ABSTRACT
BACKGROUND: Hepatitis B Virus (HBV) infection is one of the major causes of liver cirrhosis, hepatocellular carcinoma and deaths due to the acute or chronic consequences worldwide. HBV is distributed into various genotypes based on nucleic acid sequence variation. OBJECTIVES: To develop a method of HBV genotyping and drug resistance interpretation using partial sequencing of polymerase gene. METHODS: This study was performed on 98 HBV infected patients' serum samples from Western India. A nested PCR protocol was designed for amplification of pol gene from HBV genome and Sanger's sequencing of the gene fragment. Sequences were aligned with HBV reference sequences for phylogenetic analysis and for characterization of genetic diversity. Drug resistance mutations were screened using HBVSeq program from Stanford University. RESULTS: Distribution of HBV genotypes showed predominance of genotype D, circulating in 76 (77.55%) patients (p < 0.05). Genotypes A and C were less prevalent and were identified in 4 (4.08%) and 18 (18.37%) patients, respectively. Anti-retroviral drug resistance mutations were not detected in any patient. CONCLUSION: A method for determination of HBV genotypes using pol gene sequencing which simultaneously detects major drug resistance mutations has been established. HBV genetic diversity may play an important role in treatment decision.
Subject(s)
DNA, Viral/genetics , Hepatitis B virus/classification , Hepatitis B virus/genetics , Hepatitis B, Chronic/virology , Mutation , Polymerase Chain Reaction/methods , Polymorphism, Genetic/genetics , Adult , DNA, Viral/blood , DNA-Directed DNA Polymerase , Genetic Variation , Genotype , Hepatitis B virus/isolation & purification , Hepatitis B, Chronic/blood , Hepatitis B, Chronic/epidemiology , Humans , India/epidemiology , Male , Molecular Epidemiology , PhylogenyABSTRACT
Seventy-eight soil samples were collected from the various locations in the vicinity of Kaziranga National Park (Assam), India, during April to October 2009 and screened for the presence of keratinophilic fungi using the hair baiting techniques for isolation. Thirty-nine isolates were recovered and identified by recognition of their macro- and micromorphological features. Their identification was also confirmed by the BLAST search of sequences of the ITS1-5.8S-ITS2 rDNA region against the NCBI/GenBank data and compared with deposited sequences for identification purpose. Eleven species related to seven genera were recorded viz. Aphanoascus durus (1.28%), Arthroderma tuberculatum (3.84%), Arthroderma corniculatum (1.28%), Chrysosporium indicum (16.66%), C. tropicum (3.84%), Ctenomyces serratus (5.12%), Keratinophyton punsolae (1.28%), Microsporum appendiculatum (1.28%), Microsporum gypseum complex (11.53%), Trichophyton mentagrophytes (11.28%) and T. terrestre (2.56%).
Subject(s)
Fungi/isolation & purification , Fungi/metabolism , Keratins/metabolism , Soil Microbiology , Cluster Analysis , DNA, Fungal/chemistry , DNA, Fungal/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , DNA, Ribosomal Spacer/chemistry , DNA, Ribosomal Spacer/genetics , Fungi/classification , Fungi/genetics , Hair/microbiology , Incidence , India , Microbiological Techniques , Microscopy , Parks, Recreational , Phylogeny , RNA, Ribosomal, 5.8S , Sequence Analysis, DNAABSTRACT
BACKGROUND: Accurate and swift detection of viruses causing diseases in humans represent continuous challenges to diagnostic and epidemiological research. Efficient and rapid diagnosis is crucial for effective implication of disease management strategies. Multitude approaches attempted to identify individual viruses, includes serological assays and molecular methods. Detection assays based on peptides have become increasingly substantial and indispensable for its advantages over conventional methods. METHODS: We have primarily outlined the progress made in peptide based diagnostic systems for the commonly found viral infections in India - Influenza virus, Chikungunya virus, Dengue virus, Rotavirus, Japanese encephalitis virus (JEV), Epstein-Barr virus (EBV), Human Immunodeficiency virus (HIV) and Hepatitis C virus (HCV). Further, we have documented the recent advancements that could impact the upcoming developments of peptide based diagnostic assays. RESULTS: In this review we identified that very few studies in development of peptide based assays for viral infections has been reported. In a country specific scenario like India and its burdened health care system, sensitive and rapid diagnostic kits based on peptides could be considered as a better alternative to the conventional serological tests including whole antigenic proteins. CONCLUSION: The finding of this review uncovers the importance of a peptide based diagnostic system for rapid detection of viral infections. Even though, in recent times, peptide based assays have intrigued researchers, further work in this domain is entailed.
