SARS-Like Coronaviruses in Horseshoe Bats (Rhinolophus spp.) in Russia, 2020

We found and genetically described two novel SARS-like coronaviruses in feces and oral swabs of the greater (R. ferrumequinum) and the lesser (R. hipposideros) horseshoe bats in southern regions of Russia. The viruses, named Khosta-1 and Khosta-2, together with related viruses from Bulgaria and Kenya, form a separate phylogenetic lineage. We found evidence of recombination events in the evolutionary history of Khosta-1, which involved the acquisition of the structural proteins S, E, and M, as well as the nonstructural genes ORF3, ORF6, ORF7a, and ORF7b, from a virus that is related to the Kenyan isolate BtKY72. The examination of bats by RT-PCR revealed that 62.5% of the greater horseshoe bats in one of the caves were positive for Khosta-1 virus, while its overall prevalence was 14%. The prevalence of Khosta-2 was 1.75%. Our results show that SARS-like coronaviruses circulate in horseshoe bats in the region, and we provide new data on their genetic diversity.

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SARS-like coronaviruses in horseshoe bats (Rhinolophus spp.) in Russia, 2020.

10.1101/2021.05.17.444362 ◽

2021 ◽

Author(s):

Sergey V Alkhovsky ◽

Sergey V Lenshin ◽

Alexey V Romashin ◽

Tatyana V Vishnevskaya ◽

Oleg I Vyshemirsky ◽

...

Keyword(s):

Genetic Diversity ◽

Evolutionary History ◽

Southern Region ◽

Structural Proteins ◽

Rt Pcr ◽

Phylogenetic Lineage ◽

History Of ◽

Horseshoe Bats ◽

Nonstructural Genes

We found and genetically described two novel SARS-like coronaviruses in feces and oral swabs of the great (R. ferrumequinum) and the lesser (R. hipposideros) horseshoe bats in southern region of Russia. The viruses, named Khosta-1 and Khosta-2, together with related viruses from Bulgaria and Kenya, form a separate phylogenetic lineage. We found an evidence of recombination events in evolutionary history of Khosta-1, which involved the acquisition of structural proteins S, E, and M as well as nonstructural genes ORF3, ORF6, ORF7a, and ORF7b from a virus that is closely related to Kenyan isolate BtKY72. Examination of bats by RT-PCR revealed that 62,5% of great horseshoe bats in one of the caves were positive for Khosta-1 virus while its overall prevalence was 14%. The prevalence of Khosta-2 was 1,75%. Our results show that SARS-like coronaviruses circulate in horseshoe bats in the region and provide a new data on their genetic diversity.

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Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Viruses ◽

10.3390/v13050737 ◽

2021 ◽

Vol 13 (5) ◽

pp. 737

Author(s):

Issiaka Bagayoko ◽

Marcos Giovanni Celli ◽

Gustavo Romay ◽

Nils Poulicard ◽

Agnès Pinel-Galzi ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Sierra Leone ◽

Evolutionary History ◽

Molecular Diversity ◽

Genomic Data ◽

Gene Recombination ◽

Necrosis Virus ◽

History Of ◽

Complex Evolutionary History

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

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Comparative mitochondrial phylogeography of two legless lizards (Pygopodidae) from Queensland’s fragmented woodlands

Israel Journal of Ecology and Evolution ◽

10.1163/22244662-20191081 ◽

2020 ◽

Vol 66 (3-4) ◽

pp. 142-150

Author(s):

Jessica Worthington Wilmer ◽

Andrew P. Amey ◽

Carmel McDougall ◽

Melanie Venz ◽

Stephen Peck ◽

...

