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Akhter G, Ahmed I, Ahmad SM. Comparative Study of Two Himalayan Snow Trouts, Schizothorax esocinus and Schizothorax curvifrons Within the Schizothoracinae and Other Nearest Relatives of Cyprinidae, Inferred from Mitochondrial Sequences of Cytochrome b (Cyt-b) and Cytochrome Oxidase I (Co-I) Gene. Biochem Genet 2024:10.1007/s10528-024-10862-x. [PMID: 38896378 DOI: 10.1007/s10528-024-10862-x] [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: 10/31/2023] [Accepted: 06/06/2024] [Indexed: 06/21/2024]
Abstract
The Himalayan region encompasses varied aquatic ecosystems, characterized by the presence of diverse ichthyofauna, particularly represented by members of the Schizothorax genus, commonly referred to as snow trout. The primary objective of this work was to examine the molecular phylogeny of Schizothoracinae, specifically focusing on the two species, Schizothorax esocinus and Schizothorax curvifrons, which are known to inhabit the northern and north-eastern regions of the Himalayas. This investigation was conducted by analyzing the entire mitochondrial Cyt-b and Co-I gene sequences. The aligned Cyt-b and Co-I sequences for S. esocinus, S. curvifrons, and related members within the subfamily Schizothoracinae, spanned 1130 to 1141 and 1536 to 1551 base pairs, respectively. Using these gene, phylogenetic trees were created to compare Schizothoracinae species to other subfamilies of the family Cyprinidae (Barbinae, Alburninae, Leuciscinae, Xenocyprinae, Cyprininae, and Cultrinae). Genetic distances for Cyt-b and Co-I sequence at three hierarchical levels shows significant disparities in their average score. For Cyt-b, average p-distances for intraspecies, intragenus, and intrafamily were 2.13%, 4.1%, and 15.23%, respectively. Similarly, for Co-I, average p-distances were 1.19%, 3.6%, and 13.8% for intraspecies, intragenus, and intrafamily, respectively. Total number of haplotypes (h) based on Cyt-b and Co-I gene were 6 and 12 within the target Schizothorax spp. In the present study, the observed range of haplotype diversity (hd) for the Cyt-b gene varied from 0.00 to 0.847, with an average haplotype diversity of 0.847 ± 0.034. Similarly, for the Co-I gene, the observed haplotype diversity ranged from 0.00 to 0.931, with an average value of haplotype diversity estimated to be 0.931 ± 0.024. The results of the present study clearly shows that the representative species exhibited close affinities with members of Barbinae and Cyprininae, while other subfamilies formed distinct groups. The findings of the study also indicated that the Cyt-b and Co-I gene exhibits polymorphism and has the potential to serve as a marker for identifying genetic differentiation among populations based on ecological habitats. Mitochondrial Cyt-b and Co-I have been established as a universally accepted and validated genetic marker within a comprehensive bio-identification system at the species level.
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Affiliation(s)
- G Akhter
- Fish Nutrition Research Laboratory, Department of Zoology, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India
| | - I Ahmed
- Fish Nutrition Research Laboratory, Department of Zoology, University of Kashmir, Hazratbal, Srinagar, 190 006, Jammu and Kashmir, India.
| | - S M Ahmad
- Division of Biotechnology, Faculty of Veterinary Sciences & Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
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Pantier R, Brown M, Han S, Paton K, Meek S, Montavon T, Shukeir N, McHugh T, Kelly DA, Hochepied T, Libert C, Jenuwein T, Burdon T, Bird A. MeCP2 binds to methylated DNA independently of phase separation and heterochromatin organisation. Nat Commun 2024; 15:3880. [PMID: 38719804 PMCID: PMC11079052 DOI: 10.1038/s41467-024-47395-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 03/29/2024] [Indexed: 05/12/2024] Open
Abstract
Correlative evidence has suggested that the methyl-CpG-binding protein MeCP2 contributes to the formation of heterochromatin condensates via liquid-liquid phase separation. This interpretation has been reinforced by the observation that heterochromatin, DNA methylation and MeCP2 co-localise within prominent foci in mouse cells. The findings presented here revise this view. MeCP2 localisation is independent of heterochromatin as MeCP2 foci persist even when heterochromatin organisation is disrupted. Additionally, MeCP2 foci fail to show hallmarks of phase separation in live cells. Importantly, we find that mouse cellular models are highly atypical as MeCP2 distribution is diffuse in most mammalian species, including humans. Notably, MeCP2 foci are absent in Mus spretus which is a mouse subspecies lacking methylated satellite DNA repeats. We conclude that MeCP2 has no intrinsic tendency to form condensates and its localisation is independent of heterochromatin. Instead, the distribution of MeCP2 in the nucleus is primarily determined by global DNA methylation patterns.
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Affiliation(s)
- Raphaël Pantier
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh, EH9 3BF, UK
| | - Megan Brown
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh, EH9 3BF, UK
| | - Sicheng Han
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh, EH9 3BF, UK
| | - Katie Paton
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh, EH9 3BF, UK
| | - Stephen Meek
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Thomas Montavon
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Nicholas Shukeir
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Toni McHugh
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh, EH9 3BF, UK
| | - David A Kelly
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh, EH9 3BF, UK
| | - Tino Hochepied
- Center for Inflammation Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Claude Libert
- Center for Inflammation Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Thomas Jenuwein
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Tom Burdon
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Adrian Bird
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh, EH9 3BF, UK.
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Yatsuyanagi T, Kanbe T, Fujii K, Inoue S, Araki H. Environmental DNA unveils deep phylogeographic structure of a freshwater fish. Mol Ecol 2024; 33:e17337. [PMID: 38558465 DOI: 10.1111/mec.17337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
Phylogeography bears an important part in ecology and evolution. However, current phylogeographic studies are largely constrained by limited numbers of individual samples. Using an environmental DNA (eDNA) assay for phylogeographic analyses, this study provides detailed information regarding the history of Siberian stone loach Barbatula toni, a primary freshwater fish across the whole range of Hokkaido, Japan. Based on an eDNA metabarcoding on 293 river water samples, we detected eDNA from B. toni in 189 rivers. A total of 51 samples, representing the entire island, were then selected from the B. toni eDNA-positive sample set for the subsequent analyses. To elucidate the phylogeographic structure of B. toni, newly developed eDNA metabarcoding primers (Barba-cytb-F/R) were applied to these samples, specifically targeting their haplotypic variation in cytochrome b. After a bioinformatic processing to mitigate haplotypic false positives, a total of 50 eDNA haplotypes were identified. Two regionally restricted, genetically distinct lineages of the species were revealed as a result of phylogeographic analyses on the haplotypes and tissue-derived DNA from B. toni. According to a molecular clock analysis, they have been genetically isolated for at least 1.5 million years, suggesting their ancient origin and colonisation of Hokkaido, presumably in the glacial periods. These results demonstrate how freshwater fishes can alter their distributions over evolutionary timescales and how eDNA assay can deepen our understanding of phylogeography.
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Affiliation(s)
| | - Takashi Kanbe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kazuya Fujii
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
- Fukuda Hydrologic Center, Sapporo, Japan
| | - Shouko Inoue
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hitoshi Araki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Han PY, Xu FH, Tian JW, Zhao JY, Yang Z, Kong W, Wang B, Guo LJ, Zhang YZ. Molecular Prevalence, Genetic Diversity, and Tissue Tropism of Bartonella Species in Small Mammals from Yunnan Province, China. Animals (Basel) 2024; 14:1320. [PMID: 38731324 PMCID: PMC11083988 DOI: 10.3390/ani14091320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Bartonella is an intracellular parasitic zoonotic pathogen that can infect animals and cause a variety of human diseases. This study investigates Bartonella prevalence in small mammals in Yunnan Province, China, focusing on tissue tropism. A total of 333 small mammals were sampled from thirteen species, three orders, four families, and four genera in Heqing and Gongshan Counties. Conventional PCR and real-time quantitative PCR (qPCR) were utilized for detection and quantification, followed by bioinformatic analysis of obtained DNA sequences. Results show a 31.5% detection rate, varying across species. Notably, Apodemus chevrieri, Eothenomys eleusis, Niviventer fulvescens, Rattus tanezumi, Episoriculus leucops, Anourosorex squamipes, and Ochotona Thibetana exhibited infection rates of 44.4%, 27.7%, 100.0%, 6.3%, 60.0%, 23.5%, and 22.2%, respectively. Genetic analysis identified thirty, ten, and five strains based on ssrA, rpoB, and gltA genes, with nucleotide identities ranging from 92.1% to 100.0%. Bartonella strains were assigned to B. grahamii, B. rochalimae, B. sendai, B. koshimizu, B. phoceensis, B. taylorii, and a new species identified in Episoriculus leucops (GS136). Analysis of the different tissues naturally infected by Bartonella species revealed varied copy numbers across different tissues, with the highest load in spleen tissue. These findings underscore Bartonella's diverse species and host range in Yunnan Province, highlighting the presence of extensive tissue tropism in Bartonella species naturally infecting small mammalian tissues.
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Affiliation(s)
- Pei-Yu Han
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Yunnan Key Laboratory of Zoonotic Disease Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (P.-Y.H.); (F.-H.X.); (J.-W.T.); (J.-Y.Z.); (Z.Y.); (W.K.)
| | - Fen-Hui Xu
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Yunnan Key Laboratory of Zoonotic Disease Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (P.-Y.H.); (F.-H.X.); (J.-W.T.); (J.-Y.Z.); (Z.Y.); (W.K.)
| | - Jia-Wei Tian
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Yunnan Key Laboratory of Zoonotic Disease Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (P.-Y.H.); (F.-H.X.); (J.-W.T.); (J.-Y.Z.); (Z.Y.); (W.K.)
| | - Jun-Ying Zhao
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Yunnan Key Laboratory of Zoonotic Disease Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (P.-Y.H.); (F.-H.X.); (J.-W.T.); (J.-Y.Z.); (Z.Y.); (W.K.)
| | - Ze Yang
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Yunnan Key Laboratory of Zoonotic Disease Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (P.-Y.H.); (F.-H.X.); (J.-W.T.); (J.-Y.Z.); (Z.Y.); (W.K.)
| | - Wei Kong
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Yunnan Key Laboratory of Zoonotic Disease Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (P.-Y.H.); (F.-H.X.); (J.-W.T.); (J.-Y.Z.); (Z.Y.); (W.K.)
| | - Bo Wang
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA;
| | - Li-Jun Guo
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Yunnan Key Laboratory of Zoonotic Disease Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (P.-Y.H.); (F.-H.X.); (J.-W.T.); (J.-Y.Z.); (Z.Y.); (W.K.)
| | - Yun-Zhi Zhang
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Yunnan Key Laboratory of Zoonotic Disease Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (P.-Y.H.); (F.-H.X.); (J.-W.T.); (J.-Y.Z.); (Z.Y.); (W.K.)
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Kapoor S, Yang YT, Hall RN, Gasser RB, Bowles VM, Perry T, Anstead CA. Complete Mitochondrial Genome for Lucilia cuprina dorsalis (Diptera: Calliphoridae) from the Northern Territory, Australia. Genes (Basel) 2024; 15:506. [PMID: 38674440 PMCID: PMC11050061 DOI: 10.3390/genes15040506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The Australian sheep blowfly, Lucilia cuprina dorsalis, is a major sheep ectoparasite causing subcutaneous myiasis (flystrike), which can lead to reduced livestock productivity and, in severe instances, death of the affected animals. It is also a primary colonizer of carrion, an efficient pollinator, and used in maggot debridement therapy and forensic investigations. In this study, we report the complete mitochondrial (mt) genome of L. c. dorsalis from the Northern Territory (NT), Australia, where sheep are prohibited animals, unlike the rest of Australia. The mt genome is 15,943 bp in length, comprising 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a non-coding control region. The gene order of the current mt genome is consistent with the previously published L. cuprina mt genomes. Nucleotide composition revealed an AT bias, accounting for 77.5% of total mt genome nucleotides. Phylogenetic analyses of 56 species/taxa of dipterans indicated that L. c. dorsalis and L. sericata are the closest among all sibling species of the genus Lucilia, which helps to explain species evolution within the family Luciliinae. This study provides the first complete mt genome sequence for L. c. dorsalis derived from the NT, Australia to facilitate species identification and the examination of the evolutionary history of these blowflies.
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Affiliation(s)
- Shilpa Kapoor
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.T.Y.); (T.P.)
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| | - Ying Ting Yang
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.T.Y.); (T.P.)
| | - Robyn N. Hall
- CSIRO Health & Biosecurity, Acton, ACT 2601, Australia;
- Ausvet Pty Ltd., Fremantle, WA 6160, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| | - Vernon M. Bowles
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
| | - Trent Perry
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.T.Y.); (T.P.)
| | - Clare A. Anstead
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia; (R.B.G.); (V.M.B.)
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Mason B, Cervena B, Frias L, Goossens B, Hasegawa H, Keuk K, Langgeng A, Majewski K, Matsumoto T, Matsuura K, Mendonça R, Okamoto M, Peter S, Petrzelkova KJ, Sipangkui S, Xu Z, Pafco B, MacIntosh AJ. Novel insight into the genetic diversity of strongylid nematodes infecting South-East and East Asian primates. Parasitology 2024; 151:514-522. [PMID: 38629119 PMCID: PMC11106507 DOI: 10.1017/s0031182024000386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 05/18/2024]
Abstract
With many non-human primates (NHPs) showing continued population decline, there is an ongoing need to better understand their ecology and conservation threats. One such threat is the risk of disease, with various bacterial, viral and parasitic infections previously reported to have damaging consequences for NHP hosts. Strongylid nematodes are one of the most commonly reported parasitic infections in NHPs. Current knowledge of NHP strongylid infections is restricted by their typical occurrence as mixed infections of multiple genera, which are indistinguishable through traditional microscopic approaches. Here, modern metagenomics approaches were applied for insight into the genetic diversity of strongylid infections in South-East and East Asian NHPs. We hypothesized that strongylid nematodes occur in mixed communities of multiple taxa, dominated by Oesophagostomum, matching previous findings using single-specimen genetics. Utilizing the Illumina MiSeq platform, ITS-2 strongylid metabarcoding was applied to 90 samples from various wild NHPs occurring in Malaysian Borneo and Japan. A clear dominance of Oesophagostomum aculeatum was found, with almost all sequences assigned to this species. This study suggests that strongylid communities of Asian NHPs may be less species-rich than those in African NHPs, where multi-genera communities are reported. Such knowledge contributes baseline data, assisting with ongoing monitoring of health threats to NHPs.
