Rapid Detection and Differentiation of Dengue Virus Serotypes by a Real-Time Reverse Transcription-Loop-Mediated Isothermal Amplification Assay

Parida, Manmohan; Horioke, Kouhei; Ishida, Hiroyuki; Dash, Paban Kumar; Saxena, Parag; Jana, Asha Mukul; Islam, MA; Inoue, Satoshi; Hosaka, Norimitsu; Morita, Kouichi

doi:10.1128/jcm.43.6.2895-2903.2005

Cited by 310 publications

(250 citation statements)

References 19 publications

(37 reference statements)

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“…These specimens gave negative results in the sRT-LAMP assay within 90 min (data not shown). The specificity and selectivity of the RT-LAMP assay has also been demonstrated in previous studies (3,10,11).…”

supporting

confidence: 67%

Simultaneous Detection and Genogroup‐Screening Test for Norovirus Genogroups I and II from Fecal Specimens in Single Tube by Reverse Transcription‐Loop‐Mediated Isothermal Amplification Assay

Fukuda¹,

Sasaki²,

Kuwayama

et al. 2007

Microbiology and Immunology

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We developed a reverse transcription‐loop‐mediated isothermal amplification (RT‐LAMP) assay for the rapid detection of noroviruses (NoVs) in a genogroup‐specific manner in a previous study. In this study, to detect NoVs more easily and simply, we have developed an RT‐LAMP assay for the simultaneous detection of NoV genogroup I (GI) and II (GII) genomes in a single tube. The genogrouping was achieved by using fluorescence‐labeled primers, and the green and red colors for GI and GII, respectively, sometimes with yellow color for GI and GII mixture, were indicated on the agarose gel under UV light at 312 nm.

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supporting

confidence: 67%

Simultaneous Detection and Genogroup‐Screening Test for Norovirus Genogroups I and II from Fecal Specimens in Single Tube by Reverse Transcription‐Loop‐Mediated Isothermal Amplification Assay

Fukuda¹,

Sasaki²,

Kuwayama

et al. 2007

Microbiology and Immunology

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“…LAMP has already been successfully used for rapid detection of DNA and RNA viruses such as West Nile virus, severe acute respiratory syndrome (SARS), and dengue (37)(38)(39) …”

Section: Loop-mediated Isothermal Amplification (Lamp)mentioning

confidence: 99%

“…As a consequence, it is possible to evaluate the reaction in real time by measuring the turbidity or, more importantly, by visualization by the naked eye, facilitating better distinction between positive and negative samples (36). The LAMP method can synthesize 20 μg of specific DNA from 25 μL of reaction mixture in one hour (35).LAMP has already been successfully used for rapid detection of DNA and RNA viruses such as West Nile virus, severe acute respiratory syndrome (SARS), and dengue (37)(38)(39) According to a study by Lau et al (51), it is possible to detect Toxoplasma gondii in human blood with a sensitivity exceeding 85%, which is higher than the value demonstrated using nested PCR (62.5%), with all samples of both methods being 100% specific. Because of its simplicity, sensitivity, and specificity, LAMP is suggested as an appropriate method for the routine diagnosis of active infection in humans.…”

mentioning

confidence: 99%

Molecular techniques for the study and diagnosis of parasite infection

Tavares¹,

Staggemeier²,

Borges³

et al. 2011

J. Venom. Anim. Toxins incl. Trop. Dis

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Abstract:In parasitology, routine laboratory diagnosis involves conventional methods, such as optical microscopy, used for the morphological identification of parasites. Currently, molecular biology techniques are increasingly used to diagnose parasite structures in order to enhance the identification and characterization of parasites. The objective of the present study was to review the main current and new diagnostic techniques for confirmation of parasite infections, namely: polymerase chain reaction (PCR), real-time polymerase chain reaction (RT-PCR), loop-mediated isothermal amplification (LAMP), Luminex xMAP, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and restriction fragment length polymorphism (RFLP), in addition to microsatellites. Molecular assays have comprehensively assisted in the diagnosis, treatment and epidemiological studies of parasitic diseases that affect people worldwide, helping to control parasitic disease mortality.Key words: parasite infection, diagnosis, molecular techniques, molecular epidemiology. Review ARticle The Journal of Venomous Animals and Toxins including Tropical Diseases ISSN 1678-9199 | 2011 | volume 17 | issue 3 | pages 239-248 INTRODUCTIONIn parasitology, routine laboratory diagnosis involves conventional methods, such as optical microscopy, used for the morphological identification of parasites (1). However, the occasional difficulty of identifying these parasite structures may decrease the sensitivity of such methods. Currently, because of these difficulties, molecular biology has been employed to detect parasites responsible for parasitic diseases (2).Traditional parasitological analyses have the advantage of being less costly without requiring expensive reagents and equipment. Additionally, such analyses can be easily performed when a trained microscopist is available. On the other hand, molecular technology demonstrates the presence of parasites based on their antigenic components or DNA segments (3). These tests are not influenced by environmental factors that usually can interfere with the results of a stool test, for example, thus ensuring highly reliable results (4).Current laboratory diagnostic methods for the identification of parasites include: polymerase chain reaction (PCR), random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), microsatellite marker method, Luminex xMAP-based technology (areas of multianalyte profiling), loop-mediated isothermal amplification (LAMP), and the recently added real-time PCR (5-12).The objective of the present article was to review the applications of molecular biology techniques in parasitology by evaluating and discussing their uses and benefits. MOLECULAR METHODS FOR DETECTION OF PARASITE STRUCTURESSeveral molecular tests to detect parasites have been developed in the last decade. Their specificity and sensitivity have gradually increased, and parasites that were previously difficult to diagnose usi...

