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Williams RAJ, Sánchez-Llatas CJ, Doménech A, Madrid R, Fandiño S, Cea-Callejo P, Gomez-Lucia E, Benítez L. Emerging and Novel Viruses in Passerine Birds. Microorganisms 2023; 11:2355. [PMID: 37764199 PMCID: PMC10536639 DOI: 10.3390/microorganisms11092355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
There is growing interest in emerging viruses that can cause serious or lethal disease in humans and animals. The proliferation of cloacal virome studies, mainly focused on poultry and other domestic birds, reveals a wide variety of viruses, although their pathogenic significance is currently uncertain. Analysis of viruses detected in wild birds is complex and often biased towards waterfowl because of the obvious interest in avian influenza or other zoonotic viruses. Less is known about the viruses present in the order Passeriformes, which comprises approximately 60% of extant bird species. This review aims to compile the most significant contributions on the DNA/RNA viruses affecting passerines, from traditional and metagenomic studies. It highlights that most passerine species have never been sampled. Especially the RNA viruses from Flaviviridae, Orthomyxoviridae and Togaviridae are considered emerging because of increased incidence or avian mortality/morbidity, spread to new geographical areas or hosts and their zoonotic risk. Arguably poxvirus, and perhaps other virus groups, could also be considered "emerging viruses". However, many of these viruses have only recently been described in passerines using metagenomics and their role in the ecosystem is unknown. Finally, it is noteworthy that only one third of the viruses affecting passerines have been officially recognized.
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Affiliation(s)
- Richard A. J. Williams
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Christian J. Sánchez-Llatas
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
| | - Ana Doménech
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Ricardo Madrid
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Sergio Fandiño
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Pablo Cea-Callejo
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Esperanza Gomez-Lucia
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Laura Benítez
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
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2
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Huang X, Zhou J, Hou Y, Wang R, Li Q, Wang Y, Yuan R, Chen P, Wang B, Xia X. Diversity and Genetic Characteristics of Astroviruses from Animals in Yunnan Province. Viruses 2022; 14:v14102234. [PMID: 36298789 PMCID: PMC9607396 DOI: 10.3390/v14102234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 11/21/2022] Open
Abstract
Astroviruses (AstVs) are single-stranded RNA viruses, including two main genera: Mamastroviruses (MAstVs) and Avastroviruses (AAstVs). AstVs have been detected in more than 80 different mammals and birds, with the characteristics of multiple cross-species transmission and gene recombination. All these have accelerated the process of virus mutation and posed a potential threat to human beings and animal husbandry. Yunnan province is a global hotspot with rich biodiversity and abundant animal resources and an important area with significance for public health and security because it neighbors a few Southeast Asian countries. This study collected 860 samples from 13 species of animals in Yunnan province for AstVs detection. The results showed that the positive rate of AstVs was 6.05%, and its extremely high genetic diversity was observed in different animal species. Potential cross-species transmission events were also detected from rodents to birds. Therefore, AstVs, which are widely distributed with highly diverse genes and the risk of cross-species transmission to people, deserve more attention in this region.
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Affiliation(s)
- Xingyu Huang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jiuxuan Zhou
- Yunnan Academy of Forestry and Grassland, Kunming 650201, China
| | - Yutong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Rui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Yixuan Wang
- Yunnan Academy of Forestry and Grassland, Kunming 650201, China
| | - Ruiling Yuan
- Yunnan Academy of Forestry and Grassland, Kunming 650201, China
| | - Peng Chen
- Yunnan Academy of Forestry and Grassland, Kunming 650201, China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Correspondence: (B.W.); (X.X.)
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Correspondence: (B.W.); (X.X.)
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Gaunt ER, Digard P. Compositional biases in RNA viruses: Causes, consequences and applications. WILEY INTERDISCIPLINARY REVIEWS. 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] [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.
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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
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Sobhy NM, Armién AG, Pilot J, Singh V, Padhi SK, Muldoon D, Goyal SM, Mor SK. Detection and molecular characterization of astro and bocaviruses in dogs in Minnesota. Comp Immunol Microbiol Infect Dis 2021; 81:101740. [PMID: 34971935 DOI: 10.1016/j.cimid.2021.101740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 10/19/2022]
Abstract
Canine astrovirus (CAstV) and canine bocavirus (CBoV) are involved in cases of mild, and sometimes severe, gastroenteritis in dogs. Fecal samples from two dead dogs with gastroenteritis were received at the University of Minnesota Veterinary Diagnostic Laboratory to determine the cause of death. Small round viruses of 20-35 nm diameter were observed by negative contrast electron microscopy. The samples were subjected to Illumina MiSeq sequencing. Both samples were strongly positive for CAstV; all viral reads were related to CAstV. In addition, sample number 1 had a few reads of CBoV. Two complete sequences of CAstV were identified (6625 and 6627 nt in length) with 95% nt identity. RT-PCR and PCR were used to confirm CAstV and CBoV infections in successive samples of canine gastroenteritis. Sanger sequencing was done on nucleic acids from positive samples. Of a total of ten samples, CAstV and CBoV infections were confirmed in six and eight animals, respectively. Four animals had mixed infection with both viruses. All sequences of ORF1b gene of CAstVs showed closest clusters in phylogenetic tree with 96-100% nucleotide and amino acids identity. On the other hand, identity between VP2 gene of different CBoV strains in this study ranged from 93%- 100%. All strains were located close to each other except the divergent MT078234 strain, which was arranged in a separate branch and was closer to reference strain JN648103/USA/2010. This study highlights the importance of electron microscopy and next generation sequencing for early detection and characterization of viruses associated with dog gastroenteritis.
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Affiliation(s)
- N M Sobhy
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA; Department of Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia 44511, Egypt
| | - A G Armién
- California Animal Health and Food Safety Laboratory System, University of California, Davis, CA 95616, USA
| | - J Pilot
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - V Singh
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - S K Padhi
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - D Muldoon
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - S M Goyal
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - S K Mor
- Veterinary Diagnostic Laboratory and Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.
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5
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Dayaram A, Seeber P, Courtiol A, Soilemetzidou S, Tsangaras K, Franz M, McEwen GK, Azab W, Kaczensky P, Melzheimer J, East ML, Ganbaatar O, Walzer C, Osterrieder N, Greenwood AD. Seasonal host and ecological drivers may promote restricted water as a viral vector. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 773:145446. [PMID: 33588222 DOI: 10.1016/j.scitotenv.2021.145446] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/19/2021] [Accepted: 01/23/2021] [Indexed: 06/12/2023]
Abstract
In climates with seasonally limited precipitation, terrestrial animals congregate at high densities at scarce water sources. We hypothesize that viruses can exploit the recurrence of these diverse animal congregations to spread. In this study, we test the central prediction of this hypothesis - that viruses employing this transmission strategy remain stable and infectious in water. Equid herpesviruses (EHVs) were chosen as a model as they have been shown to remain stable and infectious in water for weeks under laboratory conditions. Using fecal data from wild equids from a previous study, we establish that EHVs are shed more frequently by their hosts during the dry season, increasing the probability of water source contamination with EHV. We document the presence of several strains of EHVs present in high genome copy number from the surface water and sediments of waterholes sampled across a variety of mammalian assemblages, locations, temperatures and pH. Phylogenetic analysis reveals that the different EHV strains found exhibit little divergence despite representing ancient lineages. We employed molecular approaches to show that EHVs shed remain stable in waterholes with detection decreasing with increasing temperature in sediments. Infectivity experiments using cell culture reveals that EHVs remain infectious in water derived from waterholes. The results are supportive of water as an abiotic viral vector for EHV.
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Affiliation(s)
- Anisha Dayaram
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315 Berlin, Germany; Institut für Neurophysiologie, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Peter Seeber
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315 Berlin, Germany; Limnological Institute, University of Konstanz, Mainaustrasse 252, 78467 Konstanz, Germany
| | - Alexandre Courtiol
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315 Berlin, Germany
| | - Sanatana Soilemetzidou
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315 Berlin, Germany
| | - Kyriakos Tsangaras
- Department of Life and Health Sciences, University of Nicosia, 46 Makedonitissas Avenue, CY-2417 Nicosia, Cyprus
| | - Mathias Franz
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315 Berlin, Germany
| | - Gayle K McEwen
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315 Berlin, Germany
| | - Walid Azab
- Institut für Virologie, Freie Universität Berlin, Robert-von-Ostertag-Str, 7-13, 14163 Berlin, Germany
| | - Petra Kaczensky
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Savoyenstrasse 1, A-1160 Vienna, Austria; Norwegian Institute for Nature Research, Trondheim, Norway
| | - Jörg Melzheimer
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315 Berlin, Germany
| | - Marion L East
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315 Berlin, Germany
| | - Oyunsaikhan Ganbaatar
- Department of Biology, School of Arts and Sciences, National University of Mongolia, Mongolia; Great Gobi B Strictly Protected Area, Takhiin Tal, Gobi-Altai Province, Mongolia
| | - Christian Walzer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Savoyenstrasse 1, A-1160 Vienna, Austria; Wildlife Conservation Society, 2300 Southern Blvd, 10460 Bronx, NY, USA
| | - Nikolaus Osterrieder
- Institut für Virologie, Freie Universität Berlin, Robert-von-Ostertag-Str, 7-13, 14163 Berlin, Germany; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Alex D Greenwood
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315 Berlin, Germany; Department of Veterinary Medicine, Freie Universität Berlin, Oertzenweg 19b, 14163, Germany.
