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1.
Rev. cuba. med. trop ; 74(2): e809, May.-Aug. 2022. graf
Article in Spanish | LILACS-Express | LILACS | ID: biblio-1408918

ABSTRACT

RESUMEN Introducción: El aumento de los casos de COVID-19 en Cuba requirió el desarrollo de nuevas capacidades para el diagnóstico molecular de la infección. En la Unidad Empresarial de Base Laboratorios LIORAD-AICA+, de La Habana, se estableció un Laboratorio de Biología Molecular para el diagnóstico molecular de la enfermedad. Objetivo: Analizar la experiencia de un año de trabajo, en el diagnóstico molecular de la COVID-19, del Laboratorio de Biología Molecular de la UEB LIORAD. Métodos: Para iniciar el diagnóstico molecular del SARS-CoV-2 en la UEB Laboratorios LIORAD se llevó a cabo un conjunto de acciones que estuvieron dirigidas a la evaluación de los riesgos, establecimiento de las áreas y el flujo de trabajo, y formación de equipos de trabajo. El personal se capacitó, se modificaron y elaboraron procedimientos e instructivas. Resultados: La evaluación de los riesgos permitió detectar un conjunto de riesgos asociados a la actividad de diagnóstico y se establecieron las medidas para mitigarlos. El personal del laboratorio recibió un total de 23 capacitaciones, se elaboró un total de ocho procedimientos e instructivas y dos registros. El laboratorio procesó en un año un total de 125 154 muestras. Conclusiones: Durante el año de trabajo el Laboratorio de Biología Molecular de la UEB LIORAD se realizó el diagnóstico certero de la enfermedad. Esto evidencia la importancia de la capacitación del personal y el cumplimiento de las buenas prácticas y medidas de bioseguridad en el trabajo con muestras potencialmente infecciosas.


ABSTRACT Introduction: The increase in the number of cases of COVID-19 in Cuba demanded of new capacities for the molecular diagnosis of the infection. A Laboratory of Molecular Biology for the molecular diagnosis of this disease was installed at the Base Business Unit LIORAD-AICA+ Laboratories in Havana. Objective: To analyze a one-year work experience in the molecular diagnosis of COVID-19 at the Laboratory of Molecular Biology, LIORAD-AICA+. Methods: To begin with the molecular diagnosis of SARS-CoV-2 at LIORAD-AICA+, a group of actions were carried out aimed at evaluating the risks, establishing the working areas and flow, and training the work team. Personnel were trained, and procedures and guidelines were drawn up and modified. Results: Risk assessment allowed identifying several risks associated with the diagnostic activity, and measures were established to mitigate them. The laboratory personnel received 23 training sessions; and eight procedures and guidelines, and two registers were drawn up. The laboratory processed a total of 125 154 samples in a year. Conclusions: During the work year, the accurate diagnosis of the disease was conducted at the Laboratory of Molecular Biology, LIORAD-AICA+. This evidences the importance of personnel training and the compliance with good practices and biosafety measures when working with potentially infectious samples.

2.
Braz. dent. j ; 33(2): 68-72, Mar.-Apr. 2022. tab
Article in English | LILACS-Express | LILACS, BBO | ID: biblio-1374620

ABSTRACT

Abstract The World Health Organization has declared the widespread spread of SARS-CoV-2 and its associated disease (COVID-19) a public health emergency. The standard gold test for detecting the virus is the RT-PCR, performed from nasopharyngeal swab (NPS) samples. However, this test may be uncomfortable for the patient and requires specific training and attire from the health professional responsible for collecting the sample. Therefore, the search for alternative ways to collect samples that may be used in the diagnosis of COVID-19 is relevant. This study aimed to compare the results obtained from NPS and saliva samples. NPS and saliva samples were collected from 189 symptomatic outpatients suspected of COVID-19, who came to Piquet Carneiro Polyclinic. RNA extraction was performed using the Bio-Gene DNA/RNA Viral Extraction kit (Bioclin®). Real-time reverse transcriptase-polymerase chain reaction (RT-PCR) reactions used the Molecular SARS-CoV-2 (E / RP) kit (Bio-Manguinhos). The results indicated that 142 showed a non-detectable result (ND), while 47 showed a detectable result (D). Among the 142 "ND", 137 (94.4%) saliva samples obtained the same result, while 5 samples (3.4%) were "D". Among the 47 "D" swab samples, 35 (74.4%) showed the same result in the saliva samples. The sensitivity of the saliva test was 0.74 and the specificity was 0.97. The positive predictive value was 0.88 while the negative predictive value was 0.92. The results showed that detection of Sars-CoV-2 using saliva samples showed high sensitivity and specificity compared to nasopharyngeal swabs.


