scholarly journals Detection and Phylogenetic Analysis of a Novel Tick-borne Virus in Haemaphysalis Longicornis Ticks and Sheep From Shandong, China

2021 ◽  
Author(s):  
Lijun Shao ◽  
Ruiheng Chang ◽  
Lin Liu ◽  
Yongjin Wang ◽  
Yun Gao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary Relationship ◽  
Human Remains ◽  
Domestic Animals ◽  
Molecular Evidence ◽  
Haemaphysalis Longicornis ◽  
Pathogenic Potential ◽  
Qrt Pcr ◽  
Positive Rate ◽  
Yantai City

Abstract Dabieshan tick virus (DTV) was first identified in Haemaphysalis longicornis from Hubei Province, China in 2015. However, its pathogenic potential to animals and human remains to be further explored. In this study, the presence of DTV in ticks and sheep samples was investigated. A total of 170 engorged ticks were collected from May to September 2019 from Taian and Yantai city, Shandong Province and were pooled individually to screening for DTV. The results of of qRT-PCR revealed the positive rate of 13.6% (3/22) in serum of sheep and 8.2% (14/170) in attached ticks, respectively. Phylogenetic analysis demonstrated a close evolutionary relationship among those DTV isolates from animal and ticks, and DTV was relatively conservative in evolution. These findings are the first to demonstrate molecular evidence of DTV in domestic animals. Nonetheless, whether or not could cause disease in sheep and other animals, DTV deserves further investigation.

scholarly journals Detection and phylogenetic analysis of a novel tick-borne virus in Haemaphysalis longicornis ticks and sheep from Shandong, China

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Lijun Shao ◽  
Ruiheng Chang ◽  
Lin Liu ◽  
Yongjin Wang ◽  
Yun Gao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary Relationship ◽  
Domestic Animals ◽  
Molecular Evidence ◽  
Haemaphysalis Longicornis ◽  
Serum Samples ◽  
Pathogenic Potential ◽  
Qrt Pcr ◽  
Positive Rate ◽  
Yantai City

AbstractDabieshan tick virus (DTV) was first identified in Haemaphysalis longicornis from Hubei Province, China in 2015. However, its pathogenic potential to animals and human remains to be further explored. In this study, a total of 170 engorged ticks and 22 sheep serum samples were collected from Taian and Yantai city, Shandong Province to investigate the presence of DTV. The results of qRT-PCR revealed the positive rate of 13.6% (3/22) in sheep serum and 8.2% (14/170) in attached ticks, respectively. Phylogenetic analysis demonstrated a close evolutionary relationship among those DTV isolates from animal and ticks, and DTV might be relatively conservative in evolution. These findings are the first to demonstrate molecular evidence of DTV in domestic animals. Nonetheless, whether or not causing disease in animals, DTV deserves further investigation.

scholarly journals Detection and Phylogenetic Analysis of a Novel Tick-Borne Virus in Yunnan and Guizhou Provinces, Southwestern China

Pathogens ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1143
Author(s):  
Anan Wang ◽  
Zheng Pang ◽  
Lin Liu ◽  
Qianwen Ma ◽  
Yize Han ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Yunnan Province ◽  
Evolutionary Dynamics ◽  
Guizhou Province ◽  
Southwestern China ◽  
Molecular Evidence ◽  
Haemaphysalis Longicornis ◽  
Qrt Pcr ◽  
First Time ◽  
Minimum Infection Rate

Dabieshan tick virus (DTV) is a novel tick-borne virus with the potential to infect both animals and humans. It has been confirmed that DTV is widely distributed in Shandong and Zhejiang Provinces. In this study, a total of 389 ticks were sampled from Honghe city of Yunnan Province and Bijie city of Guizhou Province, and then divided into 148 pools according to the location and species. QRT-PCR and nested PCR were performed to confirm the presence of DTV. The results showed a minimum infection rate of 2.43% (5/206) in Yunnan Province and 3.28% (6/183) in Guizhou Province, respectively. Interestingly, DTV was identified in Rhipicephalusmicroplus for the first time besides Haemaphysalis longicornis. Phylogenetic analysis showed that DTV from Yunnan and Guizhou Provinces shared over 94% identity with isolates derived from Hubei and Shandong Provinces, and DTV was relatively conservative in evolutionary dynamics. These findings provide molecular evidence of Dabieshan tick virus in different species of ticks from unrecognized endemic regions and suggest that DTV may be widely prevalent in southwestern China.

scholarly journals Detection of three pandemic causing coronaviruses from non-respiratory samples: systematic review and meta-analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chandan Mishra ◽  
Suneeta Meena ◽  
Jitendra Kumar Meena ◽  
Suman Tiwari ◽  
Purva Mathur
Keyword(s):  
Systematic Review ◽  
Detection Rate ◽  
Meta Analysis ◽  
Total Sample ◽  
Urine Samples ◽  
Pathogenic Potential ◽  
Clinical Specimens ◽  
Qrt Pcr ◽  
Corona Virus ◽  
Positive Rate