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“…Four antigenically distinct serotypes (DENV1-4) circulate simultaneously in endemic countries, with 60-70% identity in nucleotide sequences [4] and approximately 70% [5] in deduced amino acid sequence identity among the four serotypes. Secondary disease with 3 DENV-2 and -3 are more likely to result in DHF as with DENV-1 and-4.…”

Section: Introductionmentioning

confidence: 99%

Circulation of Dengue Virus Type 3 Genotype III in Africa Since 2008

Monteil¹,

Maquart²,

Caro³

et al. 2016

JHVRV

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Dengue virus type 3 (DENV-3) genotype III circulated across East Africa between 1984 and 1993, but virulent strains is now considered essential public health activity. DENV serotype 3 (DENV-3) was first isolated during a DHF epidemic in Manila in 1956 [11] and is now circulating in Asia and South America [12,13,14]. This serotype is often associated with more severe diseases and dengue hemorrhagic fever than other serotypes [15,16,17]. Little is known about DENV-3 activity in Africa. Serotype 3 was first detected in Africa during a 1984 epidemic event in Pemba (Mozambique), where at least 45% of the local population was affected [18]. This high proportion could be explained at least in part by the naïve immune status of the population against this new serotype. Since then, sporadic occurrences of the serotype 3 were reported, such as in Kenya in 1991 and in Somalia in 1993 [19]. DENV-3 was responsible for 2 epidemics in Sudan in 2004-2005 and 2010 [20]. The latter affected over 3765 people [21]. In West Africa, DENV-3 circulation was first published in 2008 in Cote d'Ivoire, during a yellow fever alert [22,23].Moreover, subtle changes such as the ones at the lineage level could alter the potential of the dengue virus to cause severity, as it has already been observed in Sri Lankan DENV-3 strains [24,25]. The E protein is the major target gene for genetic variations with a possible impact on virulence [26,27] (Table 1). Materials and Methods Virus isolationSingle T25 C6/36 cells flask (2,6.106 cells) was inoculated with a mix made of 200 μl of serum with 2 ml of L-15 cell culture medium (Gibco), 2% FCS and 20 μl of heparin and filtered on a 22μm sterile filter. Culture flask was incubated at 28 °C. After 7 days, 2 ml of media was removed and added to a new T25 C6/36 cells flask. Culture flask was incubated at 28 °C, under 5% CO2 during 5 days. The supernatant was then removed and used for RT-PCR. Reverse-Transcription and sequencingViral RNA was extracted from 140 μl of cell culture supernatant using QIAamp Viral RNA Mini Kits (Qiagen, Germany). RT-PCR and amplification was processed as previously described by Lanciotti et al. [17]: To generate two overlapping fragments covering the PrM/M and E genes region, primers pairs F1 (5'-GCTCCCCATGTCGGCATGGGACTGG-3')/ R1(5'-CATCCCTTTGAGTTTCAATTTGTCCAT-3') (1541bp) and F2 (5'-CTAGGATCTCAAGAAGGAGCAATGCA-3')/R2 (5'-CGCGGATCCATGGCTGTTGCCACTCTTTTGGGGGA-3') (865bp) were used in 2 separate reactions. These 2 overlapping fragments amplify a global region of 2272bp. RNA was first transcribed to cDNA using the Super Script III one-step RT-PCR kit (Invitrogen). The reaction mix was 25 µl of 2X reaction mix, 5 µl of template RNA, 1µl of sense primer 10µM (F1 or F2), 1µl of anti-sense primer 10 µM (R1 or R2), 2 µL of SuperScript III RT/Platinum Taq Mix and up to 50 µl of autoclaved distilled water according to manufacturer instruction. The cycle used was 56 °C during 30 min then 94 °C during 2 min followed by 40 cycles of 94 °C (15 s), 56 °C (30 s) and 68 °C (1 min 30). T...

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Rapid Detection and Differentiation of Dengue Virus Serotypes by a Real-Time Reverse Transcription-Loop-Mediated Isothermal Amplification Assay

Cited by 310 publications

References 19 publications

Simultaneous Detection and Genogroup‐Screening Test for Norovirus Genogroups I and II from Fecal Specimens in Single Tube by Reverse Transcription‐Loop‐Mediated Isothermal Amplification Assay

Simultaneous Detection and Genogroup‐Screening Test for Norovirus Genogroups I and II from Fecal Specimens in Single Tube by Reverse Transcription‐Loop‐Mediated Isothermal Amplification Assay

Molecular techniques for the study and diagnosis of parasite infection

Circulation of Dengue Virus Type 3 Genotype III in Africa Since 2008

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