Resumo A Organização Mundial da Saúde declarou a disseminação generalizada do SARS-CoV-2 e sua doença associada (COVID-19) uma emergência de saúde pública. O teste padrão ouro para detecção do vírus é o RT-PCR, realizado a partir de amostras de swab nasofaríngeo (NPS). No entanto, esse exame pode ser desconfortável para o paciente e requer treinamento específico e vestimenta do profissional de saúde responsável pela coleta da amostra. Portanto, a busca por formas alternativas de coleta de amostras que possam ser utilizadas no diagnóstico de COVID-19 é relevante. O objetivo deste estudo foi comparar os resultados obtidos em amostras de NPS e saliva. Amostras de NPS e saliva foram coletadas de 189 pacientes ambulatoriais sintomáticos com suspeita de COVID-19, que procuraram a Policlínica Piquet Carneiro. A extração de RNA foi realizada com o kit Bio-Gene DNA / RNA Viral Extraction (Bioclin®) e as reações em tempo real da reação em cadeia da polimerase-transcriptase reversa (RT-PCR) usaram o kit Molecular SARS-CoV-2 (E / RP) (Bio-Manguinhos). Os resultados indicaram que 142 apresentaram resultado não detectável (ND), enquanto 47 apresentaram resultado detectável (D). Entre os 142 "ND", 137 (94,4%) amostras de saliva obtiveram o mesmo resultado, enquanto 5 amostras (3,4%) foram "D". Dentre as 47 amostras de swab "D", 35 (74,4%) apresentaram o mesmo resultado nas amostras de saliva. A sensibilidade do teste de saliva foi de 0,74 e a especificidade foi de 0,97. O valor preditivo positivo foi de 0,88, enquanto o valor preditivo negativo foi de 0,92. Os resultados mostraram que a detecção de Sars-CoV-2 em amostras de saliva apresentou alta sensibilidade e especificidade quando comparada com swabs nasofaríngeos.

3.
Article in English | AIM | ID: biblio-1361415

ABSTRACT

Background. SARS-CoV-2 viral loads may aid in the risk stratification of patients with COVID-19. Methods. 486 patients tested positive for SARS Cov2 by real time RT-PCR were included in this study. All the tests were performed on nasopharyngeal swabs during the first week after symptom onset using Sansure Biotech™ SARS Cov2 real time RT-PCR kits. Patient's condition was monitored over a period of one month after the onset of symptoms. Results. The mean Ct value in the group of patients who developed acute respiratory distress syndrome (ARDS +) was 18.27 (95% CI: 17.43-19.10) while for the ARDS group it was 33.06 (95% CI: 32.77-33.34). Discussion. The Ct values in the group of patients who developed ARDS (ARDS +) were significantly lower than those observed in the ARDS- group. By setting a cut-off value, the determination Ct values (on a qualitative technique) from nasopharyngeal swabs performed during the first week after symptom onset will assist clinicians in risk-stratifying patients. Conclusion. Our data show that the determination of SARS CoV2 RTPCR cycle threshold values from nasopharyngeal swabs performed during the first week after symptom onset may aid in the risk stratification of patients with COVID-19


Subject(s)
Humans , Respiratory Distress Syndrome, Newborn , SARS Virus , COVID-19 Nucleic Acid Testing , COVID-19
4.
Arq. gastroenterol ; 58(3): 353-358, July-Sept. 2021. tab
Article in English | LILACS | ID: biblio-1345299

