scholarly journals Detection of Rickettsial DNA in Ticksin Irkutsk Region

2015 ◽  
Vol 14 (6) ◽  
pp. 43-46 ◽  
Author(s):  
N. . Yakovchitc ◽  
E. . Bondarenko ◽  
R. . Adelshin ◽  
O. . Melnikova ◽  
E. . Vershinin ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Citrate Synthase ◽  
Nucleotide Sequences ◽  
Surface Proteins ◽  
Rt Pcr ◽  
Rickettsia Species ◽  
Test Systems ◽  
Haemaphysalis Concinna ◽  
Irkutsk Region ◽  
Pcr Test

Individually 470 Dermacentor nuttalli and 46 Haemaphysalis concinna ticks collected in Irkutsk Region were analyzed using RT-PCR test systems. Rickettsia contamination of D. nuttalli was 82,3% including 1,3% of the ticks with R. sibirica DNA. H. concinna ticks were infected by rickettsia to 8,7% and the detected DNA in 6,5% of cases belonged to R. heilongjiangensis. PCR results were confirmed by phylogenetic analysis of the nucleotide sequences of three gene fragments: citrate synthase (gltA) and ompA and ompB surface proteins. Thus, circulation of two Rickettsia species pathogenic to humans was determined at the examined area.

scholarly journals Variety of Rickettsia Spechies in Ixodes Ticks at the Russian island (Primorsk Territory) in 2011-2012

2017 ◽  
Vol 16 (6) ◽  
pp. 27-31
Author(s):  
N. V. Yakovchits ◽  
R. V. Adelshin ◽  
E. A. Sidorova ◽  
A. Y. Nikitin ◽  
E. I. Andaev
Keyword(s):  
Phylogenetic Analysis ◽  
Infection Rate ◽  
Citrate Synthase ◽  
Surface Proteins ◽  
Ixodes Persulcatus ◽  
Haemaphysalis Concinna ◽  
Ixodes Ticks ◽  
Epidemic Typhus

Total 728 Ixodes ticks of four species: Ixodes persulcatus, I. pavlovskyi, Haemaphysalis concinna, H. japonica douglasi collected at the Russian island in 2011-2012 were investigated. Common Rickettsia infection rate in the tested vectors varied from 4.1 to 27.9%, and the most infected representatives turned out I. persulcatus and I. pavlovskyi - 27.9 and 10.0%, respectively. Sequencing and the phylogenetic analysis of fragments of citrate synthase genes (gltA) and ompA and ompB surface proteins revealed Rickettsia DNA in ticks of Ixodes genus belonging to Candidatus Rickettsia tarasevichiae, and in ticks of Haemaphysalis genus - to Candidatus R. principis. DNA of tick-borne epidemic typhus agent - R. sibirica and R. heilongjiangensis, failed to find in the ticks tested.

scholarly journals PHYLOGENETIC ANALYSIS AND VIRULENCE-CODING GENES CHARACTERIZATION OF NEWCASTLE DISEASE VIRUS ISOLATED FROM LAYING HEN BRAIN WITH TETELO SYMPTOM

2019 ◽  
Vol 13 (3) ◽  
Author(s):  
Safira Iqlima Sarah ◽  
Christian Marco Hadi Nugroho ◽  
Ryan Septa Kurnia ◽  
Dhandy Koesoemo Wardhana ◽  
Heni Puspitasari
Keyword(s):  
Phylogenetic Analysis ◽  
Newcastle Disease ◽  
Virus Infections ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Viral Genes ◽  
Poultry Disease ◽  
The Brain ◽  
Pcr Test

