scholarly journals Discovery and Evolution of a Divergent Coronavirus in the Plateau Pika From China That Extends the Host Range of Alphacoronaviruses

2021 ◽  
Vol 12 ◽  
Author(s):  
Wentao Zhu ◽  
Jing Yang ◽  
Shan Lu ◽  
Dong Jin ◽  
Shusheng Wu ◽  
...  
Keyword(s):  
Host Range ◽  
Phylogenetic Trees ◽  
Nonstructural Protein ◽  
Keystone Species ◽  
Speciation Analysis ◽  
New Order ◽  
Regulatory Sequences ◽  
Plateau Pika ◽  
Viral Pathogens ◽  
Qinghai Province

Although plateau pikas are the keystone species in the plateau ecosystem of the Qinghai Province of China, little is known about their role in the evolution and transmission of viral pathogens, especially coronaviruses. Here, we describe the characterization and evolution of a novel alphacoronavirus, termed plateau pika coronavirus (PPCoV) P83, which has a prevalence of 4.5% in plateau pika fecal samples. In addition to classical gene order, the complete viral genome contains a unique nonstructural protein (NS2), several variable transcription regulatory sequences and a highly divergent spike protein. Phylogenetic analysis indicates that the newly discovered PPCoV falls into the genus Alphacoronavirus and is most closely related to rodent alphacoronaviruses. The co-speciation analysis shows that the phylogenetic trees of the alphacoronaviruses and their hosts are not always matched, suggesting inter-species transmission is common in alphacoronaviruses. And, PPCoV origin was estimated by molecular clock based on membrane and RNA-dependent RNA polymerase encoding genes, respectively, which revealed an apparent discrepancy with that of co-speciation analysis. PPCoV was detected mainly in intestinal samples, indicating a potential enteric tropism for the virus. Overall, this study extends the host range of alphacoronaviruses to a new order (Lagomorpha), indicating that plateau pikas may be the natural reservoir of PPCoV and play an important and long-term role in alphacoronavirus evolution.

scholarly journals The burying and grazing effects of plateau pika on alpine grassland are small: a pilot study in a semiarid basin on the Qinghai-Tibet Plateau

2016 ◽  
Vol 13 (22) ◽  
pp. 6273-6284 ◽  
Author(s):  
Shuhua Yi ◽  
Jianjun Chen ◽  
Yu Qin ◽  
Gaowei Xu
Keyword(s):  
Net Primary Production ◽  
Keystone Species ◽  
Alpine Grassland ◽  
Tibet Plateau ◽  
Plateau Pika ◽  
Carbon And Nitrogen ◽  
Grazing Effects ◽  
Considerable Controversy ◽  
The One ◽  
Qinghai Tibet Plateau

Abstract. There is considerable controversy about the effects of plateau pika (Ochotona curzoniae, hereafter pika) on alpine grassland on the Qinghai-Tibet Plateau (QTP). On the one hand, pika is considered a keystone species. On the other hand, it is being poisoned. Although significant efforts have been made to study the effects of pika at a quadrat scale ( ∼  m2), our knowledge about its distribution and effects at a larger scale is very limited. In this study, we investigated the direct effects, i.e., burying and grazing, of pika by upscaling field sampling at a quadrat scale to a plot scale ( ∼  1000 m2) by aerial photographing. Altogether 168 plots were set on four different types of alpine grassland in a semiarid basin on the QTP. Results showed that (1) the effects of pika pile burying on the reduction of vegetation cover, biomass, soil carbon, and nitrogen were less than 10 %, which was much smaller than the effects of bald patches; and (2) pika consumed 8–21 % of annual net primary production of grassland. We concluded that the direct burying and grazing effects of pika on alpine grassland were minor in this region. The quadcopter is an efficient and economic tool for long-term repeated monitoring over large regions for further understanding the role of pika.

scholarly journals Complete mitochondrial genomes confirm the generic placement of the plateau vole, Neodon fuscus

2019 ◽  
Vol 39 (8) ◽  
Author(s):  
Jian-Qiu Li ◽  
Li Li ◽  
Bao-Quan Fu ◽  
Hong-Bin Yan ◽  
Wan-Zhong Jia
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Evolutionary Relationship ◽  
Sister Group ◽  
Trna Genes ◽  
Mammal Species ◽  
Qinghai Province ◽  
Loop Region ◽  
Mt Genome

