scholarly journals Peste des petits ruminants virus infection of goats in Bangladesh: Pathological investigation, molecular detection and isolation of the virus

1970 ◽  
Vol 28 (1) ◽  
pp. 1-7 ◽  
Author(s):  
MA Rahman ◽  
I Shadmin ◽  
M Noor ◽  
R Parvin ◽  
EH Chowdhury ◽  
...  
Keyword(s):  
Lymph Node ◽  
Vero Cells ◽  
Viral Rna ◽  
Sub Saharan Africa ◽  
Tissue Homogenate ◽  
Clinical Samples ◽  
Peste Des Petits Ruminants ◽  
Rt Pcr ◽  
Sub Saharan ◽  
Bronchial Lymph Node

Peste des petits ruminants (PPR), an economically important morbillivirus infection of sheep and goats, is widely distributed in sub-Saharan Africa, Middle East and western and southern Asia including Bangladesh.  A small flock of Black Bengal goats contracted PPR following introduction of new animals. A pathological investigation was conducted on the outbreak, the viral RNA corresponding to F gene was detected by RT-PCR and the virus was isolated in Vero cells. Out of 37 goats 19 (51%) developed clinnical disease, of which 5 (13.5%) died. Goats under one year of age had highest morbidity and mortality with typical signs and lesions of PPR. Viral RNA should be detected in mesenteric and bronchial lymph node tissues. Typical cytopathic effects (CPE) in Vero cells following inoculation of lymph node tissue homogenate were visible at the third passage. However, the replication of virus in cel culture was detected by RT-PCR at the first and second passage in the absence of visible CPE. RT-PCR appears to be a very useful and sensitive tool not only for the detection of PPR virus in clinical samples but also for monitoring the growth or virus in cell culture following inoculation.DOI: http://dx.doi.org/10.3329/bvet.v28i1.8808 Bangl. vet. 2011. Vol. 28, No. 1, 1–7

scholarly journals PO 8581 ZOONOTIC VIRAL ANTIGENS SURVEILLANCE IN HEALTHY POPULATIONS LIVING IN LAMBARÉNÉ, GABON

2019 ◽  
Vol 4 (Suppl 3) ◽  
pp. A58.2-A58
Author(s):  
Emmanuel Bache ◽  
Marguerite M Loembe ◽  
Selidji T Agnandji
Keyword(s):  
Disease Transmission ◽  
Disease Surveillance ◽  
Vaccine Trial ◽  
Viral Rna ◽  
Sub Saharan Africa ◽  
Surveillance Systems ◽  
Rt Pcr ◽  
Zoonotic Infections ◽  
Viral Antigens ◽  
Sub Saharan

BackgroundWorldwide, viral zoonotic infections such as filoviruses, flaviviruses, nairoviruses and arenaviruses cause self-limiting to severe diseases. They are endemic in sub-Saharan Africa, causing sporadic outbreaks warranting the development of sustainable surveillance systems. In Gabon, Ebola outbreaks occurred from 1994 to 2002 causing 214 human cases and 150 deaths, while Dengue, Zika and Chikungunya virus outbreaks occurred between 2007 and 2010. Beyond these outbreaks, little is known about the epidemiology. Recently, in collaboration with the Japanese government, the Research and Health Ministries of Gabon supported the implementation of a biosecurity level-3 (BSL-3) laboratory at CERMEL in Lambaréné as a zoonotic disease surveillance unit. Start-off involved antigen detection and characterisation of circulating antibodies to targeted viral antigens in healthy populations. This study reports data from healthy participants (18–50 years) in a phase I rVSV-ZEBOV-GP Ebola vaccine trial.MethodsHundred-six (106) baseline samples were screened for Ebola, Dengue (serotypes) 1–4 and Chikungunya viral RNA by RT-PCR on serum. IgG ELISA on plasma was used to identify antibodies against: Zaire-Ebola-(EBOV-GP and EBOV-VP40), Marburg-(MARV-GP and MARV-VP40), Crimean Congo Haemorrhagic Fever-(CCHFV-GP), Lasa-(LASV-GPC and LASV-NP), Yellow Fever-(YFV-NS1), West-Nile-(WNV-NS1), Zika virus-(ZIKV-NS1), Chikungunya-(CHIKV-VLP) and Dengue-(DENV1-NS1,DENV2-NS1,DENV3-NS1,DENV4-NS1) virus antigens.ResultsNo viral RNA was isolated by RT-PCR in 106 samples. About 9% (10/106), 3% (3/106), 6% (6/106), 24% (25/106), 51% (54/106), 38% (40/106) and 36% (38/106) participants were seropositive for antibodies specific to EBOV-GP, MARV-GP, CCHFV-GP, YFV-NS1, WNV-NS1, ZIKV-NS1 and CHIKV-VLP, respectively. Twelve percent (12%; 13/106) of participants possessed antibodies specific to Zika, Chikungunya and Dengue 1–4 antigens. Six percent (6%; 6/106) of participants were seropositive for EBOV-GP and CCHFV-GP.ConclusionWe found antibodies to viral zoonotic infections among our healthy volunteers. Further assays, including neutralisation assays are being performed to ascertain the specificity of the antibodies. These findings, once confirmed, will provide insights into disease surveillance, vaccine trial designs, evaluation of post-vaccine immune responses, variability in adverse events and overall disease transmission patterns.

