scholarly journals Long-Term Circulation of Atypical Porcine Pestivirus (APPV) within Switzerland

Viruses ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 653 ◽  
Author(s):  
Cindy Kaufmann ◽  
Hanspeter Stalder ◽  
Xaver Sidler ◽  
Sandra Renzullo ◽  
Corinne Gurtner ◽  
...  
Keyword(s):  
Diagnostic Tests ◽  
Viral Genome ◽  
The United States ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Newborn Piglets ◽  
Virus Prevalence ◽  
Virus Diversity ◽  
Congenital Tremor

In 2015, a new pestivirus was described in pig sera in the United States. This new “atypical porcine pestivirus” (APPV) was later associated with congenital tremor (CT) in newborn piglets. The virus appears to be distributed worldwide, but the limited knowledge of virus diversity and the use of various diagnostic tests prevent direct comparisons. Therefore, we developed an APPV-specific real-time RT-PCR assay in the 5′UTR of the viral genome to investigate both retro- and prospectively the strains present in Switzerland and their prevalence in domestic pigs. Overall, 1080 sera obtained between 1986 and 2018 were analyzed, revealing a virus prevalence of approximately 13% in pigs for slaughter, whereas it was less than 1% in breeding pigs. In the prospective study, APPV was also detected in piglets displaying CT. None of the samples could detect the Linda virus, which is another new pestivirus recently reported in Austria. Sequencing and phylogenetic analysis revealed a broad diversity of APP viruses in Switzerland that are considerably distinct from sequences reported from other isolates in Europe and overseas. This study indicates that APPV has already been widely circulating in Switzerland for many years, mainly in young animals, with 1986 being the earliest report of APPV worldwide.

Real-time PCR assay for sensitive organ detection and epidemic investigation of Turbot reddish body iridovirus

2009 ◽  
Vol 6 (1) ◽  
pp. 61-67 ◽  
Author(s):  
Wu Cheng-Long ◽  
Shi Cheng-Yin ◽  
Huang Jie ◽  
Kong Xiao-Yu
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Viral Genome ◽  
Sybr Green ◽  
Sybr Green I ◽  
Quantitative Detection ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Linear Coefficient ◽  
Sensitive Organ

AbstractA rapid and sensitive real-time polymerase chain reaction (PCR) assay coupled with SYBR Green I chemistry was developed for the quantitative detection of Turbot reddish body iridovirus (TRBIV) isolated from farmed turbot (Scophthalmus maximus). A 152 bp DNA fragment from the TRBIV major capsid protein (MCP) gene was involved in the real-time PCR (RT-PCR) assay using the Roter Gene 3000 sequence detection system. The PCR mixture contained a fluorescent dye, SYBR Green I, which exhibited fluorescence enhancement when bound to double-stranded (ds) DNA. The enhancement of fluorescence was proportional to the initial concentration of the template DNA. The positive control plasmid, pUCm-T/TRBIV MCP, containing the target sequence, was quantified to make a standard curve for sample detection after serial tenfold dilution. Linear coefficient correlations between the cycle threshold (CT) value and logarithmic positive plasmid concentration were close to one (R2=0.9952) and the detection limit of the assay was 102 copies of positive plasmids. The quantitative detection of virus in different tissues from TRBIV-infected fish showed that the spleen and kidney contained the largest number of viral particles (5.23×106 and 2.18×106 viral genome copies/mg tissue, respectively), while no viral DNA was detected in the muscular tissue. The molecular epidemic investigation of TRBIV showed that many cultured turbots were infected and TRBIV has become epidemic in turbot farms located along the Shandong peninsula. The virus number varied from 1.27×102 to 2.33×106 viral genome copies/mg tissue in spleens of infected turbot. These results suggest that the RT-PCR assay reported here can be used as a rapid, sensitive and quantitative method for TRBIV.

scholarly journals First Report of Barley virus G in the United States and California

Plant Disease ◽  
2021 ◽  
Author(s):  
Anna Christine Erickson ◽  
Bryce Falk
Keyword(s):  
United States ◽  
Viral Genome ◽  
The United States ◽  
Full Length ◽  
Yellow Dwarf ◽  
Rt Pcr ◽  
First Report ◽  
Query Coverage ◽  
Full Length Sequence ◽  
The U.S