AbstractSARS-CoV-2 has posed an unprecedented challenge to the world. Pandemics have been caused previously by viruses of this family like Middle East Respiratory Corona Virus (MERS CoV), Severe Acute Respiratory Syndrome Corona Virus (SARS CoV). Although these viruses are primarily respiratory viruses, but they have been isolated from non-respiratory samples as well. Presently, the detection rate of SARS‐CoV‐2 RNA from different clinical specimens using Real Time Reverse Transcriptase Polymerized Chain Reaction (qRT‐PCR) after onset of symptoms is not yet well established. Therefore, the aim of this systematic review was to establish the profile of detecting SARS‐CoV‐2, MERS CoV, SARS CoV from different types of clinical specimens other than the respiratory using a standard diagnostic test (qRT‐PCR). A total of 3429 non-respiratory specimens were recorded: SARS CoV (total sample—802), MERS CoV (total sample—155), SARS CoV-2 (total sample—2347). Out of all the samples studied high positive rate was seen for saliva with 96.7% (14/14; 95% CI 87.6–100.0%) for SARS CoV and 57.5% (58/250; 95% CI − 1.2 to 116.2%) for SARS CoV-2, while low detection rate in urine samples for SARS CoV-2 with 2.2% (8/318; 95% CI 0.6–3.7%) and 9.6% (12/61; 95% CI − 0.9 to 20.1%) for SARS CoV but there was relatively higher positivity in urine samples for MERS CoV with detection rate of 32.4% (2/38; 95% CI − 37.3 to 102.1%). In Stool sample positivity was 54.9% (396/779; 95% CI 41.0–68.8%), 45.2% (180/430; 95% CI 28.1–62.3%) and 34.7% (4/38; 95% CI − 29.5 to 98.9%) for SARS CoV-2, MERS CoV, and SARS CoV, respectively. In blood sample the positivity was 33.3% (7/21; 95% CI 13.2–53.5%), 23.7% (42/277; 95% CI 10.5–36.9%) and 2.5% (2/81; 95% CI 0.00–5.8%) for MERS CoV, SARS CoV-2 and SARS CoV respectively. SARS‐CoV‐2 along with previous two pandemic causing viruses from this family, were highly detected stool and saliva. A low positive rate was recorded in blood samples. Viruses were also detected in fluids along with unusual samples like semen and vaginal secretions thus highlighting unique pathogenic potential of SARS‐CoV‐2.

A REVISED GENERIC SYNOPSIS OF HYACINTHACEAE IN SUB-SAHARAN AFRICA, BASED ON MOLECULAR EVIDENCE, INCLUDING NEW COMBINATIONS AND THE NEW TRIBE PSEUDOPROSPEREAE

2003 ◽  
Vol 60 (3) ◽  
pp. 533-568 ◽  
Author(s):  
J. C. MANNING ◽  
P. GOLDBLATT ◽  
M. F. FAY
Keyword(s):  
Phylogenetic Analysis ◽  
Sub Saharan Africa ◽  
Molecular Evidence ◽  
New Combinations ◽  
Generic Level ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Single Genus ◽  
New Tribe ◽  
Sub Saharan

A revised generic synopsis of sub-Saharan Hyacinthaceae is presented, based on a molecular phylogenetic analysis of the family. Generic rank is accorded only to reciprocally monophyletic clades that can be distinguished by recognizable morphological discontinuities, thereby permitting an appropriate generic assignment of species not included in the analysis. Three subfamilies are recognized within the region. Subfamily Ornithogaloideae, characterized by flattened or angular seeds with tightly adhering testa, is considered to include the single genus Ornithogalum, which is expanded to include the genera Albuca, Dipcadi, Galtonia, Neopatersonia and Pseudogaltonia. Recognizing any of these segregates at generic level renders the genus Ornithogalum polyphyletic, while subdivision of Ornithogalum into smaller, morphologically distinguishable segregates in order to preserve the monophyly of each is not possible. Subfamily Urgineoideae, characterized by flattened or winged seeds with brittle, loosely adhering testa, comprises the two mainland African genera Bowiea and Drimia. The latter is well circumscribed by its deciduous, short-lived perianth and includes the previously recognized genera Litanthus, Rhadamanthus, Schizobasis and Tenicroa. The monotypic Madagascan Igidia is provisionally included in the subfamily as a third genus on the basis of its seeds, pending molecular confirmation of its relationships. Subfamily Hyacinthoideae resolves into three clades, distinguished as tribes Hyacintheae (strictly northern hemisphere and not treated further), Massonieae and Pseudoprospereae tribus nov. Full descriptions and a key to their identification are provided for all genera. New combinations reflecting the generic circumscriptions adopted here are made for most African and all Indian and Madagascan species.