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Affiliation(s)
- Bethan Mason
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Barbora Cervena
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Liesbeth Frias
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Benoit Goossens
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - Hideo Hasegawa
- Department of Biomedicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Kenneth Keuk
- Wildlife Research Center, Kyoto University, Inuyama Campus, Inuyama, Japan
| | - Abdullah Langgeng
- Wildlife Research Center, Kyoto University, Inuyama Campus, Inuyama, Japan
| | - Kasia Majewski
- Wildlife Research Center, Kyoto University, Inuyama Campus, Inuyama, Japan
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Japan
| | - Keiko Matsuura
- Department of Biomedicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Renata Mendonça
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Centre for Functional Ecology – Science for People & the Planet, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Munehiro Okamoto
- Center for the Evolutionary Origins of Human Behavior (EHUB), Kyoto University, Kyoto, Japan
| | - Steve Peter
- Kulliyah of Science, Department of Biotechnology, International Islamic University of Malaysia, Kuantan, Pahang, Malaysia
| | - Klara J. Petrzelkova
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Liberec Zoo, Liberec, Czech Republic
| | | | - Zhihong Xu
- Wildlife Research Center, Kyoto University, Inuyama Campus, Inuyama, Japan
| | - Barbora Pafco
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
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Bugarski-Stanojević V, Đokić M, Stamenković G, Barišić Klisarić N, Stojković O, Jojić V, Savić I. A Cryptic Subterranean Mammal Species, the Lesser Blind Mole Rat ( Nannospalax leucodon syrmiensis)-Retreated but Not Extinct. Animals (Basel) 2024; 14:774. [PMID: 38473158 DOI: 10.3390/ani14050774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Blind mole rats (genus Nannospalax) attract a great deal of attention because of their cancer resistance and longevity. Due to the high rate of chromosome rearrangements, 74 Nannospalax chromosomal forms have been discovered. The convergence of their external morphology complicates their taxonomy, and many cryptic species remain unrecognized. Thus, the European N. leucodon supersp. is listed in the IUCN Red List of Threatened Species with "Data Deficient" status. It is crucial for the conservation of biodiversity to clarify its taxonomy, to recognize each cryptic species, and assign to them the correct conservation status. Of the more than 20 chromosomal forms described within N. leucodon, five cryptic species occur in Serbia. The most threatened among them-N. l. syrmiensis, described and named 50 years ago in the regions of Srem, Belgrade and Mačva-has been declared extinct in the literature, which may have negative consequences for the conservation of wildlife genetic diversity. Through five years of fieldwork and comparison of 16SrRNA and MT-CYTB gene segments between old, archived teeth and recently collected material, we show that N. l. syrmiensis is not extinct. However, its habitat has been fragmented and reduced, owing primarily to anthropogenic impact. Therefore, detailed surveillance, population-structure studies, risk assessment, and appropriate conservation measures are needed.
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Affiliation(s)
- Vanja Bugarski-Stanojević
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, 11108 Belgrade, Serbia
| | - Marko Đokić
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, 11108 Belgrade, Serbia
| | - Gorana Stamenković
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, 11108 Belgrade, Serbia
| | - Nataša Barišić Klisarić
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, 11108 Belgrade, Serbia
| | - Oliver Stojković
- Institute of Forensic Medicine, Faculty of Medicine, University of Belgrade, 11060 Belgrade, Serbia
| | - Vida Jojić
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, 11108 Belgrade, Serbia
| | - Ivo Savić
- Institute of Zoology, Faculty of Biology, University of Belgrade, 11060 Belgrade, Serbia
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Huang X, Hou J, Le X, Hou Y, Yang L, Li Q, Wang B, Xia X. Diversity of astroviruses in wild animals in Yunnan province, China. Virol J 2024; 21:51. [PMID: 38414022 PMCID: PMC10900740 DOI: 10.1186/s12985-024-02314-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Astroviruses (AstVs) are single-stranded RNA viruses that have been detected in a wide range of mammals and birds. They are associated with numerous interspecies transmissions and viral recombination events, posing a threat to human and animal health. METHODS We collected 1,333 samples from wild animals, including bats, rodents, wild boars, and birds, from various states and cities in the Yunnan Province, China, between 2020 and 2023 to investigate the presence of AstVs. AstVs were detected using a polymerase chain reaction targeting the RdRp gene. Finally, the Molecular Evolutionary Genetics Analysis software was used to construct the phylogenetic tree. RESULTS The overall positivity rate for AstVs was 7.12% in four species, indicating their widespread occurrence in the region. High genetic diversity among AstVs was observed in different animal species, suggesting the potential for interspecies transmission, particularly among rodents and birds. Additionally, we identified a novel AstV strain and, for the first time, provided information on the presence of bastroviruses in Yunnan, China. CONCLUSIONS The widespread distribution and high genetic diversity of AstVs, along with the observed potential for interspecies transmission, highlight the importance of further investigation and surveillance in the region. The findings emphasize the need for increased attention to AstVs and their potential impact on human and animal health in Yunnan and other regions.
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Affiliation(s)
- Xingyu Huang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China
| | - Junjie Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China
| | - Xiang Le
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China
| | - Yutong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China
| | - Lingsi Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China
| | - Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China.
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, Yunnan, P.R. China.
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Frias L, Manin BO, Guerrero-Sánchez S, Sipangkui S, Chua TH. Detection of echinostomatid trematode eggs at the forest-oil palm interface in Sabah, Malaysia. Parasitology 2024; 151:181-184. [PMID: 38167272 PMCID: PMC10941037 DOI: 10.1017/s0031182023001257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
In this study, we report the occurrence of echinostomatid eggs in feces of wildlife, domestic animals and humans frequenting the forest–oil palm plantation interface in the Kinabatangan (Sabah, Malaysia), and discuss potential implications for public health. Using microscopy, we detected echinostomatid eggs in six host species, including Asian palm civets (Paradoxurus hermaphroditus [13/18]), leopard cats (Prionailurus bengalensis [3/4]), long-tailed macaques (Macaca fascicularis [1/10]), domestic dogs [3/5] and cats [1/1], and humans [7/9]. Molecular analysis revealed a close genetic proximity of civet echinostomatids to Artyfechinostomum malayanum, a zoonotic parasite of public health relevance. The intermediate hosts for A. malayanum have been reported in at least 3 districts in Sabah, suggesting that all the necessary elements required for the completion of the parasite's life cycle are present. Our findings point at the presence of zoonotic trematodes in an area with high human–wildlife interaction and highlight the potential public and animal health concern of zoonotic trematode infection in the context of Southeast Asia's rapidly changing ecosystems.
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Affiliation(s)
- Liesbeth Frias
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Asian School of the Environment, Nanyang Technological University, Singapore
| | - Benny Obrain Manin
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Sergio Guerrero-Sánchez
- Centre for Applied One Health Research and Policy Advice, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | | | - Tock H. Chua
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
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10
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Park K, Kim J, Noh J, Kim K, Yang E, Kim SG, Cho HK, Byun KS, Kim JH, Lee YS, Shim JO, Shin M, Kim WK, Song JW. First detection and characterization of hepatitis E virus (Rocahepevirus ratti) from urban Norway rats (Rattus norvegicus) in the Republic of Korea. J Med Virol 2024; 96:e29401. [PMID: 38235603 DOI: 10.1002/jmv.29401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/21/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Hepatitis E virus (HEV), an emerging zoonotic pathogen, poses a significant public health concern worldwide. Recently, rat HEV (Rocahepevirus ratti genotype C1; HEV-C1) has been reported to cause zoonotic infections and hepatitis in humans. Human infections with HEV-C1 are considered to be underestimated worldwide due to limited knowledge of transmission routes, genome epidemiology, and the risk assessment of zoonosis associated with these viruses. A total of 186 wild Norway rats (Rattus norvegicus) were collected from the Republic of Korea (ROK) between 2011 and 2021. The prevalence of HEV-C1 RNA was 8 of 180 (4.4%) by reverse-transcription polymerase chain reaction. We first reported three nearly whole-genome sequences of HEV-C1 newly acquired from urban rats in the ROK. Phylogenetic analysis demonstrated that Korea-indigenous HEV-C1 formed an independent genetic group with those derived from R. norvegicus rats in other countries, indicating geographical and genetic diversity. Our findings provide critical insights into the molecular prevalence, genome epidemiology, and zoonotic potential of Rocahepevirus. This report raises awareness of the presence of Rocahepevirus-related hepatitis E among physicians in the ROK.
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Affiliation(s)
- Kyungmin Park
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jongwoo Kim
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Juyoung Noh
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kijin Kim
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Eunyoung Yang
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seong-Gyu Kim
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hee-Kyung Cho
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kwan Soo Byun
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Korea University Medical Center, Seoul, Republic of Korea
| | - Ji Hoon Kim
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Korea University Medical Center, Seoul, Republic of Korea
| | - Young-Sun Lee
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Korea University Medical Center, Seoul, Republic of Korea
| | - Jung Ok Shim
- Department of Pediatrics, Korea University College of Medicine, Seoul, Republic of Korea
| | - Minsoo Shin
- Department of Pediatrics, Korea University Ansan Hospital, Ansan, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
- Institute of Medical Research, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Jin-Won Song
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
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11
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Szynwelski BE, Mares-Guia MAMM, Filippis AMB, Gonçalves GL, Tokuda M, Wagner PGC, Wu S, Oliveira VP, Lima MGM, Lynch JW, Freitas TRO. Phylogeography, genetic diversity, and intraspecific genetic structure of the black-horned capuchin (Sapajus nigritus). Am J Primatol 2024; 86:e23566. [PMID: 37855375 DOI: 10.1002/ajp.23566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/03/2023] [Accepted: 10/07/2023] [Indexed: 10/20/2023]
Abstract
Recent molecular studies have clarified the overarching taxonomy of capuchin monkeys, but intraspecific genetic diversity remains unexplored for most capuchin species. One example is Sapajus nigritus, the southernmost capuchin monkey, found in Brazil and Argentina; its phenotypic diversity has been recognized as two geographic subspecies, but the intraspecific genetic structure of this taxon is poorly known. Here, we sampled across most of this species' geographic distribution, producing a newly sequenced data set for genetic analyses that included 78 individuals from 14 populations. We investigated the intraspecific diversity, genetic structure, and evolutionary history using three mitochondrial markers. Our results indicated that S. nigritus populations exhibited high levels of genetic structure. We found strong support for two monophyletic clades within this species with a deep phylogenetic split, and clear separation from other related taxa. Vicariance events seem to have played a prevalent role in shaping S. nigritus genetic differentiation. The Paraíba do Sul River may have driven the deep divergence between southern and northern clades, whereas the Tietê River may have had a weaker, more recent effect on the divergence of populations within the southern clade.
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Affiliation(s)
- Bruna E Szynwelski
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Maria A M M Mares-Guia
- Fiocruz (Fundação Oswaldo Cruz), Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Ana M B Filippis
- Fiocruz (Fundação Oswaldo Cruz), Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Gislene L Gonçalves
- Departamento de Recursos Ambientales, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica, Chile
| | - Marcos Tokuda
- Parque Zoológico Municipal Quinzinho de Barros, Sorocaba, Brazil
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, Brazil
| | - Paulo G C Wagner
- Centro de Triagem de Animais Silvestres, Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, Porto Alegre, Rio Grande do Sul, Brazil
| | - Stacy Wu
- Departamento de Ciência Animal, Universidade Federal do Paraná, Programa de Pós-Graduação em Ciência Animal, Setor Palotina, Palotina, Brazil
| | | | - Marcela G M Lima
- Laboratório de Biogeografia da Conservação e Macroecologia, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Jessica W Lynch
- Institute for Society and Genetics and Department of Anthropology, University of California-Los Angeles, Los Angeles, California, USA
- Department of Anthropology, University of California, Los Angeles, California
| | - Thales R O Freitas
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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12
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Kim J, Park K, Kim K, Noh J, Kim SG, Yang E, Cho HK, Lee SH, No JS, Lee GY, Lee D, Song DH, Gu SH, Park MS, Cho NH, Jeong ST, Kim WK, Song JW. High-resolution phylogeographical surveillance of Hantaan orthohantavirus using rapid amplicon-based Flongle sequencing, Republic of Korea. J Med Virol 2024; 96:e29346. [PMID: 38178580 DOI: 10.1002/jmv.29346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/04/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024]
Abstract
Orthohantaviruses, etiological agents of hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome, pose a critical public health threat worldwide. Hantaan orthohantavirus (HTNV) outbreaks are particularly endemic in Gyeonggi Province in northern area of the Republic of Korea (ROK). Small mammals were collected from three regions in the Gyeonggi Province during 2017 and 2018. Serological and molecular prevalence of HTNV was 25/201 (12.4%) and 10/25 (40%), respectively. A novel nanopore-based diagnostic assay using a cost-efficient Flongle chip was developed to rapidly and sensitively detect HTNV infection in rodent specimens within 3 h. A rapid phylogeographical surveillance of HTNV at high-resolution phylogeny was established using the amplicon-based Flongle sequencing. In total, seven whole-genome sequences of HTNV were newly obtained from wild rodents collected in Paju-si (Gaekhyeon-ri) and Yeoncheon-gun (Hyeonga-ri and Wangnim-ri), Gyeonggi Province. Phylogenetic analyses revealed well-supported evolutionary divergence and genetic diversity, enhancing the resolution of the phylogeographic map of orthohantaviruses in the ROK. Incongruences in phylogenetic patterns were identified among HTNV tripartite genomes, suggesting differential evolution for each segment. These findings provide crucial insights into on-site diagnostics, genome-based surveillance, and the evolutionary dynamics of orthohantaviruses to mitigate hantaviral outbreaks in HFRS-endemic areas in the ROK.
