scholarly journals Retrieval of the Complete Coding Sequence of the UK-Endemic Tatenale Orthohantavirus Reveals Extensive Strain Variation and Supports Its Classification as a Novel Species

Viruses ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 454 ◽  
Author(s):  
Joseph G. Chappell ◽  
Theocharis Tsoleridis ◽  
Okechukwu Onianwa ◽  
Gabby Drake ◽  
Ian Ashpole ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Novel Species ◽  
Single Species ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Coding Sequence ◽  
The United Kingdom ◽  
Single Field ◽  
The Uk ◽  
Globally Distributed

Orthohantaviruses are globally distributed viruses, associated with rodents and other small mammals. However, data on the circulation of orthohantaviruses within the UK, particularly the UK-endemic Tatenale virus, is sparse. In this study, 531 animals from five rodent species were collected from two locations in northern and central England and screened using a degenerate, pan- orthohantavirus RT-PCR assay. Tatenale virus was detected in a single field vole (Microtus agrestis) from central England and twelve field voles from northern England. Unbiased high-throughput sequencing of the central English strain resulted in the recovery of the complete coding sequence of a novel strain of Tatenale virus, whilst PCR-primer walking of the northern English strain recovered almost complete coding sequence of a previously identified strain. These findings represented the detection of a third lineage of Tatenale virus in the United Kingdom and extended the known geographic distribution of these viruses from northern to central England. Furthermore, the recovery of the complete coding sequence revealed that Tatenale virus was sufficiently related to the recently identified Traemersee virus, to meet the accepted criteria for classification as a single species of orthohantavirus.

scholarly journals Retrieval of the Complete Coding Sequence of the UK-Endemic Tatenale Orthohantavirus Reveals Extensive Strain Variation and Supports its Classification as a Novel Species

2019 ◽  
Author(s):  
Joseph G. Chappell ◽  
Theocharis Tsoleridis ◽  
Okechukwu Onianwa ◽  
Gabby Drake ◽  
Ian Ashpole ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Novel Species ◽  
Accurate Analysis ◽  
Coding Sequence ◽  
Evolutionary Origins ◽  
Pcr Product ◽  
Pcr Method ◽  
The Uk ◽  
Potential Pathogenicity

AbstractHantaviruses are a diverse group of single-stranded, negative-sensed RNA viruses, known to cause sporadic outbreaks of potentially fatal human disease. To date, only two Orthohantavirus species have been detected in the UK - Seoul virus and Tatenale. Whilst Seoul is known to be pathogenic in humans, only partial fragments of Tatenale have been recovered, precluding any accurate analysis of its phylogeny or potential pathogenicity. To overcome this shortfall we used a degenerate primer PCR method to identify Tatenale-infection in rodents living in two separate locations in the UK. PCR positive samples were then subjected to either unbiased high-throughput sequencing or overlapping PCR product sequencing to recover the complete coding sequence of the Tatenale virus. This analysis provided in-depth insight into the evolutionary origins of this recently identified UK Orthohantavirus and unequivocally showed that Tatenale virus meets the established criteria for classification as a novel species. Crucially, our data will facilitate in vitro investigation into the zoonotic potential of Tatenale virus.

scholarly journals Detection of Seoul virus in wild brown rats (Rattus norvegicus) from pig farms in Northern England

2019 ◽  
Vol 184 (17) ◽  
pp. 525-525 ◽  
Author(s):  
Ellen G Murphy ◽  
Nicola J Williams ◽  
Malcolm Bennett ◽  
Daisy Jennings ◽  
Julian Chantrey ◽  
...  
Keyword(s):  
Age Differences ◽  
Rattus Norvegicus ◽  
Sanger Sequencing ◽  
Reservoir Host ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Seoul Virus ◽  
Pig Farms ◽  
Wild Rats ◽  
Globally Distributed