scholarly journals Quantitative measurement of infectious virus in SARS-CoV-2 Alpha, Delta and Epsilon variants reveals higher infectivity (viral titer:RNA ratio) in clinical samples containing the Delta and Epsilon variants.

2021 ◽  
Author(s):  
Hannah W Despres ◽  
Margaret G Mills ◽  
David J Shirley ◽  
Madaline M Schmidt ◽  
Meei-Li Huang ◽  
...  
Keyword(s):  
Quantitative Measurement ◽  
Infectious Virus ◽  
Viral Rna ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Genome Copy ◽  
Live Virus ◽  
High Degree ◽  
The Relationship ◽  
Rna Levels

ABSTRACT Background Novel SARS-CoV-2 Variants of Concern (VoC) pose a challenge to controlling the COVID-19 pandemic. Previous studies indicate that clinical samples collected from individuals infected with the Delta variant may contain higher levels of RNA than previous variants, but the relationship between viral RNA and infectious virus for individual variants is unknown. Methods We measured infectious viral titer (using a micro-focus forming assay) as well as total and subgenomic viral RNA levels (using RT-PCR) in a set of 165 clinical samples containing SARS-CoV-2 Alpha, Delta and Epsilon variants that were processed within two days of collection from the patient. Results We observed a high degree of variation in the relationship between viral titers and RNA levels. Despite the variability we observed for individual samples the overall infectivity differed among the three variants. Both Delta and Epsilon had significantly higher infectivity than Alpha, as measured by the number of infectious units per quantity of viral E gene RNA (6 and 4 times as much, p=0.0002 and 0.009 respectively) or subgenomic E RNA (11 and 7 times as much, p<0.0001 and 0.006 respectively). Conclusion In addition to higher viral RNA levels reported for the Delta variant, the infectivity (amount of replication competent virus per viral genome copy) may also be increased compared to Alpha. Measuring the relationship between live virus and viral RNA is an important step in assessing the infectivity of novel SARS-CoV-2 variants. An increase in the infectivity of the Delta variant may further explain increased spread and suggests a need for increased measures to prevent viral transmission.

scholarly journals Inactivation of SARS-CoV-2 virus in saliva using a guanidium based transport medium suitable for RT-PCR diagnostic assays

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252687
Author(s):  
Sukalyani Banik ◽  
Kaheerman Saibire ◽  
Shraddha Suryavanshi ◽  
Glenn Johns ◽  
Soumitesh Chakravorty ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Viral Rna ◽  
Clinical Samples ◽  
Sample Collection ◽  
Rt Pcr ◽  
Diagnostic Assays ◽  
Guanidinium Thiocyanate ◽  
Upper Respiratory ◽  
Polymerase Chain ◽  
The Stability