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Affiliation(s)
- Jongwoo Kim
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyungmin Park
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kijin Kim
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Juyoung Noh
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seong-Gyu Kim
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Eunyoung Yang
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hee-Kyung Cho
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seung-Ho Lee
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Jin Sun No
- Division of High-Risk Pathogens, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Geum-Young Lee
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Daesang Lee
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Dong-Hyun Song
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Se Hun Gu
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Seong Tae Jeong
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, Hallym University, Chuncheon, Republic of Korea
- Institute of Medical Research, Hallym University, Chuncheon, Republic of Korea
| | - Jin-Won Song
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
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13
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Zamoto-Niikura A, Saigo A, Sato M, Kobayashi H, Sasaki M, Nakao M, Suzuki T, Morikawa S. The presence of Ixodes pavlovskyi and I. pavlovskyi-borne microorganisms in Rishiri Island: an ecological survey. mSphere 2023; 8:e0021323. [PMID: 37930050 PMCID: PMC10871164 DOI: 10.1128/msphere.00213-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/25/2023] [Indexed: 11/07/2023] Open
Abstract
IMPORTANCE Understanding the ecology of ticks and tick-borne microorganisms is important to assess the risk of emerging tick-borne diseases. Despite the fact that the Ixodes pavlovskyi tick bites humans, we lack information including population genetics and the reason for the inadequate distribution in Japan. A 5-year survey revealed that Rishiri Island, the main stopover in the East Asian Flyway of wild birds in the northern Sea of Japan, was a refuge of I. pavlovskyi. The I. pavlovskyi included two haplogroups, which were supposed to diverge a long time before the island separated from the continent and Hokkaido mainland. The detection of microorganisms from wildlife revealed that wild birds and rodents play a role in diffusion and settlement, respectively, of not only I. pavlovskyi but also I. pavlovskyi-borne microorganisms including Candidatus Ehrlichia khabarensis and Babesia microti US lineage. Various island-specific factors control I. pavlovskyi dominance and tick-borne pathogen maintenance. The results may enable us to explain how tick-borne infectious microorganisms are transported.
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Affiliation(s)
- Aya Zamoto-Niikura
- Management Department of Biosafety, Laboratory Animal and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akiko Saigo
- Management Department of Biosafety, Laboratory Animal and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Hirotaka Kobayashi
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shigeru Morikawa
- Department of Veterinary Medicine, Okayama University of Science, Okayama, Japan
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14
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Svoboda Karić P, Anđelić Dmitrović B, Mrmić S, Paić A, Bjedov L, Štritof Z, Margaletić J, Kurolt IC. First Molecular Evidence of Seewis Virus in Croatia. Life (Basel) 2023; 13:2359. [PMID: 38137960 PMCID: PMC10744651 DOI: 10.3390/life13122359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Orthohantaviruses are mainly carried and transmitted by wild rodents, although during the last decade, they have also been identified in multiple species of shrews and moles. Orthohantavirus, Orthohantavirus seewisense (Seewis virus, SWSV), first detected in Switzerland in a single Sorex araneus (Eurasian common shrew) specimen, has been further described in several European countries, including Croatia's neighboring Slovenia and Hungary. Croatia is a well-known endemic region for several zoonotic agents including three different orthohantaviruses: Orthohantavirus puumalaense (PUUV), Orthohantavirus dobravaense (DOBV), and Orthohantavirus tulaense (TULV). In this study, nine shrews were tested and SWSV RNA was detected in liver, lung, and kidney belonging to two shrews (22.22%), one collected on Medvednica mountain in Zagreb County, and the other in the Stara Gradiška area in lowland Croatia. The phylogenetic analysis of the complete S segment's open reading frame (ORF) and partial L-segment revealed that the Croatian sequences, when compared to sequences from the adjacent geographic regions, form a specific genetic lineage. Two SWSV-positive shrew species-Sorex araneus and Neomys milleri (Mediterranean water shrew)-were identified using barcode-based sequence analysis. Therefore, the SWSV detection in N. milleri throughout the course of this study is seen as a rare find in this shrew species. To our knowledge, this is the first molecular and phylogenetic analysis of SWSV in Croatia.
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Affiliation(s)
- Petra Svoboda Karić
- Research Department, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, Mirogojska 8, 10000 Zagreb, Croatia
| | - Barbara Anđelić Dmitrović
- Research Department, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, Mirogojska 8, 10000 Zagreb, Croatia
| | - Stella Mrmić
- Research Department, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, Mirogojska 8, 10000 Zagreb, Croatia
| | - Antonia Paić
- Research Department, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, Mirogojska 8, 10000 Zagreb, Croatia
| | - Linda Bjedov
- Department of Forest Protection and Wildlife Management, Faculty of Forestry, University of Zagreb, Svetošimunska 25, 10000 Zagreb, Croatia
| | - Zrinka Štritof
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia
| | - Josip Margaletić
- Department of Forest Protection and Wildlife Management, Faculty of Forestry, University of Zagreb, Svetošimunska 25, 10000 Zagreb, Croatia
| | - Ivan-Christian Kurolt
- Research Department, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, Mirogojska 8, 10000 Zagreb, Croatia
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15
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Mora JM, Ruedas LA. Updated list of the mammals of Costa Rica, with notes on recent taxonomic changes. Zootaxa 2023; 5357:451-501. [PMID: 38220635 DOI: 10.11646/zootaxa.5357.4.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Indexed: 01/16/2024]
Abstract
Although Costa Rica occupies a mere 0.03% of the Earths land area, it nevertheless has recorded within its borders approximately 5% of the global diversity of mammals, thus making it one of the worlds megadiverse countries. Over the past ten years, 22 species have been added to the countrys inventory, bringing the total number known as here documented to 271; Chiroptera account for ten of these, having grown to 124 from 114; rodents have increased by eight species, from 47 to 55, with the caveat that we include three invasive species of Muridae that have gone feral. In contrast, the number of orders has decreased by one, by Artiodactyla incorporating the former Cetacea. Notes are provided for all taxonomic novelties since the last update. Since the first taxonomic compendium of the mammals of Costa Rica in 1869, the number of known species has grown by approximately 1.22 species year-1 (R2 = 0.96). Since 1983 however, this growth rate has been 1.64 species year-1 (R2 = 0.98). Despite this strong growth, an asymptote in the number of known species has not been reached. Conservation remains a primary need: over 60% of the countrys mammal species show population trends that are decreasing (13%), unknown (37%), or not assessed (11%), based on IUCN criteria. These analyses suggest that much remains to be known regarding the number of mammal species living in Costa Rica, but also that much more remains to be done to safeguard Costa Ricas exceptional biodiversity heritage.
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Affiliation(s)
- Jos Manuel Mora
- Department of Biology and Museum of Vertebrate Biology; Portland State University; Portland; Oregon 97207-0751; USA; Carrera de Gestin Ecoturstica; Sede Central; Universidad Tcnica Nacional; Alajuela; Costa Rica.
| | - Luis A Ruedas
- Department of Biology and Museum of Vertebrate Biology; Portland State University; Portland; Oregon 97207-0751; USA.
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16
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Liu W, Hao Y, Song X, Ma L, Li J, He J, Bu Y, Niu H. Exploring the endangerment mechanisms of Hipposideros pomona based on molecular phylogeographic methods. Ecol Evol 2023; 13:e10653. [PMID: 37869444 PMCID: PMC10587739 DOI: 10.1002/ece3.10653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/21/2023] [Accepted: 10/11/2023] [Indexed: 10/24/2023] Open
Abstract
The endangerment mechanisms of various species are a focus of studies on biodiversity and conservation biology. Hipposideros pomona is an endangered species, but the reasons behind its endangerment remain unclear. We investigated the endangerment mechanisms of H. pomona using mitochondrial DNA, nuclear DNA, and microsatellite loci markers. The results showed that the nucleotide diversity of mitochondria DNA and heterozygosity of microsatellite markers were high (π = 0.04615, H O = 0.7115), whereas the nucleotide diversity of the nuclear genes was low (THY: π = 0.00508, SORBS2: π = 0.00677, ACOX2: π = 0.00462, COPS7A: π = 0.00679). The phylogenetic tree and median-joining network based on mitochondrial DNA sequences clustered the species into three clades, namely North Vietnam-Fujian, Myanmar-West Yunnan, and Laos-Hainan clades. However, joint analysis of nuclear genes did not exhibit clustering. Analysis of molecular variance revealed a strong population genetic structure; IMa2 analysis did not reveal significant gene flow between all groups (p > .05), and isolation-by-distance analysis revealed a significant positive correlation between genetic and geographic distances (p < .05). The mismatch distribution analysis, neutral test, and Bayesian skyline plots revealed that the H. pomona population were relatively stable and exhibited a contraction trend. The results implied that H. pomona exhibits female philopatry and male-biased dispersal. The Hengduan Mountains could have acted as a geographical barrier for gene flow between the North Vietnam-Fujian clade and the Myanmar-West Yunnan clade, whereas the Qiongzhou Strait may have limited interaction between the Hainan populations and other clades. The warm climate during the second interglacial Quaternary period (c. 0.33 Mya) could have been responsible for species differentiation, whereas the cold climate during the late Quaternary last glacial maximum (c. 10 ka BP) might have caused the overall contraction of species. The lack of significant gene flow in nuclear microsatellite loci markers among the different populations investigated reflects recent habitat fragmentation due to anthropogenic activities; thus, on-site conservation of the species and restoration of gene flow corridors among populations need immediate implementation.
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Affiliation(s)
- Wei Liu
- College of Life SciencesHenan Normal UniversityXinxiangChina
| | - Yan Hao
- College of Life SciencesHenan Normal UniversityXinxiangChina
| | - Xinhang Song
- College of Life SciencesHenan Normal UniversityXinxiangChina
| | - Liqun Ma
- College of Life SciencesHenan Normal UniversityXinxiangChina
| | - Jing Li
- College of Life SciencesHenan Normal UniversityXinxiangChina
| | - Jingying He
- College of Life SciencesHenan Normal UniversityXinxiangChina
| | - Yanzhen Bu
- College of Life SciencesHenan Normal UniversityXinxiangChina
| | - Hongxing Niu
- College of Life SciencesHenan Normal UniversityXinxiangChina
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17
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Balakirev AE, Bui PX, Rozhnov VV. New data on the distribution and diversity of the Tonkin limestone rat ( Tonkinomysdaovantieni, Rodentia, Muridae). Biodivers Data J 2023; 11:e110335. [PMID: 38312342 PMCID: PMC10838083 DOI: 10.3897/bdj.11.e110335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/23/2023] [Indexed: 02/06/2024] Open
Abstract
The paper presented novel findings of little-known species of rodents the Tonkin limestone rat Tonkinomysdaovantieni in Cao Bang Province, Vietnam with its morphological and genetic characterisation. The study summarises data on the distribution of this data-deficient species, available museum collections, genetic samples, information on its taxonomy and ecology, important to establish the proper conservation status of the species. An exhaustive map of the findings is provided. It is shown that, based on the data currently available, the species does not require taxonomic revision and also, apparently, does not need a special conservation measure; its status may be established to date as Near Threatened B1a+2a and the current population trend - Stable, IUCN.
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Affiliation(s)
- Alexander E Balakirev
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Moscow Russia
- Joint Russian-Vietnamese Tropical Research and Technological Centre, Hanoi, Vietnam Joint Russian-Vietnamese Tropical Research and Technological Centre Hanoi Vietnam
| | - Phuong Xuan Bui
- Joint Russian-Vietnamese Tropical Research and Technological Centre, Hanoi, Vietnam Joint Russian-Vietnamese Tropical Research and Technological Centre Hanoi Vietnam
| | - Viatcheslav V Rozhnov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Moscow Russia
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Lanes RDEO, Bonvicino CR. Reevaluation of Rhipidomys emiliae (J.A. Allen 1916) and description of a new Rhipidomys (Rodentia: Cricetidae) species from Amazonia and Cerrado. Zootaxa 2023; 5346:581-597. [PMID: 38221321 DOI: 10.11646/zootaxa.5346.5.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Indexed: 01/16/2024]
Abstract
We present the revalidation of the sigmodontinae rodent species R. emiliae, as well as the description of a new species for the genus Rhipidomys. The maximum likelihood analysis recovers R. emiliae as sister species of the clade with Rhipidomys sp. nov. and R. ipukensis, with high bootstrap values. Comparisons between these species based on the external, cranial, and dental morphology identified several unique characters in Rhipidomys sp. nov., including more grayish brown color of the dorsal coat, subsquamosal fenestra wide and long, angular process ends in the same position of the end of condyloid process, conspicuous protostyle and enterostyle. We describe a new karyotype (2n = 44 and FN = 64) for the genus and, based on an integrative analysis together with morphology and molecular phylogeny, assign it to R. emiliae, and assign the karyotype with 2n = 44 and FN = 52 to Rhipidomys sp. nov.. The analysis integrating data indicated that R. emiliae has a geographic distribution restricted to the lowlands of eastern Amazonia, whereas Rhipidomys sp. nov. occurs in the central Amazonia and Cerrado. The data showed that some Rhipidomys species have its distribution currently limited by rivers, as Rhipidomys sp. nov. occurring west of the Araguaia-Tocantins interfluve, R. emiliae east of the Tocantins River, and R. ipukensis between the Tocantins and Araguaia rivers. This work, in addition to revealing a still unknown biodiversity describing a species, brings a new understanding to the genus, and shows how integrating different markers helps in the correct association between the nominal form and the karyotype.