IntroductionHantaviruses are maintained by mammalian hosts, such as rodents, and are shed in their excretions. Clinical disease can occur in humans from spillover infection. Brown rats (Rattus norvegicus) are the globally distributed reservoir host of Seoul virus (SEOV). Human cases of SEOV-associated haemorrhagic fever with renal syndrome (SEOV-HFRS)have been reported in Great Britain (GB) since 1977.MethodsBrown rats (n=68) were trapped from a variety of peridomestic locations, with a focus on pig farms. Kidney and lung tissues were tested for viral RNA using a pan-hantavirus RT-PCR assay followed by Sanger sequencing and analysis.ResultsSEOV RNA was detected in 19 per cent (13/68, 95% CI 11 to 30) of rats and all sequences fell within SEOV lineage 9. Twelve sequences were highly similar to each other and to the previously reported GB Humber strain of SEOV (98 per cent). One rat SEOV sequence was more distant. The SEOV prevalence in rats from pig farms was significantly greater (p=0.047) than other sites sampled. No significant sex or age differences were observed among positive and negative rats.DiscussionThe results from this study suggest that SEOV could be widespread in wild rats in GB and therefore pose a potential risk to public health.

Generic detection of poleroviruses using an RT-PCR assay targeting the RdRp coding sequence

2014 ◽  
Vol 198 ◽  
pp. 1-11 ◽  
Author(s):  
Leonidas Lotos ◽  
Konstantinos Efthimiou ◽  
Varvara I. Maliogka ◽  
Nikolaos I. Katis
Keyword(s):  
Rt Pcr ◽  
Pcr Assay ◽  
Coding Sequence

scholarly journals Performance of Real-Time Reverse Transcription Polymerase Chain Reaction for the Detection of Foot-and-Mouth Disease Virus during Field Outbreaks in the United Kingdom in 2007

2009 ◽  
Vol 21 (3) ◽  
pp. 321-330 ◽  
Author(s):  
Scott M. Reid ◽  
Katja Ebert ◽  
Katarzyna Bachanek-Bankowska ◽  
Carrie Batten ◽  
Anna Sanders ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
United Kingdom ◽  
Real Time ◽  
Reverse Transcription ◽  
Foot And Mouth Disease ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Pcr Assay ◽  
The United Kingdom ◽  
Polymerase Chain

Rapid and accurate diagnosis is essential for effective control of foot-and-mouth disease (FMD). The present report describes the practical steps undertaken to deploy a real-time reverse transcription polymerase chain reaction (real-time RT-PCR) to process the samples received during the outbreaks of FMD in the United Kingdom in 2007. Two independent real-time RT-PCR assays targeting different regions (5′UTR and 3D) of the FMD virus (FMDV) genome were used to confirm the presence of FMDV in clinical samples collected from the first infected premises. Once the FMDV strain responsible had been sequenced, a single real-time RT-PCR assay (3D) was selected to test a total of 3,216 samples, including material from all 8 infected premises. Using a 96-well automated system to prepare nucleic acid template, up to 84 samples could be processed within 5 hr of submission, and up to 269 samples were tested per working day. A conservative cut-off was used to designate positive samples, giving rise to an assay specificity of 99.9% or 100% for negative control material or samples collected from negative premises, respectively. For the first time, real-time RT-PCR results were used to recognize preclinical FMD in a cattle herd. Furthermore, during the later stages of the outbreaks, the real-time RT-PCR assay supported an active surveillance program within high-risk cattle herds. To the authors' knowledge, this is the first documented use of real-time RT-PCR as a principal laboratory diagnostic tool following introduction of FMD into a country that was FMD-free (without vaccination) and highlights the advantages of this assay to support control decisions during disease outbreaks.

scholarly journals Whole-genome sequencing of SARS-COV-2 reveals a substantially lower frequency of the UK variant than previously announced in Libya

2021 ◽  
Author(s):  
Inas M Alhudiri ◽  
Ahmad M Ramadan ◽  
Khaled Ibrahim Ibrahim ◽  
Mouna Eljilani ◽  
Adel Abdalla Aboud ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Drop Out ◽  
Whole Genome ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Gene Target ◽  
Specific Identification ◽  
S Gene ◽  
The Uk

A cluster-5 variant was detected in September 2020 in minks and humans in Denmark and currently classified as Alpha or B.1.1.7 strain. This variant presents several mutations in the spike region (S) which could increase the transmissibility of the virus 43-90% over previously circulating variants. The national center for disease control (NCDC) announced on 24th February 2021 the discovery of B.1.1.7 strain in Libya using a reverse-transcriptase PCR assay for S-gene target failure (SGTF) and reported that 25% of the tested samples were UK variant. This assay relies on the specific identification of the H69-V70 deletion in S gene which causes S gene drop out in RT-PCR; characteristic of the UK variant (B.1.1.7). This letter discusses our whole genome sequencing results of positive SARS-COV-2 samples with SGTF collected between 25th February - 4th March 2021 in Libya.