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6
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Roach SN, Langlois RA. Intra- and Cross-Species Transmission of Astroviruses. Viruses 2021; 13:v13061127. [PMID: 34208242 PMCID: PMC8230745 DOI: 10.3390/v13061127] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/30/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Astroviruses are non-enveloped, single-stranded RNA viruses that infect mammalian and avian species. In humans, astrovirus infections are one of the most common causes of gastroenteritis in children. Infection has also been linked to serious neurological complications, especially in immunocompromised individuals. More extensive disease has also been characterized in non-human mammalian and avian species. To date, astroviruses have been detected in over 80 different avian and mammalian hosts. As the number of hosts continues to rise, the need to understand how astroviruses transmit within a given species as well as to new host species becomes increasingly important. Here, we review the current understanding of astrovirus transmission, the factors that influence viral spread, and the potential for cross-species transmission. Additionally, we highlight the current gaps in knowledge and areas of future research that will be key to understanding astrovirus transmission and zoonotic potential.
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Affiliation(s)
- Shanley N. Roach
- Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Ryan A. Langlois
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence:
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Kim J, Lal A, Kil EJ, Kwak HR, Yoon HS, Choi HS, Kim M, Ali M, Lee S. Adaptation and Codon-Usage Preference of Apple and Pear-Infecting Apple Stem Grooving Viruses. Microorganisms 2021; 9:microorganisms9061111. [PMID: 34063757 PMCID: PMC8223792 DOI: 10.3390/microorganisms9061111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 11/17/2022] Open
Abstract
Apple stem grooving virus (ASGV; genus Capillovirus) is an economically important virus. It has an approx. 6.5 kb, monopartite, linear, positive-sense, single-stranded RNA genome. The present study includes identification of 24 isolates—13 isolates from apple (Pyrus malus L.) and 11 isolates from pear (Pyrus communis L.)—from different agricultural fields in South Korea. The coat protein (CP) gene of the corresponding 23 isolates were amplified, sequenced, and analyzed. The CP sequences showed phylogenetic separation based on their host species, and not on the geography, indicating host adaptation. Further analysis showed that the ASGV isolated in this study followed host adaptation influenced and preferred by the host codon-usage.
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Affiliation(s)
- Jaedeok Kim
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (J.K.); (A.L.); (E.-J.K.)
- Incheon International Airport Regional Office, Animal and Plant Quarantine Agency, Seoul 22382, Korea
| | - Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (J.K.); (A.L.); (E.-J.K.)
| | - Eui-Joon Kil
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (J.K.); (A.L.); (E.-J.K.)
- Department of Plant Medicals, Andong National University, Andong 36729, Korea
| | - Hae-Ryun Kwak
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea; (H.-R.K.); (H.-S.C.)
| | - Hwan-Su Yoon
- Department of Biological Science, Sungkyunkwan University, Suwon 16419, Korea;
| | - Hong-Soo Choi
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea; (H.-R.K.); (H.-S.C.)
| | - Mikyeong Kim
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea; (H.-R.K.); (H.-S.C.)
- College of Agriculture, Life and Environment Sciences, Chungbuk National University, Cheongju 28644, Korea
- Correspondence: (M.K.); (M.A.); (S.L.); Tel.: +82-43-261-2509 (M.K.); +92-312-9959558 (M.A.); +82-31-290-7866 (S.L.); Fax: +82-43-271-4414 (M.K.); +82-31-290-7892 (S.L.)
| | - Muhammad Ali
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Johar Town, Lahore 54770, Pakistan
- Correspondence: (M.K.); (M.A.); (S.L.); Tel.: +82-43-261-2509 (M.K.); +92-312-9959558 (M.A.); +82-31-290-7866 (S.L.); Fax: +82-43-271-4414 (M.K.); +82-31-290-7892 (S.L.)
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (J.K.); (A.L.); (E.-J.K.)
- Correspondence: (M.K.); (M.A.); (S.L.); Tel.: +82-43-261-2509 (M.K.); +92-312-9959558 (M.A.); +82-31-290-7866 (S.L.); Fax: +82-43-271-4414 (M.K.); +82-31-290-7892 (S.L.)
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8
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Franzo G, Tucciarone CM, Legnardi M, Cecchinato M. Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues. BMC Genomics 2021; 22:244. [PMID: 33827429 PMCID: PMC8025453 DOI: 10.1186/s12864-021-07559-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 03/26/2021] [Indexed: 11/10/2022] Open
Abstract
Background Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, very few of those studies focused on the effect of genome composition and the codon bias of different IBV proteins, despite the remarkable increase in available complete genomes. In the present study, all IBV complete genomes were downloaded (n = 383), and several statistics representative of genome composition and codon bias were calculated for each protein-coding sequence, including but not limited to, the nucleotide odds ratio, relative synonymous codon usage and effective number of codons. Additionally, viral codon usage was compared to host codon usage based on a collection of highly expressed genes in IBV target and nontarget tissues. Results The results obtained demonstrated a significant difference among structural, non-structural and accessory proteins, especially regarding dinucleotide composition, which appears under strong selective forces. In particular, some dinucleotide pairs, such as CpG, a probable target of the host innate immune response, are underrepresented in genes coding for pp1a, pp1ab, S and N. Although genome composition and dinucleotide bias appear to affect codon usage, additional selective forces may act directly on codon bias. Variability in relative synonymous codon usage and effective number of codons was found for different proteins, with structural proteins and polyproteins being more adapted to the codon bias of host target tissues. In contrast, accessory proteins had a more biased codon usage (i.e., lower number of preferred codons), which might contribute to the regulation of their expression level and timing throughout the cell cycle. Conclusions The present study confirms the existence of selective forces acting directly on the genome and not only indirectly through phenotype selection. This evidence might help understanding IBV biology and in developing attenuated strains without affecting the protein phenotype and therefore immunogenicity. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07559-5.
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Affiliation(s)
- Giovanni Franzo
- Microbiology and Infectious Diseases, Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16 - 35020 Legnaro, Padua, Italy.
| | - Claudia Maria Tucciarone
- Microbiology and Infectious Diseases, Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16 - 35020 Legnaro, Padua, Italy
| | - Matteo Legnardi
- Microbiology and Infectious Diseases, Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16 - 35020 Legnaro, Padua, Italy
| | - Mattia Cecchinato
- Microbiology and Infectious Diseases, Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16 - 35020 Legnaro, Padua, Italy
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Molecular survey of parvovirus, astrovirus, coronavirus, and calicivirus in symptomatic dogs. Vet Res Commun 2021; 45:31-40. [PMID: 33392909 PMCID: PMC7779159 DOI: 10.1007/s11259-020-09785-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/09/2020] [Accepted: 12/16/2020] [Indexed: 01/31/2023]
Abstract
Gastrointestinal disorders caused by enteric viruses are frequently reported in dogs worldwide, with significant mortality rates in unvaccinated individuals. This study reports the identification and molecular characterization of Canine parvovirus (CPV-2), Canine coronavirus (CcoV), Canine astrovirus (AstV), and Canine calicivirus (CcaV) in a panel of dogs showing severe enteric clinical signs sampled in a typical Mediterranean environment (Sardinia, Italy). At least one of these viral species was detected in 92.3% samples. CPV-2 was the most frequently detected virus (87.2%), followed by AsTv (20.5%), CCoV-IIa (18%), and CCoV-I (10.3%). CCoV-IIb and CaCV were not detected in any sample. Single infection was detected in 24 samples (66.7%), mainly related to CPV-2 (91.7%). Coinfections were present in 33.3% samples with constant detection of CPV-2. Canine coronavirus was present only in coinfected animals. The VP2 sequence analysis of CPV-2 positive samples confirmed the presence of all variants, with CPV-2b most frequently detected. Phylogeny based on the CcoV-IIa spike protein (S) gene allowed to identify 2 different clades among Sardinian isolates but failed to distinguish enteric from pantropic viruses. Study on presence and prevalence of enteroviruses in dogs increase our knowledge about the circulation of these pathogens in the Mediterranean area and highlight the need for dedicated routine vaccine prophylaxis. Molecular analyses of enteric viruses are fundamental to avoid failure of vaccines caused by frequent mutations observed in these enteroviruses.
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Deb B, Uddin A, Chakraborty S. Composition, codon usage pattern, protein properties, and influencing factors in the genomes of members of the family Anelloviridae. Arch Virol 2021; 166:461-474. [PMID: 33392821 PMCID: PMC7779081 DOI: 10.1007/s00705-020-04890-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 10/02/2020] [Indexed: 01/31/2023]
Abstract
The present study was carried out on 62 genome sequences of members of the family Anelloviridae, as there have been no reports of genome analysis of these DNA viruses using a bioinformatics approach. The genes were found to be rich in AC content with low codon usage bias (CUB). Relative synonymous codon usage (RSCU) values identified the preferred codons for each amino acid in the family. The codon AGA was overrepresented, while the codons TCG, TTG, CGG, CGT, ACG, GCG and GAT were underrepresented in all of the genomes. A significant correlation was found between the effective number of codons (ENC) and base constraints, indicating that compositional properties might have influenced the CUB. A highly significant correlation was observed between the overall base content and the base content at the third codon position, indicating that mutations might have affected the CUB. A highly significant positive correlation was observed between GC12 and GC3 (r = 0.904, p < 0.01), which indicated that directional mutation pressure influenced all three codon positions. A neutrality plot revealed that the contribution of mutation and natural selection in determining the CUB was 58.6% and 41.4%, respectively.
