis of ZIKV infection is still a major hurdle that must be overcome. Contributing to the inaccuracy of most serologically-based diagnostic assays for ZIKV, is the substantial geographic and antigenic overlap with other flaviviruses, including the four serotypes of dengue virus (DENV). Within this study, we have utilized a novel T cell receptor (TCR) sequencing platform to distinguish between ZIKV and DENV infections. Using high-throughput TCR sequencing of lymphocytes isolated from DENV and ZIKV infected mice, we were able to develop an algorithm which could identify virus-associated TCR sequences uniquely associated with either a prior ZIKV or DENV infection in mice. Using this algorithm, we were then able to separate mice that had been exposed to ZIKV or DENV infection with 97% accuracy. Overall this study serves as a proof-of-principle that T cell receptor sequencing can be used as a diagnostic tool capable of distinguishing between closely related viruses. Our results demonstrate the potential for this innovative platform to be used to accurately diagnose Zika virus infection and potentially the next emerging pathogen(s). Diagnostic differentiation between dengue virus and Zika virus infections is a challenge due to serological cross-reactivity. In this study, we used a novel T cell receptor sequencing platform to identify T cell receptor sequences significantly associated with either dengue or Zika virus infection in HLA-A2 transgenic mice. These libraries were used to computationally train diagnostic classifiers which were capable of distinguishing between dengue and Zika virus in independent cohorts of infected mice.
Collapse
|
34
|
da Silva FS, Cruz ACR, de Almeida Medeiros DB, da Silva SP, Nunes MRT, Martins LC, Chiang JO, da Silva Lemos P, Cunha GM, de Araujo RF, de Oliveira Monteiro HA, Nunes Neto JP. Mitochondrial genome sequencing and phylogeny of Haemagogus albomaculatus, Haemagogus leucocelaenus, Haemagogus spegazzinii, and Haemagogus tropicalis (Diptera: Culicidae). Sci Rep 2020; 10:16948. [PMID: 33046768 DOI: 10.1038/s41598-020-73790-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/14/2020] [Indexed: 12/22/2022] Open
Abstract
The genus Haemagogus (Diptera: Culicidae) comprises species of great epidemiological relevance, involved in transmission cycles of the Yellow fever virus and other arboviruses in South America. So far, only Haemagogus janthinomys has complete mitochondrial sequences available. Given the unavailability of information related to aspects of the evolutionary biology and molecular taxonomy of this genus, we report here, the first sequencing of the mitogenomes of Haemagogus albomaculatus, Haemagogus leucocelaenus, Haemagogus spegazzinii, and Haemagogus tropicalis. The mitogenomes showed an average length of 15,038 bp, average AT content of 79.3%, positive AT-skews, negative GC-skews, and comprised 37 functional subunits (13 PCGs, 22 tRNA, and 02 rRNA). The PCGs showed ATN as start codon, TAA as stop codon, and signs of purifying selection. The tRNAs had the typical leaf clover structure, except tRNASer1. Phylogenetic analyzes of Bayesian inference and Maximum Likelihood, based on concatenated sequences from all 13 PCGs, produced identical topologies and strongly supported the monophyletic relationship between the Haemagogus and Conopostegus subgenera, and corroborated with the known taxonomic classification of the evaluated taxa, based on external morphological aspects. The information produced on the mitogenomes of the Haemagogus species evaluated here may be useful in carrying out future taxonomic and evolutionary studies of the genus.
Collapse
|
35
|
de Bernadi Schneider A, Jacob Machado D, Guirales S, Janies DA. FLAVi: An Enhanced Annotator for Viral Genomes of Flaviviridae. Viruses 2020; 12:E892. [PMID: 32824044 PMCID: PMC7472247 DOI: 10.3390/v12080892] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Responding to the ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and Zika, demands a greater understanding of how these viruses emerge and spread. Updated phylogenies are central to this understanding. Most cladograms of Flaviviridae focus on specific lineages and ignore outgroups, hampering the efficacy of the analysis to test ingroup monophyly and relationships. This is due to the lack of annotated Flaviviridae genomes, which has gene content variation among genera. This variation makes analysis without partitioning difficult. Therefore, we developed an annotation pipeline for the genera of Flaviviridae (Flavirirus, Hepacivirus, Pegivirus, and Pestivirus, named "Fast Loci Annotation of Viruses" (FLAVi; http://flavi-web.com/), that combines ab initio and homology-based strategies. FLAVi recovered 100% of the genes in Flavivirus and Hepacivirus genomes. In Pegivirus and Pestivirus, annotation efficiency was 100% except for one partition each. There were no false positives. The combined phylogenetic analysis of multiple genes made possible by annotation has clear impacts over the tree topology compared to phylogenies that we inferred without outgroups or data partitioning. The final tree is largely congruent with previous hypotheses and adds evidence supporting the close phylogenetic relationship between dengue and Zika.