scholarly journals Detection of the SARS-CoV-2 UK Variant in Portugal

2021 ◽  
Vol 5 (1) ◽  
pp. 39
Author(s):  
Susana Bandarra ◽  
Lurdes Monteiro ◽  
Laura Brum
Keyword(s):  
United Kingdom ◽  
Rt Pcr ◽  
The United Kingdom ◽  
First Case ◽  
Diagnostic Samples ◽  
The Uk

At the end of 2020, a new highly transmissible variant of SARS-CoV-2 was discovered in the United Kingdom (UK). This work aims to identify potential cases of the UK variant in Portugal using routine diagnostic samples. A total of 26 out of 43 positive samples that were identified by RT-PCR as suspects were confirmed through sequencing to be the SARS-CoV-2 UK variant. The first case of the UK variant identified by us was in samples collected on 21 December 2020 at Lisbon airport in travelers from Manchester and London.

scholarly journals Integrating High throughput Sequencing into Survey Design Reveals Turnip Yellows Virus and Soybean Dwarf Virus in Pea (Pisum Sativum) in the United Kingdom

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2530
Author(s):  
Aimee R. Fowkes ◽  
Sam McGreig ◽  
Hollie Pufal ◽  
Shona Duffy ◽  
Becky Howard ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
High Throughput Sequencing ◽  
Sampling Strategy ◽  
The United Kingdom ◽  
First Finding ◽  
Turnip Yellows Virus ◽  
The Uk ◽  
Soybean Dwarf Virus ◽  
Pea Enation Mosaic Virus ◽  
Pea Seed

There is only limited knowledge of the presence and incidence of viruses in peas within the United Kingdom, therefore high-throughput sequencing (HTS) in combination with a bulk sampling strategy and targeted testing was used to determine the virome in cultivated pea crops. Bulks of 120 leaves collected from twenty fields from around the UK were initially tested by HTS, and presence and incidence of virus was then determined using specific real-time reverse-transcription PCR assays by testing smaller mixed-bulk size samples. This study presents the first finding of turnip yellows virus (TuYV) in peas in the UK and the first finding of soybean dwarf virus (SbDV) in the UK. While TuYV was not previously known to be present in UK peas, it was found in 13 of the 20 sites tested and was present at incidences up to 100%. Pea enation mosaic virus-1, pea enation mosaic virus-2, pea seed-borne mosaic virus, bean yellow mosaic virus, pea enation mosaic virus satellite RNA and turnip yellows virus associated RNA were also identified by HTS. Additionally, a subset of bulked samples were re-sequenced at greater depth to ascertain whether the relatively low depth of sequencing had missed any infections. In each case the same viruses were identified as had been identified using the lower sequencing depth. Sequencing of an isolate of pea seed-borne mosaic virus from 2007 also revealed the presence of TuYV and SbDV, showing that both viruses have been present in the UK for at least a decade, and represents the earliest whole genome of SbDV from Europe. This study demonstrates the potential of HTS to be used as a surveillance tool, or for crop-specific field survey, using a bulk sampling strategy combined with HTS and targeted diagnostics to indicate both presence and incidence of viruses in a crop.

1089: Prognostic Value of Molecular Staging of Bladder Cancer with RT -PCR Assay for KRT20: Results at 5 Year-Follow-up

2007 ◽  
Vol 177 (4S) ◽  
pp. 360-360
Author(s):  
Ana Agud ◽  
Maria J. Ribal ◽  
Lourdes Mengual ◽  
Mercedes Marin-Aguilera ◽  
Laura Izquierdo ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Prognostic Value ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Molecular Staging

İngiltere’den Türkiye’ye ‘Düzensiz’ Göçmen Dövizi Gönderme Davranışının Nedenleri Üzerine Nitel Bir İnceleme