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Affiliation(s)
- Bornali Deb
- Department of Biotechnology, Assam University, Silchar, Assam 788150 India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, Assam 788150 India
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Amimo JO, Machuka EM, Abworo EO, Vlasova AN, Pelle R. Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms. Viruses 2020; 12:v12111262. [PMID: 33167568 PMCID: PMC7694451 DOI: 10.3390/v12111262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 11/16/2022] Open
Abstract
Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of seven strains with complete (or near complete) AstV genome revealed variable nucleotide and amino acid sequence identities with known porcine astrovirus (PoAstV) strains. The U083 and K321 strains had nucleotide sequence identities ranging from 66.4 to 75.4% with the known PoAstV2 strains; U460 strain had nucleotide sequence identities of 57.0 to 65.1% regarding the known PoAstV3; and K062, K366, K451, and K456 strains had nucleotide sequence identities of 63.5 to 80% with the known PoAstV4 strains. The low sequence identities (<90%) indicate that novel genotypes of PoAstVs are circulating in the study area. Recombination analysis using whole genomes revealed evidence of multiple recombination events in PoAstV4, suggesting that recombination might have contributed to the observed genetic diversity. Linear antigen epitope prediction and a comparative analysis of capsid protein of our field strains identified potential candidate epitopes that could help in the design of immuno-diagnostic tools and a subunit vaccine. These findings provide new insights into the molecular epidemiology of porcine astroviruses in East Africa.
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Affiliation(s)
- Joshua O. Amimo
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, P.O. Box 29053, Nairobi 00625, Kenya
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, The Ohio State University, 1168 Madison Avenue, Wooster, OH 44961, USA;
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (E.M.M.); (E.O.A.); (R.P.)
- Correspondence:
| | - Eunice M. Machuka
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (E.M.M.); (E.O.A.); (R.P.)
| | - Edward O. Abworo
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (E.M.M.); (E.O.A.); (R.P.)
| | - Anastasia N. Vlasova
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, The Ohio State University, 1168 Madison Avenue, Wooster, OH 44961, USA;
| | - Roger Pelle
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (E.M.M.); (E.O.A.); (R.P.)
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12
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A Crosstalk on Codon Usage in Genes Associated with Leukemia. Biochem Genet 2020; 59:235-255. [PMID: 32989646 DOI: 10.1007/s10528-020-10000-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023]
Abstract
Leukemia is the outcome of aggregation of damaged white blood cells. Several genes were reported to be associated with the pathogenesis of leukemia. These genes were computationally analyzed to decipher their codon usage bias (CUB) and to identify the prime factors influencing the codon usage profile as no work was reported yet. The mean values of synonymous codon usage order (SCUO) parameter indicated low CUB of the genes. Significant positive association of SCUO with overall GC and positional GCs might signal the presence of mutational pressure. However, neutrality plot suggested the dominant role of natural selection across the genes. Along with natural selection, the role of mutation pressure was also prominent and that might be responsible for lower CUB (SCUO = 0.19) of genes. Low translational speed might permit accuracy in the process. A strong inverse relationship of translational rate was observed with CUB of genes and folding energy.
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13
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Wu H, Bao Z, Mou C, Chen Z, Zhao J. Comprehensive Analysis of Codon Usage on Porcine Astrovirus. Viruses 2020; 12:v12090991. [PMID: 32899965 PMCID: PMC7552017 DOI: 10.3390/v12090991] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 08/26/2020] [Accepted: 09/03/2020] [Indexed: 02/04/2023] Open
Abstract
Porcine astrovirus (PAstV), associated with mild diarrhea and neurological disease, is transmitted in pig farms worldwide. The purpose of this study is to elucidate the main factors affecting codon usage to PAstVs. Phylogenetic analysis showed that the subtype PAstV-5 sat at the bottom of phylogenetic tree, followed by PAstV-3, PAstV-1, PAstV-2, and PAstV-4, indicating that the five existing subtypes (PAstV1-PAstV5) may be formed by multiple differentiations of PAstV ancestors. A codon usage bias was found in the PAstVs-2,3,4,5 from the analyses of effective number of codons (ENC) and relative synonymous codon usage (RSCU). Nucleotides A/U are more frequently used than nucleotides C/G in the genome CDSs of the PAstVs-3,4,5. Codon usage patterns of PAstV-5 are dominated by mutation pressure and natural selection, while natural selection is the main evolutionary force that affects the codon usage pattern of PAstVs-2,3,4. The analyses of codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) showed the codon usage similarities between the PAstV and animals might contribute to the broad host range and the cross-species transmission of astrovirus. Our results provide insight into understanding the PAstV evolution and codon usage patterns.
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Affiliation(s)
- Huiguang Wu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (H.W.); (Z.B.); (C.M.)
- Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Zhengyu Bao
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (H.W.); (Z.B.); (C.M.)
| | - Chunxiao Mou
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (H.W.); (Z.B.); (C.M.)
- Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Zhenhai Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (H.W.); (Z.B.); (C.M.)
- Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (Z.C.); (J.Z.)
| | - Jingwen Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Correspondence: (Z.C.); (J.Z.)
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Deb B, Uddin A, Chakraborty S. Codon usage pattern and its influencing factors in different genomes of hepadnaviruses. Arch Virol 2020; 165:557-570. [PMID: 32036428 PMCID: PMC7086886 DOI: 10.1007/s00705-020-04533-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/07/2019] [Indexed: 12/18/2022]
Abstract
Codon usage bias (CUB) arises from the preference for a codon over codons for the same amino acid. The major factors contributing to CUB are evolutionary forces, compositional properties, gene expression, and protein properties. The present analysis was performed to investigate the compositional properties and the extent of CUB across the genomes of members of the family Hepadnaviridae, as previously no work using bioinformatic tools has been reported. The viral genes were found to be AT rich with low CUB. Analysis of relative synonymous codon usage (RSCU) was used to identify overrepresented and underrepresented codons for each amino acid. Correlation analysis of overall nucleotide composition and its composition at the third codon position suggested that mutation pressure might influence the CUB. A highly significant correlation was observed between GC12 and GC3 (r = 0.910, p < 0.01), indicating that directional mutation affected all three codon positions across the genome. Translational selection (P2) and mutational responsive index (MRI) values of genes suggested that mutation plays a more important role than translational selection in members of the family Hepadnaviridae.
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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.
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15
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Ismail SNFB, Baharum SN, Fazry S, Low CF. Comparative genome analysis reveals a distinct influence of nucleotide composition on virus-host species-specific interaction of prawn-infecting nodavirus. JOURNAL OF FISH DISEASES 2019; 42:1761-1772. [PMID: 31637743 DOI: 10.1111/jfd.13093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/21/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
Discovery of species-specific interaction between the host and virus has drawn the interest of many researchers to study the evolution of the newly emerged virus. Comparative genome analysis provides insights of the virus functional genome evolution and the underlying mechanisms of virus-host interactions. The analysis of nucleotide composition signified the evolution of nodavirus towards host specialization in a host-specific mutation manner. GC-rich genome of betanodavirus was significantly deficient in UpA and UpU dinucleotides composition, whilst the AU-rich genome of gammanodavirus was deficient in CpG dinucleotide. The capsid of MrNV and PvNV of gammanodavirus retains the highest abundance of adenine and uracil at the second codon position, respectively, which were found to be very distinctive from the other genera. ENC-GC3 plot inferred the influence of natural selection and mutational pressure in shaping the evolution of MrNV RdRp and capsid, respectively. Furthermore, CAI/eCAI analysis predicts a comparable adaptability of MrNV in squid, Sepia officinalis than its natural host, Macrobrachium rosenbergii. Thus, further study is warranted to investigate the capacity of MrNV replication in S. officinalis owing to its high codon adaptation index.
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Affiliation(s)
| | | | - Shazrul Fazry
- Tasik Chini Research Center, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Bangi, Malaysia
| | - Chen Fei Low
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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16
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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] [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.
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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
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Wohlgemuth N, Honce R, Schultz-Cherry S. Astrovirus evolution and emergence. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 69:30-37. [PMID: 30639546 PMCID: PMC7106029 DOI: 10.1016/j.meegid.2019.01.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 12/19/2022]
Abstract
Astroviruses are small, non-enveloped, positive-sense, single-stranded RNA viruses that belong to the Astroviridae family. Astroviruses infect diverse hosts and are typically associated with gastrointestinal illness; although disease can range from asymptomatic to encephalitis depending on the host and viral genotype. Astroviruses have high genetic variability due to an error prone polymerase and frequent recombination events between strains. Once thought to be species specific, recent evidence suggests astroviruses can spread between different host species, although the frequency with which this occurs and the restrictions that regulate the process are unknown. Recombination events can lead to drastic evolutionary changes and contribute to cross-species transmission events. This work reviews the current state of research on astrovirus evolution and emergence, especially as it relates to cross-species transmission and recombination of astroviruses.
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Affiliation(s)
- Nicholas Wohlgemuth
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Rebekah Honce
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38105, United States
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
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18
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Genome polarity of RNA viruses reflects the different evolutionary pressures shaping codon usage. Arch Virol 2018; 163:2883-2888. [PMID: 29987380 DOI: 10.1007/s00705-018-3930-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/10/2018] [Indexed: 10/28/2022]
Abstract
RNA viruses are classified by their genome polarity and replication strategies. Nucleotide composition and codon usage differ among virus groups, for instance positive-sense RNA (+ssRNA) viruses have higher GC-content than the other RNA virus groups. Codon usage of +ssRNA viruses is closer to humans showing significantly higher codon adaptation index (CAI) than those of negative-sense RNA (-ssRNA), double stranded RNA (dsRNA) and retroviruses. Ambisense viruses have high CAI comparable to that of +ssRNA virus despite their lower GC content, whereas dsRNA viruses have the lowest CAI. This may provide a benefit for +ssRNA viruses as their genomes are used as mRNA. However, analyses for influence of nucleotide composition on codon usage did not show a difference between +ssRNA and -ssRNA viruses. This suggests that genome composition and hence mutational pressure remain the major pressure causing the differences in codon usage among RNA viruses with different genome types.