AbstractThe plateau vole, Neodon fuscus is endemic to China and is distributed mainly in Qinghai Province. It is of public health interest, as it is, a potential reservoir of Toxoplasma gondii and the intermediate host of Echinococcus multilocularis. However, genetic data of this species are lacking, and its name and taxonomy are still a controversy. In the present study, we determined the nucleotide sequence of the entire mitochondrial (mt) genome of N. fuscus and analyzed its evolutionary relationship. The mitogenome was 16328 bp in length and contained 13 protein-coding genes, 22 genes for transfer RNAs (tRNA), two ribosomal RNA genes and two major noncoding regions (OL region and D-loop region). Most genes were located on the heavy strand. All tRNA genes had typical cloverleaf structures except for tRNASer (GCU). The mt genome of N. fuscus was rich in A+T (58.45%). Maximum likelihood (ML) and Bayesian methods yielded phylogenetic trees from 33 mt genomes of Arvicolinae, in which N. fuscus formed a sister group with Neodon irene and Neodon sikimensis to the exclusion of species of Microtus and other members of the Arvicolinae. Further phylogenetic analyses (ML only) based on the cytb gene sequences also demonstrated that N. fuscus had a close relationship with N. irene. The complete mitochondrial genome was successfully assembled and annotated, providing the necessary information for the phylogenetic analyses. Although the name Lasiopodomys fuscus was used in the book ‘Wilson & Reeder’s Mammal Species of the World’, we have confirmed here that its appropriate name is N. fuscus through an analysis of the evolutionary relationships.

scholarly journals PARASITE SPECIES ASSOCIATED WITH WILD PLATEAU PIKA (OCHOTONA CURZONIAE) IN SOUTHEASTERN QINGHAI PROVINCE, CHINA

2009 ◽  
Vol 45 (2) ◽  
pp. 288-294 ◽  
Author(s):  
Chengmin Wang ◽  
Hongxuan He ◽  
Ming Li ◽  
Fumin Lei ◽  
J. Jeffrey Root ◽  
...  
Keyword(s):  
Parasite Species ◽  
Plateau Pika ◽  
Qinghai Province ◽  
Ochotona Curzoniae

scholarly journals Marivita lacus sp. nov., isolated from a saline lake

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1889-1894 ◽  
Author(s):  
Zhi-Ping Zhong ◽  
Ying Liu ◽  
Ting-Ting Hou ◽  
Hong-Can Liu ◽  
Yu-Guang Zhou ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Saline Lake ◽  
Qaidam Basin ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Respiratory Quinone ◽  
Qinghai Province ◽  
Gram Staining ◽  
Bacterium Strain

A Gram-staining-negative, strictly heterotrophic and aerobic bacterium, strain TS-T44T, was isolated from a saline lake, Tuosu Lake in Qaidam basin, Qinghai province, China. Its taxonomic position was investigated using a polyphasic approach. Cells of strain TS-T44T were non-endospore-forming, non-motile rods, 0.8–1.2 μm wide and 1.2–3.0 μm long. Catalase- and oxidase-positive. Growth occurred in the presence of up to 8  % (w/v) NaCl (optimum, 3.0  %) and at 15–35 °C (optimum, 25 °C) and pH 7.0–10.0 (optimum, pH 7.5–8.5). C18 : 1ω7c was the predominant fatty acid. The major respiratory quinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and an unknown lipid. The DNA G+C content was 65.5 mol% [determined from the melting temperature (Tm)]. Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T44T was associated with the genus Marivita and showed highest sequence similarity to Marivita cryptomonadis CL-SK44T (97.7  %), Marivita litorea CL-JM1T (97.5  %) and Marivita geojedonensis DPG-138T (97.3  %), and < 97  % to other species. DNA–DNA relatedness of strain TS-T44T to M. cryptomonadis JCM 15447T, M. litorea JCM 15446T and M. geojedonensis KCTC 23882T was 23 ± 3  %, 33 ± 4  % and 35 ± 2  %, respectively. Based on the data presented, it is concluded that strain TS-T44T represents a novel species of the genus Marivita, for which the name Marivita lacus sp. nov. is proposed. The type strain is TS-T44T ( = CGMCC 1.12478T = JCM 19516T).

scholarly journals Pests, keystone species, and hungry ghosts: the Gesar epic and human-pika relations on the Tibetan Plateau

