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Dankaona W, Nooroong P, Poolsawat N, Srionrod N, Techangamsuwan S, Anuracpreeda P. Molecular characterization of canine circovirus based on the Capsid gene in Thailand. BMC Vet Res 2024; 20:312. [PMID: 38997779 PMCID: PMC11245861 DOI: 10.1186/s12917-024-04120-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 06/07/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Canine circovirus (CanineCV) is a single-stranded circular DNA virus that infects domestic and wild canids in many countries. CanineCV is associated with gastroenteritis and diarrhea, respiratory disease, and generalized vasculitis leading to a fatal event. The Capsid protein (Cap) is a structural protein of the virus which has high genetic variability and plays a role in the canine immune response. In this study, we cloned the full-length CanineCV Capsid gene (Cap). In-silico analyses were used to explore the genomic and amino acid variability and natural selection acting on the Cap gene. The immune relevance for T-cell and B-cell epitopes was predicted by the immunoinformatic approach. RESULTS According to the Cap gene, our results showed that CanineCV was separated into five phylogenetic groups. The obtained CanineCV strain from this study was grouped with the previously discovered Thai strain (MG737385), as supported by a haplotype network. Entropy analyses revealed high nucleotide and amino acid variability of the Capsid region. Selection pressure analysis revealed four codons at positions 24, 50, 103, and 111 in the Cap protein evolved under diversifying selection. Prediction of B-cell epitopes exhibited four consensus sequences based on physiochemical properties, and eleven peptide sequences were predicted as T-cell epitopes. In addition, the positive selection sites were located within T-cell and B-cell epitopes, suggesting the role of the host immune system as a driving force in virus evolution. CONCLUSIONS Our study provides knowledge of CanineCV genetic diversity, virus evolution, and potential epitopes for host cell immune response.
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Affiliation(s)
- Wichan Dankaona
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Pornpiroon Nooroong
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Napassorn Poolsawat
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Nitipon Srionrod
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Somporn Techangamsuwan
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Panat Anuracpreeda
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand.
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Jiang H, Qiu Q, Zhou Y, Zhang Y, Xu W, Cui A, Li X. The epidemiological and genetic characteristics of human parvovirus B19 in patients with febrile rash illnesses in China. Sci Rep 2023; 13:15913. [PMID: 37741897 PMCID: PMC10517975 DOI: 10.1038/s41598-023-43158-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023] Open
Abstract
To understand the epidemiological and genetic characteristics of B19V, a multiple-province surveillance of patients with febrile rash illnesses (FRIs) were conducted in China during 2009 ~ 2021. The clinical specimens of 3,820 FRI patients were collected and tested for B19V DNA. A total of 99 (2.59%) patients were positive for B19V, and 49 (49.49%) were children under 5 years old. B19V infections occurred throughout the year without obvious seasonal pattern. Ten NS1-VP1u sequences and seven genome sequences were obtained in this study, identified as subgenotype 1a. Combined with the globally representative genome sequences, no temporal and geographic clustering trends of B19V were observed, and there was no significant correlation between B19V sequences and clinical manifestations. The evolutionary rate of the B19V genome was 2.30 × 10-4 substitutions/site/year. The number of negative selection sites was higher than that of positive selection sites. It was the first to comprehensively describe the prevalence patterns and evolutionary characteristics of B19V in FRI patients in China. B19V played the role in FRI patients. Children under 5 years old were the main population of B19V infection. Subgenotype 1a was prevalent in FRI patients in China. B19V showed a high mutation rate, while negative selection acted on the genome.
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Affiliation(s)
- Haoran Jiang
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, WHO WPRO Regional Reference Measles/Rubella Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
- School of Public Health and Management, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Qi Qiu
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, WHO WPRO Regional Reference Measles/Rubella Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
- Shanghai Municipal Center for Disease Control and Prevention, Institute of Infectious Disease Prevention and Control, 1380 Zhongshan West Road, Xuhui District, Shanghai, 200336, People's Republic of China
| | - Yangzi Zhou
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, WHO WPRO Regional Reference Measles/Rubella Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, People's Republic of China
| | - Yan Zhang
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, WHO WPRO Regional Reference Measles/Rubella Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Wenbo Xu
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, WHO WPRO Regional Reference Measles/Rubella Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Aili Cui
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, WHO WPRO Regional Reference Measles/Rubella Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.
| | - Xiaomei Li
- School of Public Health and Management, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China.