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Franzo G, Segales J, Tucciarone CM, Cecchinato M, Drigo M. The analysis of genome composition and codon bias reveals distinctive patterns between avian and mammalian circoviruses which suggest a potential recombinant origin for Porcine circovirus 3. PLoS One 2018; 13:e0199950. [PMID: 29958294 PMCID: PMC6025852 DOI: 10.1371/journal.pone.0199950] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/15/2018] [Indexed: 01/30/2023] Open
Abstract
Members of the genus Circovirus are host-specific viruses, which are totally dependent on cell machinery for their replication. Consequently, certain mimicry of the host genome features is expected to maximize cellular replicative system exploitation and minimize the recognition by the innate immune system. In the present study, the analysis of several genome composition and codon bias parameters of circoviruses infecting avian and mammalian species demonstrated the presence of quite distinctive patterns between the two groups. Remarkably, a higher deviation from the expected values based only on mutational patterns was observed for mammalian circoviruses both at dinucleotide and codon levels. Accordingly, a stronger selective pressure was estimated to shape the genome of mammalian circoviruses, particularly in the Cap encoding gene, compared to avian circoviruses. These differences could be attributed to different physiological and immunological features of the two host classes and suggest a trade-off between a tendency to optimize the capsid protein translation while minimizing the recognition of the genome and the transcript molecules. Interestingly, the recently identified Porcine circovirus 3 (PCV-3) had an intermediate pattern in terms of genome composition and codon bias. Particularly, its Rep gene appeared closely related to other mammalian circoviruses (especially bat circoviruses) while the Cap gene more closely resembled avian circoviruses. These evidences, coupled with the high selective forces apparently modelling the PCV-3 Cap gene composition, suggest the potential recombinant origin, followed or preceded by a host jump, of this virus.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Padua, Italy
- * E-mail:
| | - Joaquim Segales
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA- UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Claudia Maria Tucciarone
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Padua, Italy
| | - Mattia Cecchinato
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Padua, Italy
| | - Michele Drigo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Padua, Italy
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De Grazia S, Lanave G, Bonura F, Urone N, Cappa V, Li Muli S, Pepe A, Gellért A, Banyai K, Martella V, Giammanco GM. Molecular evolutionary analysis of type-1 human astroviruses identifies putative sites under selection pressure on the capsid protein. INFECTION GENETICS AND EVOLUTION 2017; 58:199-208. [PMID: 29288011 DOI: 10.1016/j.meegid.2017.12.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/06/2017] [Accepted: 12/22/2017] [Indexed: 12/23/2022]
Abstract
Human astroviruses (HAstV) are important enteric pathogens that can be classified into eight sero/genotypes (HAstV-1 to -8). Although the various HAstV types show global spread, type-1 strains tend to be predominant. Molecular analysis of the genomic region encoding the capsid protein (ORF2) has revealed discrete sequence variation, with different lineages within each HAstV type and at least three major lineages have been identified within HAstV-1. Longitudinal epidemiological surveillance has revealed temporal shift of the various HAstV-1 lineages. Metadata analysis of HAstV-1 sequences available in the databases also revealed temporal shifts of the circulation of HAstV-1 lineages, suggesting possible antigenic-related mechanisms of selection at the sub-genotype level. By comparison of HAstV-1 capsid sequences, lineage-defining residues under positive selection were identified. Structural analysis of HAstV-1 capsid allowed identifying at least six residues exposed on the virion surface. Two residues were located in the VP34 (shell region) whilst four residues were mapped in the VP25/27 (protruding region) of HAstV capsid protein, in proximity of the putative receptor binding S site. These findings suggest that mechanisms similar to those observed and/or hypothesized for other enteric viruses are also shaping the evolution of HAstVs, with intra-typic diversification being a possible mechanism to decrease the antigenic pressure to which these viruses are exposed.
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Affiliation(s)
- Simona De Grazia
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy.
| | - Gianvito Lanave
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy
| | - Floriana Bonura
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Noemi Urone
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Vincenzo Cappa
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Sara Li Muli
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Arcangelo Pepe
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Akos Gellért
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest H-1143, Hungary
| | - Krisztian Banyai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest H-1143, Hungary
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy
| | - Giovanni M Giammanco
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
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PHYLOGENETIC ANALYSIS OF THE GENOME OF AN ENTERITIS-ASSOCIATED BOTTLENOSE DOLPHIN MASTADENOVIRUS SUPPORTS A CLADE INFECTING THE CETARTIODACTYLA. J Wildl Dis 2017; 54:112-121. [PMID: 29077545 DOI: 10.7589/2017-03-052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
: Adenoviruses are nonenveloped, double-stranded DNA viruses, known to infect members of all tetrapod classes, with a similarity between phylogenies of hosts and viruses observed. We characterized bottlenose dolphin adenovirus 2 (BdAdV-2) found in a bottlenose dolphin ( Tursiops truncatus) with enteritis. Virions were seen by negative staining electron microscopy of feces. Initial sequences obtained using conserved PCR primers were expanded using primer walking techniques, and the complete coding sequence was obtained. Phylogenetic analyses were consistent with coevolution of this virus and its bottlenose dolphin host, placing BdAdV-2 into a monophyletic group with other mastadenoviruses of Cetartiodactyla. When considering the low guanine/cytosine (G/C) content of BdAdV-2 with the phylogenetic data, this virus may represent a host-jumping event from another member of Cetartiodactyla. Analysis of partial polymerase indicated that bottlenose dolphin adenovirus 1, previously identified in Spain, and BdAdV-2 are sister taxa with harbor porpoise adenovirus 1, forming a cetacean clade. Bottlenose dolphin adenovirus 2 includes a highly divergent fiber gene. Two genes homologous to the dUTPase superfamily are also present which could play a role in enabling viral replication in nondividing cells. We used sequence data to develop a probe hybridization quantitative PCR assay specific to BdAdV-2 with a limit of detection of 10 copies.
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22
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Phakaratsakul S, Sirihongthong T, Boonarkart C, Suptawiwat O, Auewarakul P. Codon usage of HIV regulatory genes is not determined by nucleotide composition. Arch Virol 2017; 163:337-348. [PMID: 29067529 DOI: 10.1007/s00705-017-3597-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/30/2017] [Indexed: 11/27/2022]
Abstract
Codon usage bias can be a result of either mutational bias or selection for translational efficiency and/or accuracy. Previous data has suggested that nucleotide composition constraint was the main determinant of HIV codon usage, and that nucleotide composition and codon usage were different between the regulatory genes, tat and rev, and other viral genes. It is not clear whether translational selection contributed to the codon usage difference and how nucleotide composition and translational selection interact to determine HIV codon usage. In this study, a model of codon bias due to GC composition with modification for the A-rich third codon position was used to calculate predicted HIV codon frequencies based on its nucleotide composition. The predicted codon usage of each gene was compared with the actual codon frequency. The predicted codon usage based on GC composition matched well with the actual codon frequencies for the structural genes (gag, pol and env). However, the codon usage of the regulatory genes (tat and rev) could not be predicted. Codon usage of the regulatory genes was also relatively unbiased showing the highest effective number of codons (ENC). Moreover, the codon adaptation index (CAI) of the regulatory genes showed better adaptation to human codons when compared to other HIV genes. Therefore, the early expressed genes responsible for regulation of the replication cycle, tat and rev, were more similar to humans in terms of codon usage and GC content than other HIV genes. This may help these genes to be expressed efficiently during the early stages of infection.
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Affiliation(s)
- Supinya Phakaratsakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Thanyaporn Sirihongthong
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Chompunuch Boonarkart
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Ornpreya Suptawiwat
- Research and International Relations Division, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
| | - Prasert Auewarakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
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Malmberg M, Rubio-Guerri C, Hayer J, García-Párraga D, Nieto-Pelegrín E, Melero M, Álvaro T, Valls M, Sánchez-Vizcaíno JM, Belák S, Granberg F. Phylogenomic analysis of the complete sequence of a gastroenteritis-associated cetacean adenovirus (bottlenose dolphin adenovirus 1) reveals a high degree of genetic divergence. INFECTION GENETICS AND EVOLUTION 2017; 53:47-55. [PMID: 28506838 DOI: 10.1016/j.meegid.2017.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/09/2017] [Accepted: 05/11/2017] [Indexed: 10/19/2022]
Abstract
Adenoviruses are common pathogens in vertebrates, infecting a wide range of hosts, but only having rarely been detected and correlated with disease in cetaceans. This article describes the first complete genomic sequence of a cetacean adenovirus, bottlenose dolphin adenovirus 1 (BdAdV-1), detected in captive bottlenose dolphin population (Tursiops truncatus) suffering from self-limiting gastroenteritis. The complete genome sequence of BdAdV-1 was recovered from data generated by high-throughput sequencing and validated by Sanger sequencing. The genome is 34,080bp long and has 220 nucleotides long inverted terminal repeats. A total of 29 coding sequences were identified, 26 of which were functionally annotated. Among the unusual features of this genome is a remarkably long 4380bp E3 ORF1, that displays no sequence homology with the corresponding E3 regions of other adenoviruses. In addition, the fiber protein only has 26% identity with fiber proteins described in other adenoviruses. Three hypothetical proteins were predicted. The phylogenetic analysis indicates that the closest known relative to BdAdV-1 is an adenovirus detected in bottlenose dolphin (KR024710), with an amino acid sequence identity between 36 and 79% depending on the protein. Based on the phylogenic analysis, the BdAdV-1 appears to have co-evolved with its host. The results indicate that BdAdV-1 belongs to the Mastadenovirus genus of the Adenoviridae family, however, it is clearly different from other adenoviruses, especially in the 3'-end of the viral genome. The high degree of sequence divergence suggests that BdAdV-1 should be considered as a novel species in the Mastadenovirus genus. The study also demonstrates the usefulness of high-throughput sequencing to obtain full-length genomes of genetically divergent viruses.