ABSTRACT

ABSTRACT BACKGROUND: The Prex2 protein is a member of the Rac family proteins that belongs to small G proteins with a critical role in cell migration, cell proliferation, and apoptosis through its effects on PI3K cell signaling pathway and phosphatase activity of PTEN protein. The effect of PREX2 gene expression has been shown in some cancer cells. A survey of PREX2 gene expression in gastric antral epithelial cells of gastric cancer patients with Helicobacter pylori various genotypes infection can conduct to better understanding H. pylori infection's carcinogenesis. METHODS: In a case-control study, PREX2 gene expression was evaluated in gastric antral biopsy samples on four groups of patients referred to Sanandaj hospitals, including gastritis with (n=23) and without (n=27) H. pylori infection and gastric cancer with (n=21) and without (n=32) H. pylori infection. Each gastric biopsy sample's total RNA was extracted and cDNA synthesized by using Kits (Takara Company). The PREX2 gene expression was measured using the relative quantitative real-time RT-PCR method and ΔΔCt formula. RESULTS: The PREX2 gene expression increased in gastric antral biopsy samples of gastritis and gastric cancer patients with H. pylori infection (case groups) than patients without H. pylori infection (control groups) 2.38 and 2.27 times, respectively. The patients with H. pylori vacA s1m1 and sabB genotypes infection showed a significant increase of PREX2 gene expression in gastric cancer antral epithelial cells. CONCLUSION: H. pylori vacA s1m1 and sabB genotypes have the positive correlations with PREX2 gene expression in gastric antral epithelial cells of gastritis and gastric cancer patients.


RESUMO CONTEXTO: A proteína Prex2 é membro das proteínas da família Rac que pertencem a pequenas proteínas G com um papel crítico na migração celular, na proliferação celular e na apoptose através de seus efeitos na via de sinalização celular PI3K e atividade fosfatase da proteína PTEN. O efeito da expressão genética PREX2 tem sido mostrada em algumas células cancerosas. Um levantamento da expressão genética PREX2 em células epiteliais antrais gástricas de pacientes infectados com vários genótipos de Helicobacter pylori pode conduzir a um melhor entendimento da carcinogênese da infecção por H. pylori. MÉTODOS: Em estudo de caso-controle, a expressão genética PREX2 foi avaliada em amostras de biópsia antral gástrica em quatro grupos de pacientes encaminhados aos hospitais de Sanandaj, incluindo gastrite com (n=23) e sem (n=27) infecção por H. pylori e de câncer gástrico com (n=21) e sem (n=32) infecção por H. pylori. O RNA total de cada amostra de biópsia gástrica foi extraído e cDNA sintetizado por meio de kits (Takara Company). A expressão genética PREX2 foi medida utilizando-se o método RT-PCR em tempo real quantitativo relativo e a fórmula ΔΔCt. RESULTADOS: A expressão genética PREX2 aumentou em amostras de biópsia antral gástrica de pacientes com gastrite e câncer gástrico com infecção por H. pylori (grupos de casos) em relação aos sem infecção por H. pylori (grupos de controle) 2,38 e 2,27 vezes, respectivamente. Os pacientes com infecção por genótipos H. pylori vacA s1m1 e sabB apresentaram um aumento significativo da expressão genética PREX2 em células epiteliais antrais de câncer gástrico. CONCLUSÃO: Os genótipos H. pylori vacA s1m1 e sabB têm correlações positivas com a expressão genética PREX2 em células epiteliais antrais gástricas de pacientes com câncer gástrico e gastrites.


Subject(s)
Humans , Helicobacter Infections , Guanine Nucleotide Exchange Factors/genetics , Gastritis/genetics , Gastritis/microbiology , Case-Control Studies , Helicobacter pylori , Epithelial Cells/metabolism , Epithelial Cells/microbiology , Gastric Mucosa
5.
Braz. j. infect. dis ; 25(2): 101542, 2021. tab
Article in English | LILACS | ID: biblio-1278571

ABSTRACT

ABSTRACT In response to the Zika epidemics in Brazil, the ZDC molecular assay (Bio-Manguinhos) was developed and registered at the Brazilian Regulatory Agency of Health Surveillance - ANVISA. The circulation of Zika (ZIKV) Dengue (DENV) and Chikungunya (CHIKV) viruses and their clinical similarities are challenges to correctly diagnose these viruses. The simultaneous detection of ZIKV, DENV and CHIKV is an important tool for diagnosis and surveillance. Here, we present the analytical and clinical performance evaluation of ZDC molecular assay (Bio-Manguinhos) at the public health laboratories three years after its registration at ANVISA. The clinical performance demonstrates the ZDC molecular assay (Bio-Manguinhos) has 100% sensitivity and 100% specificity to detect and discriminate ZIKV, CHIKV, and DENV from clinical plasma samples. The ZDC molecular assay (Bio-Manguinhos) results were highly reproducible and no cross-reactivity was seen during testing with a panel of other infectious agents. In conclusion, the ZDC molecular assay (Bio-Manguinhos) is an accurate and reliable tool to monitor Zika, dengue and chikungunya infections in countries like Brazil with simultaneous circulation of the three viruses.