Collapse
Affiliation(s)
- Adriano de Bernadi Schneider
- AntiViral Research Center, Department of Medicine, University of California San Diego, San Diego, CA 92103, USA;
| | - Denis Jacob Machado
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; (S.G.); (D.A.J.)
| | - Sayal Guirales
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; (S.G.); (D.A.J.)
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; (S.G.); (D.A.J.)
| |
Collapse
|
36
|
Oberemok VV, Laikova KV, Yurchenko KA, Marochkin NA, Fomochkina II, Kubyshkin AV. SARS-CoV-2 will constantly sweep its tracks: a vaccine containing CpG motifs in 'lasso' for the multi-faced virus. Inflamm Res 2020; 69:801-12. [PMID: 32656668 DOI: 10.1007/s00011-020-01377-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/28/2020] [Accepted: 07/06/2020] [Indexed: 12/11/2022] Open
Abstract
During the current COVID-19 pandemic, the global ratio between the dead and the survivors is approximately 1 to 10, which has put humanity on high alert and provided strong motivation for the intensive search for vaccines and drugs. It is already clear that if we follow the most likely scenario, which is similar to that used to create seasonal influenza vaccines, then we will need to develop improved vaccine formulas every year to control the spread of the new, highly mutable coronavirus SARS-CoV-2. In this article, using well-known RNA viruses (HIV, influenza viruses, HCV) as examples, we consider the main successes and failures in creating primarily highly effective vaccines. The experience accumulated dealing with the biology of zoonotic RNA viruses suggests that the fight against COVID-19 will be difficult and lengthy. The most effective vaccines against SARS-CoV-2 will be those able to form highly effective memory cells for both humoral (memory B cells) and cellular (cross-reactive antiviral memory T cells) immunity. Unfortunately, RNA viruses constantly sweep their tracks and perhaps one of the most promising solutions in the fight against the COVID-19 pandemic is the creation of 'universal' vaccines based on conservative SARS-CoV-2 genome sequences (antigen-presenting) and unmethylated CpG dinucleotides (adjuvant) in the composition of the phosphorothioate backbone of single-stranded DNA oligonucleotides (ODN), which can be effective for long periods of use. Here, we propose a SARS-CoV-2 vaccine based on a lasso-like phosphorothioate oligonucleotide construction containing CpG motifs and the antigen-presenting unique ACG-containing genome sequence of SARS-CoV-2. We found that CpG dinucleotides are the most rare dinucleotides in the genomes of SARS-CoV-2 and other known human coronaviruses, and hypothesized that their higher frequency could be responsible for the unwanted increased lethality to the host, causing a ‘cytokine storm’ in people who overexpress cytokines through the activation of specific Toll-like receptors in a manner similar to TLR9-CpG ODN interactions. Interestingly, the virus strains sequenced in China (Wuhan) in February 2020 contained on average one CpG dinucleotide more in their genome than the later strains from the USA (New York) sequenced in May 2020. Obviously, during the first steps of the microevolution of SARS-CoV-2 in the human population, natural selection tends to select viral genomes containing fewer CpG motifs that do not trigger a strong innate immune response, so the infected person has moderate symptoms and spreads SARS-CoV-2 more readily. However, in our opinion, unmethylated CpG dinucleotides are also capable of preparing the host immune system for the coronavirus infection and should be present in SARS-CoV-2 vaccines as strong adjuvants.
Collapse
|
37
|
Melo Lucio FN, Da Silva JE, Marinho EM, Da Silva Mendes FR, Marinho MM, Marinho ES. METHYLCYTISINE ALCALOID POTENTIALLY ACTIVE AGAINST DENGUE VIRUS: A MOLECULAR DOCKING STUDY AND ELECTRONIC STRUCTURAL CHARACTERIZATION. ACTA ACUST UNITED AC 2020. [DOI: 10.29121/granthaalayah.v8.i1.2020.270] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Dengue fever is a serious disease acquired from the Aedes aegypti mosquito present in tropical and subtropical regions, deeply impacting the population's quality of life. Its control requires combating the virus, and the use of substances that do not cause damage to the environment is of fundamental importance. The present work was carried out in silico to perform the structural-electronic characterization of the alkaloid Methylcytisine, a tricyclic quinolizidine alkaloid that has insecticidal activities, identifying the molecular boundary orbitals and descriptors of global chemical reactivity and assessing the inhibitory potential of methylcytisine on NS5 methyltransferase enzyme dengue virus, as well as identifying possible biological targets in humans. Methylcytisine was geometrically optimized through semi-empirical quantum calculations with thermodynamically more stable conformation, characterizing its structure (atoms, angles and bonds) and its reactivity descriptors. The analysis of the molecular docking simulations showed that methylcytisine is coupled in the same active site of the NS5 enzyme methyltransferase DENV, very similar to the complexed ligand S-adenosyl-L-homocysteine. The intermolecular interactions found for the complex formed and the distance values of the enzyme residues, indicate that methylcytisine has potential application as a new inhibitor of the dengue virus, however it has a high possibility of interaction with human neuronal acetylcholine receptors.