Newcastle disease (ND) is an acute poultry disease caused by Paramyxovirus group. It has characteristic neurological symptoms, called torticollis. The molecular assay to find out the presence of viral genes in the brain can be an option in detecting ND virus infections since it penetrates brain barrier system. The purpose of this study was to identify ND viruses in the brain of chickens with torticollis symptoms, to analyze its phylogenetic and to characterize its virulence genetic code. Samples used were 12 dead chickens with historically had torticollis symptoms, obtained from poultry farms at several areas in West Java and Banten. Chicken brains were prepared for reverse transcriptasepolymerase chain reaction (RT-PCR) test. All positive samples then sequenced to obtain its nucleotide sequences from some of Fusion (F) genes analyzed its phylogenetic by comparing with Indonesian ND isolate virus from GenBank using Mega X software. The results of RT-PCR test showed that only one sample (Virus MSL.03) contained genes of ND virus. Based on homology tests and phylogenetic analysis, the virus belonged to subgenotype VIIh with an identical level of 95.34-95.86% when compared to several isolates from Indonesia. The MSL.03 ND virus has 112RRRKRF117 pattern in F0 indicatest its virulent category.

scholarly journals Rickettsia lusitaniae in Ornithodoros Porcinus Ticks, Zambia

Pathogens ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1306
Author(s):  
Simbarashe Chitanga ◽  
Herman M. Chambaro ◽  
Lavel C. Moonga ◽  
Kyoko Hayashida ◽  
Junya Yamagishi ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
National Parks ◽  
Citrate Synthase ◽  
Sequence Similarity ◽  
Ixodid Ticks ◽  
Sub Saharan Africa ◽  
Public Health Importance ◽  
Rickettsia Species ◽  
Ornithodoros Moubata

Rickettsial pathogens are amongst the emerging and re-emerging vector-borne zoonoses of public health importance. Though traditionally considered to be transmitted by ixodid ticks, the role of argasid ticks as vectors of these pathogens is increasingly being recognized. While bat-feeding (Ornithodoros faini) and chicken-feeding (Argas walkerae) argasid ticks have been shown to harbor Rickettsia pathogens in Zambia, there are currently no reports of Rickettsia infection in southern Africa from warthog-feeding (Phacochoerus africanus) soft ticks, particularly Ornithodoros moubata and Ornithodoros porcinus. Our study sought to expand on the existing knowledge on the role of soft ticks in the epidemiology of Rickettsia species through screening for Rickettsia pathogens in warthog burrow-dwelling soft ticks from two national parks in Zambia. The tick species from which Rickettsia were detected in this study were identified as Ornithodoros porcinus, and an overall minimal Rickettsia infection rate of 19.8% (32/162) was observed. All of the sequenced Rickettsia were identified as Rickettsia lusitaniae based on nucleotide sequence similarity and phylogenetic analysis of the citrate synthase (gltA) and 17kDa common antigen (htrA) genes. Utilizing all of the gltA (n = 10) and htrA (n = 12) nucleotide sequences obtained in this study, BLAST analysis showed 100% nucleotide similarity to Rickettsia lusitaniae. Phylogenetic analysis revealed that all of the Zambian gltA and htrA gene sequences could be grouped with those of Rickettsia lusitaniae obtained in various parts of the world. Our data suggest that Rickettsia lusitaniae has a wider geographic and vector range, enhancing to our understanding of Rickettsia lusitaniae epidemiology in sub-Saharan Africa.

scholarly journals Waterborne Outbreak of Acute Gastroenteritis Caused by Recombinant Norovirus GII.P7–GII.6 in Khabarovsk in 2019

2020 ◽  
pp. 50-54
Author(s):  
LV Butakova ◽  
EYu Sapega ◽  
OE Trotsenko ◽  
TA Zaytseva ◽  
TN Karavyanskaya ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Acute Gastroenteritis ◽  
Molecular Genetic ◽  
Disease Onset ◽  
Molecular Genetic Analysis ◽  
Nucleotide Sequences ◽  
Contaminated Water ◽  
Rt Pcr ◽  
Waterborne Outbreak ◽  
Causative Agents