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Affiliation(s)
- Maja Malmberg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden; SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden; World Organisation for Animal Health (OIE) Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Box 7028, 750 07 Uppsala, Sweden.
| | - Consuelo Rubio-Guerri
- VISAVET Center and Animal Health Department, Veterinary School, Complutense University of Madrid, Av Puerta del Hierro s/n, 28040 Madrid, Spain; Fundación Oceanografic, Ciudad de las Artes y las Ciencias, Primo Yúfera 1B, 46013, Valencia, Spain.
| | - Juliette Hayer
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden
| | - Daniel García-Párraga
- Fundación Oceanografic, Ciudad de las Artes y las Ciencias, Primo Yúfera 1B, 46013, Valencia, Spain; Veterinary Services, Avanqua Oceanogràfic-Ágora, C/Eduardo Primo Yúfera 1B, 46013, Valencia, Spain.
| | - Elvira Nieto-Pelegrín
- VISAVET Center and Animal Health Department, Veterinary School, Complutense University of Madrid, Av Puerta del Hierro s/n, 28040 Madrid, Spain
| | - Mar Melero
- VISAVET Center and Animal Health Department, Veterinary School, Complutense University of Madrid, Av Puerta del Hierro s/n, 28040 Madrid, Spain.
| | - Teresa Álvaro
- Veterinary Services, Avanqua Oceanogràfic-Ágora, C/Eduardo Primo Yúfera 1B, 46013, Valencia, Spain.
| | - Mónica Valls
- Veterinary Services, Avanqua Oceanogràfic-Ágora, C/Eduardo Primo Yúfera 1B, 46013, Valencia, Spain.
| | - Jose Manuel Sánchez-Vizcaíno
- VISAVET Center and Animal Health Department, Veterinary School, Complutense University of Madrid, Av Puerta del Hierro s/n, 28040 Madrid, Spain.
| | - Sándor Belák
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden; World Organisation for Animal Health (OIE) Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Box 7028, 750 07 Uppsala, Sweden.
| | - Fredrik Granberg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden; World Organisation for Animal Health (OIE) Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Box 7028, 750 07 Uppsala, Sweden.
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24
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Lacroix A, Duong V, Hul V, San S, Davun H, Omaliss K, Chea S, Hassanin A, Theppangna W, Silithammavong S, Khammavong K, Singhalath S, Afelt A, Greatorex Z, Fine AE, Goldstein T, Olson S, Joly DO, Keatts L, Dussart P, Frutos R, Buchy P. Diversity of bat astroviruses in Lao PDR and Cambodia. INFECTION GENETICS AND EVOLUTION 2016; 47:41-50. [PMID: 27871796 PMCID: PMC7106329 DOI: 10.1016/j.meegid.2016.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/12/2016] [Accepted: 11/14/2016] [Indexed: 12/24/2022]
Abstract
Astroviruses are known to infect humans and a wide range of animal species, and can cause gastroenteritis in their hosts. Recent studies have reported astroviruses in bats in Europe and in several locations in China. We sampled 1876 bats from 17 genera at 45 sites from 14 and 13 provinces in Cambodia and Lao PDR respectively, and tested them for astroviruses. Our study revealed a high diversity of astroviruses among various Yangochiroptera and Yinpterochiroptera bats. Evidence for varying degrees of host restriction for astroviruses in bats was found. Furthermore, additional Pteropodid hosts were detected. The astroviruses formed distinct phylogenetic clusters within the genus Mamastrovirus, most closely related to other known bat astroviruses. The astrovirus sequences were found to be highly saturated indicating that phylogenetic relationships should be interpreted carefully. An astrovirus clustering in a group with other viruses from diverse hosts, including from ungulates and porcupines, was found in a Rousettus bat. These findings suggest that diverse astroviruses can be found in many species of mammals, including bats. Diverse astroviruses detected in bats in Lao PDR and Cambodia High polymorphism of astroviruses found in insectivorous and frugivorous bats High level of genome saturation and hypermutation potential evidenced in astrovirus Detection of additional astrovirus bat hosts, i.e. nectar bats from the genus Eonycteris Discovery of a new species of astrovirus in fruit bats (Rousettus sp.)
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Affiliation(s)
- Audrey Lacroix
- Institut Pasteur du Cambodge, Virology Unit, Phnom Penh, Cambodia
| | - Veasna Duong
- Institut Pasteur du Cambodge, Virology Unit, Phnom Penh, Cambodia
| | - Vibol Hul
- Institut Pasteur du Cambodge, Virology Unit, Phnom Penh, Cambodia
| | - Sorn San
- National Veterinary Research Institute, Department of Animal Health and Production, Ministry of Agriculture Forestry and Fisheries, Cambodia
| | - Holl Davun
- National Veterinary Research Institute, Department of Animal Health and Production, Ministry of Agriculture Forestry and Fisheries, Cambodia
| | - Keo Omaliss
- Forest Administration, Ministry of Agriculture Forestry and Fisheries, Cambodia
| | | | - Alexandre Hassanin
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 MNHN CNRS UPMC, EPHE, Muséum national d'Histoire naturelle, Paris, France; Muséum national d'Histoire naturelle, Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 MNHN CNRS UPMC, France
| | - Watthana Theppangna
- National Animal Health Laboratory, Ministry of Agriculture Forestry and Fisheries, Laos
| | | | | | | | - Aneta Afelt
- Institute of Physical Geography, Faculty of Geography and Regional Studies, University of Warsaw, Warsaw, Poland
| | | | - Amanda E Fine
- Wildlife Conservation Society, Wildlife Health Program, Bronx, N.Y., USA
| | - Tracey Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, USA
| | - Sarah Olson
- Wildlife Conservation Society, Wildlife Health Program, Bronx, N.Y., USA
| | - Damien O Joly
- Wildlife Conservation Society, Wildlife Health Program, Bronx, N.Y., USA; Metabiota Inc., Nanaimo, British Columbia, Canada
| | | | - Philippe Dussart
- Institut Pasteur du Cambodge, Virology Unit, Phnom Penh, Cambodia
| | - Roger Frutos
- Cirad, UMR 17, Cirad-Ird, TA-A17/G, Montpellier, France; Université de Montpellier, IES, UMR 5214, CNRS-UM, Montpellier, France.
| | - Philippe Buchy
- Institut Pasteur du Cambodge, Virology Unit, Phnom Penh, Cambodia; GSK Vaccines R&D, 150 Beach road, # 22-00, 189720, Singapore.
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25
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Avian nephritis virus (ANV) on Brazilian chickens farms: circulating genotypes and intra-genotypic diversity. Arch Virol 2016; 161:3455-3462. [PMID: 27638777 DOI: 10.1007/s00705-016-3057-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/08/2016] [Indexed: 10/21/2022]
Abstract
Avian nephritis virus (ANV), which belongs to the family Astroviridae, is associated with different clinical manifestations (including enteric disorders). Despite being frequently found in the avian industry worldwide, information regarding genetic features of these viruses in Brazil is scarce. Therefore, sixty fecal sample pools (5-6 birds of the same flock), representing 60 poultry farms from six Brazilian States, were screened using an astrovirus-specific hemi-nested-PCR assay targeting the conserved ORF1b gene, followed by nucleotide sequencing of amplified products. PCR and phylogenetic analysis confirmed the detection of 21 positive samples to ANV (35 %). In order to investigate the genetic diversity represented by these viruses, amplification, cloning and phylogenetic analysis of the deduced amino acid sequence of ORF2 gene were attempted. Eight samples were successfully cloned (generating 32 clones in total) and sequenced. Based on phylogenetic analysis of ORF2, sequences defined in this study were classified into three genotypes: genotype 5, which has already been described in birds, and two other novel genotypes, tentatively named genotype 8 and 9, all of which occurred in single or mixed infections. Moreover, high intra-genotypic diversity and co-circulation of distinct strains in a same host population were observed. This study revealed the presence of new strains of ANV in Brazilian poultry and their circulation in commercial chicken flocks.
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26
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van Hemert F, van der Kuyl AC, Berkhout B. Impact of the biased nucleotide composition of viral RNA genomes on RNA structure and codon usage. J Gen Virol 2016; 97:2608-2619. [PMID: 27519195 DOI: 10.1099/jgv.0.000579] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We are interested in the influence of nucleotide composition on the fundamental characteristics of the virus RNA genome. Most RNA viruses have genomes with a distinct nucleotide composition, e.g. ranging from minimally 12.9 % to maximally 40.3 % (C- and U-count, respectively, in coronavirus HKU). We present a global analysis of diverse virus types, including plus-strand, minus-strand and double-strand RNA viruses, for the impact of this nucleotide preference on the predicted structure of the RNA genome that is packaged in virion particles and on the codon usage in the viral open reading frames. Several virus-specific features will be described, but also some general conclusions were drawn. Without exception, the virus-specific nucleotide bias was enriched in the unpaired, single-stranded regions of the RNA genome, thus creating an even more striking virus-specific signature. We present a simple mechanism that is based on elementary aspects of RNA structure folding to explain this general trend. In general, the nucleotide bias was the major determinant of the virus-specific codon usages, thus limiting a role for codon selection and translational control. We will discuss molecular and evolutionary scenarios that may be responsible for the diverse nucleotide biases of RNA viruses.