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3
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Bichicchi F, Guglietta N, Rocha Alves AD, Fasano E, Manaresi E, Bua G, Gallinella G. Next Generation Sequencing for the Analysis of Parvovirus B19 Genomic Diversity. Viruses 2023; 15:217. [PMID: 36680257 PMCID: PMC9863757 DOI: 10.3390/v15010217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/02/2023] [Accepted: 01/07/2023] [Indexed: 01/15/2023] Open
Abstract
Parvovirus B19 (B19V) is a ssDNA human virus, responsible for an ample range of clinical manifestations. Sequencing of B19V DNA from clinical samples is frequently reported in the literature to assign genotype (genotypes 1-3) and for finer molecular epidemiological tracing. The increasing availability of Next Generation Sequencing (NGS) with its depth of coverage potentially yields information on intrinsic sequence heterogeneity; however, integration of this information in analysis of sequence variation is not routinely obtained. The present work investigated genomic sequence heterogeneity within and between B19V isolates by application of NGS techniques, and by the development of a novel dedicated bioinformatic tool and analysis pipeline, yielding information on two newly defined parameters. The first, α-diversity, is a measure of the amount and distribution of position-specific, normalised Shannon Entropy, as a measure of intra-sample sequence heterogeneity. The second, σ-diversity, is a measure of the amount of inter-sample sequence heterogeneity, also incorporating information on α-diversity. Based on these indexes, further cluster analysis can be performed. A set of 24 high-titre viraemic samples was investigated. Of these, 23 samples were genotype 1 and one sample was genotype 2. Genotype 1 isolates showed low α-diversity values, with only a few samples showing distinct position-specific polymorphisms; a few genetically related clusters emerged when analysing inter-sample distances, correlated to the year of isolation; the single genotype 2 isolate showed the highest α-diversity, even if not presenting polymorphisms, and was an evident outlier when analysing inter-sample distance. In conclusion, NGS analysis and the bioinformatic tool and pipeline developed and used in the present work can be considered effective tools for investigating sequence diversity, an observable parameter that can be incorporated into the quasispecies theory framework to yield a better insight into viral evolution dynamics.
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Affiliation(s)
- Federica Bichicchi
- Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy
| | - Niccolò Guglietta
- Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy
| | - Arthur Daniel Rocha Alves
- Laboratory of Technological Development in Virology, Oswaldo Cruz Foundation/FIOCRUZ, Brasil Avenue 4365, Manguinhos, Rio de Janeiro 21040-900, Brazil
| | - Erika Fasano
- Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy
| | - Elisabetta Manaresi
- Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy
| | - Gloria Bua
- Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy
| | - Giorgio Gallinella
- Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy
- Microbiology Section, IRCCS Sant’Orsola Hospital, 40138 Bologna, Italy
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4
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Morais P, Trovão N, Abecasis A, Parreira R. Insect-specific viruses in the Parvoviridae family: genetic lineage characterization and spatiotemporal dynamics of the recently established Brevihamaparvovirus genus. Virus Res 2022; 313:198728. [DOI: 10.1016/j.virusres.2022.198728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 10/18/2022]
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5
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Pavesi A. Origin, Evolution and Stability of Overlapping Genes in Viruses: A Systematic Review. Genes (Basel) 2021; 12:genes12060809. [PMID: 34073395 PMCID: PMC8227390 DOI: 10.3390/genes12060809] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 12/11/2022] Open
Abstract
During their long evolutionary history viruses generated many proteins de novo by a mechanism called “overprinting”. Overprinting is a process in which critical nucleotide substitutions in a pre-existing gene can induce the expression of a novel protein by translation of an alternative open reading frame (ORF). Overlapping genes represent an intriguing example of adaptive conflict, because they simultaneously encode two proteins whose freedom to change is constrained by each other. However, overlapping genes are also a source of genetic novelties, as the constraints under which alternative ORFs evolve can give rise to proteins with unusual sequence properties, most importantly the potential for novel functions. Starting with the discovery of overlapping genes in phages infecting Escherichia coli, this review covers a range of studies dealing with detection of overlapping genes in small eukaryotic viruses (genomic length below 30 kb) and recognition of their critical role in the evolution of pathogenicity. Origin of overlapping genes, what factors favor their birth and retention, and how they manage their inherent adaptive conflict are extensively reviewed. Special attention is paid to the assembly of overlapping genes into ad hoc databases, suitable for future studies, and to the development of statistical methods for exploring viral genome sequences in search of undiscovered overlaps.