Subject(s)
Humans , Zika Virus/genetics , Zika Virus Infection/diagnosis , Brazil , Chikungunya virus/genetics , Dengue/diagnosis , Dengue Virus/genetics , Chikungunya Fever/diagnosis , Laboratories
6.
Article | IMSEAR | ID: sea-209679

ABSTRACT

Covid-19 pandemic has affected the whole word medically, economically and emotionally. It is being considered as the biggest pandemic after the Spanish flu, with very high degree of morbidity and mortality in those with complications. The diagnostic and treatment criteria of this novel virus are being updated frequentlyas nothing much is known about it. This highlights the importance of hematology lab parametersin Coviddiagnosis and prediction of disease progression. Multiple studieson complete blood counts and it’s derived parametershave beenconductedin patients of Covid-19however limited literature is available whichdiscussesthe morphology of circulatingblood cellsin Covid-19 cases.This short communicationis presentedwith the purpose of highlighting theperipheral blood findings of 50 lab confirmed Covid-19 cases admitted atSuper SpecialtyPediatric Hospital and Post Graduate Teaching Hospital, NOIDA.Keywords: Covid-19; morbidity and mortality; SARS CoV2; real time RT-PCR.Short Communication

7.
Int J Pharm Pharm Sci ; 2019 May; 11(5): 19-26
Article | IMSEAR | ID: sea-205891

ABSTRACT

Objective: Centella asiatica (L.) Urb from Umbelliferae is a potential source of secondary metabolites having immense medicinal value. Asiaticoside is the major therapeutic compound. In the present study, Identification of a possible relationship between concentration/transcript level expression of asiaticoside and concentrations of growth hormones at different growth stages was observed. The current study includes molecular and biochemical evaluation of stress generated in C. asiatica at different time intervals in vitro. Methods: The enhancement in auxin, cytokinin and final asiaticoside content were determined using immunoassay kits for auxin, cytokinin and HPLC analysis respectively. Transcript level expression at different growth phases was carried out using real-time RT-PCR. For isolation of stress-related miRNAs, reverse transcription of total RNA using miScript II RT Kit PCR System was carried out as per instructions. The differential expression of five selected miRNAs was done by Real-Time RT-PCR. The analysis of stress in vitro was done by quantification of Hydrogen Peroxide (H2O2), total phenolics and total antioxidants by H2O2 assay kit, total antioxidant assay kit and Folin Ciocalteau reagent respectively. The final asiaticoside content was determined by HPLC. Results: Differential expression of key genes involved in asiaticoside pathway showed significantly higher transcript expression, which is in correlation with the final asiaticoside content. The enhanced expression of miRNAs and the analysis of H2O2, total antioxidant capacity and total phenolics are suggestive of generation of oxidative stress under controlled conditions. Conclusion: The present study shows a direct correlation between oxidative stress and transcript/phytochemical estimation of asiaticoside content under in vitro conditions.

8.
Article in Chinese | WPRIM | ID: wpr-805390

ABSTRACT

Objective@#To establish a method for the simultaneous identification of Zika, Chikungunya and Mayaro viruses.@*Methods@#The complete genome sequences of Zika, Chikungunya and Mayaro virus were retrieved from Global Shared Database for comparative analysis, estimate its conservative region and determine the target gene location, specific primers and probes were designed, then a triplex real-time RT-PCR assay was developed. The specificity, sensitivity and repeatability of the assay were assessed by viral nucleic acid of Zika virus, Chikungunya virus a, in vitro transcriptional RNA of Mayaro virus, normal human serum and related virus simulation sample.@*Results@#The result showed that the established method could detect Zika virus, Chikungunya virus, as well as simulated Mayaro virus samples, the limit of detection (LOD) of Zika and Chikungunya virus was 16.22 Copy/PCR and 12.02 Copy/PCR, respectively, the LOD for simulated Mayaro virus RNA was 2.82 Copy/PCR, no significant difference was detected between the triplex and monoplex assays. No cross reaction was found in the detection of dengue virus, Hantavirus, severe fever with thrombocytopenia syndrome (SFTS) virus, yellow fever virus and influenza virus, and 100 healthy adults blood samples, the specificity of the method was 100%. The repeatability result showed that the standard deviation of all three detections were blow 0.5 and the coefficient of variation was less than 2% by selecting viral nucleic acids or transcribed RNA with high, medium and low concentration gradients.@*Conclusions@#A triplex real-time RT-PCR assay for detection of Zika, Chikungunya and Mayaro virus has been established with an acceptable specificity, sensitivity and repeatability.

