Dengue virus type 1 (DENV-1) Asian and American/African (AM/AF) genotypes were reported to be co-circulating in southern and western states of India based on envelope (E) gene sequencing of few representative samples. The objective of the present study was to develop a one-step real-time RT-PCR to discriminate between Asian and AM/AF genotypes of DENV-1 and investigate the spatio-temporal distribution of the DENV-1 genotypes in southern and western states of India. A one-step real-time RT-PCR to discriminate the Asian and AM/AF genotypes of DENV-1 was developed and validated using 40 samples (17 Asian and 23 AM/AF), for which the envelope (E) gene sequence data was available. DENV-2, DENV-3 and DENV-4 isolates, one each and DENV negative samples (n = 17) were also tested by the assay. Additional 296 samples positive for DENV-1 from selected Southern and Western states of India were genotyped using the real-time RT-PCR assay. Among the samples used for validation, the genotyping results were concordant with sequencing results for 39 samples. In the one discordant sample which was positive for AM/AF by sequencing, the genotyping assay tested positive for both Asian and AM/AF genotype. DENV-2, DENV-3 and DENV-4 isolates were not reactive in the assay. None of the DENV negative samples were positive (sensitivity 100% and specificity 98.2%). A total of 336 samples (40 samples with sequence data and 296 samples without sequence data) were used for spatio-temporal distribution analysis. The results revealed that the Asian genotype was the predominant genotype in Tamil Nadu and Kerala, the southern states. The AM/AF genotype was the predominant genotype in Maharashtra, a western state of India. In Nashik district of Maharashtra, Asian genotype was observed in 32.6% of DENV-1 samples during 2017 while the same decreased to 7.3% during 2018. In Pune district, Asian genotype was observed in 40.0% of DENV-1 samples during 2018 only. To conclude, a one step real-time RT-PCR has been developed for discriminating Asian and AM/AF genotypes of DENV-1. This assay can act as a complement to sequencing but not a substitute and can be utilized in resource limited settings for molecular surveillance of DENV-1. DENV-1 Asian genotype was the dominant genotype in South India while, AM/AF genotype was dominant in Western India.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6832813 | PMC |
| http://dx.doi.org/10.1016/j.meegid.2019.103989 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Identification of Anoikis-Related Genes in Chronic Kidney Disease Based on Bioinformatics Analysis Combined with Experimental Validation.
J Inflamm Res
January 2025
Department of Pharmacology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, People's Republic of China.
Background: Chronic kidney disease (CKD) is a progressive condition that arises from diverse etiological factors, resulting in structural alterations and functional impairment of the kidneys. We aimed to establish the Anoikis-related gene signature in CKD by bioinformatics analysis.
Methods: We retrieved 3 datasets from the Gene Expression Omnibus (GEO) database to obtain differentially expressed genes (DEGs), followed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) of them, which were intersected with Anoikis-related genes (ARGs) to derive Anoikis-related differentially expressed genes (ARDEGs).
Circ-PAN3 facilitates hepatocellular carcinoma growth via sponging miR-153 and upregulating cyclin D1.
Oncol Res
January 2025
Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
Background: Circular RNAs (circRNAs) play a pivotal role in the development and advancement of various cancer types. However, the involvement of circ-PAN3 in hepatocellular carcinoma (HCC) is not well understood. To shed light on this, we conducted a comprehensive study through biochemistry, cell biology, molecular biology, and bioinformatics techniques to investigate the role of circ-PAN3 and its associated pathway in the progression of HCC.
View Article and Find Full Text PDFDevelopment of a SYBR Green-based RT-qPCR assay for the rapid detection of peste-des-petits-ruminants virus.
J Vet Diagn Invest
January 2025
Departments of Veterinary Microbiology, College of Veterinary and Animal Sciences, Kerala Veterinary and Animal Sciences University, Pookode, Kerala, India.
Peste-des-petits-ruminants (PPR) is primarily a disease of small ruminants caused by peste-des-petits-ruminants virus (PPRV; , ), formerly the small ruminant morbillivirus. PPRV can cause significant morbidity and mortality in small ruminants and a significant economic impact. Conventional reverse-transcription PCR (RT-PCR), and probe-based and SYBR Green-based RT quantitative real-time PCR (RT-qPCR), are employed for the molecular detection of PPRV.
View Article and Find Full Text PDFOverexpressing OsNF-YB12 elevated the content of jasmonic acid and impaired drought tolerance in rice.
Plant Sci
January 2025
Shanghai Agrobiological Gene Center, Shanghai, 201106 China; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China. Electronic address:
Nuclear factor Y (NF-Y) is an evolutionarily conserved heterotrimeric transcription factor in eukaryotes. In a previous study, OsNF-YB12 was confirmed to be associated with drought tolerance using the Ecotilling method. In this study, real-time quantitative RT-PCR revealed that OsNF-YB12 was induced by various abiotic stresses and phytohormones, with expression levels differing between leaves and roots.
View Article and Find Full Text PDFSelection and validation of reference genes for the normalization of RT-qPCR gene expression data in Rheum tanguticum (Polygonaceae) under various abiotic stresses.
J Plant Physiol
January 2025
School of Life Sciences, Qinghai Normal University, Xining, 810008, China.
Rheum tanguticum, an endemic species from the Qinghai-Xizang Plateau, is a significant perennial and medicinal plant recognized for its robust resistance to abiotic stresses, including drought, cold, and salinity. To advance the understanding of stress-response mechanisms in R. tanguticum, this study aimed to establish a reliable set of housekeeping genes as references for normalizing RT-qPCR gene expression analyses.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!