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Affiliation(s)
- Angelo Pavesi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, I-43124 Parma, Italy
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6
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Seetha D, Pillai HR, Nori SRC, Kalpathodi SG, Thulasi VP, Nair RR. Molecular-genetic characterization of human parvovirus B19 prevalent in Kerala State, India. Virol J 2021; 18:96. [PMID: 33952289 PMCID: PMC8097873 DOI: 10.1186/s12985-021-01569-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/30/2021] [Indexed: 01/21/2023] Open
Abstract
Background Human parvovirus B19V is a DNA virus, and a member of the family Parvoviridae, that causes various clinical manifestations, from asymptomatic to persistent infection that is associated with different autoimmune diseases. The parvovirus B19 evolves with a very high mutation rate that is closer to those of existing RNA viruses. Globally circulating B19V is currently classified into three genotypes, but their distribution is not spatially and temporally correlated. Except for a few recent reports on B19V entry into the human host and its genetic diversity, there is a lack of sufficient studies on this virus from distinct geographical locations and no clear understanding of its evolution has been documented. Methods To better understand the evolution of the Human parvo B19V virus from India's southern part, a geographically distinct location with no reports of B19V genomes, we have screened for B19V in 456 suspected cases using VP1/2 surface marker genes, and its characteristics were studied in detail. Amongst 456 clinically suspected B19V samples, 7.2% (33/456) were found positive by nested PCR (nPCR) were subsequently validated by real-time PCR, Sanger sequencing, and metagenome analysis. Results Human parvovirus B19 infection was shown among 33 of 456 patients when tested by nPCR; 30 among these were also positive by qPCR and were subsequently confirmed by sequencing 75% nPCR positive samples and 76% qPCR positive samples were from patients with age. ≥ 50 years respectively (Additional file 1: Table S1). The complete VP1/2 gene assembly from the South Indian strain showed three novel mutations (T122A, V128I, I283V), which might significantly impact the stability and virulence of the B19V virus circulating in this part of the world. These mutations might be crucial for its adaptive evolutionary strategies facilitating the spread and infectivity potential of the virus. In maximum likelihood phylogeny of VP1/2 sequences, the South Indian B19V strain forms a separate clade closer to the existing genotype two strains circulating worldwide. Conclusion Our study contributes to a better understanding of the human parvovirus's genetic and evolutionary characteristics in South India. Also, it highlights the possibility that a positive selection pressure acting on VP1/2 could increase the survival and replication capabilities of the viruses. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01569-1.
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Affiliation(s)
- Dayakar Seetha
- Laboratory Medicine and Molecular Diagnostics Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695585, India
| | - Heera R Pillai
- Laboratory Medicine and Molecular Diagnostics Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695585, India
| | - Sai Ravi Chandra Nori
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Sanu Ghosh Kalpathodi
- Laboratory Medicine and Molecular Diagnostics Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695585, India
| | - Vineetha P Thulasi
- Laboratory Medicine and Molecular Diagnostics Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695585, India
| | - Radhakrishnan R Nair
- Laboratory Medicine and Molecular Diagnostics Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695585, India.