Collapse
|
38
|
Tian HF, Hu QM, Xiao HB, Zeng LB, Meng Y, Li Z. Genetic and codon usage bias analyses of major capsid protein gene in Ranavirus. Infect Genet Evol 2020; 84:104379. [PMID: 32497680 DOI: 10.1016/j.meegid.2020.104379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/07/2020] [Accepted: 05/22/2020] [Indexed: 12/29/2022]
Abstract
The Ranavirus (one genus of Iridovidae family) is an emerging pathogen that infects fish, amphibian, and reptiles, and causes great economical loss and ecological threat to farmed and wild animals globally. The major capsid protein (MCP) has been used as genetic typing marker and as target to design vaccines. Herein, the codon usage pattern of 73 MCP genes of Ranavirus and Lymphocystivirus are studied by calculating effective number of codons (ENC), relative synonymous codon usage (RSCU), codon adaptation index (CAI), and relative codon deoptimization index (RCDI), and similarity index (SiD). The Ranavirus are confirmed to be classified into five groups by using phylogenetic analysis, and varied nucleotide compositions and hierarchical cluster analysis based on RSCU. The results revealed different codon usage patterns among Lymphocystivirus and five groups of Ranavirus. Ranavirus had six over-represented codons ended with G/C nucleotide, while Lymphocystivirus had six over-represented codons ended with A/T nucleotide. A comparative analysis of parameters that define virus and host relatedness in terms of codon usage were analyzed indicated that Amphibian-like ranaviruses (ALRVs) seem to possess lower ENC values and higher CAIs in contrast to other ranaviruses isolated from fishes, and two groups (FV3-like and CMTV-like group) of them had received higher selection pressure from their hosts as having higher relative codon deoptimization index (RCDI) and similarity index (SiD). The correspondence analysis (COA) and Spearman's rank correlation analyses revealed that nucleotide compositions, relative dinucleotide frequency, mutation pressure, and natural translational selection shape the codon usage pattern in MCP genes and the ENC-GC3S and neutrality plots indicated that the natural selection is the predominant factor. These results contribute to understanding the evolution of Ranavirus and their adaptions to their hosts.
Collapse
Affiliation(s)
- Hai-Feng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Qiao-Mu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Han-Bing Xiao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Ling-Bing Zeng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| | - Zhong Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| |
Collapse
|
39
|
Young F, Rogers S, Robertson DL. Predicting host taxonomic information from viral genomes: A comparison of feature representations. PLoS Comput Biol 2020; 16:e1007894. [PMID: 32453718 PMCID: PMC7307784 DOI: 10.1371/journal.pcbi.1007894] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 06/22/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022] Open
Abstract
The rise in metagenomics has led to an exponential growth in virus discovery. However, the majority of these new virus sequences have no assigned host. Current machine learning approaches to predicting virus host interactions have a tendency to focus on nucleotide features, ignoring other representations of genomic information. Here we investigate the predictive potential of features generated from four different ‘levels’ of viral genome representation: nucleotide, amino acid, amino acid properties and protein domains. This more fully exploits the biological information present in the virus genomes. Over a hundred and eighty binary datasets for infecting versus non-infecting viruses at all taxonomic ranks of both eukaryote and prokaryote hosts were compiled. The viral genomes were converted into the four different levels of genome representation and twenty feature sets were generated by extracting k-mer compositions and predicted protein domains. We trained and tested Support Vector Machine, SVM, classifiers to compare the predictive capacity of each of these feature sets for each dataset. Our results show that all levels of genome representation are consistently predictive of host taxonomy and that prediction k-mer composition improves with increasing k-mer length for all k-mer based features. Using a phylogenetically aware holdout method, we demonstrate that the predictive feature sets contain signals reflecting both the evolutionary relationship between the viruses infecting related hosts, and host-mimicry. Our results demonstrate that incorporating a range of complementary features, generated purely from virus genome sequences, leads to improved accuracy for a range of virus host prediction tasks enabling computational assignment of host taxonomic information. Elucidating the host of a newly identified virus species is an important challenge, with applications from knowing the source species of a newly emerged pathogen to understanding the bacteriophage-host relationships within the microbiome of any of earth’s ecosystems. Current high throughput methods used to identify viruses within biological or environmental samples have resulted in an unprecedented increase in virus discovery. However, for the majority of these virus genomes the host species/taxonomic classification remains unknown. To address this gap in our knowledge there is a need for fast, accurate computational methods for the assignment of putative host taxonomic information. Machine learning is an ideal approach but to maximise predictive accuracy the viral genomes need to be represented in a format (sets of features) that makes the discriminative information available to the machine learning algorithm. Here, we compare different types of features derived from the same viral genomes for their ability to predict host information. Our results demonstrate that all these feature sets are predictive of host taxonomy and when combined have the potential to improve accuracy over the use of individual feature sets across many virus host prediction applications.