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Affiliation(s)
- Rayque DE Oliveira Lanes
- Postgraduate program in Genetics; Universidade Federal do Rio de Janeiro; Rio de Janeiro Brazil.
| | - Cibele Rodrigues Bonvicino
- Laboratrio de Biologia e Parasitologia de Mamferos Silvestres Reservatrios; IOC; Fiocruz; Rio de Janeiro; Brasil.
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Peeters M, Champagne M, Ndong Bass I, Goumou S, Ndimbo Kumugo SP, Lacroix A, Esteban A, Meta Djomsi D, Soumah AK, Mbala Kingebeni P, Mba Djonzo FA, Lempu G, Thaurignac G, Mpoudi Ngole E, Kouanfack C, Mukadi Bamuleka D, Likofata J, Muyembe Tamfum JJ, De Nys H, Capelle J, Toure A, Delaporte E, Keita AK, Ahuka Mundeke S, Ayouba A. Extensive Survey and Analysis of Factors Associated with Presence of Antibodies to Orthoebolaviruses in Bats from West and Central Africa. Viruses 2023; 15:1927. [PMID: 37766333 PMCID: PMC10536003 DOI: 10.3390/v15091927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The seroprevalence to orthoebolaviruses was studied in 9594 bats (5972 frugivorous and 3622 insectivorous) from Cameroon, the Democratic Republic of Congo (DRC) and Guinea, with a Luminex-based serological assay including recombinant antigens of four orthoebolavirus species. Seroprevalence is expressed as a range according to different cut-off calculations. Between 6.1% and 18.9% bat samples reacted with at least one orthoebolavirus antigen; the highest reactivity was seen with Glycoprotein (GP) antigens. Seroprevalence varied per species and was higher in frugivorous than insectivorous bats; 9.1-27.5% versus 1.3-4.6%, respectively. Seroprevalence in male (13.5%) and female (14.4%) bats was only slightly different and was higher in adults (14.9%) versus juveniles (9.4%) (p < 0.001). Moreover, seroprevalence was highest in subadults (45.4%) when compared to mature adults (19.2%), (p < 0.001). Our data suggest orthoebolavirus circulation is highest in young bats. More long-term studies are needed to identify birthing pulses for the different bat species in diverse geographic regions and to increase the chances of detecting viral RNA in order to document the genetic diversity of filoviruses in bats and their pathogenic potential for humans. Frugivorous bats seem more likely to be reservoirs of orthoebolaviruses, but the role of insectivorous bats has also to be further examined.
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Affiliation(s)
- Martine Peeters
- TransVIHMI, University of Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), 34394 Montpellier, France; (M.C.); (A.L.); (A.E.); (G.T.); (E.D.)
| | - Maëliss Champagne
- TransVIHMI, University of Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), 34394 Montpellier, France; (M.C.); (A.L.); (A.E.); (G.T.); (E.D.)
| | - Innocent Ndong Bass
- Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Yaounde P.O. Box 1857, Cameroon; (I.N.B.); (D.M.D.); (F.A.M.D.); (C.K.)
| | - Souana Goumou
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abdel Nasser de Conakry, Conakry BP6629, Guinea; (S.G.); (A.K.S.); (A.T.); (A.K.K.)
| | - Simon-Pierre Ndimbo Kumugo
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of the Congo; (S.-P.N.K.); (P.M.K.); (G.L.); (D.M.B.); (J.-J.M.T.); (S.A.M.)
| | - Audrey Lacroix
- TransVIHMI, University of Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), 34394 Montpellier, France; (M.C.); (A.L.); (A.E.); (G.T.); (E.D.)
| | - Amandine Esteban
- TransVIHMI, University of Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), 34394 Montpellier, France; (M.C.); (A.L.); (A.E.); (G.T.); (E.D.)
| | - Dowbiss Meta Djomsi
- Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Yaounde P.O. Box 1857, Cameroon; (I.N.B.); (D.M.D.); (F.A.M.D.); (C.K.)
| | - Abdoul Karim Soumah
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abdel Nasser de Conakry, Conakry BP6629, Guinea; (S.G.); (A.K.S.); (A.T.); (A.K.K.)
| | - Placide Mbala Kingebeni
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of the Congo; (S.-P.N.K.); (P.M.K.); (G.L.); (D.M.B.); (J.-J.M.T.); (S.A.M.)
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa P.O. Box 1197, Democratic Republic of the Congo
| | - Flaubert Auguste Mba Djonzo
- Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Yaounde P.O. Box 1857, Cameroon; (I.N.B.); (D.M.D.); (F.A.M.D.); (C.K.)
| | - Guy Lempu
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of the Congo; (S.-P.N.K.); (P.M.K.); (G.L.); (D.M.B.); (J.-J.M.T.); (S.A.M.)
| | - Guillaume Thaurignac
- TransVIHMI, University of Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), 34394 Montpellier, France; (M.C.); (A.L.); (A.E.); (G.T.); (E.D.)
| | - Eitel Mpoudi Ngole
- Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Yaounde P.O. Box 1857, Cameroon; (I.N.B.); (D.M.D.); (F.A.M.D.); (C.K.)
| | - Charles Kouanfack
- Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Yaounde P.O. Box 1857, Cameroon; (I.N.B.); (D.M.D.); (F.A.M.D.); (C.K.)
| | - Daniel Mukadi Bamuleka
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of the Congo; (S.-P.N.K.); (P.M.K.); (G.L.); (D.M.B.); (J.-J.M.T.); (S.A.M.)
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa P.O. Box 1197, Democratic Republic of the Congo
| | - Jacques Likofata
- Laboratoire Provincial de Mbandaka, Equateur, Democratic Republic of the Congo;
| | - Jean-Jacques Muyembe Tamfum
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of the Congo; (S.-P.N.K.); (P.M.K.); (G.L.); (D.M.B.); (J.-J.M.T.); (S.A.M.)
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa P.O. Box 1197, Democratic Republic of the Congo
| | - Helene De Nys
- Astre, CIRAD, INRAE, University of Montpellier, 34398 Montpellier, France; (H.D.N.); (J.C.)
- Astre, CIRAD, 6 Lanark Road, Harare, Zimbabwe
| | - Julien Capelle
- Astre, CIRAD, INRAE, University of Montpellier, 34398 Montpellier, France; (H.D.N.); (J.C.)
| | - Abdoulaye Toure
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abdel Nasser de Conakry, Conakry BP6629, Guinea; (S.G.); (A.K.S.); (A.T.); (A.K.K.)
| | - Eric Delaporte
- TransVIHMI, University of Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), 34394 Montpellier, France; (M.C.); (A.L.); (A.E.); (G.T.); (E.D.)
| | - Alpha Kabinet Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abdel Nasser de Conakry, Conakry BP6629, Guinea; (S.G.); (A.K.S.); (A.T.); (A.K.K.)
| | - Steve Ahuka Mundeke
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of the Congo; (S.-P.N.K.); (P.M.K.); (G.L.); (D.M.B.); (J.-J.M.T.); (S.A.M.)
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa P.O. Box 1197, Democratic Republic of the Congo
| | - Ahidjo Ayouba
- TransVIHMI, University of Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD), 34394 Montpellier, France; (M.C.); (A.L.); (A.E.); (G.T.); (E.D.)
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Huang H, Fu M, Han P, Yin H, Yang Z, Kong Y, Wang B, Yang X, Ren T, Zhang Y. Clinical and Molecular Epidemiology of Hemorrhagic Fever with Renal Syndrome Caused by Orthohantaviruses in Xiangyun County, Dali Prefecture, Yunnan Province, China. Vaccines (Basel) 2023; 11:1477. [PMID: 37766153 PMCID: PMC10537480 DOI: 10.3390/vaccines11091477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Hemorrhagic fever with renal syndrome (HFRS) is a zoonotic disease transmitted by several rodent species. We obtained clinical data of HFRS patients from the medical records of the People's Hospital of Xiangyun County in Dali Prefecture from July 2019 to August 2021. We collected epidemiological data of HFRS patients through interviews and investigated host animals using the night clip or night cage method. We systematically performed epidemiological analyses of patients and host animals. The differences in the presence of rodent activity at home (χ2 = 8.75, p = 0.031 < 0.05), of rodent-proof equipment in the food (χ2 = 9.19, p = 0.025 < 0.05), and of rodents or rodent excrement in the workplace (χ2 = 10.35, p = 0.014 < 0.05) were statistically different in the four clinical types, including mild, medium, severe, and critical HFRS-associated diseases. Furthermore, we conducted molecular detection of orthohantavirus in host animals. The total orthohantavirus infection rate of rodents was 2.72% (9/331); the specific infection rate of specific animal species was 6.10% (5/82) for the Apodemus chevrieri, 100% (1/1) for the Rattus nitidus, 3.77% (2/53) for the Rattus norvegicus, and 12.50% (1/8) for the Crocidura dracula. In this study, a total of 21 strains of orthohantavirus were detected in patients and rodents. The 12 orthohantavirus strains from patients showed a closer relationship with Seoul orthohantavirus (SEOOV) L0199, DLR2, and GZRn60 strains; the six orthohantavirus strains from Rattus norvegicus and Apodemus chevrieri were closely related to SEOOV GZRn60 strain. One strain (XYRn163) from Rattus norvegicus and one strain (XYR.nitidus97) from Rattus nitidus were closely related to SEOOV DLR2 strain; the orthohantavirus strain from Crocidura dracula was closely related to the Luxi orthohantavirus (LUXV) LX309 strain. In conclusion, patients with HFRS in Xuangyun County of Dali Prefecture are predominantly affected by SEOOV, with multiple genotypes of orthohantavirus in host animals, and, most importantly, these orthohantavirus strains constantly demonstrated zoonotic risk in humans.
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Affiliation(s)
- Hao Huang
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Key Laboratory for Cross-Border Control and Quarantine of Zoonoses in Universities of Yunnan Province, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China
| | - Meng Fu
- School of Public Health, Kunming Medical University, Kunming 650000, China
| | - Peiyu Han
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Key Laboratory for Cross-Border Control and Quarantine of Zoonoses in Universities of Yunnan Province, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China
| | - Hongmin Yin
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Key Laboratory for Cross-Border Control and Quarantine of Zoonoses in Universities of Yunnan Province, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China
| | - Zi Yang
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Key Laboratory for Cross-Border Control and Quarantine of Zoonoses in Universities of Yunnan Province, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China
| | - Yichen Kong
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Key Laboratory for Cross-Border Control and Quarantine of Zoonoses in Universities of Yunnan Province, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China
| | - Bo Wang
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Xinglou Yang
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650023, China
| | - Tilian Ren
- Department of Infection, People's Hospital of Xiangyun County, Dali 671000, China
| | - Yunzhi Zhang
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Key Laboratory for Cross-Border Control and Quarantine of Zoonoses in Universities of Yunnan Province, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China
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Han Y, Xu P, Wang Y, Zhao W, Zhang J, Zhang S, Wang J, Jin Q, Wu Z. Panoramic analysis of coronaviruses carried by representative bat species in Southern China to better understand the coronavirus sphere. Nat Commun 2023; 14:5537. [PMID: 37684236 PMCID: PMC10491624 DOI: 10.1038/s41467-023-41264-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Bats, recognized as considerable reservoirs for coronaviruses (CoVs), serve as natural hosts for several highly pathogenic CoVs, including SARS-CoV and SARS-CoV-2. Investigating the bat CoV community provides insights into the origin for highly pathogenic CoVs and highlights bat CoVs with potential spillover risks. This study probes the evolution, recombination, host range, geographical distribution, and cross-species transmission characteristics of bat CoVs across China and its associated CoVs in other regions. Through detailed research on 13,064 bat samples from 14 provinces of China, 1141 CoV strains are found across 10 subgenera and one unclassified Alpha-CoV, generating 399 complete genome sequences. Within bat CoVs, 11 new CoV species are identified and 425 recombination events are detected. Bats in southern China, particularly in Yunnan province, exhibit a pronounced diversity of CoVs. Limited sampling and low detection rates exist for CoVs in Myotacovirus, Nyctacovirus, Hibecovirus, Nobecovirus in China. The genus Myotis is highlighted as a potential ancestral host for Alpha-CoV, with the genus Hipposideros suggested as a likely progenitor host for bat-associated Beta-CoV, indicating the complexity of cross-species transmission dynamics. Through the comprehensive analysis, this study enriches the understanding of bat CoVs and offers a valuable resource for future research.
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Affiliation(s)
- Yelin Han
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences, Beijing, China
| | - Panpan Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuyang Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences, Beijing, China
| | - Wenliang Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences, Beijing, China
| | - Junpeng Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China.
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences, Beijing, China.
| | - Zhiqiang Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China.
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences, Beijing, China.
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Talebzadeh F, Ghadipasha M, Gharehdaghi J, Raoofian R, Azam K, Koosha M, Oshaghi MA. Efficiency of mitochondrial genes and nuclear Alu elements in detecting human DNA in blood meals of Anopheles stephensi mosquitoes: a time-course study. Parasit Vectors 2023; 16:284. [PMID: 37580774 PMCID: PMC10426119 DOI: 10.1186/s13071-023-05884-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/14/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND The time required for PCR detection of DNA in human blood meals in vector mosquitoes may vary, depending on the molecular markers used, based on the size and copy number of the amplicons. Detailed knowledge of the blood-feeding behavior of mosquito populations in nature is an essential component for evaluating their vectorial capacity and for assessing the roles of individual vertebrates as potential hosts involved in the transmission of vector-borne diseases. METHODS Laboratory experiments were conducted to compare the time course of PCR detection of DNA in human blood meals from individual blood-fed Anopheles stephensi mosquitoes, using loci with different characteristics, including two mitochondrial DNA (mtDNA) genes, cytB (228 bp) and 16S ribosomal RNA (rRNA) (157 bp) and nuclear Alu-repeat elements (226 bp) at different time points after the blood meal. RESULTS Human DNA was detectable up to 84-120 h post-blood-feeding, depending on the length and copy number of the loci. Our results suggest that 16S rRNA and Alu-repeat markers can be successfully recovered from human DNA up to 5 days post-blood-meal. The 16S rDNA and Alu-repeat loci have a significantly (P = 0.008) slower decline rate than the cytB locus. Median detection periods (T50) for the amplicons were 117, 113 and 86.4 h for Alu-repeat, 16S rDNA and cytB, respectively, suggesting an inverse linear relationship between amplicon size/copy number and digestion time. CONCLUSION This comparative study shows that the Alu-repeat locus is the most efficient marker for time-course identification of human DNA from blood meals in female mosquitoes. It is also a promising tool for determining the anthropophilic index (AI) or human blood index (HBI), i.e. the proportion of blood meals from humans, which is often reported as a relative measure of anthropophagy of different mosquito vectors, and hence a measure of the vector competence of mosquito species collected in the field.