2020 ◽  
pp. 147447402096314
Author(s):  
Emily T. Yeh ◽  
Gaerrang
Keyword(s):  
Tibetan Plateau ◽  
Large Scale ◽  
Keystone Species ◽  
Chinese Government ◽  
The Tibetan Plateau ◽  
Grassland Degradation ◽  
Plateau Pika ◽  
Political Ontology ◽  
The Earth ◽  
Asymmetric Power

For over half a century, the Chinese government has carried out large-scale poisoning campaigns on the Tibetan Plateau in an effort to exterminate the plateau pika, which is viewed as a pest that competes with livestock and causes grassland degradation. Since the 1990s, an ecological counternarrative has emerged in which pikas are keystone species rather than pests, and indicators rather than prime causes of grassland degradation. Virtually ignored in this debate are the ways in which Tibetan pastoralists understand and relate to pikas. We investigate Tibetan analytics of what pikas are, and what draws them to specific sites, based on interviews and observations in two pastoral communities, as well as readings of the Epic of King Gesar. Performed by bards since the twelfth century, the epic is grounded in the cultural milieu of Tibetan nomadic society and continues to be an important part of everyday life. As such, it shapes Tibetan analytics, a term we use to refer to forms of reason that cannot be reduced to ‘cultural belief.’ Because large numbers of pikas, as hungry ghosts, are drawn to places where the essence or fertility of the earth has been depleted, causing irritation to territorial deities, Tibetan practices include rituals to feed hungry ghosts, appease territorial deities, and return treasures to restore the fertility of the earth. Bringing Tibetan analytics together with proposals for political ontology, the article examines the ways in which these different ontologies, or practices of worlding, cooperate and conflict in a context of asymmetric power relations and non-liberal recognition of difference. This approach takes seriously both the agency of the nonhuman as well as human difference, while rejecting notions of rigidly bounded ontologies.

scholarly journals Genetic Structure and Biology of Xylella fastidiosa Strains Causing Disease in Citrus and Coffee in Brazil

2008 ◽  
Vol 74 (12) ◽  
pp. 3690-3701 ◽  
Author(s):  
Rodrigo P. P. Almeida ◽  
Fernanda E. Nascimento ◽  
John Chau ◽  
Simone S. Prado ◽  
Chi-Wei Tsai ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Host Range ◽  
Multilocus Sequence Typing ◽  
Phylogenetic Trees ◽  
Xylella Fastidiosa ◽  
Microsatellite Analysis ◽  
The Other ◽  
Plant Pathogenic Bacterium ◽  
Vector Borne ◽  
Coffee Plants

ABSTRACT Xylella fastidiosa is a vector-borne, plant-pathogenic bacterium that causes disease in citrus (citrus variegated chlorosis [CVC]) and coffee (coffee leaf scorch [CLS]) plants in Brazil. CVC and CLS occur sympatrically and share leafhopper vectors; thus, determining whether X. fastidiosa isolates can be dispersed from one crop to another and cause disease is of epidemiological importance. We sought to clarify the genetic and biological relationships between CVC- and CLS-causing X. fastidiosa isolates. We used cross-inoculation bioassays and microsatellite and multilocus sequence typing (MLST) approaches to determine the host range and genetic structure of 26 CVC and 20 CLS isolates collected from different regions in Brazil. Our results show that citrus and coffee X. fastidiosa isolates are biologically distinct. Cross-inoculation tests showed that isolates causing CVC and CLS in the field were able to colonize citrus and coffee plants, respectively, but not the other host, indicating biological isolation between the strains. The microsatellite analysis separated most X. fastidiosa populations tested on the basis of the host plant from which they were isolated. However, recombination among isolates was detected and a lack of congruency among phylogenetic trees was observed for the loci used in the MLST scheme. Altogether, our study indicates that CVC and CLS are caused by two biologically distinct strains of X. fastidiosa that have diverged but are genetically homogenized by frequent recombination.

scholarly journals Molecular detection of parvovirus in Manchurian chipmunks (Tamias sibiricus asiaticus) captured in Korea

Intervirology ◽  
2021 ◽  
Author(s):  
Jin Il Kim ◽  
Kwangsook Park ◽  
Hyunho Shin ◽  
Soo Min Choi ◽  
Ki-Joon Song
Keyword(s):  
Nonstructural Protein ◽  
Specific Gene ◽  
Wild Animals ◽  
Korean Strain ◽  
Viral Pathogens ◽  
Positive Rate ◽  
Genetic Sequences ◽  
Tamias Sibiricus ◽  
Bovine Parvovirus ◽  
Kidney Liver