Collapse
Affiliation(s)
- Francesca Young
- MRC-University of Glasgow Centre For Virus Research, Glasgow, United Kingdom
| | - Simon Rogers
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
| | - David L. Robertson
- MRC-University of Glasgow Centre For Virus Research, Glasgow, United Kingdom
- * E-mail:
| |
Collapse
|
40
|
Randhawa GS, Soltysiak MPM, El Roz H, de Souza CPE, Hill KA, Kari L. Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study. PLoS One 2020; 15:e0232391. [PMID: 32330208 PMCID: PMC7182198 DOI: 10.1371/journal.pone.0232391] [Citation(s) in RCA: 195] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/14/2020] [Indexed: 12/24/2022] Open
Abstract
The 2019 novel coronavirus (renamed SARS-CoV-2, and generally referred to as the COVID-19 virus) has spread to 184 countries with over 1.5 million confirmed cases. Such major viral outbreaks demand early elucidation of taxonomic classification and origin of the virus genomic sequence, for strategic planning, containment, and treatment. This paper identifies an intrinsic COVID-19 virus genomic signature and uses it together with a machine learning-based alignment-free approach for an ultra-fast, scalable, and highly accurate classification of whole COVID-19 virus genomes. The proposed method combines supervised machine learning with digital signal processing (MLDSP) for genome analyses, augmented by a decision tree approach to the machine learning component, and a Spearman's rank correlation coefficient analysis for result validation. These tools are used to analyze a large dataset of over 5000 unique viral genomic sequences, totalling 61.8 million bp, including the 29 COVID-19 virus sequences available on January 27, 2020. Our results support a hypothesis of a bat origin and classify the COVID-19 virus as Sarbecovirus, within Betacoronavirus. Our method achieves 100% accurate classification of the COVID-19 virus sequences, and discovers the most relevant relationships among over 5000 viral genomes within a few minutes, ab initio, using raw DNA sequence data alone, and without any specialized biological knowledge, training, gene or genome annotations. This suggests that, for novel viral and pathogen genome sequences, this alignment-free whole-genome machine-learning approach can provide a reliable real-time option for taxonomic classification.
Collapse
Affiliation(s)
- Gurjit S. Randhawa
- Department of Computer Science, The University of Western Ontario, London, ON, Canada
| | | | - Hadi El Roz
- Department of Biology, The University of Western Ontario, London, ON, Canada
| | - Camila P. E. de Souza
- Department of Statistical and Actuarial Sciences, The University of Western Ontario, London, ON, Canada
| | - Kathleen A. Hill
- Department of Biology, The University of Western Ontario, London, ON, Canada
| | - Lila Kari
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada
| |
Collapse
|
41
|
Sotomayor-Bonilla J, Tolsá-García MJ, García-Peña GE, Santiago-Alarcon D, Mendoza H, Alvarez-Mendizabal P, Rico-Chávez O, Sarmiento-Silva RE, Suzán G. Insights into the Host Specificity of Mosquito-Borne Flaviviruses Infecting Wild Mammals. Ecohealth 2019; 16:726-733. [PMID: 31664588 DOI: 10.1007/s10393-019-01442-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
Mosquito-borne flaviviruses (MBFVs) are of public and animal health concern because they cause millions of human deaths annually and impact domestic animals and wildlife globally. MBFVs are phylogenetically divided into two clades, one is transmitted by Aedes mosquitoes (Ae-MBFVs) associated with mammals and the other by Culex mosquitoes (Cx-MBFVs) associated with birds. However, this assumption has not been evaluated. Here, we synthesized 79 published reports of MBFVs from wild mammals, estimating their host. Then, we tested whether the host specificity was biased to sampling and investigation efforts or to phylogenetic relationships using a viral phylogenetic tree drawn from analyzing whole flavivirus genomes obtained in GenBank. We found in total 18 flaviviruses, nine related to Aedes spp. and nine to Culex spp. infecting 129 mammal species. Thus, this supports that vectors are transmitting MBFV across available host clades and that ornithophilic mosquitoes are readily infecting mammals. Although most of the mosquito species are generalists in their host-feeding preferences, we also found a certain degree of MBFV's specificity, as most of them infect closely related mammal species. The present study integrates knowledge regarding MBFVs, and it may help to understand their transmission dynamics between viruses, vectors, and mammal hosts.