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Affiliation(s)
- Fahimeh Talebzadeh
- Department of Vector Biology and Control of Diseases, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Ghadipasha
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Jaber Gharehdaghi
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Reza Raoofian
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Kamal Azam
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mona Koosha
- Department of Vector Biology and Control of Diseases, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Oshaghi
- Department of Vector Biology and Control of Diseases, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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Kapoor S, Young ND, Yang YT, Batterham P, Gasser RB, Bowles VM, Anstead CA, Perry T. Mitochondrial genomic investigation reveals a clear association between species and genotypes of Lucilia and geographic origin in Australia. Parasit Vectors 2023; 16:279. [PMID: 37573420 PMCID: PMC10423422 DOI: 10.1186/s13071-023-05902-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/27/2023] [Indexed: 08/14/2023] Open
Abstract
BACKGROUND Lucilia cuprina and L. sericata (family Calliphoridae) are globally significant ectoparasites of sheep. Current literature suggests that only one of these blowfly subspecies, L. cuprina dorsalis, is a primary parasite causing myiasis (flystrike) in sheep in Australia. These species and subspecies are difficult to distinguish using morphological features. Hence, being able to accurately identify blowflies is critical for diagnosis and for understanding their relationships with their hosts and environment. METHODS In this study, adult blowflies (5 pools of 17 flies; n = 85) were collected from five locations in different states [New South Wales (NSW), Queensland (QLD), Tasmania (TAS), Victoria (VIC) and Western Australia (WA)] of Australia and their mitochondrial (mt) genomes were assembled. RESULTS Each mt genome assembled was ~ 15 kb in size and encoded 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region. The Lucilia species mt genomes were conserved in structure, and the genes retained the same order and direction. The overall nucleotide composition was heavily biased towards As and Ts-77.7% of the whole genomes. Pairwise nucleotide diversity suggested divergence between Lucilia cuprina cuprina, L. c. dorsalis and L. sericata. Comparative analyses of these mt genomes with published data demonstrated that the blowflies collected from sheep farm in TAS clustered within a clade with L. sericata. The flies collected from an urban location in QLD were more closely related to L. sericata and represented the subspecies L. c. cuprina, whereas the flies collected from sheep farms in NSW, VIC and WA represented the subspecies L. c. dorsalis. CONCLUSIONS Phylogenetic analyses of the mt genomes representing Lucilia from the five geographic locations in Australia supported the previously demonstrated paraphyly of L. cuprina with respect to L. sericata and revealed that L. c. cuprina is distinct from L. c. dorsalis and that L. c. cuprina is more closely related to L. sericata than L. c. dorsalis. The mt genomes reported here provide an important molecular resource to develop tools for species- and subspecies-level identification of Lucilia from different geographical regions across Australia.
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Affiliation(s)
- Shilpa Kapoor
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia
- Department of Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, The University of Melbourne, Building 400, Parkville, VIC 3010 Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, The University of Melbourne, Building 400, Parkville, VIC 3010 Australia
| | - Ying Ting Yang
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Philip Batterham
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, The University of Melbourne, Building 400, Parkville, VIC 3010 Australia
| | - Vernon M. Bowles
- Department of Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, The University of Melbourne, Building 400, Parkville, VIC 3010 Australia
| | - Clare A. Anstead
- Department of Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, The University of Melbourne, Building 400, Parkville, VIC 3010 Australia
| | - Trent Perry
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia
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Martínez‐Borrego D, Arellano E, González‐Cózatl FX, Ospina‐Garcés SM, Rogers DS. Species delimitation and integrative taxonomy of the Reithrodontomys mexicanus (Rodentia: Cricetidae) cryptic complex. Ecol Evol 2023; 13:e10355. [PMID: 37529589 PMCID: PMC10387591 DOI: 10.1002/ece3.10355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/12/2023] [Accepted: 07/12/2023] [Indexed: 08/03/2023] Open
Abstract
Species boundaries are difficult to establish in groups with very similar morphology. As an alternative, it has been suggested to integrate multiple sources of data to clarify taxonomic problems in taxa where cryptic speciation processes have been reported. This is the case of the harvest mouse Reithrodontomys mexicanus, which has a problematic taxonomy history as it is considered a complex species. Here, we evaluate the cryptic diversity of R. mexicanus using an integrative taxonomy approach in order to detect candidate lineages at the species level. The molecular analysis used one mitochondrial (cytb) and two nuclear (Fgb-I7 and IRBP) genes. Species hypotheses were suggested based on three molecular delimitation methods (mPTP, bGMYC, and STACEY) and cytb genetic distance values. Skull and environmental space differences between the delimited species were also tested to complement the discrimination of candidate species. Based on the consensus across the delimitation methods and genetic distance values, four species were proposed, which were mostly supported by morphometric and ecological data: R. mexicanus clade I, R. mexicanus clade IIA, R. mexicanus clade IIIA, and R. mexicanus clade IIIB. In addition, the evolutionary relationships between the species that comprise the R. mexicanus group were discussed from a phylogenetic approach. Our findings present important taxonomic implications for Reithrodontomys, as the number of known species for this genus increases. Furthermore, we highlight the importance of the use of multiple sources of data in systematic studies to establish robust delimitations between species considered taxonomically complex.
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Affiliation(s)
- Daily Martínez‐Borrego
- Centro de Investigación en Biodiversidad y ConservaciónUniversidad Autónoma del Estado de MorelosCuernavacaMorelosMexico
| | - Elizabeth Arellano
- Centro de Investigación en Biodiversidad y ConservaciónUniversidad Autónoma del Estado de MorelosCuernavacaMorelosMexico
| | - Francisco X. González‐Cózatl
- Centro de Investigación en Biodiversidad y ConservaciónUniversidad Autónoma del Estado de MorelosCuernavacaMorelosMexico
| | | | - Duke S. Rogers
- Department of Biology and Monte L Bean Life Science MuseumBrigham Young UniversityProvoUtahUSA
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25
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Gonzalez P, Salazar JR, Salinas TP, Avila M, Colella JP, Dunnum JL, Glass GE, Gonzalez G, Juarez E, Lindblade K, Pile E, Mendoza Y, Pascale JM, Armien AG, Cook JA, Armien B. Two Decades of Wildlife Pathogen Surveillance: Case Study of Choclo orthohantavirus and Its Wild Reservoir Oligoryzomys costaricensis. Viruses 2023; 15:1390. [PMID: 37376689 DOI: 10.3390/v15061390] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/04/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The Costa Rican pygmy rice rat (Oligoryzomys costaricensis) is the primary reservoir of Choclo orthohantavirus (CHOV), the causal agent of hantavirus disease, pulmonary syndrome, and fever in humans in Panama. Since the emergence of CHOV in early 2000, we have systematically sampled and archived rodents from >150 sites across Panama to establish a baseline understanding of the host and virus, producing a permanent archive of holistic specimens that we are now probing in greater detail. We summarize these collections and explore preliminary habitat/virus associations to guide future wildlife surveillance and public health efforts related to CHOV and other zoonotic pathogens. Host sequences of the mitochondrial cytochrome b gene form a single monophyletic clade in Panama, despite wide distribution across Panama. Seropositive samples were concentrated in the central region of western Panama, consistent with the ecology of this agricultural commensal and the higher incidence of CHOV in humans in that region. Hantavirus seroprevalence in the pygmy rice rat was >15% overall, with the highest prevalence in agricultural areas (21%) and the lowest prevalence in shrublands (11%). Host-pathogen distribution, transmission dynamics, genomic evolution, and habitat affinities can be derived from the preserved samples, which include frozen tissues, and now provide a foundation for expanded investigations of orthohantaviruses in Panama.
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Affiliation(s)
- Publio Gonzalez
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
| | - Jacqueline R Salazar
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
| | - Tybbysay P Salinas
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
| | - Mario Avila
- Department of Vector Control-Herrera Health Region, Ministry of Health, Panama City 0843-03441, Panama
| | - Jocelyn P Colella
- Biodiversity Institute & Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Jonathan L Dunnum
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Gregory E Glass
- Department of Geography & Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Gloria Gonzalez
- Department of Genomics and Proteomics, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
| | - Enos Juarez
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
| | - Kimberly Lindblade
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Edwin Pile
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
| | - Yaxelis Mendoza
- Department of Genomics and Proteomics, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
- Sistema Nacional de Investigación (SNI), Secretaria Nacional de Ciencia y Tecnología (SENACYT), Panama City 0816-02852, Panama
| | - Juan Miguel Pascale
- Department of Genomics and Proteomics, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
| | - Anibal G Armien
- California Animal Health & Food Safety Laboratory System (CAHFS), School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Blas Armien
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
- Sistema Nacional de Investigación (SNI), Secretaria Nacional de Ciencia y Tecnología (SENACYT), Panama City 0816-02852, Panama
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26
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Filip E, Strzała T, Stępień E, Cembrowska-Lech D. Universal mtDNA fragment for Cervidae barcoding species identification using phylogeny and preliminary analysis of machine learning approach. Sci Rep 2023; 13:9133. [PMID: 37277428 DOI: 10.1038/s41598-023-35637-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023] Open
Abstract
The aim of the study was to use total DNA obtained from bone material to identify species of free-living animals based on the analysis of mtDNA fragments by molecular methods using accurate bioinformatics tools Bayesian approach and the machine learning approach. In our research, we present a case study of successful species identification based on degraded samples of bone, with the use of short mtDNA fragments. For better barcoding, we used molecular and bioinformatics methods. We obtained a partial sequence of the mitochondrial cytochrome b (Cytb) gene for Capreolus capreolus, Dama dama, and Cervus elaphus, that can be used for species affiliation. The new sequences have been deposited in GenBank, enriching the existing Cervidae mtDNA base. We have also analysed the effect of barcodes on species identification from the perspective of the machine learning approach. Machine learning approaches of BLOG and WEKA were compared with distance-based (TaxonDNA) and tree-based (NJ tree) methods based on the discrimination accuracy of the single barcodes. The results indicated that BLOG and WEKAs SMO classifier and NJ tree performed better than TaxonDNA in discriminating Cervidae species, with BLOG and WEKAs SMO classifier performing the best.
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Affiliation(s)
- Ewa Filip
- Institute of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland.
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, Szczecin, Poland.
| | - Tomasz Strzała
- Department of Genetics, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Edyta Stępień
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16, 70-383, Szczecin, Poland
| | - Danuta Cembrowska-Lech
- Institute of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland
- Sanprobi Sp. z o. o. Sp. k., Kurza Stopka 5C, 70-535, Szczecin, Poland
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27
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Gu SH, Miñarro M, Feliu C, Hugot JP, Forrester NL, Weaver SC, Yanagihara R. Multiple Lineages of Hantaviruses Harbored by the Iberian Mole ( Talpa occidentalis) in Spain. Viruses 2023; 15:1313. [PMID: 37376613 DOI: 10.3390/v15061313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/26/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
The recent detection of both Nova virus (NVAV) and Bruges virus (BRGV) in European moles (Talpa europaea) in Belgium and Germany prompted a search for related hantaviruses in the Iberian mole (Talpa occidentalis). RNAlater®-preserved lung tissue from 106 Iberian moles, collected during January 2011 to June 2014 in Asturias, Spain, were analyzed for hantavirus RNA by nested/hemi-nested RT-PCR. Pairwise alignment and comparison of partial L-segment sequences, detected in 11 Iberian moles from four parishes, indicated the circulation of genetically distinct hantaviruses. Phylogenetic analyses, using maximum-likelihood and Bayesian methods, demonstrated three distinct hantaviruses in Iberian moles: NVAV, BRGV, and a new hantavirus, designated Asturias virus (ASTV). Of the cDNA from seven infected moles processed for next generation sequencing using Illumina HiSeq1500, one produced viable contigs, spanning the S, M and L segments of ASTV. The original view that each hantavirus species is harbored by a single small-mammal host species is now known to be invalid. Host-switching or cross-species transmission events, as well as reassortment, have shaped the complex evolutionary history and phylogeography of hantaviruses such that some hantavirus species are hosted by multiple reservoir species, and conversely, some host species harbor more than one hantavirus species.