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Affiliation(s)
- Formijn van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands
| | - Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands
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27
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Sewage surveillance reveals the presence of canine GVII norovirus and canine astrovirus in Uruguay. Arch Virol 2015; 160:2839-43. [PMID: 26280526 DOI: 10.1007/s00705-015-2571-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/10/2015] [Indexed: 12/11/2022]
Abstract
Canine norovirus (NoV) and astrovirus (AstV) were studied in 20 domestic sewage samples collected in two cities in Uruguay. Four samples were characterized as canine AstV after phylogenetic analysis clustering with strains detected in Italy and Brazil in 2008 and 2012, respectively. One sample was characterized as canine NoV and clustered with a strain detected in Hong Kong and recently classified as GVII. This study shows the occurrence of a canine NoV GVII strain for the first time in the American continent and also warns about possible zoonotic infection, since canine strains were detected in domestic sewage.
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28
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Cortés-Hinojosa G, Gulland FMD, Goldstein T, Venn-Watson S, Rivera R, Waltzek TB, Salemi M, Wellehan JFX. Phylogenomic characterization of California sea lion adenovirus-1. INFECTION GENETICS AND EVOLUTION 2015; 31:270-6. [PMID: 25660039 DOI: 10.1016/j.meegid.2015.01.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 01/27/2015] [Accepted: 01/27/2015] [Indexed: 11/30/2022]
Abstract
Significant adenoviral diversity has been found in humans, but in domestic and wild animals the number of identified viruses is lower. Here we present the complete genome of a recently discovered mastadenovirus, California sea lion adenovirus 1 (CSLAdV-1) isolated from California sea lions (Zalophus californianus), an important pathogen associated with hepatitis in pinnipeds. The genome of this virus has the typical mastadenoviral structure with some notable differences at the carboxy-terminal end, including a dUTPase that does not cluster with other mastadenoviral dUTPases, and a fiber that shows similarity to a trans-sialidase of Trypanosoma cruzi and choline-binding protein A (CbpA) of Streptococcus pneumoniae. The GC content is low (36%), and phylogenetic analyses placed the virus near the root of the clade infecting laurasiatherian hosts in the genus Mastadenovirus. These findings support the hypothesis that CSLAdV-1 in California sea lions represents a host jump from an unknown mammalian host in which it is endemic.
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Affiliation(s)
- Galaxia Cortés-Hinojosa
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | | | - Tracey Goldstein
- Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | | | - Rebecca Rivera
- Hubbs-SeaWorld Research Institute, 2595 Ingraham St., San Diego, CA, USA
| | - Thomas B Waltzek
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine University of Florida, Gainesville, FL, USA
| | - Marco Salemi
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - James F X Wellehan
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA.
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29
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Abstract
Human astroviruses (HAtVs) are positive-sense single-stranded RNA viruses that were discovered in 1975. Astroviruses infecting other species, particularly mammalian and avian, were identified and classified into the genera Mamastrovirus and Avastrovirus. Through next-generation sequencing, many new astroviruses infecting different species, including humans, have been described, and the Astroviridae family shows a high diversity and zoonotic potential. Three divergent groups of HAstVs are recognized: the classic (MAstV 1), HAstV-MLB (MAstV 6), and HAstV-VA/HMO (MAstV 8 and MAstV 9) groups. Classic HAstVs contain 8 serotypes and account for 2 to 9% of all acute nonbacterial gastroenteritis in children worldwide. Infections are usually self-limiting but can also spread systemically and cause severe infections in immunocompromised patients. The other groups have also been identified in children with gastroenteritis, but extraintestinal pathologies have been suggested for them as well. Classic HAstVs may be grown in cells, allowing the study of their cell cycle, which is similar to that of caliciviruses. The continuous emergence of new astroviruses with a potential zoonotic transmission highlights the need to gain insights on their biology in order to prevent future health threats. This review focuses on the basic virology, pathogenesis, host response, epidemiology, diagnostic assays, and prevention strategies for HAstVs.
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Affiliation(s)
- Albert Bosch
- Enteric Virus Laboratory, Department of Microbiology and Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
| | - Rosa M Pintó
- Enteric Virus Laboratory, Department of Microbiology and Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Microbiology and Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
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30
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Emerging trends in the epidemiology of human astrovirus infection among infants, children and adults hospitalized with acute watery diarrhea in Kolkata, India. INFECTION GENETICS AND EVOLUTION 2012; 12:1685-93. [DOI: 10.1016/j.meegid.2012.07.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/19/2012] [Accepted: 07/31/2012] [Indexed: 11/17/2022]
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31
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Molenaar-de Backer MWA, Lukashov VV, van Binnendijk RS, Boot HJ, Zaaijer HL. Global co-existence of two evolutionary lineages of parvovirus B19 1a, different in genome-wide synonymous positions. PLoS One 2012; 7:e43206. [PMID: 22912828 PMCID: PMC3418230 DOI: 10.1371/journal.pone.0043206] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 07/18/2012] [Indexed: 11/18/2022] Open
Abstract
Parvovirus B19 (B19V) can cause infection in humans. To date, three genotypes of B19V, with subtypes, are known, of which genotype 1a is the most prevalent genotype in the Western world. We sequenced the genome of B19V strains of 65 asymptomatic, recently infected Dutch blood donors, to investigate the spatio-temporal distribution of B19V strains, in the years 2003-2009. The sequences were compared to B19V sequences from Dutch patients with fifth disease, and to global B19V sequences as available from GenBank. All Dutch B19V strains belonged to genotype 1a. Phylogenetic analysis of the strains from Dutch blood donors showed that two groups of genotype 1a co-exist. A clear-cut division into the two groups was also found among the B19V strains from Dutch patients, and among the B19V sequences in GenBank. The two groups of genotype 1a co-exist around the world and do not appear to differ in their ability to cause disease. Strikingly, the two groups of B19V predominantly differ in synonymous mutations, distributed throughout the entire genome of B19V. We propose to call the two groups of B19V genotype 1a respectively subtype 1a1 and 1a2.
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32
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Prevalence and risk factors of astrovirus infection in puppies from French breeding kennels. Vet Microbiol 2012; 157:214-9. [DOI: 10.1016/j.vetmic.2011.11.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 11/04/2011] [Accepted: 11/15/2011] [Indexed: 01/13/2023]
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33
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Hyndman TH, Marschang RE, Wellehan JFX, Nicholls PK. Isolation and molecular identification of Sunshine virus, a novel paramyxovirus found in Australian snakes. INFECTION GENETICS AND EVOLUTION 2012; 12:1436-46. [PMID: 22575820 DOI: 10.1016/j.meegid.2012.04.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 04/18/2012] [Accepted: 04/20/2012] [Indexed: 01/17/2023]
Abstract
This paper describes the isolation and molecular identification of a novel paramyxovirus found during an investigation of an outbreak of neurorespiratory disease in a collection of Australian pythons. Using Illumina® high-throughput sequencing, a 17,187 nucleotide sequence was assembled from RNA extracts from infected viper heart cells (VH2) displaying widespread cytopathic effects in the form of multinucleate giant cells. The sequence appears to contain all the coding regions of the genome, including the following predicted paramyxoviral open reading frames (ORFs): 3'--Nucleocapsid (N)--putative Phosphoprotein (P)--Matrix (M)--Fusion (F)--putative attachment protein--Polymerase (L)--5'. There is also a 540 nucleotide ORF between the N and putative P genes that may be an additional coding region. Phylogenetic analyses of the complete N, M, F and L genes support the clustering of this virus within the family Paramyxoviridae but outside both of the current subfamilies: Paramyxovirinae and Pneumovirinae. We propose to name this new virus, Sunshine virus, after the geographic origin of the first isolate--the Sunshine Coast of Queensland, Australia.
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Affiliation(s)
- Timothy H Hyndman
- School of Veterinary and Biomedical Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia.
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34
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Genetic characterization of astroviruses detected in guinea fowl (Numida meleagris) reveals a distinct genotype and suggests cross-species transmission between turkey and guinea fowl. Arch Virol 2012; 157:1329-37. [PMID: 22527867 DOI: 10.1007/s00705-012-1311-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 03/17/2012] [Indexed: 10/28/2022]
Abstract
Astroviruses can infect mammalian and avian species and are often responsible for gastroenteric disease symptoms. In this study, the complete open reading frame (ORF) 2, the 3' end of ORF1b and the corresponding intergenic region of astroviruses identified in farmed guinea fowl (Numida meleagris) were sequenced and genetically analysed. Overall, the genetic sequence of guinea fowl astroviruses was related to turkey astrovirus type 2 (TastV2), although a marked genetic distance was revealed based on ORF2, which might indicate the circulation of a distinct virus genotype and serotype in guinea fowl. Furthermore, the genetic data presented herein suggest that either recombination between different astroviruses infecting distinct hosts or adaptation of a given astrovirus to a new host had occurred. In either case, direct or indirect interspecies transmission of astroviruses is likely to have occurred between turkey and guinea fowl, indicating the ability of viruses belonging to the family Astroviridae to cross species barriers.