scholarly journals Molecular identification of the Trypanosoma (Herpetosoma) lewisi clade in black rats (Rattus rattus) from Australia

2019 ◽  
Author(s):  
Siobhon L. Egan ◽  
Casey L. Taylor ◽  
Jill M. Austen ◽  
Peter B. Banks ◽  
Liisa A. Ahlstrom ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Identification ◽  
Ribosomal Rna ◽  
Rattus Rattus ◽  
Molecular Evidence ◽  
Diverse Range ◽  
Blood Samples ◽  
Trypanosoma Lewisi ◽  
Sydney Australia ◽  
Black Rats

AbstractInvasive rodent species are known hosts for a diverse range of infectious microorganisms and have long been associated with the spread of disease globally. The present study describes molecular evidence for the presence of a Trypanosoma sp. from black rats (Rattus rattus) in northern Sydney, Australia. Sequences of the 18S ribosomal RNA (rRNA) locus were obtained in two out of eleven (18%) blood samples with subsequent phylogenetic analysis confirming the identity within the Trypanosoma lewisi clade.

Reassignment of 'Triplophysa' jiarongensis (Cypriniformes: Nemacheilidae) to Oreonectes Günther, 1868

Zootaxa ◽  
2019 ◽  
Vol 4565 (3) ◽  
pp. 398 ◽  
Author(s):  
XUAN LIU ◽  
HUAIQING DENG ◽  
ZHIJIN LIU ◽  
JIANG ZHOU
Keyword(s):  
Phylogenetic Analysis ◽  
Short Distance ◽  
River System ◽  
Genetic Distances ◽  
Molecular Evidence ◽  
Karst Cave ◽  
Bayesian Phylogenetic Analysis ◽  
As Species ◽  
Secondary Sexual Dimorphism ◽  
Underground River

Specimens identified as Oreonectes jiarongensis (Cypriniformes: Nemacheilidae) were collected from a karst cave in Jiarong Town and Banzhai Township, Libo County, Guizhou, China. Several lines of morphological and molecular evidence suggested that this species was similar to species of Oreonectes Günther 1868 and not closely related to species of Triplophysa Rendal, 1933. The anterior and posterior nostrils of 'Triplophysa' jiarongensis were separated by a short distance, and there was no secondary sexual dimorphism in male specimens. The Bayesian phylogenetic analysis based on cytochrome b recovered 'T.' jiarongensis in a well-supported clade with Oreonectes daqikongensis, O. shuilongensis, O. furcocaudalis and O. platycephalus, sister to the Triplophysa clade. In addition, the genetic distances between 'T.' jiarongensis and species of Oreonectes were low (O. daqikongensis: 0.114; O. shuilongensis: 0.106; O. platycephalus: 0.180), while distances to species of Triplophysa were higher (T. dorsalis: 0.233; T. yarkandensis: 0.282). Therefore, we reassign 'T.' jiarongensis to Oreonectes. Based on this result, it is now clear that species of both Oreonectes and Triplophysa inhabit the same underground river system in Guizhou. However, as species of Oreonectes are only known from the southern part of Guizhou, it may be that O. jiarongensis inhabits the most northerly part of the range of this genus. 

scholarly journals Phylogenetic Analysis ofStenotrophomonasspp. Isolates Contributes to the Identification of Nosocomial and Community-Acquired Infections

2014 ◽  
Vol 2014 ◽  
pp. 1-13 ◽  
Author(s):  
Vinicius Godoy Cerezer ◽  
Silvia Yumi Bando ◽  
Jacyr Pasternak ◽  
Marcia Regina Franzolin ◽  
Carlos Alberto Moreira-Filho
Keyword(s):  
Phylogenetic Analysis ◽  
Multidrug Resistance ◽  
Phylogenetic Profile ◽  
Opportunistic Pathogen ◽  
Clinical Isolates ◽  
Environmental Distribution ◽  
Pathogenic Potential ◽  
Clinical Strains ◽  
Specific Fragment ◽  
Clonal Variability