Keyword(s):

Genetic Diversity ◽

Evolutionary History ◽

The West ◽

European Settlement ◽

Low Genetic Diversity ◽

Eastern Australia ◽

Wide Range ◽

History Of ◽

Open Forests ◽

Fossorial Species

Sclerophyll woodlands and open forests once covered vast areas of eastern Australia, but have been greatly fragmented and reduced in extent since European settlement. The biogeographic and evolutionary history of the biota of eastern Australia’s woodlands also remains poorly known, especially when compared to rainforests to the east, or the arid biome to the west. Here we present an analysis of patterns of mitochondrial genetic diversity in two species of Pygopodid geckos with distributions centred on the Brigalow Belt Bioregion of eastern Queensland. One moderately large and semi-arboreal species, Paradelma orientalis, shows low genetic diversity and no clear geographic structuring across its wide range. In contrast a small and semi-fossorial species, Delma torquata, consists of two moderately divergent clades, one from the ranges and upland of coastal areas of south-east Queensland, and other centred in upland areas further inland. These data point to varying histories of geneflow and refugial persistance in eastern Australia’s vast but now fragmented open woodlands. The Carnarvon Ranges of central Queensland are also highlighted as a zone of persistence for cool and/or wet-adapted taxa, however the evolutionary history and divergence of most outlying populations in these mountains remains unstudied.

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Study of molecular genetic diversity and evolutionary history of medicinally important endangered genus Chlorophytum using DNA barcodes

Biochemical Systematics and Ecology ◽

10.1016/j.bse.2016.02.035 ◽

2016 ◽

Vol 65 ◽

pp. 245-252 ◽

Cited By ~ 2

Author(s):

Swapnil M. Patil ◽

Niraj R. Rane ◽

Avinash A. Adsul ◽

Avinash R. Gholave ◽

Shrirang R. Yadav ◽

...

Keyword(s):

Genetic Diversity ◽

Evolutionary History ◽

Molecular Genetic ◽

Dna Barcodes ◽

Molecular Genetic Diversity ◽

History Of

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Genetic diversity and evolutionary history of the Tyrrhenian treefrog Hyla sarda (Anura: Hylidae): adding pieces to the puzzle of Corsica-Sardinia biota

Biological Journal of the Linnean Society ◽

10.1111/j.1095-8312.2011.01643.x ◽

2011 ◽

Vol 103 (1) ◽

pp. 159-167 ◽

Cited By ~ 13

Author(s):

ROBERTA BISCONTI ◽

DANIELE CANESTRELLI ◽

GIUSEPPE NASCETTI

Keyword(s):

Genetic Diversity ◽

Evolutionary History ◽

History Of

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Sequence Diversity in the Tetraploid Zea perennis and the Closely Related Diploid Z. diploperennis: Insights From Four Nuclear Loci

Genetics ◽

10.1093/genetics/158.1.401 ◽

2001 ◽

Vol 158 (1) ◽

pp. 401-412 ◽

Cited By ~ 1

Author(s):

Peter Tiffin ◽

Brandon S Gaut

Keyword(s):

Genetic Diversity ◽

Evolutionary History ◽

Molecular Data ◽

Sequence Diversity ◽

Common Phenomenon ◽

Factors Associated ◽

History Of ◽

Recent Origin ◽

Nuclear Loci ◽

Few Data

Abstract Polyploidy has been an extremely common phenomenon in the evolutionary history of angiosperms. Despite this there are few data available to evaluate the effects of polyploidy on genetic diversity and to compare the relative effects of drift and selection in polyploids and related diploids. We investigated DNA sequence diversity at four nuclear loci (adh1, glb1, c1, and waxy) from the tetraploid Zea perennis and the closely related diploid Z. diploperennis. Contrary to expectations, we detected no strong evidence for greater genetic diversity in the tetraploid, or for consistent differences in the effects of either drift or selection between the tetraploid and the diploid. Our failure to find greater genetic diversity in Z. perennis may result from its relatively recent origin or demographic factors associated with its origin. In addition to comparing genetic diversity in the two species, we constructed genealogies to infer the evolutionary origin of Z. perennis. Although these genealogies are equivocal regarding the mode of origin, several aspects of these genealogies support an autotetraploid origin. Consistent with previous molecular data the genealogies do not, however, support the division of Zea into two sections, the section Zea and the section Luxuriantes.