Collapse
Affiliation(s)
- Jesús Sotomayor-Bonilla
- Laboratorio de Ecología de Enfermedades y Una Salud, Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Circuito Interior S/N, Ciudad Universitaria, Coyoacán, 04520, Ciudad de México, Mexico
- Asociación Mexicana de Medicina de la Conservación Kalaan Kab AC, Ciclistas 63 Col. Country Club, Coyoacán, Ciudad de Mexico, Mexico
| | - María José Tolsá-García
- Laboratorio de Ecología de Enfermedades y Una Salud, Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Circuito Interior S/N, Ciudad Universitaria, Coyoacán, 04520, Ciudad de México, Mexico.
- Asociación Mexicana de Medicina de la Conservación Kalaan Kab AC, Ciclistas 63 Col. Country Club, Coyoacán, Ciudad de Mexico, Mexico.
| | - Gabriel E García-Peña
- Laboratorio de Ecología de Enfermedades y Una Salud, Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Circuito Interior S/N, Ciudad Universitaria, Coyoacán, 04520, Ciudad de México, Mexico
- Asociación Mexicana de Medicina de la Conservación Kalaan Kab AC, Ciclistas 63 Col. Country Club, Coyoacán, Ciudad de Mexico, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Circuito Interior S/N, Ciudad Universitaria, Coyoacán, Ciudad de México, Mexico
| | - Diego Santiago-Alarcon
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología AC, Carretera Antigua a Coatepec 351, Xalapa, Veracruz, Mexico
| | - Hugo Mendoza
- Laboratorio de Ecología de Enfermedades y Una Salud, Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Circuito Interior S/N, Ciudad Universitaria, Coyoacán, 04520, Ciudad de México, Mexico
- Asociación Mexicana de Medicina de la Conservación Kalaan Kab AC, Ciclistas 63 Col. Country Club, Coyoacán, Ciudad de Mexico, Mexico
| | - Paulina Alvarez-Mendizabal
- Laboratorio de Ecología de Enfermedades y Una Salud, Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Circuito Interior S/N, Ciudad Universitaria, Coyoacán, 04520, Ciudad de México, Mexico
- Asociación Mexicana de Medicina de la Conservación Kalaan Kab AC, Ciclistas 63 Col. Country Club, Coyoacán, Ciudad de Mexico, Mexico
| | - Oscar Rico-Chávez
- Laboratorio de Ecología de Enfermedades y Una Salud, Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Circuito Interior S/N, Ciudad Universitaria, Coyoacán, 04520, Ciudad de México, Mexico
- Asociación Mexicana de Medicina de la Conservación Kalaan Kab AC, Ciclistas 63 Col. Country Club, Coyoacán, Ciudad de Mexico, Mexico
| | - Rosa Elena Sarmiento-Silva
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Circuito Interior S/N, Ciudad Universitaria, Coyoacán, Ciudad de México, Mexico
| | - Gerardo Suzán
- Laboratorio de Ecología de Enfermedades y Una Salud, Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Circuito Interior S/N, Ciudad Universitaria, Coyoacán, 04520, Ciudad de México, Mexico
- Asociación Mexicana de Medicina de la Conservación Kalaan Kab AC, Ciclistas 63 Col. Country Club, Coyoacán, Ciudad de Mexico, Mexico
| |
Collapse
|
42
|
Zeghbib S, Herczeg R, Kemenesi G, Zana B, Kurucz K, Urbán P, Madai M, Földes F, Papp H, Somogyi B, Jakab F. Genetic characterization of a novel picornavirus in Algerian bats: co-evolution analysis of bat-related picornaviruses. Sci Rep 2019; 9:15706. [PMID: 31673141 PMCID: PMC6823487 DOI: 10.1038/s41598-019-52209-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/15/2019] [Indexed: 12/13/2022] Open
Abstract
Bats are reservoirs of numerous zoonotic viruses. The Picornaviridae family comprises important pathogens which may infect both humans and animals. In this study, a bat-related picornavirus was detected from Algerian Minioptreus schreibersii bats for the first time in the country. Molecular analyses revealed the new virus originates to the Mischivirus genus. In the operational use of the acquired sequence and all available data regarding bat picornaviruses, we performed a co-evolutionary analysis of mischiviruses and their hosts, to authentically reveal evolutionary patterns within this genus. Based on this analysis, we enlarged the dataset, and examined the co-evolutionary history of all bat-related picornaviruses including their hosts, to effectively compile all possible species jumping events during their evolution. Furthermore, we explored the phylogeny association with geographical location, host-genus and host-species in both data sets.
Collapse
Affiliation(s)
- Safia Zeghbib
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Róbert Herczeg
- Bioinformatics Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Gábor Kemenesi
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Brigitta Zana
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Kornélia Kurucz
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Péter Urbán
- Bioinformatics Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Mónika Madai
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Fanni Földes
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Henrietta Papp
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Balázs Somogyi
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Ferenc Jakab
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary.