Cross-species transmission of viral diseases alarms our global community for its potential of novel pandemic events. Of various viral pathogens noted recently, parvoviruses have posed public health threats not only to humans but to wild animals. To investigate the prevalence of parvoviruses in wild Manchurian chipmunks, here we detected genetic fragments of the nonstructural protein of parvovirus by polymerase chain reaction in wild Manchurian chipmunk specimens captured in the central and southern regions of South Korea and compared their sequence homology with references. Of a total of 348 specimens examined, chipmunk parvovirus (ChpPV)-specific gene fragments were detected with a 31.32 % rate (109 chipmunks of 348) in their kidney, liver, lung, and spleen samples, and the chipmunks captured in Gangwon Province exhibited the highest positive rate (45.37%), followed by Gyeongsang (35.29%), Gyeonggi (31.03%), Chungcheong (20.00%), and Jeolla (19.70%). When compared with the reference sequences registered in GenBank, a partial ChpPV sequence showed 97.70% identity to the previously reported Korean strain at the nucleic acid level. In the phylogenetic analysis, ChpPV exhibited closer relationship to primate parvoviruses, erythroviruses, and bovine parvovirus than to adeno-associated viruses. Despite limited sample size and genetic sequences examined in this study, our results underline the prevalence of ChpPV in Korea and emphasize the need of close surveillance of parvoviruses in wild animals.

scholarly journals Eilat Virus Host Range Restriction Is Present at Multiple Levels of the Virus Life Cycle

2014 ◽  
Vol 89 (2) ◽  
pp. 1404-1418 ◽  
Author(s):  
Farooq Nasar ◽  
Rodion V. Gorchakov ◽  
Robert B. Tesh ◽  
Scott C. Weaver
Keyword(s):  
Host Range ◽  
Nonstructural Protein ◽  
Rna Replication ◽  
Encephalitis Virus ◽  
Broad Host Range ◽  
Genomic Rna ◽  
Range Restriction ◽  
Entry Level ◽  
Equine Encephalitis Virus ◽  
Host Range Restriction

ABSTRACTMost alphaviruses are mosquito-borne and exhibit a broad host range, infecting many different vertebrates, including birds, rodents, equids, humans, and nonhuman primates. This ability of most alphaviruses to infect arthropods and vertebrates is essential for their maintenance in nature. Recently, a new alphavirus, Eilat virus (EILV), was described, and in contrast to all other mosquito-borne viruses, it is unable to replicate in vertebrate cell lines. Investigations into the nature of its host range restriction showed the inability of genomic EILV RNA to replicate in vertebrate cells. Here, we investigated whether the EILV host range restriction is present at the entry level and further explored the viral factors responsible for the lack of genomic RNA replication. Utilizing Sindbis virus (SINV) and EILV chimeras, we show that the EILV vertebrate host range restriction is also manifested at the entry level. Furthermore, the EILV RNA replication restriction is independent of the 3′ untranslated genome region (UTR). Complementation experiments with SINV suggested that RNA replication is restricted by the inability of the EILV nonstructural proteins to form functional replicative complexes. These data demonstrate that the EILV host range restriction is multigenic, involving at least one gene from both nonstructural protein (nsP) and structural protein (sP) open reading frames (ORFs). As EILV groups phylogenetically within the mosquito-borne virus clade of pathogenic alphaviruses, our findings have important evolutionary implications for arboviruses.IMPORTANCEOur work explores the nature of host range restriction of the first “mosquito-only alphavirus,” EILV. EILV is related to pathogenic mosquito-borne viruses (Eastern equine encephalitis virus [EEEV], Western equine encephalitis virus [WEEV], Venezuelan equine encephalitis virus [VEEV], and Chikungunya virus [CHIKV]) that cause severe disease in humans. Our data demonstrate that EILV is restricted both at entry and genomic RNA replication levels in vertebrate cells. These findings have important implications for arbovirus evolution and will help elucidate the viral factors responsible for the broad host range of pathogenic mosquito-borne alphaviruses, facilitate vaccine development, and inform potential strategies to reduce/prevent alphavirus transmission.

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