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Bat-borne polyomaviruses in Europe reveal an evolutionary history of intrahost divergence with horseshoe bats distributed across the African and Eurasian continents

Journal of General Virology ◽

10.1099/jgv.0.001467 ◽

2020 ◽

Vol 101 (10) ◽

pp. 1119-1130

Author(s):

Márton Z. Vidovszky ◽

Zhizhou Tan ◽

Michael J. Carr ◽

Sándor Boldogh ◽

Balázs Harrach ◽

...

Keyword(s):

Evolutionary History ◽

Genetic Relatedness ◽

Relationship Analysis ◽

Geographical Distances ◽

Pathogenic Viruses ◽

History Of ◽

Capsid Protein Vp1 ◽

Horseshoe Bat ◽

Dsdna Viruses ◽

Horseshoe Bats

Polyomaviruses (PyVs) are small, circular dsDNA viruses carried by diverse vertebrates, including bats. Although previous studies have reported several horseshoe bat PyVs collected in Zambia and China, it is still unclear how PyVs evolved in this group of widely dispersed mammals. Horseshoe bats (genus Rhinolophus) are distributed across the Old World and are natural reservoirs of numerous pathogenic viruses. Herein, non-invasive bat samples from European horseshoe bat species were collected in Hungary for PyV identification and novel PyVs with complete genomes were successfully recovered from two different European horseshoe bat species. Genomic and phylogenetic analysis of the Hungarian horseshoe bat PyVs supported their classification into the genera Alphapolyomavirus and Betapolyomavirus. Notably, despite the significant geographical distances between the corresponding sampling locations, Hungarian PyVs exhibited high genetic relatedness with previously described Zambian and Chinese horseshoe bat PyVs, and phylogenetically clustered with these viruses in each PyV genus. Correlation and virus–host relationship analysis suggested that these PyVs co-diverged with their European, African and Asian horseshoe bat hosts distributed on different continents during their evolutionary history. Additionally, assessment of selective pressures over the major capsid protein (VP1) of horseshoe bat PyVs showed sites under positive selection located in motifs exposed to the exterior of the capsid. In summary, our findings revealed a pattern of stable intrahost divergence of horseshoe bat PyVs with their mammalian hosts on the African and Eurasian continents over evolutionary time.

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Genetic diversity and evolutionary history of Korean isolates of severe fever with thrombocytopenia syndrome virus from 2013–2016

Archives of Virology ◽

10.1007/s00705-020-04733-0 ◽

2020 ◽

Vol 165 (11) ◽

pp. 2599-2603

Author(s):

Mi-ran Yun ◽

Jungsang Ryou ◽

Wooyoung Choi ◽

Joo-Yeon Lee ◽

Sun-Whan Park ◽

...

Keyword(s):

Infectious Disease ◽

Genetic Diversity ◽

Amino Acid ◽

Evolutionary History ◽

Public Database ◽

Korean Strain ◽

Future Studies ◽

History Of ◽

Phylogeny And Evolution ◽

Severe Fever

AbstractSevere fever with thrombocytopenia syndrome (SFTS) is caused by SFTS virus (SFTSV). Although SFTS originated in China, it is an emerging infectious disease with prevalence confirmed in Japan, Korea, and Vietnam. The full-length genomes of 51 Korean SFTSV isolates from 2013 to 2016 were sequenced, and the sequences were deposited into a public database (GenBank) and analyzed to elucidate the phylogeny and evolution of the virus. Although most of the Korean SFTSV isolates were closely related to previously reported Japanese isolates, some were closely related to previously reported Chinese isolates. We identified one Korean strain that appears to have resulted from multiple inter-lineage reassortments. Several nucleotide and amino acid variations specific to the Korean isolates were identified. Future studies should focus on how these variations affect virus pathogenicity and evolution.

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