9.
Braz. j. med. biol. res ; 51(6): e7221, 2018. tab
Article in English | LILACS | ID: biblio-889096

ABSTRACT

Clinical manifestations of Zika, dengue, and chikungunya virus infections are very similar, making it difficult to reach a diagnosis based only on clinical grounds. In addition, there is an intense cross-reactivity between antibodies directed to Zika virus and other flaviviruses, and an accurate Zika diagnosis is best achieved by real-time RT-PCR. However, some real-time RT-PCR show better performance than others. To reach the best possible Zika diagnosis, the analytic sensitivity of some probe-based real-time RT-PCR amplifying Zika virus RNA was evaluated in spiked and clinical samples. We evaluated primers and probes to detect Zika virus, which had been published before, and tested sensitivity using serum spiked and patient samples by real-time RT-PCR. When tested against spiked samples, the previously described primers showed different sensitivity, with very similar results when samples from patients (serum and urine) were analyzed. Real-time RT-PCR designed to amplify Zika virus NS1 showed the best analytical sensitivity for all samples.


Subject(s)
Humans , RNA, Viral/genetics , Dengue/diagnosis , Chikungunya Fever/diagnosis , Zika Virus/genetics , Zika Virus Infection/diagnosis , Clinical Protocols , Sensitivity and Specificity , Reverse Transcriptase Polymerase Chain Reaction , Coinfection , Real-Time Polymerase Chain Reaction
10.
Article in Chinese | WPRIM | ID: wpr-806847

ABSTRACT

Objective@#To investigate the presence of hepatitis E virus (HEV) RNA and HEV antigen (HEV-Ag) and to evaluate the infectivity of HEV in urine through a SPF rabbit model of HEV infection.@*Methods@#Serum, fecal and urine samples collected from SPF rabbits with HEV infection were tested for viral and biochemical markers using real-time RT-PCR and ELISA. Liver and kidney biopsies were performed for observing histopathological changes and immunohistochemical staining. Rabbits were challenged with HEV isolated in urine samples to evaluate the infectivity.@*Results@#Rabbit R1# that was injected with rabbit HEV presented viremia, fecal shedding of HEV, high serum level of HEV-Ag, elevated aspartate transaminase (AST) and alanine transaminase (ALT) and typical symptoms of hepatitis. Urine samples of rabbit R1# continued to be positive for HEV RNA and HEV-Ag. Ratios of HEV-Ag to RNA in urine samples of rabbit R1# were significantly higher than those in serum and feces samples. The parameters quantified in routine urinalysis remained within the normal ranges in rabbit R1#. However, pathological changes and the presence of HEV-Ag were observed in kidney tissues. Furthermore, serum and fecal samples that were collected from one of the two rabbits injected with rabbit R1# urine-derived HEV were HEV positive and the virus strains isolated form feces remained infective to rabbits.@*Conclusion@#HEV infection may result in kidney injury and the urine may pose a risk of transmission. HEV-Ag detection in urine may be valuable for the diagnosis of ongoing HEV infection.

11.
Article in English | WPRIM | ID: wpr-690669

ABSTRACT

<p><b>OBJECTIVE</b>To detect Japanese encephalitis virus (JEV) rapidly and distinguish its genotypes, a TaqMan-based reverse transcriptase quantitative polymerase chain reaction (RT-PCR) detection system was developed.</p><p><b>METHODS</b>By aligning the full-length sequences of JEV (G1-G5), six sets of highly specific TaqMan real-time RT-PCR primers and probes were designed based on the highly conserved NS1, NS2, and M genes of JEV, which included one set for non-specific JEV detection and five sets for the detection of specific JEV genotypes. Twenty batches of mosquito samples were used to evaluate our quantitative PCR assay.</p><p><b>RESULTS</b>With the specific assay, no other flavivirus were detected. The lower limits of detection of the system were 1 pfu/mL for JEV titers and 100 RNA copies/µL. The coefficients of variation of this real-time RT-PCR were all < 2.8%. The amplification efficiency of this method was between 90% and 103%.</p><p><b>CONCLUSION</b>A TaqMan real-time RT-PCR detection system was successfully established to detect and differentiate all five JEV genotypes.</p>


