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S. Celina S, Černý J. Genetic background of adaptation of Crimean-Congo haemorrhagic fever virus to the different tick hosts. PLoS One 2024; 19:e0302224. [PMID: 38662658 PMCID: PMC11045102 DOI: 10.1371/journal.pone.0302224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Crimean-Congo haemorrhagic fever orthonairovirus (CCHFV) is a negative-sense, single-stranded RNA virus with a segmented genome and the causative agent of a severe Crimean-Congo haemorrhagic fever (CCHF) disease. The virus is transmitted mainly by tick species in Hyalomma genus but other ticks such as representatives of genera Dermacentor and Rhipicephalus may also be involved in virus life cycle. To improve our understanding of CCHFV adaptation to its tick species, we compared nucleotide composition and codon usage patterns among the all CCHFV strains i) which sequences and other metadata as locality of collection and date of isolation are available in GenBank and ii) which were isolated from in-field collected tick species. These criteria fulfilled 70 sequences (24 coding for S, 23 for M, and 23 for L segment) of virus isolates originating from different representatives of Hyalomma and Rhipicephalus genera. Phylogenetic analyses confirmed that Hyalomma- and Rhipicephalus-originating CCHFV isolates belong to phylogenetically distinct CCHFV clades. Analyses of nucleotide composition among the Hyalomma- and Rhipicephalus-originating CCHFV isolates also showed significant differences, mainly in nucleotides located at the 3rd codon positions indicating changes in codon usage among these lineages. Analyses of codon adaptation index (CAI), effective number of codons (ENC), and other codon usage statistics revealed significant differences between Hyalomma- and Rhipicephalus-isolated CCHFV strains. Despite both sets of strains displayed a higher adaptation to use codons that are preferred by Hyalomma ticks than Rhipicephalus ticks, there were distinct codon usage preferences observed between the two tick species. These findings suggest that over the course of its long co-evolution with tick vectors, CCHFV has optimized its codon usage to efficiently utilize translational resources of Hyalomma species.
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Affiliation(s)
- Seyma S. Celina
- Faculty of Tropical AgriSciences, Center for Infectious Animal Diseases, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jiří Černý
- Faculty of Tropical AgriSciences, Center for Infectious Animal Diseases, Czech University of Life Sciences Prague, Prague, Czech Republic
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3
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Hussain S, Rasool ST, Pottathil S. The Evolution of Severe Acute Respiratory Syndrome Coronavirus-2 during Pandemic and Adaptation to the Host. J Mol Evol 2021; 89:341-356. [PMID: 33993372 PMCID: PMC8123100 DOI: 10.1007/s00239-021-10008-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/25/2021] [Indexed: 12/02/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 is a zoonotic virus with a possible origin in bats and potential transmission to humans through an intermediate host. When zoonotic viruses jump to a new host, they undergo both mutational and natural selective pressures that result in non-synonymous and synonymous adaptive changes, necessary for efficient replication and rapid spread of diseases in new host species. The nucleotide composition and codon usage pattern of SARS-CoV-2 indicate the presence of a highly conserved, gene-specific codon usage bias. The codon usage pattern of SARS-CoV-2 is mostly antagonistic to human and bat codon usage. SARS-CoV-2 codon usage bias is mainly shaped by the natural selection, while mutational pressure plays a minor role. The time-series analysis of SARS-CoV-2 genome indicates that the virus is slowly evolving. Virus isolates from later stages of the outbreak have more biased codon usage and nucleotide composition than virus isolates from early stages of the outbreak.
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Affiliation(s)
- Snawar Hussain
- Department of Biomedical Sciences, College of Clinical Pharmacy, King Faisal University, P.O Box. 400, Al-Ahsa, 31982, Kingdom of Saudi Arabia.
| | - Sahibzada Tasleem Rasool
- Department of Biomedical Sciences, College of Clinical Pharmacy, King Faisal University, P.O Box. 400, Al-Ahsa, 31982, Kingdom of Saudi Arabia
| | - Shinu Pottathil
- Department of Biomedical Sciences, College of Clinical Pharmacy, King Faisal University, P.O Box. 400, Al-Ahsa, 31982, Kingdom of Saudi Arabia
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4
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Mechanisms Underlying Host Range Variation in Flavivirus: From Empirical Knowledge to Predictive Models. J Mol Evol 2021; 89:329-340. [PMID: 34059925 DOI: 10.1007/s00239-021-10013-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [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.