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7
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Molecular analysis of goose parvovirus field strains from a Derzsy's disease outbreak reveals local European-associated variants. Arch Virol 2021; 166:1931-1942. [PMID: 33934195 DOI: 10.1007/s00705-021-05086-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
Since its first recognition in the early 1960s, Derzsy's disease has caused significant economic losses in the goose meat industry through the world. Today, Derzsy's disease still maintains its importance for small-scale waterfowl farming, despite not having a significant impact on public health. In the present study, we investigated the distribution of goose parvovirus (GPV) and its potential variants from a 2019 outbreak in Turkey. Tissue samples were obtained from infected eggs and goslings that were raised in distinct farming areas of the various provinces. For this purpose, a novel primer set for amplification of a 630-bp region of VP3 was designed to confirm GPV infection by conventional PCR method. A 4709-base nucleotide sequence including the structural, non-structural, and 5' inverted terminal repeat regions was obtained from three samples from the Central Anatolian region. Multiple sequence comparisons and phylogenetic analysis demonstrated that the field strains clustered with European group 2 and contained a series of unique amino acid substitutions that might affect the virulence of the virus. These results confirmed that European-related field strains caused the outbreak in Asia Minor, and this might assist in understanding the circulation of GPV in Asia and Europe.
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8
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Abdelrahman D, Al-Sadeq DW, Smatti MK, Taleb SA, AbuOdeh RO, Al-Absi ES, Al-Thani AA, Coyle PV, Al-Dewik N, Qahtani AAA, Yassine HM, Nasrallah GK. Prevalence and Phylogenetic Analysis of Parvovirus (B19V) among Blood Donors with Different Nationalities Residing in Qatar. Viruses 2021; 13:v13040540. [PMID: 33805034 PMCID: PMC8063948 DOI: 10.3390/v13040540] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 12/16/2022] Open
Abstract
Human parvovirus (B19V) is the causative agent of erythema infectiosum in children and is linked to a wide range of clinical manifestations. Studies related to B19V prevalence in the Middle East and North Africa (MENA) region and other parts of Asia are very scarce. The objectives of this study were to estimate the seroprevalence (anti-B19V IgM and IgG), the viremia rate (B19V DNA), and the circulating genotypes of B19V among blood donors in Qatar. Methods: Donors’ blood samples (n = 5026) from different nationalities, mainly from the MENA region and South East Asia, were collected from 2014–2016. Samples were tested for the B19V DNA using RT-PCR. Furthermore, 1000 selected samples were tested to determine the seroprevalence of B19V antibodies using enzyme-linked immunosorbent assay (ELISA). Genotyping was performed on 65 DNA positive samples by sequencing of nested PCR fragments (NS1-VP1u region, 927 nt). Results: Only 1.4% (70/5026) of the samples had detectible B19V DNA in their blood. B19V DNA prevalence statistically decreased with age (p = 0.03). Anti-B19V IgG was detected in 60.3% (561/930) of the tested samples, while only 2.1% (20/930) were IgM-positive and 1.2% (11/930) were both IgM- and IgG-positive. B19V genotyping showed a predominance of Genotype 1 (100%). Sequence analysis of the NS1-VP1u region revealed 139 mutation sites, some of which were amino acid substitutions. Conclusion: Our results indicated a relatively high seroprevalence of B19V in Qatar. Most importantly, B19 DNA was detected among Qatari and non-Qatari blood donors. Therefore, blood banks in Qatar might need to consider screening for B19V, especially when transfusion is intended for high-risk populations, including immunocompromised patients.
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Affiliation(s)
| | - Duaa W. Al-Sadeq
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar; (D.W.A.-S.); (M.K.S.); (E.S.A.-A.); (A.A.A.-T.); (H.M.Y.)
- College of Medicine, Member of QU Health, Qatar University, Doha, Qatar
| | - Maria K. Smatti
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar; (D.W.A.-S.); (M.K.S.); (E.S.A.-A.); (A.A.A.-T.); (H.M.Y.)