Background: Noroviruses are common causative agents of acute gastroenteritis worldwide. Person-to-person transmission is the dominant transmission route for norovirus infection but contaminated water also often leads to outbreaks. Objectives: Our purpose was to do epidemiologic and molecular genetic analyses of waterborne norovirus infection outbreak among children in Khabarovsk in 2019. Materials and methods: Clinical and water samples were screened for the presence of norovirus RNA using real-time RT-PCR detection kit. The norovirus nucleotide sequences were determined by Sanger sequencing. The obtained sequences were subjected to a phylogenetic analysis. Results: In July 2019, 34 children developed acute gastroenteritis in Khabarovsk. The epidemiologic investigation showed that on the eve of the disease onset all patients played and bathed in a pedestrian fountain complex. A molecular genetic analysis of 18 biological samples from children with acute gastroenteritis and a water sample from the fountain revealed a recombinant norovirus GII.P7-GII.6. We established a 100.0% identity of all obtained nucleotide sequences to each other. A phylogenetic analysis of ORF2 partial sequences showed that the capsid protein of the Khabarovsk GII.P7-GII.6 strains belonged to the variant GII.6a. Conclusions: Contaminated water in the pedestrian interactive fountain complex was the most likely cause of the norovirus infection outbreak among children in Khabarovsk in 2019 associated with the lack of proper maintenance and regular disinfection measures.

scholarly journals Superiority of MALDI-TOF Mass Spectrometry over Real-Time PCR for SARS-CoV-2 RNA Detection

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 730
Author(s):  
Magda Rybicka ◽  
Ewa Miłosz ◽  
Krzysztof Piotr Bielawski
Keyword(s):  
Mass Spectrometry ◽  
Gold Standard ◽  
Viral Genome ◽  
False Negative ◽  
Rt Pcr ◽  
Rna Detection ◽  
Maldi Tof ◽  
Negative Results ◽  
False Negative Results ◽  
Pcr Test

At present, the RT-PCR test remains the gold standard for early diagnosis of SARS-CoV-2. Nevertheless, there is growing evidence demonstrating that this technique may generate false-negative results. Here, we aimed to compare the new mass spectrometry-based assay MassARRAY® SARS-CoV-2 Panel with the RT-PCR diagnostic test approved for clinical use. The study group consisted of 168 suspected patients with symptoms of a respiratory infection. After simultaneous analysis by RT-PCR and mass spectrometry methods, we obtained discordant results for 17 samples (10.12%). Within fifteen samples officially reported as presumptive positive, 13 were positive according to the MS-based assay. Moreover, four samples reported by the officially approved RT-PCR as negative were positive in at least one MS assay. We have successfully demonstrated superior sensitivity of the MS-based assay in SARS-CoV-2 detection, showing that MALDI-TOF MS seems to be ideal for the detection as well as discrimination of mutations within the viral genome.

scholarly journals The role of CT imaging for management of COVID-19 in epidemic area: early experience from a University Hospital

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Vikram rao Bollineni ◽  
Koenraad Hans Nieboer ◽  
Seema Döring ◽  
Nico Buls ◽  
Johan de Mey
Keyword(s):  
Ct Scan ◽  
Predictive Value ◽  
Ct Imaging ◽  
Chest Ct ◽  
University Hospital ◽  
Rt Pcr ◽  
Ct Findings ◽  
Epidemic Area ◽  
Chest Ct Scan ◽  
Pcr Test

Abstract Background To evaluate the clinical value of the chest CT scan compared to the reference standard real-time polymerase chain reaction (RT-PCR) in COVID-19 patients. Methods From March 29th to April 15th of 2020, a total of 240 patients with respiratory distress underwent both a low-dose chest CT scan and RT-PCR tests. The performance of chest CT in diagnosing COVID-19 was assessed with reference to the RT-PCR result. Two board-certified radiologists (mean 24 years of experience chest CT), blinded for the RT-PCR result, reviewed all scans and decided positive or negative chest CT findings by consensus. Results Out of 240 patients, 60% (144/240) had positive RT-PCR results and 89% (213/240) had a positive chest CT scans. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of chest CT in suggesting COVID-19 were 100% (95% CI: 97–100%, 144/240), 28% (95% CI: 19–38%, 27/240), 68% (95% CI: 65–70%) and 100%, respectively. The diagnostic accuracy of the chest CT suggesting COVID-19 was 71% (95% CI: 65–77%). Thirty-three patients with positive chest CT scan and negative RT-PCR test at baseline underwent repeat RT-PCR assay. In this subgroup, 21.2% (7/33) cases became RT-PCR positive. Conclusion Chest CT imaging has high sensitivity and high NPV for diagnosing COVID-19 and can be considered as an alternative primary screening tool for COVID-19 in epidemic areas. In addition, a negative RT-PCR test, but positive CT findings can still be suggestive of COVID-19 infection.