Barley (Hordeum vulgare) is a valuable annual cereal crop grown widely throughout the United States and the world. The majority of barley grown commercially in California and throughout the U.S. is used for livestock feed, with the remainder being used by the malting industry and, to a lesser extent, direct food consumption; it is also often employed as a cover crop (Lazicki et al. 2016). Yellow dwarf viruses (YDVs), in the family Luteoviridae, that infect barley and other cereal crops are common and widely distributed throughout California and the U.S. (Griesbach et al. 1989; Seabloom et al. 2009). In April 2018, five barley samples exhibiting typical symptoms of YDV infection (primarily yellowing of leaf margins and tips) collected from fields in Yolo county planted with cultivar Butta 12 , were tested for viruses. Total RNA was extracted from leaf tissue using Trizol reagent, according to the manufacturer’s protocol. RNA was used as template in a multiplexed RT-PCR assay designed for the generic detection of barley and cereal infecting YDVs, using the protocol established by Malmstrom and Shu (2004). A 372 basepair amplicon indicative of Polerovirus infection was amplified from two of the samples and sequenced (Quintara Biosciences), and the resulting data analyzed via a BLASTn search. No further testing or work was done with the three samples that tested negative. Not unexpectedly, the top result returned for one of the positive samples was Cereal yellow dwarf virus-RPV (CYDV-RPV; 98% identity), a virus common to cereals in California and the U.S.. Unexpectedly, however, the top result returned for the other sample was Barley virus G (BVG), sharing 98.43% identity with the Uiseong BVG isolate (GenBank accession LC259081). To further confirm the presence of BVG in the sample, the full-length viral genome was amplified using two-step RT-PCR with primers targeting the extreme 5’ and 3’ ends of the viral genome, using the PrimeScript RT and PrimeSTAR GXL DNA Polymerase kits (Takara Bio), cloned into the binary vector pJL89 and a BLAST search of the resulting 5621 nucleotide full-length sequence (100% query coverage) once again returned results showing the YDV to be BVG. The full-length sequence was deposited into GenBank (MW853785). Nucleotide sequence comparisons showed that the CA BVG isolate shares 96.62%, 96.57%, and 96.02% identity with the sequences of the BVG-Gimje (KT962089), BVG-Uiseong (LC259081), and BVG-Aus8 (LC500836) isolates, respectively. To our knowledge, this is the first report of barley virus G in California and in the United states. Currently the prevalence, host range and mode and timing of introduction of BVG in California and the U.S. are unknown; its impact on cereal production and yield in any location in which it has been identified thus far is also unknown and may warrant further investigation.

scholarly journals Acceptable Performance of the Abbott ID NOW Among Symptomatic Individuals with Confirmed COVID-19

2020 ◽  
Author(s):  
William Stokes ◽  
Byron M. Berenger ◽  
Takshveer Singh ◽  
Ifueko Adeghe ◽  
Angela Schneider ◽  
...  
Keyword(s):  
Throat Swab ◽  
Small Sample Size ◽  
Point Of Care ◽  
The United States ◽  
Small Sample ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Specimen Collection ◽  
United States Food ◽  
States Food

INTRODUCTIONPoint of care diagnostic tests for SARS-CoV-2, such as the ID NOW, have great potential to help combat the COVID-19 pandemic. The ID NOW is approved by the United States Food and Drug Administration (FDA) for the detection of SARS-CoV-2 in symptomatic individuals within the first 7 days of symptom onset for COVID-19 if tested within 1 hour of specimen collection. However, clinical data on the performance of the ID NOW is limited, with many studies deviating from the manufacturer’s instructions and/or having small sample size.METHODSAdults with COVID-19 in the community or hospital were recruited into the study. Paired throat swabs were collected, with one throat swab transported immediately in an empty sterile tube to the laboratory for ID NOW testing, and the other transported in universal transport media and tested by an in-house SARS-CoV-2 RT-PCR assay targeting the E-gene. Positive percent agreement (PPA) was calculated.RESULTS133 individuals were included in the study. 129 samples were positive on either the ID NOW and/or RT-PCR. Assuming any positive result on either assay represents a true positive, PPA of the ID NOW compared to RT-PCR with 95% confidence intervals was 89.1% [82.0% - 94.1%] and 91.6% [85.1% - 95.9%], respectively. When analyzing individuals with symptoms ≤ 7 days and who had the ID NOW performed within an hour, ID NOW PPA increased to 98.2%.DISCUSSIONIn this study, SARS-CoV-2 results from the ID NOW were reliable, especially when testing was adhered to manufacturer’s recommendations.

scholarly journals Development and Evaluation of an Enterovirus D68 Real-Time Reverse Transcriptase PCR Assay

2015 ◽  
Vol 53 (8) ◽  
pp. 2641-2647 ◽  
Author(s):  
Todd N. Wylie ◽  
Kristine M. Wylie ◽  
Richard S. Buller ◽  
Maria Cannella ◽  
Gregory A. Storch
Keyword(s):  
Reverse Transcriptase ◽  
Real Time ◽  
Limit Of Detection ◽  
Respiratory Illness ◽  
The United States ◽  
Human Enterovirus ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Reverse Transcriptase Pcr ◽  
Enterovirus D68