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de Oliveira Ribeiro G, da Costa AC, Gill DE, Ribeiro ESD, Rego MODS, Monteiro FJC, Villanova F, Nogueira JS, Maeda AY, de Souza RP, Tahmasebi R, Morais VS, Pandey RP, Raj VS, Scandar SAS, da Silva Vasami FG, D'Agostino LG, Maiorka PC, Deng X, Nogueira ML, Sabino EC, Delwart E, Leal É, Cunha MS. Guapiaçu virus, a new insect-specific flavivirus isolated from two species of Aedes mosquitoes from Brazil. Sci Rep 2021; 11:4674. [PMID: 33633167 PMCID: PMC7907106 DOI: 10.1038/s41598-021-83879-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
Classical insect-flaviviruses (cISFVs) and dual host-related insect-specific flavivirus (dISFV) are within the major group of insect-specific flavivirus. Remarkably dISFV are evolutionarily related to some of the pathogenic flavivirus, such as Zika and dengue viruses. The Evolutionary relatedness of dISFV to flavivirus allowed us to investigate the evolutionary principle of host adaptation. Additionally, dISFV can be used for the development of flavivirus vaccines and to explore underlying principles of mammalian pathogenicity. Here we describe the genetic characterization of a novel putative dISFV, termed Guapiaçu virus (GUAPV). Distinct strains of GUAPV were isolated from pools of Aedes terrens and Aedes scapularis mosquitoes. Additionally, we also detected viral GUAPV RNA in a plasma sample of an individual febrile from the Amazon region (North of Brazil). Although GUAPV did not replicate in tested mammalian cells, 3′UTR secondary structures duplication and codon usage index were similar to pathogenic flavivirus.
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Affiliation(s)
| | | | - Danielle Elise Gill
- Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil
| | - Edcelha Soares D'Athaide Ribeiro
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Rua Tancredo Neves, 1.118, Macapá, AP, CEP 68905-230, Brazil
| | - Marlisson Octavio da S Rego
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Rua Tancredo Neves, 1.118, Macapá, AP, CEP 68905-230, Brazil
| | - Fred Julio Costa Monteiro
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Rua Tancredo Neves, 1.118, Macapá, AP, CEP 68905-230, Brazil
| | - Fabiola Villanova
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, 66075-000, Brazil
| | - Juliana Silva Nogueira
- Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, SP, 01246-000, Brazil
| | - Adriana Yurika Maeda
- Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, SP, 01246-000, Brazil
| | - Renato Pereira de Souza
- Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, SP, 01246-000, Brazil
| | - Roozbeh Tahmasebi
- Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil
| | - Vanessa S Morais
- Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat, Haryana, India
| | - V Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat, Haryana, India
| | | | | | | | - Paulo César Maiorka
- Department of Pathology, Faculty of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118-4417, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | | | - Ester Cerdeira Sabino
- Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118-4417, USA. .,Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA.
| | - Élcio Leal
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, 66075-000, Brazil.
| | - Mariana Sequetin Cunha
- Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil. .,Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, SP, 01246-000, Brazil.
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Mycobacterium lepromatosis genome exhibits unusually high CpG dinucleotide content and selection is key force in shaping codon usage. INFECTION GENETICS AND EVOLUTION 2020; 84:104399. [PMID: 32512206 DOI: 10.1016/j.meegid.2020.104399] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 01/06/2023]
Abstract
Mycobacterium lepromatosis was identified as a causative agent for leprosy in the year 2008 in the United States and later more cases were identified in Canada, Singapore, Brazil, and Myanmar. It is known to cause diffuse lepromatosis leprosy among humans. Since it is invasive, the mortality rates are higher in comparison to the M. leprae. At genomic level, there exists 90.9% similarity between M. lepromatosis and M. leprae. Codon usage analysis based on analyses of 228 coding sequences (CDSs) of M. lepromatosis, revealed that the genome is GC rich. Among the total 16 dinucleotides, CpG dinucleotide possesses the highest dinucleotide frequency in M. lepromatosis, that is strikingly an unobvious observation since higher CpG is associated with higher proinflammatory cytokine production and NF-κB activation that eventually leads to high pathogenicity. To evade immune response, CpG content is generally less in pathogens. The unusually high CpG content can be explained by the fact that the nucleotide composition of M. lepromatosis is CG rich. Various forces interplay to shape codon usage pattern of any organism including selection; mutation, nucleotide composition as well as GC biased gene conversion. To understand the interplay between various forces; neutrality, parity, Nc-GC3 (Effective number of codons-GC content at 3rd position of the codon), aromaticity (AROMO) and the general average hydropathicity score (GRAVY) analyses have been carried out. The analyses revealed that selection force is the major contributory force. Along with the selection; mutation, nucleotide composition as well as GC biased gene conversion also play role in shaping codon usage bias in M. lepromatosis. This is the first report on the codon usage in M. lepromatosis.