Background Upper respiratory samples used to test for SARS-CoV-2 virus may be infectious and present a hazard during transport and testing. A buffer with the ability to inactivate SARS-CoV-2 at the time of sample collection could simplify and expand testing for COVID-19 to non-conventional settings. Methods We evaluated a guanidium thiocyanate-based buffer, eNAT™ (Copan) as a possible transport and inactivation medium for downstream Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) testing to detect SARS-CoV-2. Inactivation of SARS-CoV-2 USA-WA1/2020 in eNAT and in diluted saliva was studied at different incubation times. The stability of viral RNA in eNAT was also evaluated for up to 7 days at room temperature (28°C), refrigerated conditions (4°C) and at 35°C. Results SARS-COV-2 virus spiked directly in eNAT could be inactivated at >5.6 log10 PFU/ml within a minute of incubation. When saliva was diluted 1:1 in eNAT, no cytopathic effect (CPE) on VeroE6 cells was observed, although SARS-CoV-2 RNA could be detected even after 30 min incubation and after two cell culture passages. A 1:2 (saliva:eNAT) dilution abrogated both CPE and detectable viral RNA after as little as 5 min incubation in eNAT. SARS-CoV-2 RNA from virus spiked at 5X the limit of detection remained positive up to 7 days of incubation in all tested conditions. Conclusion eNAT and similar guanidinium thiocyanate-based media may be of value for transport, stabilization, and processing of clinical samples for RT-PCR based SARS-CoV-2 detection.

scholarly journals Analytical Performances of Human Immunodeficiency Virus Type 1 RNA-Based Amplix® Real-Time PCR Platform for HIV-1 RNA Quantification

2016 ◽  
Vol 2016 ◽  
pp. 1-12
Author(s):  
Christian Diamant Mossoro-Kpinde ◽  
Ralph-Sydney Mboumba Bouassa ◽  
Mohammad-Ali Jenabian ◽  
Serge Tonen Wolyec ◽  
Leman Robin ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Dynamic Range ◽  
Limit Of Detection ◽  
Central Africa ◽  
Sub Saharan Africa ◽  
Clinical Samples ◽  
Absolute Bias ◽  
Sub Saharan ◽  
Hiv 1

Objectives. We evaluated the performances of Amplix real-time PCR platform developed by Biosynex (Strasbourg, France), combining automated station extraction (Amplix station 16 Dx) and real-time PCR (Amplix NG), for quantifying plasma HIV-1 RNA by lyophilized HIV-1 RNA-based Amplix reagents targeting gag and LTR, using samples from HIV-1-infected adults from Central African Republic. Results. Amplix real-time PCR assay showed low limit of detection (28 copies/mL), across wide dynamic range (1.4–10 log copies/mL), 100% sensitivity and 99% specificity, high reproducibility, and accuracy with mean bias < 5%. The assay showed excellent correlations and concordance of 95.3% with the reference HIV-1 RNA load assay (Roche), with mean absolute bias of +0.097 log copies/mL by Bland-Altman analysis. The assay was able to detect and quantify the most prevalent HIV-1 subtype strains and the majority of non-B subtypes, CRFs of HIV-1 group M, and HIV-1 groups N and O circulating in Central Africa. The Amplix assay showed 100% sensitivity and 99.6% specificity to diagnose virological failure in clinical samples from antiretroviral drug-experienced patients. Conclusions. The HIV-1 RNA-based Amplix real-time PCR platform constitutes sensitive and reliable system for clinical monitoring of HIV-1 RNA load in HIV-1-infected children and adults, particularly adapted to intermediate laboratory facilities in sub-Saharan Africa.

scholarly journals Typing of Dengue Viruses in Clinical Specimens and Mosquitoes by Single-Tube Multiplex Reverse Transcriptase PCR

1998 ◽  
Vol 36 (9) ◽  
pp. 2634-2639 ◽  
Author(s):  
Eva Harris ◽  
T. Guy Roberts ◽  
Leila Smith ◽  
John Selle ◽  
Laura D. Kramer ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Dengue Fever ◽  
Internal Control ◽  
Extraction Procedure ◽  
Rna Degradation ◽  
Viral Rna ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Single Tube ◽  
Dengue Viruses