Subject(s)
Animals , Culicidae , Virology , Encephalitis Virus, Japanese , Genetics , Polymerase Chain Reaction , Methods , Reproducibility of Results , Sensitivity and Specificity
12.
Chinese Journal of Biotechnology ; (12): 1579-1586, 2018.
Article in Chinese | WPRIM | ID: wpr-687662

ABSTRACT

The HA gene of H9N2 influenza virus (A/chicken/Hunan/04.14 (H9N2)) was amplified and sequenced. The RNA was synthesized by in vitro transcription. The RNA transcription solutions were diluted to 10⁹ copies/μL using the RNA storage solution. The aliquoted RNA solutions were used to evaluate the homogeneity and stability. The results were determined by the average value obtained from four independent laboratories. Furthermore, the fluorescence quantitative RT-PCR method was also developed to verify the detection accuracy of clinical samples. The detection limit of this method is approximately 10 copies. Taken together, the RNA transcription solution established in our study can used as positive standard reference for rapid detection of H9N2 influenza virus.

13.
Electron. j. biotechnol ; 27: 80-83, May. 2017. ilus, graf
Article in English | LILACS | ID: biblio-1010415

ABSTRACT

Background: A protocol for the micropropagation of the grape (Vitis vinifera L.) cultivar 'Monastrell' was developed. Initial plant material was obtained from the sanitary selection of grapevine plants performed by real-time RT-PCR to confirm the absence of Grapevine fanleaf virus, Arabis mosaic virus, Grapevine leafroll-associated virus 1, Grapevine leafroll-associated virus 3, and Grapevine fleck virus. Results: The effects of the salt composition (comparing Lloyd and McCown woody plant medium and Murashige and Skoog medium 1/2 macronutrients) and the growth regulator benzylaminopurine (BAP), at 0 and 8.9 µM, on plant propagation were evaluated using nodes as explants. The most efficient procedure consisted of bud induction in the medium with Lloyd and McCown woody plant salts and 8.9 µM BAP for 30 d along with elongation in cytokinin-free medium for 60 d, which gave 22 nodes/explant (174 plants/initial plant). A second cycle of propagation in a medium without BAP for another 60 d could give approximately 10,000 nodes, which can be obtained after an additional 2 months of culture. All plants acclimatized after the second cycle of multiplication were successfully transferred to soil. Conclusion: We developed an optimal protocol for V. vinifera cv. 'Monastrell' micropropagation, the first described for this cultivar.


Subject(s)
Vitis/growth & development , Purines/metabolism , Benzyl Compounds/metabolism , In Vitro Techniques , Sodium Chloride/metabolism , Vitis/virology , Real-Time Polymerase Chain Reaction , Acclimatization
14.
Chinese Journal of Zoonoses ; (12): 1002-1006,1017, 2017.
Article in Chinese | WPRIM | ID: wpr-664371

ABSTRACT

In order to establish a real-time RT-PCR based on SYBR Green Ⅱ for detection of hepatitis E virus (HEV),a pair of special primers was designed according to the conserved sequences of ORF2 in GenBank.Result showed that the standard curve of established SYBR Green Ⅱ real-time RT-PCR had a wide dynamic range from 4.10 × 102-4.10 × 108 copies/μL with a linear correlation(r2) of 0.996.The sensitivity could reach 1.00 × 102 copies/μL.The melting curve analysis using SYBR Green Ⅱ dye showed one specific peak with a melting temperature(Tm) of 84.0 C ±0.1 C.No amplification was detected from the RNA samples of porcine reproductive and respiratory syndrome virus,classial swine fever virus,transmissible gastroenteritis virus,porcine bocavirus,porcine epidemic dearrhoea virus porcine kobuvirus and porcine rotavirus by this PCR,respectively.Excellent reproducibility was obtained for detecting constructed positive plasmid DNA with intra-assay of 0.83 %-0.94 % and inter-assay of 0.83%-0.94%.Further detection of 61 specimens showed that 9 of them were HEV positive,and the results of the quantitative RT-PCR were the same as that of the conventional RT-PCR.In conclusion,the real-time quantitative RT-PCR for HEV is feasible,the real-time RT-PCR established in this study will be useful for earlier rapid laboratory diagnosis and pathogenesis of HEV.