2019 ◽  
Vol 6 (2) ◽  
pp. 173-190
Author(s):  
Fethiye Tilbe
Keyword(s):  
Cultural Values ◽  
Host Country ◽  
Regulatory Framework ◽  
Face To Face ◽  
Migrant Communities ◽  
The United Kingdom ◽  
Main Determinants ◽  
Money Transfers ◽  
The Uk ◽  
Migrant Groups

Bu makale, göçmen dövizi  akımlarında “düzensizlik” olarak ifade ettiğimiz, Türkiye’ye resmi kanallar dışında gönderilen enformel  göçmen dövizlerini, Birleşik Krallık’ta (özellikle Londra’da) yaşayan Türkiye kökenli göçmenler açısından incelemektedir. Her göçmen grubu, gerek ev sahibi ülkedeki düzenleyici çerçeve ve sosyo-ekonomik koşullar, gerek göçmen topluluğunun sosyo-kültürel değerleri tarafından belirlenen biçimde, farklı göçmen dövizi transfer biçimlerine eğilim sergilemektedir. Dolayısıyla farklı ülkelerdeki aynı kökenden göçmen toplulukları, ev sahibi ülkedeki dinamikler nedeniyle göçmen dövizlerinin formel ya da enformel (düzenli ya da düzensiz) gönderiminde farklılaşabilirken, aynı ülkedeki farklı ülke kökenli göçmen grupları da pek çok örüntünün etkisiyle farklı eğilim gösterebilmektedir. Nitel araştırma tasarımı kapsamında 27 göçmen ve 7 anahtar statüdeki katılımcıyla gerçekleştirilen yüz yüze görüşmelere dayalı olan bu çalışma, Birleşik Krallık’tan Türkiye’ye göçmen dövizi gönderimindeki düzensizlik olgusunu, her iki ülkenin sosyal, ekonomik ve kültürel dinamikleriyle ilişkilendirerek incelemeyi ve nedenlerini ortaya çıkarmayı amaç edinmektedir. Elde edilen sonuçlar, göçmenlik statüsü, gönderilen para miktar ve sıklığı ile geleneksel ilişki ağlarına olan güvenin yanında, Birleşik Krallık’taki sosyal yardım ve çalışma biçimine ilişkinin düzenleyici çerçevenin ve göçmenlerin sosyo-ekonomik durumlarının Türkiye’ye enformel göçmen dövizi gönderiminde temel belirleyici olduğunu ortaya koymaktadır.ABSTRACT IN ENGLISHA Qualitative Examination of Determinants of Remittances Sending Behaviour Among Immigrants from Turkey in the UKThis article examines the causes of irregularity in remittances flows from the United Kingdom (UK) to Turkey, from the perspective of migrants from Turkey living in the UK. Each group of migrants prefers different types of remittance sending methods, as determined by the regulatory framework and socio-economic conditions in the host country and the socio-cultural values of the migrant community. Therefore, migrant communities of the same origin in different countries may differ in using formal or informal sending methods of remittances due to the dynamics in the host country. Similarly, migrant groups of different nationalities in the same country may show different tendencies due to the influence of many patterns. Similarly, migrant groups of different nationalities in the same country may show different tendencies due to the influence of many patterns. This study aims to examine the phenomenon of irregularities in sending remittances by associating with the social, economic and cultural dynamics of both countries. For this purpose, face-to-face in-depth interviews were conducted with 27 immigrants and 7 key status participants by using qualitative research method. The obtained results reveal that the regulatory framework relating to social assistance and labour market in the UK, immigration status, the frequency and the amount of money sent and confidence in traditional relationship networks is the main determinants of informal money transfers to Turkey.

TBE in United Kingdom

2020 ◽  
Keyword(s):  
United Kingdom ◽  
Clinical Disease ◽  
England And Wales ◽  
Probable Case ◽  
The United Kingdom ◽  
South West ◽  
Louping Ill ◽  
The Uk ◽  
North And South ◽  
South West England

Until 2019, TBE was considered only to be an imported disease to the United Kingdom. In that year, evidence became available that the TBEV is likely circulating in the country1,2 and a first “probable case” of TBE originating in the UK was reported.3 In addition to TBEV, louping ill virus (LIV), a member of the TBEV-serocomplex, is also endemic in parts of the UK. Reports of clinical disease caused by LIV in livestock are mainly from Scotland, parts of North and South West England and Wales.4

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