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Affiliation(s)
- Se Hun Gu
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Marcos Miñarro
- Department of Horticultural and Forestry Crops, Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), 33300 Villaviciosa, Spain
| | - Carlos Feliu
- Department of Biology, Health and Environment, Faculty of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
| | - Jean-Pierre Hugot
- Department of Systematics and Evolution, Muséum National d'Histoire Naturelle, 75005 Paris, France
| | | | - Scott C Weaver
- Institute for Human Infections and Immunity and World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Richard Yanagihara
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
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28
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Everson KM, McGinnis RC, Burdine OP, Huddleston TR, Hylick TM, Keith AL, Moore SC, O’Brien AE, Vilardo AL, Krupa JJ. Disentangling morphology and genetics in two voles ( Microtus pennsylvanicus and M. ochrogaster) in a region of sympatry. J Mammal 2023; 104:532-545. [PMID: 37287702 PMCID: PMC10243968 DOI: 10.1093/jmammal/gyac119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 11/17/2022] [Indexed: 10/09/2023] Open
Abstract
Species in recent, rapid radiations can be difficult to distinguish from one another due to incomplete sorting of traits, insufficient time for novel morphologies to evolve, and elevated rates of hybridization and gene flow. The vole genus Microtus (58 spp.) is one such system where all three factors are likely at play. In the central United States, the prairie vole, Microtus ochrogaster, and the eastern meadow vole, M. pennsylvanicus, occur in sympatry and can be distinguished on the basis of molar cusp patterns but are known to be exceptionally difficult to distinguish using external morphological characters. Using a combination of morphometrics, pelage color analyses, and phylogenetics, we explored which traits are most effective for species identification and whether these same traits can be used to identify the subspecies M. o. ohionensis. While we were able to identify six traits that differed significantly between M. ochrogaster and M. pennsylvanicus, we also found substantial measurement overlap which limits the utility of these traits for species identification. The subspecies M. o. ohionensis was particularly difficult to distinguish from M. p. pennsylvanicus, and we did not find any evidence that this subspecies forms a distinct genetic clade. Furthermore, the full species M. ochrogaster and M. pennsylvanicus did not form reciprocal clades in phylogenetic analyses. We discuss several possible reasons for these patterns, including unrecognized variation in molar cusp patterns and/or localized hybridization. Overall, our results provide useful information that will aid in the identification of these species and subspecies in the future, and provides a case study of how genetics, morphometrics, and fur color analyses can be used to disentangle signatures of evolutionary history and hybridization.
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Affiliation(s)
- Kathryn M Everson
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Robert C McGinnis
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Olivia P Burdine
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Taniece R Huddleston
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Tyler M Hylick
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Audrey L Keith
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Savannah C Moore
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Aidan E O’Brien
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - Ava L Vilardo
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
| | - James J Krupa
- Department of Biology, T.H. Morgan Building, University of Kentucky, 675 Rose Street, Lexington, Kentucky 40506, USA
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29
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Kim Y, Leopardi S, Scaravelli D, Zecchin B, Priori P, Festa F, Drzewnioková P, De Benedictis P, Nouvellet P. Transmission dynamics of lyssavirus in Myotis myotis: mechanistic modelling study based on longitudinal seroprevalence data. Proc Biol Sci 2023; 290:20230183. [PMID: 37072038 PMCID: PMC10113028 DOI: 10.1098/rspb.2023.0183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
We investigated the transmission dynamics of lyssavirus in Myotis myotis and Myotis blythii, using serological, virological, demographic and ecological data collected between 2015 and 2022 from two maternity colonies in northern Italian churches. Despite no lyssavirus detection in 556 bats sampled over 11 events by reverse transcription-polymerase chain reaction (RT-PCR), 36.3% of 837 bats sampled over 27 events showed neutralizing antibodies to European bat lyssavirus 1, with a significant increase in summers. By fitting sets of mechanistic models to seroprevalence data, we investigated factors that influenced lyssavirus transmission within and between years. Five models were selected as a group of final models: in one model, a proportion of exposed bats (median model estimate: 5.8%) became infectious and died while the other exposed bats recovered with immunity without becoming infectious; in the other four models, all exposed bats became infectious and recovered with immunity. The final models supported that the two colonies experienced seasonal outbreaks driven by: (i) immunity loss particularly during hibernation, (ii) density-dependent transmission, and (iii) a high transmission rate after synchronous birthing. These findings highlight the importance of understanding ecological factors, including colony size and synchronous birthing timing, and potential infection heterogeneities to enable more robust assessments of lyssavirus spillover risk.
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Affiliation(s)
- Younjung Kim
- Department of Evolution, Behaviour, and Environment, School of Life Sciences, University of Sussex, BN1 9RH Brighton, UK
| | - Stefania Leopardi
- FAO and National Reference Centre for Rabies, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, Legnaro, 35020 Padua, Italy
| | - Dino Scaravelli
- S.T.E.R.N.A. and Museo Ornitologico 'F. Foschi', via Pedrali 12, 47121 Forlì, Italy
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Barbara Zecchin
- FAO and National Reference Centre for Rabies, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, Legnaro, 35020 Padua, Italy
| | - Pamela Priori
- S.T.E.R.N.A. and Museo Ornitologico 'F. Foschi', via Pedrali 12, 47121 Forlì, Italy
| | - Francesca Festa
- FAO and National Reference Centre for Rabies, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, Legnaro, 35020 Padua, Italy
| | - Petra Drzewnioková
- FAO and National Reference Centre for Rabies, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, Legnaro, 35020 Padua, Italy
| | - Paola De Benedictis
- FAO and National Reference Centre for Rabies, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, Legnaro, 35020 Padua, Italy
| | - Pierre Nouvellet
- Department of Evolution, Behaviour, and Environment, School of Life Sciences, University of Sussex, BN1 9RH Brighton, UK
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, SW7 2AZ London, UK
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30
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Li Z, Guo J, Hong Y, Zhang N, Zhang M. The Effect of Landscape Environmental Factors on Gene Flow of Red Deer ( Cervus canadensis xanthopygus) in the Southern of the Greater Khingan Mountains, China. BIOLOGY 2023; 12:biology12040576. [PMID: 37106776 PMCID: PMC10135690 DOI: 10.3390/biology12040576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/30/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023]
Abstract
Red deer (Cervus canadensis xanthopygus) living in the north of China are restricted and threatened due to human activities and the changes in the natural environment, which influence the dispersal and effective gene flow between different groups of red deer. Effective gene flow plays an important role in maintaining genetic diversity and structure and ensuring population health. In order to evaluate the genetic diversity level and understand the gene flow between different red deer groups, 231 fresh fecal samples were collected from the southern part of the Greater Khingan Mountains, China. A microsatellite marker was used for genetic analysis. The results showed that the genetic diversity of red deer was intermediate in this region. Significant genetic differentiation among different groups was found in the main distribution area (p < 0.01) using F-statistics and the program STRUCTURE. Different degrees of gene flow existed in red deer groups, and the roads (importance = 40.9), elevation (importance = 38.6), and settlements (importance = 14.1) exerted main effects on gene flow between red deer groups. Human-made factors should be noticed and strictly supervised in this region to avoid excessive disturbance to the normal movement of the red deer. Further conservation and management of red deer should reduce the intensity of vehicular traffic in the concentrated distribution areas of red deer, especially during the heat season. This research helps us better understand the genetic level and health status of red deer in the southern part of the Greater Khingan Mountains and provides theoretical references for protecting and restoring the red deer populations in China.
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Affiliation(s)
- Zheng Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Jinhao Guo
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yang Hong
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Ning Zhang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Minghai Zhang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
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31
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Liu Y, Pu Y, Chen S, Wang X, Murphy RW, Wang X, Liao R, Tang K, Yue B, Liu S. Revalidation and expanded description of Mustela aistoodonnivalis (Mustelidae: Carnivora) based on a multigene phylogeny and morphology. Ecol Evol 2023; 13:e9944. [PMID: 37082328 PMCID: PMC10111237 DOI: 10.1002/ece3.9944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 04/22/2023] Open
Abstract
The lacked-teeth pygmy weasel, Mustela aistoodonnivalis Wu & Kao, 1991, was originally described as being from Taibai Mountain and Zhashui county, Shaanxi, China. Subsequently, it was considered a subspecies or synonym of Mustela nivalis. In a faunal survey of northwestern Sichuan, eight specimens of M. aistoodonnivalis were collected. A molecular phylogenetic analysis of one mitochondrial and six nuclear genes clustered the specimens as a distinct clade and not with M. nivalis. Morphologically, the lack of the second lower molar differentiated them from M. nivalis, and genetic distances were typical of discrete species. These analyses confirmed that M. aistoodonnivalis is an independent species in the genus Mustela.
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Affiliation(s)
- Yingxun Liu
- College of Life SciencesSichuan UniversityChengduSichuanChina
| | - Yingting Pu
- College of Life SciencesSichuan Normal UniversityChengduSichuanChina
| | - Shunde Chen
- College of Life SciencesSichuan Normal UniversityChengduSichuanChina
| | - Xuming Wang
- Sichuan Academy of ForestryChengduSichuanChina
| | | | - Xin Wang
- Sichuan Academy of ForestryChengduSichuanChina
| | - Rui Liao
- Sichuan Academy of ForestryChengduSichuanChina
| | - Keyi Tang
- College of Life SciencesSichuan Normal UniversityChengduSichuanChina
| | - Bisong Yue
- College of Life SciencesSichuan UniversityChengduSichuanChina
| | - Shaoying Liu
- Sichuan Academy of ForestryChengduSichuanChina
- Ecological Restoration and Conservation for Forest and Wetland Key Laboratory of Sichuan ProvinceSichuan Academy of ForestryChengduSichuanChina
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32
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Genetic Diversity and Insights about Distribution of Brown Howler Monkeys (Alouatta guariba Group) (Atelidae, Alouattinae). INT J PRIMATOL 2023. [DOI: 10.1007/s10764-023-00352-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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33
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Blair ME, Cao GTH, López-Nandam EH, Veronese-Paniagua DA, Birchette MG, Kenyon M, Md-Zain BM, Munds RA, Nekaris KAI, Nijman V, Roos C, Thach HM, Sterling EJ, Le MD. Molecular Phylogenetic Relationships and Unveiling Novel Genetic Diversity among Slow and Pygmy Lorises, including Resurrection of Xanthonycticebus intermedius. Genes (Basel) 2023; 14:643. [PMID: 36980915 PMCID: PMC10048081 DOI: 10.3390/genes14030643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Genetic analysis of historical museum collections presents an opportunity to clarify the evolutionary history of understudied primate groups, improve taxonomic inferences, and inform conservation efforts. Among the most understudied primate groups, slow and pygmy lorises (genera Nycticebus and Xanthonycticebus) are nocturnal strepsirrhines found in South and Southeast Asia. Previous molecular studies have supported five species, but studies using morphological data suggest the existence of at least nine species. We sequenced four mitochondrial loci, CO1, cytb, d-loop, and ND4, for a total of 3324 aligned characters per sample from 41 historical museum specimens for the most comprehensive geographic coverage to date for these genera. We then combined these sequences with a larger dataset composed of samples collected in Vietnam as well as previously published sequences (total sample size N = 62). We inferred phylogenetic relationships using Bayesian inference and maximum likelihood methods based on data from each locus and on concatenated sequences. We also inferred divergence dates for the most recent common ancestors of major lineages using a BEAST analysis. Consistent with previous studies, we found support for Xanthonycticebus pygmaeus as a basal taxon to the others in the group. We also confirmed the separation between lineages of X. pygmaeus from northern Vietnam/Laos/China and southern Vietnam/Cambodia and included a taxonomic revision recognizing a second taxon of pygmy loris, X. intermedius. Our results found support for multiple reciprocally monophyletic taxa within Borneo and possibly Java. The study will help inform conservation management of these trade-targeted animals as part of a genetic reference database for determining the taxonomic unit and provenance of slow and pygmy lorises confiscated from illegal wildlife trade activities.
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Affiliation(s)
- Mary E. Blair
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
| | - Giang T. H. Cao
- Department of Genetics, Vietnam National University, Hanoi 10000, Vietnam
| | - Elora H. López-Nandam
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
- Institute for Biodiversity and Sustainability Science, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Daniel A. Veronese-Paniagua
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
- The Division of Biology & Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Mark G. Birchette
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
- Department of Biology, Long Island University Brooklyn, Brooklyn, NY 11201, USA
| | - Marina Kenyon
- Dao Tien Endangered Primate Species Centre, Dong Nai 76000, Vietnam
| | - Badrul M. Md-Zain
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi Selangor 43600, Malaysia
| | - Rachel A. Munds
- Department of Anthropology & Archeology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - K. Anne-Isola Nekaris
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford OX3 0BP, UK
- School of Social Sciences and Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Vincent Nijman
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford OX3 0BP, UK
- School of Social Sciences and Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Hoàng M. Thach
- Department of Anthropology, Vietnam National University, Hanoi 10000, Vietnam
- Department of Geography & Human Ecology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854, USA
| | - Eleanor J. Sterling
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
| | - Minh D. Le
- Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi 10000, Vietnam
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Kim YR, Kim HR, Kim JY, Myeong HH, Kang JH, Kim BJ, Lee HJ. Spatio-temporal genetic structure of the striped field mouse (Apodemus agrarius) populations inhabiting national parks in South Korea: Implications for conservation and management of protected areas. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1038058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Population or habitat connectivity is a key component in maintaining species and community-level regional biodiversity as well as intraspecific genetic diversity. Ongoing human activities cause habitat destruction and fragmentation, which exacerbate the connectivity due to restricted animal movements across local habitats, eventually resulting in the loss of biodiversity. The Baekdudaegan Mountain Range (BMR) on the Korean Peninsula represents “biodiversity hotspots” and eight of the 22 Korean national parks are located within the BMR. Given the striped field mouse (Apodemus agrarius) is the most common and ecologically important small mammals in these protected areas, the population genetic assessment of this species will allow for identifying “genetic diversity hotspots” and also “genetic barriers” that may hinder gene flow, and will therefore inform on effective conservation and management efforts for the national park habitats. We collected samples from hair, tail, or buccal swabs for 252 A. agrarius individuals in 2015 and 2019. By using mitochondrial DNA cytochrome b (cyt b) sequences and nine microsatellite loci, we determined levels of genetic diversity, genetic differentiation, and gene flow among eight national park populations of A. agrarius along the BMR. We found high levels of genetic diversity but the occurrences of inbreeding for all the nine samples analyzed. Our results also indicated that there was detectable temporal genetic variation between the 2015 and 2019 populations in the Jirisan National Park, which is probably due to a short-term decline in genetic diversity caused by reduced population sizes. We also found a well-admixed shared gene pool among the national park populations. However, a significant positive correlation between geographic and genetic distances was detected only in mtDNA but not microsatellites, which might be attributed to different dispersal patterns between sexes. There was a genetic barrier to animal movements around the Woraksan National Park areas. The poor habitat connectivity surrounding these areas can be improved by establishing an ecological corridor. Our findings of the presence of genetic barriers in some protected areas provide insights into the conservation and management efforts to improve the population or habitat connectivity among the national parks.