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar;
| | - Sara A. Taleb
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar;
| | - Raed O AbuOdeh
- Medical Laboratory Sciences Department, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates;
| | - Enas S. Al-Absi
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar; (D.W.A.-S.); (M.K.S.); (E.S.A.-A.); (A.A.A.-T.); (H.M.Y.)
| | - Asmaa A. Al-Thani
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar; (D.W.A.-S.); (M.K.S.); (E.S.A.-A.); (A.A.A.-T.); (H.M.Y.)
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University, Doha, Qatar
| | - Peter. V. Coyle
- Division of Virology, Department of Pathology and Laboratory Medicine, Hamad Medical Corporation, Doha, Qatar;
| | - Nader Al-Dewik
- Department of Pediatrics, Clinical and Metabolic Genetics, Hamad Medical Corporation, Doha, Qatar;
| | - Ahmed A. Al Qahtani
- Department of Infection and Immunity, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia;
- Department of Microbiology and Immunology, Alfaisal University School of Medicine, Riyadh 11533, Saudi Arabia
| | - Hadi M. Yassine
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar; (D.W.A.-S.); (M.K.S.); (E.S.A.-A.); (A.A.A.-T.); (H.M.Y.)
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University, Doha, Qatar
| | - Gheyath K. Nasrallah
- Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar; (D.W.A.-S.); (M.K.S.); (E.S.A.-A.); (A.A.A.-T.); (H.M.Y.)
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University, Doha, Qatar
- Correspondence:
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Altinli M, Lequime S, Courcelle M, François S, Justy F, Gosselin-Grenet AS, Ogliastro M, Weill M, Sicard M. Evolution and phylogeography of Culex pipiens densovirus. Virus Evol 2019; 5:vez053. [PMID: 31807318 PMCID: PMC6884738 DOI: 10.1093/ve/vez053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Viruses of the Parvoviridae family infect a wide range of animals including vertebrates and invertebrates. So far, our understanding of parvovirus diversity is biased towards medically or economically important viruses mainly infecting vertebrate hosts, while invertebrate infecting parvoviruses—namely densoviruses—have been largely neglected. Here, we investigated the prevalence and the evolution of the only mosquito-infecting ambidensovirus, Culex pipiens densovirus (CpDV), from laboratory mosquito lines and natural populations collected worldwide. CpDV diversity generally grouped in two clades, here named CpDV-1 and -2. The incongruence of the different gene trees for some samples suggested the possibility of recombination events between strains from different clades. We further investigated the role of selection on the evolution of CpDV genome and detected many individual sites under purifying selection both in non-structural and structural genes. However, some sites in structural genes were under diversifying selection, especially during the divergence of CpDV-1 and -2 clades. These substitutions between CpDV-1 and -2 clades were mostly located in the capsid protein encoding region and might cause changes in host specificity or pathogenicity of CpDV strains from the two clades. However, additional functional and experimental studies are necessary to fully understand the protein conformations and the resulting phenotype of these substitutions between clades of CpDV.
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Affiliation(s)
- Mine Altinli
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Sebastian Lequime
- KU Leuven, Department of Microbiology, Immunology, and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, Leuven, Belgium
| | - Maxime Courcelle
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Sarah François
- DGIMI, INRA, Université de Montpellier, Montpellier, France.,Department of Zoology, University of Oxford, Oxford, UK
| | - Fabienne Justy
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | | | | | - Mylene Weill
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Mathieu Sicard
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
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10
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Pavesi A. Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation. Virology 2019; 532:39-47. [PMID: 31004987 PMCID: PMC7125799 DOI: 10.1016/j.virol.2019.03.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/29/2022]
Abstract
Overlapping genes represent an intriguing puzzle, as they encode two proteins whose ability to evolve is constrained by each other. Overlapping genes can undergo “symmetric evolution” (similar selection pressures on the two proteins) or “asymmetric evolution” (significantly different selection pressures on the two proteins). By sequence analysis of 75 pairs of homologous viral overlapping genes, I evaluated their accordance with one or the other model. Analysis of nucleotide and amino acid sequences revealed that half of overlaps undergo asymmetric evolution, as the protein from one frame shows a number of substitutions significantly higher than that of the protein from the other frame. Interestingly, the most variable protein (often known to interact with the host proteins) appeared to be encoded by the de novo frame in all cases examined. These findings suggest that overlapping genes, besides to increase the coding ability of viruses, are also a source of selective protein adaptation. A dataset of 80 pairs of homologous overlapping genes from viruses is examined. Its analysis reveals that half of overlapping genes undergo asymmetric evolution. The most variable gene product is that encoded by the de novo overlapping gene. Overlapping genes evolving asymmetrically are a source of selective protein adaptation.