We have developed and evaluated a real-time reverse transcriptase PCR (RT-PCR) assay for the detection of human enterovirus D68 (EV-D68) in clinical specimens. This assay was developed in response to the unprecedented 2014 nationwide EV-D68 outbreak in the United States associated with severe respiratory illness. As part of our evaluation of the outbreak, we sequenced and published the genome sequence of the EV-D68 virus circulating in St. Louis, MO. This sequence, along with other GenBank sequences from past EV-D68 occurrences, was used to computationally select a region of EV-D68 appropriate for targeting in a strain-specific RT-PCR assay. The RT-PCR assay amplifies a segment of the VP1 gene, with an analytic limit of detection of 4 copies per reaction, and it was more sensitive than commercially available assays that detect enteroviruses and rhinoviruses without distinguishing between the two, including three multiplex respiratory panels approved for clinical use by the FDA. The assay did not detect any other enteroviruses or rhinoviruses tested and did detect divergent strains of EV-D68, including the first EV-D68 strain (Fermon) identified in California in 1962. This assay should be useful for identifying and studying current and future outbreaks of EV-D68 viruses.

scholarly journals Role of Rapid Antigen Test in the Diagnosis of COVID-19 in India

2020 ◽  
pp. 77-80
Author(s):  
Aroop Mohanty ◽  
Ankita Kabi ◽  
Subodh Kumar ◽  
Vivek Hada
Keyword(s):  
Diagnostic Tests ◽  
Early Stage ◽  
The United States ◽  
Antigen Test ◽  
Rt Pcr ◽  
Is Development ◽  
Detection And Diagnosis ◽  
Antigen Tests ◽  
Spread Of Infection

In the current world scenario where we are seeing of an alarming increase in the number of SARS-CoV-2 infections, it is necessary that in addition to RT-PCR assays, there is development and standardization of other rapid and efficient diagnostic tests. In relation to the total number of confirmed cases, India ranks second only behind the United States and according to forecasts it will not be long before it reaches the first place. As in developing countries, such as India, it is difficult to implement molecular biology facilities in all centres, the creation of rapid antigen tests is increasingly common in the detection and diagnosis of cases of COVID-19 in an early stage limiting the spread of infection.”

scholarly journals Rapid Detection of West Nile Virus from Human Clinical Specimens, Field-Collected Mosquitoes, and Avian Samples by a TaqMan Reverse Transcriptase-PCR Assay

2000 ◽  
Vol 38 (11) ◽  
pp. 4066-4071 ◽  
Author(s):  
Robert S. Lanciotti ◽  
Amy J. Kerst ◽  
Roger S. Nasci ◽  
Marvin S. Godsey ◽  
Carl J. Mitchell ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
The United States ◽  
Taqman Assay ◽  
Rt Pcr ◽  
Pcr Assay ◽  
West Nile ◽  
Diagnostic Laboratory ◽  
Tissue Samples ◽  
Clinical Specimens ◽  
Culture Positive

The authors report on the development and application of a rapid TaqMan assay for the detection of West Nile (WN) virus in a variety of human clinical specimens and field-collected specimens. Oligonucleotide primers and FAM- and TAMRA-labeled WN virus-specific probes were designed by using the nucleotide sequence of the New York 1999 WN virus isolate. The TaqMan assay was compared to a traditional reverse transcriptase (RT)-PCR assay and to virus isolation in Vero cells with a large number (≈500) of specimens obtained from humans (serum, cerebrospinal fluid, and brain tissue), field-collected mosquitoes, and avian tissue samples. The TaqMan assay was specific for WN virus and demonstrated a greater sensitivity than the traditional RT-PCR method and correctly identified WN virus in 100% of the culture-positive mosquito pools and 98% of the culture-positive avian tissue samples. The assay should be of utility in the diagnostic laboratory to complement existing human diagnostic testing and as a tool to conduct WN virus surveillance in the United States.

scholarly journals Patient Characteristics in Cases of Reinfection or Prolonged viral shedding in SARS-CoV-2

2021 ◽  
Author(s):  
Richard M. Yoo ◽  
Roland A. Romero ◽  
Joseph Mabajen ◽  
Suchit Mehrotra ◽  
Isaac S. Kohane ◽  
...  
Keyword(s):  
United States ◽  
Diagnostic Tests ◽  
Statistical Power ◽  
Sequence Data ◽  
Serological Test ◽  
Patient Characteristics ◽  
The United States ◽  
Administrative Claims ◽  
Rt Pcr ◽  
Viral Shedding