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Meta Djomsi D, Lacroix A, Soumah AK, Kinganda Lusamaki E, Mesdour A, Raulino R, Esteban A, Ndong Bass I, Mba Djonzo FA, Goumou S, Ndimbo-Kimugu SP, Lempu G, Mbala Kingebeni P, Bamuleka DM, Likofata J, Muyembe Tamfum JJ, Toure A, Mpoudi Ngole E, Kouanfack C, Delaporte E, Keita AK, Ahuka-Mundeke S, Ayouba A, Peeters M. Coronaviruses Are Abundant and Genetically Diverse in West and Central African Bats, including Viruses Closely Related to Human Coronaviruses. Viruses 2023; 15:337. [PMID: 36851551 PMCID: PMC9967053 DOI: 10.3390/v15020337] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
Bats are at the origin of human coronaviruses, either directly or via an intermediate host. We tested swabs from 4597 bats (897 from the Democratic Republic of Congo (DRC), 2191 from Cameroon and 1509 from Guinea) with a broadly reactive PCR in the RdRp region. Coronaviruses were detected in 903 (19.6%) bats and in all species, with more than 25 individuals tested. The highest prevalence was observed in Eidolon helvum (239/733; 39.9%) and Rhinolophus sp. (306/899; 34.1%), followed by Hipposideros sp. (61/291; 20.9%). Frugivorous bats were predominantly infected with beta coronaviruses from the Nobecovirus subgenus (93.8%), in which at least 6 species/genus-specific subclades were observed. In contrast, insectivorous bats were infected with beta-coronaviruses from different subgenera (Nobecovirus (8.5%), Hibecovirus (32.8%), Merbecovirus (0.5%) and Sarbecovirus (57.6%)) and with a high diversity of alpha-coronaviruses. Overall, our study shows a high prevalence and genetic diversity of coronaviruses in bats and illustrates that Rhinolophus bats in Africa are infected at high levels with the Sarbecovirus subgenus, to which SARS-CoV-2 belongs. It is important to characterize in more detail the different coronavirus lineages from bats for their potential to infect human cells, their evolution and to study frequency and modes of contact between humans and bats in Africa.
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Affiliation(s)
- Dowbiss Meta Djomsi
- Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Yaounde P.O. Box 1857, Cameroon
| | - Audrey Lacroix
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
| | - Abdoul Karim Soumah
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Gamal Abdel Nasser University (UGANC), Conakry BP6629, Guinea
| | - Eddy Kinganda Lusamaki
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of Congo
| | - Asma Mesdour
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
| | - Raisa Raulino
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
| | - Amandine Esteban
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
| | - Innocent Ndong Bass
- Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Yaounde P.O. Box 1857, Cameroon
| | | | - Souana Goumou
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Gamal Abdel Nasser University (UGANC), Conakry BP6629, Guinea
| | | | - Guy Lempu
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of Congo
| | - Placide Mbala Kingebeni
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa P.O. Box 1197, Democratic Republic of Congo
| | - Daniel Mukadi Bamuleka
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa P.O. Box 1197, Democratic Republic of Congo
- Institut National de Recherche Biomédicale (INRB), Kinshasa P.O. Box 1197, Democratic Republic of Congo
| | - Jacques Likofata
- Laboratoire Provincial de Mbandaka, Mbandaka, Democratic Republic of Congo
| | - Jean-Jacques Muyembe Tamfum
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa P.O. Box 1197, Democratic Republic of Congo
| | - Abdoulaye Toure
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Gamal Abdel Nasser University (UGANC), Conakry BP6629, Guinea
- Department of Public Health, Faculty of Health Sciences and Techniques, Gamal Abdel Nasser University (UGANC), Conakry P.O. Box 1147, Guinea
| | - Eitel Mpoudi Ngole
- Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Yaounde P.O. Box 1857, Cameroon
| | - Charles Kouanfack
- Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Yaounde P.O. Box 1857, Cameroon
| | - Eric Delaporte
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
| | - Alpha Kabinet Keita
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Gamal Abdel Nasser University (UGANC), Conakry BP6629, Guinea
- Department of Public Health, Faculty of Health Sciences and Techniques, Gamal Abdel Nasser University (UGANC), Conakry P.O. Box 1147, Guinea
| | - Steve Ahuka-Mundeke
- National Institute of Biomedical Research (INRB), Kinshasa P.O. Box 1197, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa P.O. Box 1197, Democratic Republic of Congo
| | - Ahidjo Ayouba
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
| | - Martine Peeters
- TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, 34394 Montpellier, France
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Kasap EY, Parfenova ОK, Kurkin RV, Grishin DV. Bioinformatic analysis of the coding region of the melatonin receptor 1b gene as a reliable DNA marker to resolve interspecific mammal phylogenetic relationships. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:5430-5447. [PMID: 36896552 DOI: 10.3934/mbe.2023251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
This research looks into the main DNA markers and the limits of their application in molecular phylogenetic analysis. Melatonin 1B (MTNR1B) receptor genes were analyzed from various biological sources. Based on the coding sequences of this gene, using the class Mammalia as example, phylogenetic reconstructions were made to study the potential of mtnr1b as a DNA marker for phylogenetic relationships investigating. The phylogenetic trees were constructed using NJ, ME and ML methods that establish the evolutionary relationships between different groups of mammals. The resulting topologies were generally in good agreement with topologies established on the basis of morphological and archaeological data as well as with other molecular markers. The present divergences provided a unique opportunity for evolutionary analysis. These results suggest that the coding sequence of the MTNR1B gene can be used as a marker to study the relationships of lower evolutionary levels (order, species) as well as to resolve deeper branches of the phylogenetic tree at the infraclass level.
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Affiliation(s)
- Ekaterina Y Kasap
- Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya St, Moscow, 119121, Russia
| | - Оlga K Parfenova
- Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya St, Moscow, 119121, Russia
| | - Roman V Kurkin
- Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya St, Moscow, 119121, Russia
| | - Dmitry V Grishin
- Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya St, Moscow, 119121, Russia
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Rached A, Abi Rizk G, Mahamat AB, Khoury GE, El Hage J, Harran E, Lattard V. Investigation of anticoagulant rodenticide resistance induced by Vkorc1 mutations in rodents in Lebanon. Sci Rep 2022; 12:22502. [PMID: 36577759 PMCID: PMC9797475 DOI: 10.1038/s41598-022-26638-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 12/19/2022] [Indexed: 12/29/2022] Open
Abstract
Anticoagulant rodenticides (AR) remain the most effective chemical substances used to control rodents in order to limit their agricultural and public health damage in both rural and urban environments. The emergence of genetically based resistance to AR worldwide has threatened effective rodent control. This study gives a first overview of the distribution and frequency of single nucleotide polymorphism in the vitamin K epoxide reductase subcomponent 1 (Vkorc1) gene in rodents in Lebanon. In the Mus genus, we detected two missense mutations Leu128Ser and Tyr139Cys, that confer resistance to anticoagulant rodenticides in house mice and a new missense mutation Ala72Val in the Mus macedonicus species, not previously described. In the Rattus genus, we found one missense mutation Leu90Ile in the roof rat and one missense mutation Ser149Ile in the Norway rat. This is the first study to demonstrate potential resistance to AR in Lebanese rodents and therefore it provides data to pest control practitioners to choose the most suitable AR to control rodents in order to keep their efficacy.
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Affiliation(s)
- Antoine Rached
- USC 1233 RS2GP, VetAgro Sup, INRAe, Univ Lyon, 69280 Marcy l’Étoile, France
| | - Georges Abi Rizk
- grid.411324.10000 0001 2324 3572Animal Production department, Faculty of Agricultural Engineering and Veterinary Medicine, Lebanese University, Beirut, Lebanon
| | - Ali Barka Mahamat
- USC 1233 RS2GP, VetAgro Sup, INRAe, Univ Lyon, 69280 Marcy l’Étoile, France ,Department of Biomedical and Pharmaceutical Sciences, National Higher Institute of Science and Technology, Abeche, Chad
| | | | - Jeanne El Hage
- grid.435574.4Animal Health Laboratory, Lebanese Agricultural Research Institute, Beirut, Lebanon
| | - Elena Harran
- USC 1233 RS2GP, VetAgro Sup, INRAe, Univ Lyon, 69280 Marcy l’Étoile, France
| | - Virginie Lattard
- USC 1233 RS2GP, VetAgro Sup, INRAe, Univ Lyon, 69280 Marcy l’Étoile, France
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Howard A, Monadjem A, MacFadyen D, Chimimba CT. Testing the efficacy of bat monitoring methods for identification and species surveys in KwaZulu-Natal province, South Africa. AFRICAN ZOOLOGY 2022. [DOI: 10.1080/15627020.2022.2138722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Alexandra Howard
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- Department of Zoology and Entomology, University of the Free State, Phuthaditjhaba, South Africa
| | - Ara Monadjem
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- Department of Biological Sciences, University of Eswatini, Kwaluseni, Eswatini
| | - Duncan MacFadyen
- Department of Research and Conservation, Oppenheimer Generations, Johannesburg, South Africa
| | - Christian T Chimimba
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- DSI-NRF Centre of Excellence for Invasion Biology (CIB), Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
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Characterising Mitochondrial Capture in an Iberian Shrew. Genes (Basel) 2022; 13:genes13122228. [PMID: 36553495 PMCID: PMC9777731 DOI: 10.3390/genes13122228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/08/2022] [Accepted: 11/19/2022] [Indexed: 11/29/2022] Open
Abstract
Mitochondrial introgression raises questions of biogeography and of the extent of reproductive isolation and natural selection. Previous phylogenetic work on the Sorex araneus complex revealed apparent mitonuclear discordance in Iberian shrews, indicating past hybridisation of Sorex granarius and the Carlit chromosomal race of S. araneus, enabling introgression of the S. araneus mitochondrial genome into S. granarius. To further study this, we genetically typed 61 Sorex araneus/coronatus/granarius from localities in Portugal, Spain, France, and Andorra at mitochondrial, autosomal, and sex-linked loci and combined our data with the previously published sequences. Our data are consistent with earlier data indicating that S. coronatus and S. granarius are the most closely related of the three species, confirming that S. granarius from the Central System mountain range in Spain captured the mitochondrial genome from a population of S. araneus. This mitochondrial capture event can be explained by invoking a biogeographical scenario whereby S. araneus was in contact with S. granarius during the Younger Dryas in central Iberia, despite the two species currently having disjunct distributions. We discuss whether selection favoured S. granarius with an introgressed mitochondrial genome. Our data also suggest recent hybridisation and introgression between S. coronatus and S. granarius, as well as between S. araneus and S. coronatus.
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Jacquet S, Culbertson M, Zhang C, El Filali A, De La Myre Mory C, Pons JB, Filippi-Codaccioni O, Lauterbur ME, Ngoubangoye B, Duhayer J, Verez C, Park C, Dahoui C, Carey CM, Brennan G, Enard D, Cimarelli A, Rothenburg S, Elde NC, Pontier D, Etienne L. Adaptive duplication and genetic diversification of protein kinase R contribute to the specificity of bat-virus interactions. SCIENCE ADVANCES 2022; 8:eadd7540. [PMID: 36417524 PMCID: PMC9683710 DOI: 10.1126/sciadv.add7540] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/05/2022] [Indexed: 05/29/2023]
Abstract
Several bat species act as asymptomatic reservoirs for many viruses that are highly pathogenic in other mammals. Here, we have characterized the functional diversification of the protein kinase R (PKR), a major antiviral innate defense system. Our data indicate that PKR has evolved under positive selection and has undergone repeated genomic duplications in bats in contrast to all studied mammals that have a single copy of the gene. Functional testing of the relationship between PKR and poxvirus antagonists revealed how an evolutionary conflict with ancient pathogenic poxviruses has shaped a specific bat host-virus interface. We determined that duplicated PKRs of the Myotis species have undergone genetic diversification, allowing them to collectively escape from and enhance the control of DNA and RNA viruses. These findings suggest that viral-driven adaptations in PKR contribute to modern virus-bat interactions and may account for bat-specific immunity.
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Affiliation(s)
- Stéphanie Jacquet
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Michelle Culbertson
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Chi Zhang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - Adil El Filali
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | - Clément De La Myre Mory
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Jean-Baptiste Pons
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | | | - M. Elise Lauterbur
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Barthélémy Ngoubangoye
- International Centre of Medical Research of Franceville, Primatology Centre, Franceville, Gabon
| | - Jeanne Duhayer
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | - Clément Verez
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Chorong Park
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Clara Dahoui
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Clayton M. Carey
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Greg Brennan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - David Enard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Andrea Cimarelli
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Stefan Rothenburg
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - Nels C. Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
| | - Dominique Pontier
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | - Lucie Etienne
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
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Mitochondrial DNA variation of the caracal (Caracal caracal) in Iran and range-wide phylogeographic comparisons. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00328-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Nacif CL, Bastos DL, Mello B, Lazar A, Hingst-Zaher E, Geise L, Bonvicino CR. Hidden diversity of the genus Trinomys (Rodentia: Echimyidae): phylogenetic and populational structure analyses uncover putative new lineages. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Trinomys, one of the most species-rich spiny rat genera in Brazil, is widely distributed in Caatinga, Cerrado and Atlantic Forest biomes, and currently includes ten recognized species, three of which are polytypic. Although some studies employing molecular data have been conducted to better characterize phylogenetic relationships among species, 19 nominal taxa have been suggested, implying considerable incongruence regarding species boundaries. We addressed this incongruence by intensively sampling all species across the geographic distribution of the genus. In addition to publicly available data, we generated 182 mt-Cytb gene sequences, and employed phylogenetic and computational species delimitation methods to obtain a clearer picture of the genus diversity. Moreover, we evaluated populational diversity within each accepted species, considering their geographical distribution and a timescale for the evolution of the genus. Beyond confirming the general patterns described for the evolution of the group, this new analysis suggests that Trinomys is comprised of at least 16 evolutionary lineages, 13 of them recognized as species or subspecies, and three never before characterized. This study highlights the importance of increased sample sizes and computational species delimitation methods in uncovering hidden diversity in Trinomys.