scholarly journals Delayed pulmonary embolism after COVID-19 pneumonia: a case report

2020 ◽  
Author(s):  
Mohamad Kanso ◽  
Thomas Cardi ◽  
Halim Marzak ◽  
Alexandre Schatz ◽  
Loïc Faucher ◽  
...  
Keyword(s):  
Risk Factors ◽  
Intensive Care Unit ◽  
Pulmonary Embolism ◽  
Acute Pulmonary Embolism ◽  
Index Hospitalization ◽  
Rt Pcr ◽  
Moderate Severity ◽  
Respiratory Status ◽  
Case Summary ◽  
Pcr Test

Abstract Background  Since the onset of the COVID-19 pandemic, several cardiovascular manifestations have been described. Among them, venous thromboembolism (VTE) seems to be one of the most frequent, particularly in intensive care unit patients. We report two cases of COVID-19 patients developing acute pulmonary embolism (PE) after discharge from a first hospitalization for pneumonia of moderate severity. Case summary  Two patients with positive RT-PCR test were initially hospitalized for non-severe COVID-19. Both received standard thromboprophylaxis during the index hospitalization and had no strong predisposing risk factors for VTE. Few days after discharge, they were both readmitted for worsening dyspnoea due to PE. One patient was positive for lupus anticoagulant. Discussion  Worsening respiratory status in COVID-19 patients must encourage physicians to search for PE since SARS-CoV-2 infection may act as a precipitant risk factor for VTE. Patients may thus require more aggressive and longer thromboprophylaxis after COVID-19 related hospitalization.

Death and COVID-19 Anxiety in Home-Quarantined Individuals Aged 65 and Over During the Pandemic

2021 ◽  
pp. 003022282110598
Author(s):  
Hümeyra Aslaner ◽  
Betül Özen ◽  
Zeliha K. Erten ◽  
Mebrure Beyza Gökçek
Keyword(s):  
Polymerase Chain Reaction ◽  
Death Anxiety ◽  
Short Form ◽  
Anxiety Score ◽  
Test Results ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Test Result ◽  
Pcr Test

Urgent measures were taken for those at the age of 65 and over who were at the risk group all over the world due to the COVID-19 pandemic. It is known that many individuals at the age of 65 and over have experienced anxiety due to the uncertainties. This study aimed to determine the anxiety and death anxiety in individuals aged 65 and over who were isolation at home due to being diagnosed with COVID-19 or being in contact during the pandemic process. The study is descriptive and cross-sectional. It was performed with 656 home-quarantined individuals aged between 65–80 years with positive or negative real-time polymerase chain reaction (RT-PCR) test result. A form including questions about the death anxiety and the Coronavirus Anxiety Scale Short Form prepared by the researchers were administered to the individuals by phone call. Of the participants, 49.5% were male. Median COVID-19 anxiety score was 4 (0–18). Anxiety scores of the male and female participants were similar. Participants with negative polymerase chain reaction (PCR) results and those with death anxiety had higher COVID anxiety scores. Death anxiety has increased by 1.661 times in male gender, 1.983 times in RT-PCR positivity and 0.146 times in the presence of symptoms. Individuals with positive COVID-19 test results or those aged 65 and over who had death anxiety and negative COVID-19 test result but who were in home-isolation due to being a contact had higher anxiety score. For this reason, those with death anxiety can be supported in line with their religious beliefs to reduce anxiety. Those with negative PCR test results in quarantine can be adequately informed about the COVID-19.

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