In recent years, dengue viruses (serotypes 1 to 4) have spread throughout tropical regions worldwide. In many places, multiple dengue virus serotypes are circulating concurrently, which may increase the risk for the more severe form of the disease, dengue hemorrhagic fever. For the control and prevention of dengue fever, it is important to rapidly detect and type the virus in clinical samples and mosquitoes. Assays based on reverse transcriptase (RT) PCR (RT-PCR) amplification of dengue viral RNA can offer a rapid, sensitive, and specific approach to the typing of dengue viruses. We have reduced a two-step nested RT-PCR protocol to a single-tube reaction with sensitivity equivalent to that of the two-step protocol (1 to 50 PFU) in order to maximize simplicity and minimize the risk of sample cross-contamination. This assay was also optimized for use with a thermostable RT-polymerase. We designed a plasmid-based internal control that produces a uniquely sized product and can be used to control for both reverse transcription or amplification steps without the risk of generating false-positive results. This single-tube RT-PCR procedure was used to type dengue viruses during the 1995 and 1997-1998 outbreaks in Nicaragua. In addition, an extraction procedure that permits the sensitive detection of viral RNA in pools of up to 50 mosquitoes without PCR inhibition or RNA degradation was developed. This assay should serve as a practical tool for use in countries where dengue fever is endemic, in conjunction with classical methods for surveillance and epidemiology of dengue viruses.

scholarly journals First Report of the Green Rosette Variant of Groundnut Rosette Disease in Kenya

Plant Disease ◽  
1999 ◽  
Vol 83 (8) ◽  
pp. 782-782 ◽  
Author(s):  
A. W. Wangai ◽  
S. S. Pappu ◽  
H. R. Pappu ◽  
N. Okoko ◽  
C. M. Deom ◽  
...  
Keyword(s):  
Sub Saharan Africa ◽  
Satellite Rna ◽  
Rt Pcr ◽  
Crop Season ◽  
Production Constraints ◽  
Pcr Product ◽  
Arachis Hypogaea L ◽  
Disease Surveys ◽  
Polymerase Chain ◽  
Sub Saharan

Groundnut (Arachis hypogaea L.) is an important food crop in sub-Saharan Africa. One of the major production constraints is groundnut rosette disease, which is caused by a complex of two viruses, groundnut rosette assistor luteovirus (GRAV) and groundnut rosette umbravirus (GRV) together with the associated satellite RNA (satRNA) (1). Two main forms of the disease have been described: chlorotic and the green rosette. Variants of the satRNA have been shown to be largely responsible for the different forms of the disease (1). Chlorotic rosette has been the predominant form in all of sub-Saharan Africa while green rosette has been reported in the western and southern regions of Africa (2). During the 1997-1998 crop season, disease surveys conducted in Kenya showed the incidence of the rosette disease in farmers' fields to be 24 to 40% in a total of 23 fields surveyed in the western regions of the country (Homabay, Kendubay, Kisumu) and 30% in 8 fields sampled in the Rift Valley (Cheplamus, Marigat) regions. Representative peanut plants showing rosette symptoms were analyzed for the presence of GRV by reverse transcription polymerase chain reaction (RT-PCR). With primers specific to a portion of ORF4 of GRV RNA (3), RT-PCR gave a product of expected size (approximately 300 bp). The PCR product was cloned in pGEM-T vector and sequenced. The sequenced region showed 89% nucleotide sequence identity with published GRV sequences. Green rosette was observed on groundnut cultivars Nyaela Red and Homabay Local in the Kendu Bay region. The incidence of the green rosette was 5.3% of the plants with rosette symptoms. References: (1) A. F. Murant and I. K. Kumar. Ann. Appl. Biol. 117:85, 1990. (2) R. A. Naidu et al. Ann. Appl. Biol. 132:525, 1998. (3). M. E. Taliansky et al. J. Gen. Virol. 77:2335, 1996.

scholarly journals Biosafety level-2 laboratory diagnosis of Zaire Ebola virus disease imported from Liberia to Nigeria

2016 ◽  
Vol 5 (1) ◽  
Author(s):  
Olumuyiwa B. Salu ◽  
Ayorinde B. James ◽  
Bamidele O. Oke ◽  
Mercy R. Orenolu ◽  
Roosevelt A. Anyanwu ◽  
...  
Keyword(s):  
Ebola Virus ◽  
Virus Disease ◽  
Rna Extraction ◽  
Molecular Techniques ◽  
Viral Rna ◽  
Sub Saharan Africa ◽  
Ebola Virus Disease ◽  
Rt Pcr ◽  
Route Of Transmission ◽  
Biosafety Level