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Affiliation(s)
- Camila Leitão Nacif
- Graduate Genetics Program, Institute of Biology, Department of Genetics, Universidade Federal do Rio de Janeiro (UFRJ) , 21941-617, Rio de Janeiro, RJ , Brazil
| | - Diogo Lisbôa Bastos
- Graduate Program in Pathology, School of Medicine, Universidade Federal Fluminense (UFF) , Niterói, RJ , Brazil
| | - Beatriz Mello
- Department of Genetics, Federal University of Rio de Janeiro , Brazil
| | - Ana Lazar
- National Museum, Department of Vertebrates, Sector of Mastozoology, Universidade Federal do Rio de Janeiro (UFRJ) , 20940-040, Rio de Janeiro, RJ , Brazil
| | - Erika Hingst-Zaher
- Museu Biológico, Instituto Butantan , Avenida Vital Brazil, 1500, São Paulo , Brazil
| | - Lena Geise
- Laboratory of Mastozoology, Department of Zoology, Institute of Biology, Universidade do Estado do Rio de Janeiro (UERJ) , Rua São Francisco Xavier 524, 220559-900, Rio de Janeiro, RJ , Brazil
| | - Cibele Rodrigues Bonvicino
- Division of Genetics, National Cancer Institute (INCA) , Rua André Cavalcanti , 37, 4° andar, 20231-050, Rio de Janeiro, RJ , Brazil
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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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Bonvicino CR, Lazar A, Povill C, Caramaschi FP, de Freitas TPT, Crisóstomo CF, Botelho ALM, D’Andrea PS. Phylogeny of Didelphid marsupials (Didelphimorphia) from Acre, western Amazonia. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00314-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
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45
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Barros T, Fernandes JM, Ferreira E, Carvalho J, Valldeperes M, Lavín S, Fonseca C, Ruiz-Olmo J, Serrano E. Genetic signature of blind reintroductions of Iberian ibex (Capra pyrenaica) in Catalonia, Northeast Spain. PLoS One 2022; 17:e0269873. [PMID: 36129880 PMCID: PMC9491545 DOI: 10.1371/journal.pone.0269873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/29/2022] [Indexed: 11/18/2022] Open
Abstract
The Iberian ibex is one of the most singular species of the Iberian Peninsula. Throughout the years, this species suffered several threats which led the population to its decline. Many reintroductions and translocations were made, however, none of those actions took into account the genetic patterns of both reintroduced individuals and the target populations. In this paper, we explored the genetic traits of three populations of Iberian ibex in Catalonia, which experienced blind reintroductions in past years: The populations of Iberian ibex from Els Ports de Tortosa i Beseit National Game Reserve (TBNGR), Montserrat Natural Park (Monserrat) and Montgrí, les Illes Medes i el Baix Ter Natural Park (Montgrí) Based on the genetic patterns of the three populations coupled with the absence of genetic introgression with domestic goats–inferred using mitochondrial and nuclear markers–we propose that these should be regarded as two different management units: TBNGR coupled with Montserrat, and Montgrí. Montserrat population should be targeted as a population model for ecology and evolution studies. Although we did not detect evidences of recent bottleneck events, this population seems to be monomorphic for the mtDNA haplotype. Our results suggest that the blind reintroductions from TBNGR to Montserrat failed on maximizing the genetic diversity of the latter. We enhance the importance of genetic monitoring of both the source population and the selected individuals to be re-introduced. We conclude that the three studied population of Iberian ibex must be monitored to explore which strategy would be advantageous for maintaining the genetic diversity. On the other hand, TBNGR should be monitored to assess the existence of its singular genetic variation, where stochastic events could preserve this lost genetic variation.
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Affiliation(s)
- Tânia Barros
- Departamento de Biologia & CESAM (Centro de Estudos do Ambiente e do Mar) Universidade de Aveiro, Campus Universitário Santiago, Aveiro, Portugal
- * E-mail:
| | - Joana M. Fernandes
- Departamento de Biologia & CESAM (Centro de Estudos do Ambiente e do Mar) Universidade de Aveiro, Campus Universitário Santiago, Aveiro, Portugal
| | - Eduardo Ferreira
- Departamento de Biologia & CESAM (Centro de Estudos do Ambiente e do Mar) Universidade de Aveiro, Campus Universitário Santiago, Aveiro, Portugal
| | - João Carvalho
- Departamento de Biologia & CESAM (Centro de Estudos do Ambiente e do Mar) Universidade de Aveiro, Campus Universitário Santiago, Aveiro, Portugal
- Dept Medicina i Cirurgia Animals Facultat de Veterinària, Wildlife Ecology & Health group (WE&H) Servei d’ Ecopatologia de Fauna (SEFaS), Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, España
| | - Marta Valldeperes
- Dept Medicina i Cirurgia Animals Facultat de Veterinària, Wildlife Ecology & Health group (WE&H) Servei d’ Ecopatologia de Fauna (SEFaS), Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, España
| | - Santiago Lavín
- Dept Medicina i Cirurgia Animals Facultat de Veterinària, Wildlife Ecology & Health group (WE&H) Servei d’ Ecopatologia de Fauna (SEFaS), Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, España
| | - Carlos Fonseca
- Departamento de Biologia & CESAM (Centro de Estudos do Ambiente e do Mar) Universidade de Aveiro, Campus Universitário Santiago, Aveiro, Portugal
- ForestWISE—Collaborative Laboratory for Integrated Forest & Fire Management, Vila Real, Portugal
| | - Jordi Ruiz-Olmo
- Dirección General de Ecosistemas Forestales y Gestión del Medio (DARP), Barcelona, España
| | - Emmanuel Serrano
- Dept Medicina i Cirurgia Animals Facultat de Veterinària, Wildlife Ecology & Health group (WE&H) Servei d’ Ecopatologia de Fauna (SEFaS), Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, España
- Dipartimento di Scienze Veterinarie, Universitá di Torino, Grugliasco, Torino, Italy
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A Portable Diagnostic Assay, Genetic Diversity, and Isolation of Seoul Virus from Rattus norvegicus Collected in Gangwon Province, Republic of Korea. Pathogens 2022; 11:pathogens11091047. [PMID: 36145479 PMCID: PMC9503505 DOI: 10.3390/pathogens11091047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/11/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022] Open
Abstract
Seoul virus (SEOV), an etiological agent for hemorrhagic fever with renal syndrome, poses a significant public health threat worldwide. This study evaluated the feasibility of a mobile Biomeme platform for facilitating rapid decision making of SEOV infection. A total of 27 Rattus norvegicus were collected from Seoul Metropolitan City and Gangwon Province in Republic of Korea (ROK), during 2016–2020. The serological and molecular prevalence of SEOV was 5/27 (18.5%) and 2/27 (7.4%), respectively. SEOV RNA was detected in multiple tissues of rodents using the Biomeme device, with differences in Ct values ranging from 0.6 to 2.1 cycles compared to a laboratory benchtop system. Using amplicon-based next-generation sequencing, whole-genome sequences of SEOV were acquired from lung tissues of Rn18-1 and Rn19-5 collected in Gangwon Province. Phylogenetic analysis showed a phylogeographical diversity of rat-borne orthohantavirus collected in Gangwon Province. We report a novel isolate of SEOV Rn19-5 from Gangwon Province. Our findings demonstrated that the Biomeme system can be applied for the molecular diagnosis of SEOV comparably to the laboratory-based platform. Whole-genome sequencing of SEOV revealed the phylogeographical diversity of orthohantavirus in the ROK. This study provides important insights into the field-deployable diagnostic assays and genetic diversity of orthohantaviruses for the rapid response to hantaviral outbreaks in the ROK.
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Predicting the potential for zoonotic transmission and host associations for novel viruses. Commun Biol 2022; 5:844. [PMID: 35986178 PMCID: PMC9390964 DOI: 10.1038/s42003-022-03797-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 08/04/2022] [Indexed: 01/14/2023] Open
Abstract
Host-virus associations have co-evolved under ecological and evolutionary selection pressures that shape cross-species transmission and spillover to humans. Observed virus-host associations provide relevant context for newly discovered wildlife viruses to assess knowledge gaps in host-range and estimate pathways for potential human infection. Using models to predict virus-host networks, we predicted the likelihood of humans as hosts for 513 newly discovered viruses detected by large-scale wildlife surveillance at high-risk animal-human interfaces in Africa, Asia, and Latin America. Predictions indicated that novel coronaviruses are likely to infect a greater number of host species than viruses from other families. Our models further characterize novel viruses through prioritization scores and directly inform surveillance targets to identify host ranges for newly discovered viruses.
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Matamba E, Richards LR, Cherry MI, Rambau RV. Phylogeography of the mesic-adapted striped mouse, Rhabdomys dilectus chakae (Rodentia: Muridae) in forest margins of the Eastern Cape and southern KwaZulu-Natal provinces of South Africa. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Rhabdomys is a genus that occupies a variety of habitats, including forest margins. Among the Rhabdomys taxa, Rhabdomys dilectus chakae has a distribution that covers the eastern seaboard of South Africa, with a poorly defined divergence date from its sister taxon Rhabdomys dilectus dilectus. Here, we study three mitochondrial markers (cytochrome b, cytochrome c oxidase I and partial control region) of R. d. chakae across the Eastern Cape and KwaZulu-Natal forests of South Africa, aiming to determine the cladogenesis (molecular dating) and effective population size of this subspecies through time, in addition to its cladogenesis in relationship to other species within the genus. A phylogenetic analysis revealed six clades within Rhabdomys, confirming that our study area is occupied solely by R. d. chakae, to the exclusion of other recognized sibling species. A fossil-calibrated Bayesian relaxed molecular clock estimated a recent split between R. d. chakae and R. d. dilectus ~1.4 ± 0.35 Mya and between two Rhabdomys pumilio groups, coastal A and B, at 1.16 ± 0.44 Mya. Coalescent Bayesian skyline plots revealed a stable population of R. d. chakae in the study area that was in slow decline until 2500 years ago, when there was an expansion in the late Holocene. Radiation within Rhabdomys dates as far back as 4.27 Mya, and subsequent demographic fluctuations primarily reflect palaeoclimatic changes.
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Affiliation(s)
- Emmanuel Matamba
- Department of Botany and Zoology, Stellenbosch University , Matieland , South Africa
| | | | - Michael I Cherry
- Department of Botany and Zoology, Stellenbosch University , Matieland , South Africa
| | - Ramugondo V Rambau
- Department of Botany and Zoology, Stellenbosch University , Matieland , South Africa
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Ochola GO, Li B, Obanda V, Ommeh S, Ochieng H, Yang XL, Onyuok SO, Shi ZL, Agwanda B, Hu B. Discovery of novel DNA viruses in small mammals from Kenya. Virol Sin 2022; 37:491-502. [PMID: 35680114 PMCID: PMC9437603 DOI: 10.1016/j.virs.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/17/2022] [Indexed: 11/29/2022] Open
Abstract
Emergence and re-emergence of infectious diseases of wildlife origin have led pre-emptive pathogen surveillances in animals to be a public health priority. Rodents and shrews are among the most numerically abundant vertebrate taxa and are known as natural hosts of important zoonotic viruses. Many surveillance programs focused more on RNA viruses. In comparison, much less is known about DNA viruses harbored by these small mammals. To fill this knowledge gap, tissue specimens of 232 animals including 226 rodents, five shrews and one hedgehog were collected from 5 counties in Kenya and tested for the presence of DNA viruses belonging to 7 viral families by PCR. Diverse DNA sequences of adenoviruses, adeno-associated viruses, herpesviruses and polyomaviruses were detected. Phylogenetic analyses revealed that most of these viruses showed distinction from previously described viruses and formed new clusters. Furthermore, this is the first report of the discovery and full-length genome characterization of a polyomavirus in Lemniscomys species. This novel polyomavirus, named LsPyV KY187, has less than 60% amino acid sequence identity to the most related Glis glis polyomavirus 1 and Sciurus carolinensis polyomavirus 1 in both large and small T-antigen proteins and thus can be putatively allocated to a novel species within Betapolyomavirus. Our findings help us better understand the genetic diversity of DNA viruses in rodent and shrew populations in Kenya and provide new insights into the evolution of those DNA viruses in their small mammal reservoirs. It demonstrates the necessity of ongoing pathogen discovery studies targeting rodent-borne viruses in East Africa.
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Affiliation(s)
- Griphin Ochieng Ochola
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; Mammalogy Section, National Museums of Kenya, Nairobi, 40658-00100, Kenya; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bei Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Vincent Obanda
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, 40241-00100, Kenya
| | - Sheila Ommeh
- Institute of Biotechnology Research, Jomo Kenyatta University of Science and Technology, Nairobi, 62000-00200, Kenya
| | - Harold Ochieng
- Mammalogy Section, National Museums of Kenya, Nairobi, 40658-00100, Kenya
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Samson Omondi Onyuok
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Mammalogy Section, National Museums of Kenya, Nairobi, 40658-00100, Kenya
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Bernard Agwanda
- Mammalogy Section, National Museums of Kenya, Nairobi, 40658-00100, Kenya.
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
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Pereverzeva VV, Dokuchaev NE, Primak AA, Dubinin EA. Variability of the Cytochrome b Polypeptide in the Gray Red-Backed Vole (Craseomys rufocanus). BIOL BULL+ 2022. [DOI: 10.1134/s1062359022020145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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