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35
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Tian XT, Li BY, Zhang L, Jiao WQ, Liu JX. Bioinformatics analysis of rabbit haemorrhagic disease virus genome. Virol J 2011; 8:494. [PMID: 22044910 PMCID: PMC3377956 DOI: 10.1186/1743-422x-8-494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 11/01/2011] [Indexed: 11/10/2022] Open
Abstract
Background Rabbit haemorrhagic disease virus (RHDV), as the pathogeny of Rabbit haemorrhagic disease, can cause a highly infectious and often fatal disease only affecting wild and domestic rabbits. Recent researches revealed that it, as one number of the Caliciviridae, has some specialties in its genome, its reproduction and so on. Results In this report, we firstly analyzed its genome and two open reading frameworks (ORFs) from this aspect of codon usage bias. Our researches indicated that mutation pressure rather than natural is the most important determinant in RHDV with high codon bias, and the codon usage bias is nearly contrary between ORF1 and ORF2, which is maybe one of factors regulating the expression of VP60 (encoding by ORF1) and VP10 (encoding by ORF2). Furthermore, negative selective constraints on the RHDV whole genome implied that VP10 played an important role in RHDV lifecycle. Conclusions We conjectured that VP10 might be beneficial for the replication, release or both of virus by inducing infected cell apoptosis initiate by RHDV. According to the results of the principal component analysis for ORF2 of RSCU, we firstly separated 30 RHDV into two genotypes, and the ENC values indicated ORF1 and ORF2 were independent among the evolution of RHDV.
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Affiliation(s)
- Xiao-ting Tian
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujia ping 1, Yanchang bu, Lanzhou, Gansu, China
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36
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Rivera R, Robles-Sikisaka R, Hoffman EM, Stacy BA, Jensen ED, Nollens HH, Wellehan JFX. Characterization of a novel papillomavirus species (ZcPV1) from two California sea lions (Zalophus californianus). Vet Microbiol 2011; 155:257-66. [PMID: 22005176 DOI: 10.1016/j.vetmic.2011.09.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 09/16/2011] [Accepted: 09/23/2011] [Indexed: 12/24/2022]
Abstract
A seven-year old California sea lion (Zalophus californianus) presented with focally extensive, bilaterally symmetric, proliferative axillary skin lesions and preputial lesions. A second California sea lion in the same population presented with similar proliferative lesions on the underside of the tail. Histopathology revealed epidermal hyperplasia with severe hyperkeratosis, with proliferating keratinocytes forming broad, branching pegs that extended into the dermis. Pan-papillomaviral consensus PCR was used to obtain initial E1 sequence template and the complete genome was determined using a combination of rolling circle amplification and specific-primer PCR. Analysis revealed a novel papillomavirus, Zalophus californianus papillomavirus 1 (ZcPV1), with seven open reading frames encoding five early proteins (E6, E7, E1, E2 and E4) and two late proteins (L1 and L2). Phylogenetic analysis revealed that (ZcPV1) is most closely related to Equine papillomavirus 1 (EcPV1) in the genus Zetapapillomavirus, and Canine papillomaviruses 3 and 4 (CPV3, CPV4) in the genus Chipapillomavirus. The lesions regressed without intervention over a period of several months.
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Affiliation(s)
- Rebecca Rivera
- Hubbs-SeaWorld Research Institute, Center for Marine Veterinary Virology, 2595 Ingraham St., San Diego, CA 92109, USA.
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Zhao KN, Chen J. Codon usage roles in human papillomavirus. Rev Med Virol 2011; 21:397-411. [PMID: 22025363 DOI: 10.1002/rmv.707] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 07/07/2011] [Accepted: 07/11/2011] [Indexed: 12/14/2022]
Abstract
Human papillomavirus (HPV) genomes, similar to other virus genomes, frequently have a G + C content significantly different from their host species. The HPV genomes show a strong codon usage bias to 18 codons, with 14 showing T at the third position amongst degenerately encoded amino acids. The codon usage pattern in HPV genome plays an important role, which regulates low or non-translational expression of the viral capsid genes and results in very weak protein expression of oncogenes in a wide range of mammalian cells. Codon modification has been proved to be a powerful technology to overcome the translational blockage and weak expression of both HPV capsid genes and oncogenes in different expression systems. Furthermore, keratinocytes are the host cells of HPV infection; the codon usage in HPV capsid genes matches available aminoacyl-tRNAs in differentiated keratinocytes to modulate their protein expression. HPV DNA vaccines with codon optimization have been shown to have higher immunogenicity and induce both strong cellular and humoral responses in animal models, which may be a promising form of therapeutic HPV vaccines.
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Affiliation(s)
- Kong-Nan Zhao
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia.
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38
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De Benedictis P, Schultz-Cherry S, Burnham A, Cattoli G. Astrovirus infections in humans and animals - molecular biology, genetic diversity, and interspecies transmissions. INFECTION GENETICS AND EVOLUTION 2011; 11:1529-44. [PMID: 21843659 PMCID: PMC7185765 DOI: 10.1016/j.meegid.2011.07.024] [Citation(s) in RCA: 297] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 07/28/2011] [Accepted: 07/30/2011] [Indexed: 01/09/2023]
Abstract
Astroviruses are small, non-enveloped, positive sense, single-stranded RNA viruses first identified in 1975 in children suffering from diarrhea and then described in a wide variety of animals. To date, the list of animal species susceptible to astrovirus infection has expanded to 22 animal species or families, including domestic, synantropic and wild animals, avian, and mammalian species in the terrestrial and aquatic environments. Astrovirus infections are considered among the most common cause of gastroenteritis in children, second only to rotavirus infections, but in animals their association with enteric diseases is not well documented, with the exception of turkey and mink astrovirus infection. Genetic variability has been described in almost all astrovirus species sufficiently examined infecting mammals and birds; however, antigenic variability has been demonstrated for human astroviruses but is far less investigated in animal viruses. Interestingly, there is an increasing evidence of recombination events occurring in astroviruses, which contributes to increase the genetic variability of this group of viruses. A wide variety of species infected, the evident virus genetic diversity and the occurrence of recombination events indicate or imply either cross-species transmission and subsequent virus adaptation to new hosts or the co-infection of the same host with different astroviruses. This can also favor the emergence of novel astroviruses infecting animals or with a zoonotic potential. After more than 30 years from their first description in humans, there are many exciting streams of research to be explored and intriguing questions that remain to be answered about the relatively under-studied Astroviridae family. In the present work, we will review the existing knowledge concerning astrovirus infections in humans and animals, with particular focus on the molecular biology, interspecies transmission and zoonotic potential of this group of viruses.
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Affiliation(s)
- Paola De Benedictis
- OIE Collaborating Centre for Diseases at the Animal-Human Interface, Research & Innovation Department, Division of Biomedical Science, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
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39
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Gu YX, Zhang J, Zhou JH, Zhao F, Liu WQ, Wang M, Chen HT, Ma LN, Ding YZ, Liu YS. Comparative analysis of ovine adenovirus 287 and human adenovirus 2 and 5 based on their codon usage. DNA Cell Biol 2011; 31:360-6. [PMID: 21810025 DOI: 10.1089/dna.2011.1256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Ovine adenovirus 287 (OAdV287) emerges as one of the most promising gene vectors resulting from its unique biological characteristics. To obtain a more detailed knowledge about the codon usage of OAdV287, a comparative study based on the codon usage of OAdV287 and the prototypes of human adenovirus serotypes 2 and 5 (HAdV2/5) was carried out. Some commonly used indices measuring the codon usage patterns, including effective number of codons, relative synonymous codon usage, and statistical methods, were adopted. Overall, OAdV287 had a more biased and conservative codon usage pattern than that of HAdV2/5. Both mutation pressure and natural selection played important roles in shaping the codon usage patterns of these three adenoviruses. All the preference codons of OAdV287 had A/U ends and were totally different from those of sheep and humans; however, the preference codons of HAdV2/5 mostly had G/C ends and were mostly coincident with those of sheep and humans. The codon usage analysis in this study supplies some clues for further comprehending the unique biological characteristics of OAdV287 as gene vectors.
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Affiliation(s)
- Yuan-xing Gu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, PR China
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40
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Wellehan JF, Rivera R, Archer LL, Benham C, Muller JK, Colegrove KM, Gulland FM, St. Leger JA, Venn-Watson SK, Nollens HH. Characterization of California sea lion polyomavirus 1: Expansion of the known host range of the Polyomaviridae to Carnivora. INFECTION GENETICS AND EVOLUTION 2011; 11:987-96. [DOI: 10.1016/j.meegid.2011.03.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 02/11/2011] [Accepted: 03/17/2011] [Indexed: 11/29/2022]
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Pepin KM, Lass S, Pulliam JRC, Read AF, Lloyd-Smith JO. Identifying genetic markers of adaptation for surveillance of viral host jumps. Nat Rev Microbiol 2010; 8:802-13. [PMID: 20938453 PMCID: PMC7097030 DOI: 10.1038/nrmicro2440] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Adaptation is often thought to affect the likelihood that a virus will be able to successfully emerge in a new host species. If so, surveillance for genetic markers of adaptation could help to predict the risk of disease emergence. However, adaptation is difficult to distinguish conclusively from the other processes that generate genetic change. In this Review we survey the research on the host jumps of influenza A, severe acute respiratory syndrome-coronavirus, canine parvovirus and Venezuelan equine encephalitis virus to illustrate the insights that can arise from combining genetic surveillance with microbiological experimentation in the context of epidemiological data. We argue that using a multidisciplinary approach for surveillance will provide a better understanding of when adaptations are required for host jumps and thus when predictive genetic markers may be present.