Stenotrophomonasssp. has a wide environmental distribution and is also found as an opportunistic pathogen, causing nosocomial or community-acquired infections. One species,S. maltophilia, presents multidrug resistance and has been associated with serious infections in pediatric and immunocompromised patients. Therefore, it is relevant to conduct resistance profile and phylogenetic studies in clinical isolates for identifying infection origins and isolates with augmented pathogenic potential. Here, multilocus sequence typing was performed for phylogenetic analysis of nosocomial isolates ofStenotrophomonasspp. and, environmental and clinical strains ofS. maltophilia. Biochemical and multidrug resistance profiles of nosocomial and clinical strains were determined. The inferred phylogenetic profile showed high clonal variability, what correlates with the adaptability process ofStenotrophomonasto different habitats. Two clinical isolates subgroups ofS. maltophiliasharing high phylogenetic homogeneity presented intergroup recombination, thus indicating the high permittivity to horizontal gene transfer, a mechanism involved in the acquisition of antibiotic resistance and expression of virulence factors. For most of the clinical strains, phylogenetic inference was made using only partialppsA gene sequence. Therefore, the sequencing of just one specific fragment of this gene would allow, in many cases, determining whether the infection withS. maltophiliawas nosocomial or community-acquired.

scholarly journals Cocirculation of Two Distinct Genetic and Antigenic Lineages of Proposed Influenza D Virus in Cattle

2014 ◽  
Vol 89 (2) ◽  
pp. 1036-1042 ◽  
Author(s):  
Emily A. Collin ◽  
Zizhang Sheng ◽  
Yuekun Lang ◽  
Wenjun Ma ◽  
Ben M. Hause ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Influenza Virus ◽  
Respiratory Disease ◽  
New Genus ◽  
Cross Reactivity ◽  
Surface Glycoprotein ◽  
Clinical Samples ◽  
Genome Sequences ◽  
Antigenic Analysis ◽  
Pathogenic Potential

ABSTRACTViruses with approximately 50% homology to human influenza C virus (ICV) have recently been isolated from swine and cattle. The overall low homology to ICV, lack of antibody cross-reactivity to ICV in hemagglutination inhibition (HI) and agar gel immunodiffusion assays, and inability to productively reassort with ICV led to the proposal that these viruses represented a new genus of influenza virus, influenzavirus D (IDV). To further our understanding of the epidemiology of IDV, real-time reverse transcription-PCR was performed on a set of 208 samples from bovines with respiratory disease. Ten samples (4.8%) were positive and six viruses were successfully isolatedin vitro. Phylogenetic analysis of full-genome sequences of these six new viruses and four previously reported viruses revealed two distinct cocirculating lineages represented by D/swine/Oklahoma/1334/2011 (D/OK) and D/bovine/Oklahoma/660/2013 (D/660), which frequently reassorted with one another. Antigenic analysis using the HI assay and lineage-representative D/OK and D/660 antiserum found up to an approximate 10-fold loss in cross-reactivity against heterologous clade antiserum. One isolate, D/bovine/Texas/3-13/2011 (D/3-13), clustered with the D/660 lineage, but also had high HI titers to heterologous (D/OK) clade antiserum. Molecular modeling of the hemagglutinin esterase fusion protein of D/3-13 identified a mutation at position 212 as a possible antigenic determinant responsible for the discrepant HI results. These results suggest that IDV is common in bovines with respiratory disease and that at least two genetic and antigenically distinct clades cocirculate.IMPORTANCEA novel bovine influenza virus was recently identified. Detailed genetic and antigenic studies led to the proposal that this virus represents a new genus of influenza, influenzavirus D (IDV). Here, we show that IDV is common in clinical samples of bovine respiratory disease complex (BRDC), with a prevalence similar to that of other established BRDC etiological agents. These results are in good agreement with the near-ubiquitous seroprevalence of IDV previously found. Phylogenetic analysis of complete genome sequences found evidence for two distinct cocirculating lineages of IDV which freely reassort. Significant antigenic differences, which generally agreed with the surface glycoprotein hemagglutinin esterase phylogeny, were observed between the two lineages. Based on these results, and on the ability of IDV to infect and transmit in multiple mammalian species, additional studies to determine the pathogenic potential of IDV are warranted.

Ceriporia albomellea (Phanerochaetaceae, Basidiomycota), a new species from tropical China based on morphological and molecular evidences

Phytotaxa ◽  
2017 ◽  
Vol 298 (1) ◽  
pp. 20 ◽  
Author(s):  
YUAN YUAN ◽  
XIAO-HONG JI ◽  
FANG WU ◽  
JIA-JIA CHEN
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Morphological Characteristics ◽  
Molecular Evidence ◽  
Its Regions ◽  
Tropical China ◽  
A New Species

A new polypore, Ceriporia albomellea, collected from tropical China, is described and illustrated based on morphological characteristics and molecular evidence. It is characterized by thin, resupinate basidiome with a white subiculum, cottony margin, white to cinnamon-buff pores, clavate cystidia and oblong-ellipsoid basidiospores measured as 3.1–3.8 × 1.7–2 µm. Phylogenetic analysis based on the internal transcribed spacer (ITS) regions and nuclear large subunit (nLSU) ribosomal RNA gene regions supported C. albomellea as a distinctive species belonging to Ceriporia.

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