Importance: As testing options increase for COVID-19, their interpretability is challenged by the increasing variety of clinical contexts in which results are obtained. In particular, positive COVID-19 diagnostic (RT-PCR) tests that occur after a patient has seroconverted may be indicative of reinfection. However, in the absence of SARS-CoV-2 sequence data, the possibility of prolonged viral shedding may not be excluded. We highlight a testing pattern that identifies such cases and study its statistical power in identifying potential reinfection. We also study the medical records of patients that matched the pattern. Objective: To describe the frequency and demographic information of people with a testing pattern indicative of SARS-CoV-2 reinfection. Design: We examined 4.2 million test results from a large national health insurer in the United States. Specifically, we identified the pattern of a positive RT-PCR test followed by a positive IgG test, again followed by a positive RT-PCR. Setting: Data from outpatient laboratories across the United States was joined with claims data from a single large commercial insurer's administrative claims database. Participants: Study participants are those whose insurance, either commercial or Medicare, is provided by a single US based insurer. Exposures: People who received at least two positive diagnostic tests via RT-PCR for SARS-Cov-2 separated by 42 or more days with at least one serological test (IgG) indicating the presence of antibodies between diagnostic tests. Main Outcomes and Measures: Count and characteristics of people with the timeline of three tests as described in Exposures. Results: We identified 79 patients who had two positive RT-PCR tests separated by more than six weeks, with a positive IgG test in between. These patients tended to be older than those COVID-19 patients without this pattern (median age 56 vs. 42), and they exhibited comorbidities typically attributed to a compromised immune system and heart disease. Conclusions and Relevance: While the testing pattern alone was not sufficient to distinguish potential reinfection from prolonged viral shedding, we were able to identify common traits of the patients identified through the pattern.

Speech-Language Pathology in the Peace Corps: Necessity and Sustainability

2012 ◽  
Vol 2 (1) ◽  
pp. 11-18
Author(s):  
Melissa A. Pierce
Keyword(s):  
United States ◽  
Special Education ◽  
Peace Corps ◽  
People With Disabilities ◽  
Communication Disorders ◽  
The United States ◽  
Speech Language Pathology ◽  
Speech Language Pathologists ◽  
Language Pathology

In countries other than the United States, the study and practice of speech-language pathology is little known or nonexistent. Recognition of professionals in the field is minimal. Speech-language pathologists in countries where speech-language pathology is a widely recognized and respected profession often seek to share their expertise in places where little support is available for individuals with communication disorders. The Peace Corps offers a unique, long-term volunteer opportunity to people with a variety of backgrounds, including speech-language pathologists. Though Peace Corps programs do not specifically focus on speech-language pathology, many are easily adapted to the profession because they support populations of people with disabilities. This article describes how the needs of local children with communication disorders are readily addressed by a Special Education Peace Corps volunteer.

Multidisciplinary Evidence to Treat Bilingual Individuals with Aphasia

2008 ◽  
Vol 15 (3) ◽  
pp. 66-72 ◽  
Author(s):  
José G. Centeno
Keyword(s):  
Stroke Rehabilitation ◽  
Culturally Diverse ◽  
Treatment Strategies ◽  
The United States ◽  
Intervention Strategies ◽  
Steady Increase ◽  
Clinical Procedures ◽  
Bilingual Speakers ◽  
Aphasic Clients

Abstract The steady increase in linguistic and cultural diversity in the country, including the number of bilingual speakers, has been predicted to continue. Minorities are expected to be the majority by 2042. Strokes, the third leading cause of death and the leading cause of long-term disability in the U.S., are quite prevalent in racial and ethnic minorities, so population estimates underscore the imperative need to develop valid clinical procedures to serve the predicted increase in linguistically and culturally diverse bilingual adults with aphasia in post-stroke rehabilitation. Bilingualism is a complex phenomenon that interconnects culture, cognition, and language; thus, as aphasia is a social phenomenon, treatment of bilingual aphasic persons would benefit from conceptual frameworks that exploit the culture-cognition-language interaction in ways that maximize both linguistic and communicative improvement leading to social re-adaptation. This paper discusses a multidisciplinary evidence-based approach to develop ecologically-valid treatment strategies for bilingual aphasic individuals. Content aims to spark practitioners' interest to explore conceptually broad intervention strategies beyond strictly linguistic domains that would facilitate linguistic gains, communicative interactions, and social functioning. This paper largely emphasizes Spanish-English individuals in the United States. Practitioners, however, are advised to adapt the proposed principles to the unique backgrounds of other bilingual aphasic clients.

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