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary.
| |
Collapse
|
43
|
Goz E, Zafrir Z, Tuller T. Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code. Bioinformatics 2019; 34:3241-3248. [PMID: 29718236 PMCID: PMC7109696 DOI: 10.1093/bioinformatics/bty351] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 04/27/2018] [Indexed: 01/09/2023] Open
Abstract
Motivation Understanding how viruses co-evolve with their hosts and adapt various genomic level strategies in order to ensure their fitness may have essential implications in unveiling the secrets of viral evolution, and in developing new vaccines and therapeutic approaches. Here, based on a novel genomic analysis of 2625 different viruses and 439 corresponding host organisms, we provide evidence of universal evolutionary selection for high dimensional ‘silent’ patterns of information hidden in the redundancy of viral genetic code. Results Our model suggests that long substrings of nucleotides in the coding regions of viruses from all classes, often also repeat in the corresponding viral hosts from all domains of life. Selection for these substrings cannot be explained only by such phenomena as codon usage bias, horizontal gene transfer and the encoded proteins. Genes encoding structural proteins responsible for building the core of the viral particles were found to include more host-repeating substrings, and these substrings tend to appear in the middle parts of the viral coding regions. In addition, in human viruses these substrings tend to be enriched with motives related to transcription factors and RNA binding proteins. The host-repeating substrings are possibly related to the evolutionary pressure on the viruses to effectively interact with host's intracellular factors and to efficiently escape from the host's immune system. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Eli Goz
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.,SynVaccineLtd, Ramat Hachayal, Tel Aviv, Israel
| | - Zohar Zafrir
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.,SynVaccineLtd, Ramat Hachayal, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.,SynVaccineLtd, Ramat Hachayal, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
44
|
Sexton NR, Ebel GD. Effects of Arbovirus Multi-Host Life Cycles on Dinucleotide and Codon Usage Patterns. Viruses 2019; 11:v11070643. [PMID: 31336898 PMCID: PMC6669465 DOI: 10.3390/v11070643] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
Arthropod-borne viruses (arboviruses) of vertebrates including dengue, zika, chikungunya, Rift Valley fever, and blue tongue viruses cause extensive morbidity and mortality in humans, agricultural animals, and wildlife across the globe. As obligate intercellular pathogens, arboviruses must be well adapted to the cellular and molecular environment of both their arthropod (invertebrate) and vertebrate hosts, which are vastly different due to hundreds of millions of years of separate evolution. Here we discuss the comparative pressures on arbovirus RNA genomes as a result of a dual host life cycle, focusing on pressures that do not alter amino acids. We summarize what is currently known about arboviral genetic composition, such as dinucleotide and codon usage, and how cyclical infection of vertebrate and invertebrate hosts results in different genetic profiles compared with single-host viruses. To serve as a comparison, we compile what is known about arthropod tRNA, dinucleotide, and codon usages and compare this with vertebrates. Additionally, we discuss the potential roles of genetic robustness in arboviral evolution and how it may vary from other viruses. Overall, both arthropod and vertebrate hosts influence the resulting genetic composition of arboviruses, but a great deal remains to be investigated.
Collapse
Affiliation(s)
- Nicole R Sexton
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| |
Collapse
|
45
|
Parry R, Asgari S. Discovery of Novel Crustacean and Cephalopod Flaviviruses: Insights into the Evolution and Circulation of Flaviviruses between Marine Invertebrate and Vertebrate Hosts. J Virol 2019; 93:e00432-19. [PMID: 31068424 DOI: 10.1128/JVI.00432-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
Most described flaviviruses (family Flaviviridae) are disease-causing pathogens of vertebrates maintained in zoonotic cycles between mosquitoes or ticks and vertebrate hosts. Poor sampling of flaviviruses outside vector-borne flaviviruses such as Zika virus and dengue virus has presented a narrow understanding of flavivirus diversity and evolution. In this study, we discovered three crustacean flaviviruses (Gammarus chevreuxi flavivirus, Gammarus pulex flavivirus, and Crangon crangon flavivirus) and two cephalopod flaviviruses (Southern Pygmy squid flavivirus and Firefly squid flavivirus). Bayesian and maximum likelihood phylogenetic methods demonstrate that crustacean flaviviruses form a well-supported clade and share a more closely related ancestor with terrestrial vector-borne flaviviruses than with classical insect-specific flaviviruses. In addition, we identify variants of Wenzhou shark flavivirus in multiple gazami crab (Portunus trituberculatus) populations, with active replication supported by evidence of an active RNA interference response. This suggests that Wenzhou shark flavivirus moves horizontally between sharks and gazami crabs in ocean ecosystems. Analyses of the mono- and dinucleotide composition of marine flaviviruses compared to that of flaviviruses with known host status suggest that some marine flaviviruses share a nucleotide bias similar to that of vector-borne flaviviruses. Furthermore, we identify crustacean flavivirus endogenous viral elements that are closely related to elements of terrestrial vector-borne flaviviruses. Taken together, these data provide evidence of flaviviruses circulating between marine vertebrates and invertebrates, expand our understanding of flavivirus host range, and offer potential insights into the evolution and emergence of terrestrial vector-borne flaviviruses.IMPORTANCE Some flaviviruses are known to cause disease in vertebrates and are typically transmitted by blood-feeding arthropods such as ticks and mosquitoes. While an ever-increasing number of insect-specific flaviviruses have been described, we have a narrow understanding of flavivirus incidence and evolution. To expand this understanding, we discovered a number of novel flaviviruses that infect a range of crustaceans and cephalopod hosts. Phylogenetic analyses of these novel marine flaviviruses suggest that crustacean flaviviruses share a close ancestor to all terrestrial vector-borne flaviviruses, and squid flaviviruses are the most divergent of all known flaviviruses to date. Additionally, our results indicate horizontal transmission of a marine flavivirus between crabs and sharks. Taken together, these data suggest that flaviviruses move horizontally between invertebrates and vertebrates in ocean ecosystems. This study demonstrates that flavivirus invertebrate-vertebrate host associations have arisen in flaviviruses at least twice and may potentially provide insights into the emergence or origin of terrestrial vector-borne flaviviruses.