15.
Article in Chinese | WPRIM | ID: wpr-807984

ABSTRACT

Objective@#To establish a TaqMan-MGB probe-based real-time fluorescence RT-PCR assay for avian influenza H5N6 virus used in rapid diagnosis for suspected cases and surveillance for outer environment of live poultry markets.@*Methods@#Based on the conservative sequences of avian influenza H5N6 virus for HA and NA gene published on GenBank, specific primers and TaqMan-MGB probes were designed to develop and optimize for the dual real-time RT-PCR assay. Specificity, sensitivity, repeatability and comparison tests were carried out.@*Results@#This dual real-time RT-PCR detection can be completed within 80 minutes. There was no cross-reaction with other subtypes of influenza virus and common respiratory pathogens. The minimum detection limit could be up to 10 copies/reaction. The correlation coefficient of standard curve for the gene of H5 and N6 were 0.999 and 0.993, and the coefficients of variation for cycle threshold were range from 0.151%-0.549%and 0.213%-0.575%, respectively. The positive and negative coincidence rates of the validation test were 100%.@*Conclusions@#This TaqMan-MGB probe-based dual real-time RT-PCR for avian influenza H5N6 virus was rapid, specific and sensitive. It will have a good use in early emergency detection of suspected cases and continuous monitoring of external environment in live poultry trade market.

16.
Chinese Journal of Biotechnology ; (12): 1265-1275, 2017.
Article in Chinese | WPRIM | ID: wpr-242259

ABSTRACT

Porcine deltacoronavirus (PDCoV) has been recently recognized as an emerging viral pathogen that causes diarrhea in newborn piglets. A total of 254 small intestinal or fecal samples collected from 10 provinces including Henan, Hunan, Zhejiang, Jiangxi, Anhui, Hebei, Heilongjiang, Jiangsu, Shandong and Shanghai between 2014 and 2015, were screened by quantitative RT-PCR targeting the viral M gene. Eleven PDCoV positive samples were identified with a total positive rate of 4.33%. An indirect enzyme-linked immunosorbent assay (ELISA) was developed based on the recombinant S1 protein of PDCoV. This assay was used to test 609 serum samples of pigs with diarrhea symptoms collected from 10 provinces between 2015 and 2016. The positive rate of PDCoV antibody was 44.17% (269/609). The two methods can be used to monitor the PDCoV epidemiology in the levels of PDCoV specific RNA or antibody, helping better prevent and control PDCoV.

17.
Article in English | WPRIM | ID: wpr-8647

ABSTRACT

From 2013 to 2015, the National Institute of Health, Pakistan, received 1,270 blood samples of suspected dengue cases reported from inpatient and outpatient departments of various hospitals in Khyber Pakhtunkhwa (KPK) province. In this study, we determined the circulating dengue virus (DENV) serotypes using real-time reverse transcriptase (RT)-PCR to understand the serotype-based epidemiology of DENV. All four serotypes (DENV-1 [6%], DENV-2 [33%], DENV-3 [47%], and DENV-4 [0.1%]) were found circulating during the study period. Our findings suggest the need for an active surveillance system coupled with the laboratory diagnosis, especially in the chronic endemic areas of the country. Public awareness programs are needed for effective control and prevention of outbreaks in the future.


Subject(s)
Adolescent , Adult , Dengue/diagnosis , Dengue Virus/genetics , Disease Outbreaks , Female , Humans , Male , Middle Aged , Pakistan/epidemiology , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Serogroup , Young Adult
18.
Mem. Inst. Oswaldo Cruz ; 111(6): 385-390, June 2016. tab, graf
Article in English | LILACS | ID: lil-784246

ABSTRACT

Vesiculoviruses (VSV) are zoonotic viruses that cause vesicular stomatitis disease in cattle, horses and pigs, as well as sporadic human cases of acute febrile illness. Therefore, diagnosis of VSV infections by reliable laboratory techniques is important to allow a proper case management and implementation of strategies for the containment of virus spread. We show here a sensitive and reproducible real-time reverse transcriptase polymerase chain reaction (RT-PCR) for detection and quantification of VSV. The assay was evaluated with arthropods and serum samples obtained from horses, cattle and patients with acute febrile disease. The real-time RT-PCR amplified the Piry, Carajas, Alagoas and Indiana Vesiculovirus at a melting temperature 81.02 ± 0.8ºC, and the sensitivity of assay was estimated in 10 RNA copies/mL to the Piry Vesiculovirus. The viral genome has been detected in samples of horses and cattle, but not detected in human sera or arthropods. Thus, this assay allows a preliminary differential diagnosis of VSV infections.