Introduction: Global travel is an efficient route of transmission for highly infectious pathogens and increases the chances of such pathogens moving from high disease-endemic areas to new regions. We describe the rapid and safe identification of the first imported case of Ebola virus disease in a traveler to Lagos, Nigeria, using conventional reverse transcription polymerase chain reaction (RT-PCR) in a biosafety level (BSL)-2 facility.Case presentation: On 20 July 2014, a traveler arrived from Liberia at Lagos International Airport and was admitted to a private hospital in Lagos, with clinical suspicion of Ebola virus disease.Methodology and Outcome: Blood and urine specimens were collected, transported to the Virology Unit Laboratory at the College of Medicine, University of Lagos, and processed under stringent biosafety conditions for viral RNA extraction. RT-PCR was set-up to query the Ebola, Lassa and Dengue fever viruses. Amplicons for pan-filoviruses were detected as 300 bp bands on a 1.5% agarose gel image; there were no detectable bands for Lassa and Dengue viral RNA. Nucleotide BLAST and phylogenetic analysis of sequence data of the RNA-dependent RNA polymerase (L) gene confirmed the sequence to be Zaire ebolavirus (EBOV/Hsap/ NGA/2014/LIB-NIG 01072014; Genbank: KM251803.1).Conclusion: Our BSL-2 facility in Lagos, Nigeria, was able to safely detect Ebola virus disease using molecular techniques, supporting the reliability of molecular detection of highly infectious viral pathogens under stringent safety guidelines in BSL-2 laboratories. This is a significant lesson for the many under-facilitated laboratories in resource-limited settings, as is predominantly found in sub-Saharan Africa.

Diagnosis of foot-and-mouth disease by RT-PCR: use of phylogenetic data to evaluate primers for the typing of viral RNA in clinical samples

2001 ◽  
Vol 146 (12) ◽  
pp. 2421-2434 ◽  
Author(s):  
S. M. Reid ◽  
N. P. Ferris ◽  
G. H. Hutchings ◽  
K. De Clercq ◽  
B. J. Newman ◽  
...  
Keyword(s):  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Viral Rna ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Phylogenetic Data ◽  
Foot And Mouth

scholarly journals Ex-ante assessment of different vaccination-based control schedules against the peste des petits ruminants virus in sub-Saharan Africa

PLoS ONE ◽  
2018 ◽  
Vol 13 (1) ◽  
pp. e0190296 ◽  
Author(s):  
Pachka Hammami ◽  
Renaud Lancelot ◽  
Joseph Domenech ◽  
Matthieu Lesnoff
Keyword(s):  
Sub Saharan Africa ◽  
Peste Des Petits Ruminants ◽  
Ex Ante ◽  
Sub Saharan

scholarly journals Molecular and Virological Investigation of a Focal Chikungunya Outbreak in Northern India

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Manisha Soni ◽  
Anil Kumar Singh ◽  
Shashi Sharma ◽  
Ankita Agarwal ◽  
Natarajan Gopalan ◽  
...  
Keyword(s):  
Aedes Aegypti ◽  
Chikungunya Virus ◽  
Viral Rna ◽  
Clinical Samples ◽  
Nucleotide Sequencing ◽  
The Novel ◽  
Rt Pcr ◽  
Northern India ◽  
Genotype Identification ◽  
Mosquito Pool

Chikungunya (CHIK) fever is one of the most important arboviral infections of medical significance. The objective of the present study is to identify and characterize the etiology of a focal febrile arthritis outbreak from Gwalior, northern India, during October-November 2010. A detailed virological (isolation) and molecular (end-point RT-PCR, quantitative RT-PCR, and nucleotide sequencing) investigation of this outbreak was carried out by collecting and studying 52 clinical samples and 15 mosquito pools from the affected region. The investigation revealed the presence of CHIK viral RNA in 29% of clinical samples and 13% mosquito pool by RT-PCR. The quantification of CHIK viral RNA in samples varied from 102.50to 106.67 copies/mL, as demonstrated through quantitative RT-PCR. In addition, six CHIK viruses were isolated from RT-PCR positive samples. The nucleotide sequences of partial E1 gene of five representative CHIK viruses were deciphered, which revealed that all the viral strains from this outbreak belong to the recently emerging ECS African genotype. Identification of Chikungunya virus ECSA African genotype as the etiology of the present outbreak confirms the continued circulation of the novel genotype, since 2006, in India. The identification of CHIK virus inAedes aegyptialso confirmed it as the major vector in northern India.

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