Collapse
|
46
|
Alonso-Palomares LA, Moreno-García M, Lanz-Mendoza H, Salazar MI. Molecular Basis for Arbovirus Transmission by Aedes aegypti Mosquitoes. Intervirology 2019; 61:255-264. [PMID: 31082816 DOI: 10.1159/000499128] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 02/17/2019] [Indexed: 11/19/2022] Open
Abstract
Mosquitoes are considered the most important vectors for the transmission of pathogens to humans. Aedes aegypti is a unique species, not only by its highly anthropophilic and peridomestic habits but also because it can transmit an important variety of pathogenic viruses. Examples are dengue, yellow fever, chikungunya, Zika, and Mayaro viruses. After ingesting viremic blood, a wide range of mechanisms are activated in the mosquito to counteract viral infection. Nevertheless, these arboviruses possess strategies to overcome barriers in the mosquito and eventually reach the salivary glands to continue the transmission cycle. However, the infection and eventual transmission of arbovirus depends on multiple factors. The current review focuses in detail on the anatomic, physiological, and molecular characteristics of the mosquito A. aegypti that participate in response to a viral infection. In the past decades, the awareness of the importance of this mosquito as a disease vector and its impact on human health was largely recognized. We need to improve our comprehension of molecular mechanisms that determine the outcome of successful virus replication or control of infection for each arbovirus in the vector; this could lead to the design of effective control strategies in the future.
Collapse
Affiliation(s)
- Luis A Alonso-Palomares
- Laboratorio de Virología e Inmunovirología, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional (ENCB-IPN), Unidad Profesional "Lázaro Cárdenas", Mexico City, Mexico.,Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública (CISEI-INSP), Cuernavaca, Mexico
| | - Miguel Moreno-García
- Centro Regional de Control de Vectores, Secretaría de Salud (CERECOVE-SS), Panchimalco, Mexico
| | - Humberto Lanz-Mendoza
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública (CISEI-INSP), Cuernavaca, Mexico
| | - Ma Isabel Salazar
- Laboratorio de Virología e Inmunovirología, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional (ENCB-IPN), Unidad Profesional "Lázaro Cárdenas", Mexico City, Mexico,
| |
Collapse
|
47
|
Wang Z, Yu C, Peng Y, Ding C, Li Q, Wang D, Yuan X. Close evolutionary relationship between rice black-streaked dwarf virus and southern rice black-streaked dwarf virus based on analysis of their bicistronic RNAs. Virol J 2019; 16:53. [PMID: 31029143 PMCID: PMC6486993 DOI: 10.1186/s12985-019-1163-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/15/2019] [Indexed: 11/30/2022] Open
Abstract
Background Rice black-streaked dwarf virus (RBSDV) and Southern rice black-streaked dwarf virus (SRBSDV) seriously interfered in the production of rice and maize in China. These two viruses are members of the genus Fijivirus in the family Reoviridae and can cause similar dwarf symptoms in rice. Although some studies have reported the phylogenetic analysis on RBSDV or SRBSDV, the evolutionary relationship between these viruses is scarce. Methods In this study, we analyzed the evolutionary relationships between RBSDV and SRBSDV based on the data from the analysis of codon usage, RNA recombination and phylogenetic relationship, selection pressure and genetic characteristics of the bicistronic RNAs (S5, S7 and S9). Results RBSDV and SRBSDV showed similar patterns of codon preference: open reading frames (ORFs) in S7 and S5 had with higher and lower codon usage bias, respectively. Some isolates from RBSDV and SRBSDV formed a clade in the phylogenetic tree of S7 and S9. In addition, some recombination events in S9 occurred between RBSDV and SRBSDV. Conclusions Our results suggest close evolutionary relationships between RBSDV and SRBSDV. Selection pressure, gene flow, and neutrality tests also supported the evolutionary relationships. Electronic supplementary material The online version of this article (10.1186/s12985-019-1163-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zenghui Wang
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China.,College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Chengming Yu
- College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Yuanhao Peng
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China
| | - Chengshi Ding
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China
| | - Qingliang Li
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China
| | - Deya Wang
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, People's Republic of China.