Subject(s)
Humans , Animals , Vesicular Stomatitis/diagnosis , Vesiculovirus/genetics , Cattle , Horses/virology , Real-Time Polymerase Chain Reaction , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction , RNA, Viral/genetics , Sensitivity and Specificity
19.
Rev. Soc. Bras. Med. Trop ; 49(3): 279-285, tab, graf
Article in English | LILACS | ID: lil-785796

ABSTRACT

Abstract: INTRODUCTION: The genus Flavivirus includes several pathogenic species that cause severe illness in humans. Therefore, a rapid and accurate molecular method for diagnosis and surveillance of these viruses would be of great importance. Here, we evaluate and optimize a quantitative real-time reverse transcription polymerase chain reaction (RT-PCR) method for the diagnosis of the Flavivirus genus. METHODS: We evaluated different commercial kits that use the SYBR Green system for real-time RT-PCR with a primer set that amplifies a fragment of the NS5 flavivirus gene. The specificity and sensitivity of the assay were tested using twelve flaviviruses and ribonucleic acid (RNA) transcribed from the yellow fever virus. Additionally, this assay was evaluated using the sera of 410 patients from different regions of Brazil with acute febrile illness and a negative diagnosis for the dengue virus. RESULTS: The real-time RT-PCR amplified all flaviviruses tested at a melting temperature of 79.92 to 83.49°C. A detection limit of 100 copies per ml was determined for this assay. Surprisingly, we detected dengue virus in 4.1% (17/410) of samples from patients with febrile illness and a supposedly negative dengue infection diagnosis. The viral load in patients ranged from 2.1×107to 3.4×103copies per ml. CONCLUSIONS: The real-time RT-PCR method may be very useful for preliminary diagnoses in screenings, outbreaks, and other surveillance studies. Moreover, this assay can be easily applied to monitor viral activity and to measure viral load in pathogenesis studies.


Subject(s)
Humans , Flavivirus Infections/diagnosis , Flavivirus/genetics , Organic Chemicals , Reagent Kits, Diagnostic , Brazil , RNA, Viral/genetics , Sensitivity and Specificity , Flavivirus Infections/virology , DNA Primers , Reverse Transcriptase Polymerase Chain Reaction/methods , Flavivirus/isolation & purification , Flavivirus/classification , Fluorescent Dyes
20.
Article in English | IMSEAR | ID: sea-178824

ABSTRACT

Chandipura virus (CHPV) (Vesiculovirus: Rhabdoviridae) garnered global attention as an emerging neurotropic pathogen inflicting high mortality in children within 24 h of commencement of symptoms. The 2003-2004 outbreaks in Central India witnessed case fatality rates ranging from 56-75 per cent in Andhra Pradesh and Gujarat with typical encephalitic symptoms. Due to the acute sickness and rapid deterioration, the precise mechanism of action of the virus is still unknown. Recent studies have shown increased expression of CHPV phosphoprotein upto 6 h post infection (PI) demonstrating CHPV replication in neuronal cells and the rapid destruction of the cells by apoptosis shed light on the probable mechanism of rapid death in children. Phlebotomine sandflies are implicated as vectors due to their predominance in endemic areas, repeated virus isolations and their ability to transmit the virus by transovarial and venereal routes. Significant contributions have been made in the development of diagnostics and prophylactics, vaccines and antivirals. Two candidate vaccines, viz. a recombinant vaccine and a killed vaccine and siRNAs targeting P and M proteins have been developed and are awaiting clinical trials. Rhabdomyosarcoma and Phlebotomus papatasi cell lines as well as embryonated chicken eggs have been found useful in virus isolation and propagation. Despite these advancements, CHPV has been a major concern in Central India and warrants immediate attention from virologists, neurologists, paediatricians and the government for containing the virus.

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