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Affiliation(s)
- Angelo Pavesi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, I-43124, Parma, Italy.
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11
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Evolutionary aspects of Parvovirus B-19V associated diseases and their pathogenesis patterns with an emphasis on vaccine development. Virusdisease 2019; 30:32-42. [PMID: 31143830 DOI: 10.1007/s13337-019-00525-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 03/15/2019] [Indexed: 12/16/2022] Open
Abstract
Parvovirus B-19, a single human pathogenic member of the Parvoviridae family with it's small ssDNA and non-enveloped structure, is known to cause diseases in erythroid progenitor cells. But a wide range of clinical association of this virus with cells of non-erythroid origins has recently been discovered and many of those are being investigated for such association. Higher substitution rates in due course of evolution has been suggested for this cellular tropism and persistence. In this report, we have summarized the different disease manifestations of B-19 virus and have tried to find out a pattern of pathogenesis. Finally, we have focused on the vaccination strategies available against B-19 virus to correlate these with the mechanisms involved in various diseases caused by this virus.
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Stanojevic M, Cirkovic V, Siljic M, Gligic A, Stamenkovic G. Molecular characterization of Dobrava-Belgrade hantavirus in Serbia, 2007-2011. J Infect Public Health 2019; 12:645-649. [PMID: 30910417 DOI: 10.1016/j.jiph.2019.02.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/13/2018] [Accepted: 02/27/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Hantaviruses are etiological agents of emerging zoonotic diseases worldwide, including hemorrhagic fever with renal syndrome (HFRS). A number of hantavirus species is known to be present in Europe. In Serbia, existing data on hantavirus presence and prevalence rely in serological findings. In this study, molecular analysis was performed in order to characterize HFRS causing hantaviruses in Serbia. METHODS Sixty four serum samples of HFRS cases, previously found seropositive to anti-hantaviral antibodies, were included in the study. Partial hantaviral L and S segments were PCR amplified producing 390nt and 598nt amplicons, respectively, in parallel with human beta-actin mRNA as external reverse transcription positive control. Hantavirus specific PCR products were DNA sequenced in both direction and the obtained sequences phylogenetically confirmed and analyzed. RESULTS PCR detection of hantavirus L and S genome segments was positive in 18/64 and 11/64 tested samples, respectively. Positive PCR results involved samples obtained from different locations, mostly from central and southern parts of Serbia. All the obtained sequences were identified as Dobrava-Belgrade virus (DOBV). In the phylogenetic analysis sequences from Serbia tended to cluster in distinctive, geographically related clusters. CONCLUSIONS Our findings indicate DOBV as the main HFRS causing hantavirus in Serbia, the site of its initial isolation.
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Affiliation(s)
- Maja Stanojevic
- University of Belgrade Faculty of Medicine, Institute of Microbiology and Immunology, Belgrade, Serbia.
| | - Valentina Cirkovic
- University of Belgrade Faculty of Medicine, Institute of Microbiology and Immunology, Belgrade, Serbia
| | - Marina Siljic
- University of Belgrade Faculty of Medicine, Institute of Microbiology and Immunology, Belgrade, Serbia
| | - Ana Gligic
- Institute of Virology, Vaccines and Sera - Torlak, National Center for Arboviruses and HF Viruses, Belgrade, Serbia
| | - Gorana Stamenkovic
- University of Belgrade Institute for Biological Research "S. Stankovic", Department of Genetics, Belgrade, Serbia
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Affiliation(s)
- Giorgio Gallinella
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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