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Affiliation(s)
- Kim M Pepin
- Department of Physics, Pennsylvania State University, University Park, PA 16802, USA.
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42
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Ahn I, Jeong BJ, Son HS. Comparative study of synonymous codon usage variations between the nucleocapsid and spike genes of coronavirus, and C-type lectin domain genes of human and mouse. Exp Mol Med 2010; 41:746-56. [PMID: 19561398 PMCID: PMC2772977 DOI: 10.3858/emm.2009.41.10.081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Coronaviruses (CoVs) are single-stranded RNA viruses which contain the largest RNA genomes, and severe acute respiratory syndrome coronavirus (SARS-CoV), a newly found group 2 CoV, emerged as infectious disease with high mortality rate. In this study, we compared the synonymous codon usage patterns between the nucleocapsid and spike genes of CoVs, and C-type lectin domain (CTLD) genes of human and mouse on the codon basis. Findings indicate that the nucleocapsid genes of CoVs were affected from the synonymous codon usage bias than spike genes, and the CTLDs of human and mouse partially overlapped with the nucleocapsid genes of CoVs. In addition, we observed that CTLDs which showed the similar relative synonymous codon usage (RSCU) patterns with CoVs were commonly derived from the human chromosome 12, and mouse chromosome 6 and 12, suggesting that there might be a specific genomic region or chromosomes which show a more similar synonymous codon usage pattern with viral genes. Our findings contribute to developing the codon-optimization method in DNA vaccines, and further study is needed to determine a specific correlation between the codon usage patterns and the chromosomal locations in higher organisms.
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Affiliation(s)
- Insung Ahn
- Supercomputing Center, Korea Institute of Science and Technology Information, Daejon 305-806, Korea
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43
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Cladel NM, Bertotto A, Christensen ND. Human alpha and beta papillomaviruses use different synonymous codon profiles. Virus Genes 2010; 40:329-40. [PMID: 20157772 PMCID: PMC3752370 DOI: 10.1007/s11262-010-0451-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 01/22/2010] [Indexed: 01/11/2023]
Abstract
Human papillomaviruses use rare codons relative to their hosts. It has been theorized that this is a mechanism to allow the virus to escape immune surveillance. In the present study, we examined the codings of four major genes of 21 human alpha (mucosatropic) viruses and 16 human beta (cutaneous-tropic) viruses. We compared the codon usage of different genes from a given papillomavirus and also the same genes from different papillomaviruses. Our data showed that codon usage was not always uniform between two genes of a given papillomavirus or between the same genes of papillomaviruses from different genera. We speculate as to why this might be and conclude that codon usage in the papillomaviruses may not only play a role in facilitating escape from immune surveillance but may also underlie some of the unanswered questions in the papillomavirus field.
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Affiliation(s)
- Nancy M Cladel
- Jake Gittlen Cancer Research Foundation, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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Evolution of the sequence composition of Flaviviruses. INFECTION GENETICS AND EVOLUTION 2010; 10:129-36. [DOI: 10.1016/j.meegid.2009.11.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 10/26/2009] [Accepted: 11/03/2009] [Indexed: 11/20/2022]
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45
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Characterization of San Miguel sea lion virus populations using pyrosequencing-based methods. INFECTION GENETICS AND EVOLUTION 2009; 10:254-60. [PMID: 19931646 PMCID: PMC7106084 DOI: 10.1016/j.meegid.2009.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 10/09/2009] [Accepted: 11/16/2009] [Indexed: 01/13/2023]
Abstract
San Miguel Sea Lion Virus (SMSV) is a small RNA virus in the genus Vesivirus with an unusually broad host range. Three populations of SMSV were examined by PCR amplification of the capsid precursor and putative helicase genes, followed by pyrosequencing. The populations were nasal swabs from two SMSV infected California sea lions (Zalophus californianus) from two different years, and a virus isolate from the earlier swab that was passaged in cell culture five times. In the capsid precursor, extensive deletions were prevalent in the passaged virus but uncommon in the clinical samples. A greater prevalence of point mutations was seen in the capsid precursor gene than in the putative helicase gene. In culture, the minority sequence in the capsid precursor at nucleotide position 5826 rapidly shifted after five passages to become the majority sequence. Levels of diversity at individual sites showed much more similarity between the two clinical samples than between the earlier clinical sample and the passaged culture from the same sample. SMSV appears to behave as a quasispecies. Assessment of original patient samples is preferable for understanding clinical SMSV populations.
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Hiraoka Y, Kawamata K, Haraguchi T, Chikashige Y. Codon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe. Genes Cells 2009; 14:499-509. [PMID: 19335619 DOI: 10.1111/j.1365-2443.2009.01284.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Usage of synonymous codons represents a characteristic pattern of preference in each organism. It has been inferred that such bias of codon usage has evolved as a result of adaptation for efficient synthesis of proteins. Here we examined synonymous codon usage in genes of the fission yeast Schizosaccharomyces pombe, and compared codon usage bias with expression levels of the gene. In this organism, synonymous codon usage bias was correlated with expression levels of the gene; the bias was most obvious in two-codon amino acids. A similar pattern of the codon usage bias was also observed in Saccharomyces cerevisiae, Arabidopsis thaliana and Caenorhabditis elegans, but was not obvious in Oryza sativa, Drosophila melanogaster, Takifugu rubripes and Homo sapiens. As codons of the highly expressed genes have greater influence on translational efficiency than codons of genes expressed at lower levels, it is likely that codon usage in the S. pombe genome has been optimized by translational selection through evolution.
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Affiliation(s)
- Yasushi Hiraoka
- Department of Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, 560-0043, Japan.
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Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences. Mol Syst Biol 2009; 5:311. [PMID: 19888206 PMCID: PMC2779085 DOI: 10.1038/msb.2009.71] [Citation(s) in RCA: 172] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Accepted: 08/05/2009] [Indexed: 01/30/2023] Open
Abstract
Viruses differ markedly in their specificity toward host organisms. Here, we test the level of general sequence adaptation that viruses display toward their hosts. We compiled a representative data set of viruses that infect hosts ranging from bacteria to humans. We consider their respective amino acid and codon usages and compare them among the viruses and their hosts. We show that bacteria-infecting viruses are strongly adapted to their specific hosts, but that they differ from other unrelated bacterial hosts. Viruses that infect humans, but not those that infect other mammals or aves, show a strong resemblance to most mammalian and avian hosts, in terms of both amino acid and codon preferences. In groups of viruses that infect humans or other mammals, the highest observed level of adaptation of viral proteins to host codon usages is for those proteins that appear abundantly in the virion. In contrast, proteins that are known to participate in host-specific recognition do not necessarily adapt to their respective hosts. The implication for the potential of viral infectivity is discussed.
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48
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Atkins A, Wellehan JFX, Childress AL, Archer LL, Fraser WA, Citino SB. Characterization of an outbreak of astroviral diarrhea in a group of cheetahs (Acinonyx jubatus). Vet Microbiol 2008; 136:160-5. [PMID: 19171442 PMCID: PMC7117330 DOI: 10.1016/j.vetmic.2008.10.035] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 10/12/2008] [Accepted: 10/16/2008] [Indexed: 01/08/2023]
Abstract
A Mamastrovirus was identified in an outbreak of diarrhea in cheetahs (Acinonyx jubatus). Five young adult and two adult cheetahs presented with lethargy, anorexia, watery diarrhea and regurgitation over an 11-day period. Fecal samples were submitted for electron microscopy and culture. Electron microscopy results revealed particles morphologically consistent with an astrovirus, and no other viral pathogens or significant bacterial pathogens were identified. The astrovirus was confirmed and sequenced using consensus astroviral PCR, resulting in a 367 base pair partial RNA-dependent-RNA polymerase (RdRp) product and a 628 base pair partial capsid product. Bayesian and maximum likelihood phylogenetic analyses were performed on both the RdRp and the capsid protein segments. All animals were monitored and treated with bismuth subsalicylate tablets (524mg PO BID for 5 days), and recovered without additional intervention. This is the first report we are aware of documenting an astrovirus outbreak in cheetah.
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Affiliation(s)
- Adrienne Atkins
- Department of Small Animal Clinical Sciences, University of Florida, Gainesville, FL 32610, USA.
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49
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Analysis of synonymous codon usage in classical swine fever virus. Virus Genes 2008; 38:104-12. [PMID: 18958611 PMCID: PMC7089228 DOI: 10.1007/s11262-008-0296-z] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 10/09/2008] [Indexed: 01/27/2023]
Abstract
Using the complete genome sequences of 35 classical swine fever viruses (CSFV) representing all three genotypes and all three kinds of virulence, we analyzed synonymous codon usage and the relative dinucleotide abundance in CSFV. The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in CSFV. Furthermore, we observed that the relative abundance of dinucleotides in CSFV is independent of the overall base composition but is still the result of differential mutational pressure, which also shapes codon usage. In addition, other factors, such as the subgenotypes and aromaticity, also influence the codon usage variation among the genomes of CSFV. This study represents the most comprehensive analysis to date of CSFV codon usage patterns and provides a basic understanding of the mechanisms for codon usage bias.
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Abstract
To understand astrovirus biology, it is essential to understand factors associated with its evolution. The current study reports the genomic sequences of nine novel turkey astrovirus (TAstV) type 2-like clinical isolates. This represents, to our knowledge, the largest genomic-length data set available for any one astrovirus type. The comparison of these TAstV sequences suggests that the TAstV species contains multiple subtypes and that recombination events have occurred across the astrovirus genome. In addition, the analysis of the capsid gene demonstrated evidence for both site-specific positive selection and purifying selection.
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