| | - Xuefeng Yuan
- College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
| |
Collapse
|
48
|
Gałan W, Bąk M, Jakubowska M. Host Taxon Predictor - A Tool for Predicting Taxon of the Host of a Newly Discovered Virus. Sci Rep 2019; 9:3436. [PMID: 30837511 PMCID: PMC6400966 DOI: 10.1038/s41598-019-39847-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/30/2019] [Indexed: 12/04/2022] Open
Abstract
Recent advances in metagenomics provided a valuable alternative to culture-based approaches for better sampling viral diversity. However, some of newly identified viruses lack sequence similarity to any of previously sequenced ones, and cannot be easily assigned to their hosts. Here we present a bioinformatic approach to this problem. We developed classifiers capable of distinguishing eukaryotic viruses from the phages achieving almost 95% prediction accuracy. The classifiers are wrapped in Host Taxon Predictor (HTP) software written in Python which is freely available at https://github.com/wojciech-galan/viruses_classifier. HTP’s performance was later demonstrated on a collection of newly identified viral genomes and genome fragments. In summary, HTP is a culture- and alignment-free approach for distinction between phages and eukaryotic viruses. We have also shown that it is possible to further extend our method to go up the evolutionary tree and predict whether a virus can infect narrower taxa.
Collapse
Affiliation(s)
- Wojciech Gałan
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, ul. Gronostajowa 7, 30-387, Kraków, Poland.
| | - Maciej Bąk
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Małgorzata Jakubowska
- AGH University of Science and Technology, Faculty of Materials Science and Ceramics, al. Mickiewicza 30, 30-059, Kraków, Poland
| |
Collapse
|
49
|
Babayan SA, Orton RJ, Streicker DG. Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes. Science 2018; 362:577-580. [PMID: 30385576 DOI: 10.1126/science.aap9072] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 05/21/2018] [Accepted: 09/12/2018] [Indexed: 12/25/2022]
Abstract
Identifying the animal origins of RNA viruses requires years of field and laboratory studies that stall responses to emerging infectious diseases. Using large genomic and ecological datasets, we demonstrate that animal reservoirs and the existence and identity of arthropod vectors can be predicted directly from viral genome sequences via machine learning. We illustrate the ability of these models to predict the epidemiology of diverse viruses across most human-infective families of single-stranded RNA viruses, including 69 viruses with previously elusive or never-investigated reservoirs or vectors. Models such as these, which capitalize on the proliferation of low-cost genomic sequencing, can narrow the time lag between virus discovery and targeted research, surveillance, and management.
Collapse
Affiliation(s)
- Simon A Babayan
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, Scotland, UK.,The Moredun Research Institute, Pentlands Science Park, Penicuik EH26 0PZ, Scotland, UK
| | - Richard J Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Daniel G Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, Scotland, UK. .,MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| |
Collapse
|
50
|
Lavezzo E, Berselli M, Frasson I, Perrone R, Palù G, Brazzale AR, Richter SN, Toppo S. G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide. PLoS Comput Biol 2018; 14:e1006675. [PMID: 30543627 PMCID: PMC6307822 DOI: 10.1371/journal.pcbi.1006675] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/27/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022] Open
Abstract
G-quadruplexes are non-canonical nucleic-acid structures that control transcription, replication, and recombination in organisms. G-quadruplexes are present in eukaryotes, prokaryotes, and viruses. In the latter, mounting evidence indicates their key biological activity. Since data on viruses are scattered, we here present a comprehensive analysis of potential quadruplex-forming sequences (PQS) in the genome of all known viruses that can infect humans. We show that occurrence and location of PQSs are features characteristic of each virus class and family. Our statistical analysis proves that their presence within the viral genome is orderly arranged, as indicated by the possibility to correctly assign up to two-thirds of viruses to their exact class based on the PQS classification. For each virus we provide: i) the list of all PQS present in the genome (positive and negative strands), ii) their position in the viral genome, iii) the degree of conservation among strains of each PQS in its genome context, iv) the statistical significance of PQS abundance. This information is accessible from a database to allow the easy navigation of the results: http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=g4virus. The availability of these data will greatly expedite research on G-quadruplex in viruses, with the possibility to accelerate finding therapeutic opportunities to numerous and some fearsome human diseases.
Collapse
Affiliation(s)
- Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Michele Berselli
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Rosalba Perrone
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Sara N. Richter
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| |
Collapse
|