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McArthur MA, Zhang SL, Li L, Tesh RB, Barrett ADT. Molecular Characterization of Hamster-Adapted Yellow Fever Virus. Vector Borne Zoonotic Dis 2019; 20:222-227. [PMID: 31794691 DOI: 10.1089/vbz.2019.2495] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We previously reported two hamster models for viscerotropic yellow fever virus (YFV) infection: one using a YFV strain (Jiménez), isolated from a fatal human case in Panama in 1974, and the other using the prototype YFV strain (Asibi). Asibi hamster passage 7 (P7) was associated with accumulation of seven amino acid substitutions, including five in the envelope protein. In this study we report the genome sequences of the hamster Jiménez P0 and P10 viruses in which we identified only two amino acid substitutions during passage, one each in the nonstructural proteins NS3 and NS5, indicating a role for the nonstructural proteins in increased YFV viscerotropism in the Jiménez hamster model. Thus, there are multiple molecular mechanisms involved in viscerotropism of YFV in the hamster model. Neither Asibi P7 nor Jiménez P10 viruses were viscerotropic in mice or guinea pigs. Thus, the hamster viscerotropic phenotype did not translate to other laboratory rodent species.
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Affiliation(s)
- Monica A McArthur
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland.,Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland
| | - Shuliu L Zhang
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Li Li
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas.,Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, Texas
| | - Robert B Tesh
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Alan D T Barrett
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas.,Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, Texas
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Quintero-Gil C, Rendon-Marin S, Martinez-Gutierrez M, Ruiz-Saenz J. Origin of Canine Distemper Virus: Consolidating Evidence to Understand Potential Zoonoses. Front Microbiol 2019; 10:1982. [PMID: 31555226 PMCID: PMC6722215 DOI: 10.3389/fmicb.2019.01982] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/12/2019] [Indexed: 11/15/2022] Open
Affiliation(s)
- Carolina Quintero-Gil
- Grupo de Investigación en Ciencias Animales-GRICA, Universidad Cooperativa de Colombia, Bucaramanga, Colombia
| | - Santiago Rendon-Marin
- Grupo de Investigación en Ciencias Animales-GRICA, Universidad Cooperativa de Colombia, Bucaramanga, Colombia
| | - Marlen Martinez-Gutierrez
- Grupo de Investigación en Ciencias Animales-GRICA, Universidad Cooperativa de Colombia, Bucaramanga, Colombia.,Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
| | - Julian Ruiz-Saenz
- Grupo de Investigación en Ciencias Animales-GRICA, Universidad Cooperativa de Colombia, Bucaramanga, Colombia.,Asociación Colombiana de Virología, Bogotá, Colombia
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Ulrich K, Wehner S, Bekaert M, Di Paola N, Dilcher M, Muir KF, Taggart JB, Matejusova I, Weidmann M. Molecular epidemiological study on Infectious Pancreatic Necrosis Virus isolates from aquafarms in Scotland over three decades. J Gen Virol 2018; 99:1567-1581. [PMID: 30358526 DOI: 10.1099/jgv.0.001155] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In order to obtain an insight into genomic changes and associated evolution and adaptation of Infectious Pancreatic Necrosis Virus (IPNV), the complete coding genomes of 57 IPNV isolates collected from Scottish aquafarms from 1982 to 2014 were sequenced and analysed. Phylogenetic analysis of the sequenced IPNV strains showed separate clustering of genogroups I, II, III and V. IPNV isolates with genetic reassortment of segment A/B of genogroup III/II were determined. About 59 % of the IPNV isolates belonged to the persistent type and 32 % to the low-virulent type, and only one highly pathogenic strain (1.79 %) was identified. Codon adaptation index calculations indicated that the IPNV major capsid protein VP2 has adapted to its salmonid host. Under-representation of CpG dinucleotides in the IPNV genome to minimize detection by the innate immunity receptors, and observed positive selection in the virulence determination sites of VP2 embedded in the variable region of the main antigenic region, suggest an immune escape mechanism driving virulence evolution. The prevalence of mostly persistent genotypes, together with the assumption of adaptation and immune escape, indicates that IPNV is evolving with the host.
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Affiliation(s)
- Kristina Ulrich
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
| | | | - Michaël Bekaert
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
| | - Nicholas Di Paola
- 3Biomedical Sciences Institute, University of Sao Paulo, Sao Paulo, Brazil
| | - Meik Dilcher
- 4Canterbury Health Laboratories, Christchurch, New-Zealand
| | | | - John B Taggart
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
| | | | - Manfred Weidmann
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
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