A Rare HBV Subgenotype D4 with Unique Genomic Signatures Identified in North-Eastern India –An Emerging Clinical Challenge?

BACKGROUND/AIMS: HBV has been classified into ten genotypes (A-J) and multiple subgenotypes, some of which strongly influence disease outcome and their distribution also correlate with human migration. HBV infection is highly prevalent in India and its diverse population provides an excellent opportunity to study the distinctiveness of HBV, its evolution and disease biology in variegated ethnic groups. The North-East India, having international frontiers on three sides, is one of the most ethnically and linguistically diverse region of the country. Given the paucity of information on molecular epidemiology of HBV in this region, the study aimed to carry out an in-depth genetic characterization of HBV prevailing in North-East state of Tripura. METHODS: From sera of chronically HBV infected patients biochemical/serological tests, HBV DNA quantification, PCR-amplification, sequencing of PreS/S or full-length HBV genomes were done. HBV genotype/subgenotype determination and sequence variability were assessed by MEGA5-software. The evolutionary divergence times of different HBV subgenotypes were estimated by DNAMLK/PHYLIP program while jpHMM method was used to detect any recombination event in HBV genomes. RESULTS: HBV genotypes D (89.5%), C (6.6%) and A (3.9%) were detected among chronic carriers. While all HBV/A and HBV/C isolates belonged to subgenotype-A1 and C1 respectively, five subgenotypes of HBV/D (D1-D5) were identified including the first detection of rare D4. These non-recombinant Indian D4 (IndD4) formed a distinct phylogenetic clade, had 2.7% nucleotide divergence and recent evolutionary radiation than other global D4. Ten unique amino acids and 9 novel nucleotide substitutions were identified as IndD4 signatures. All IndD4 carried T120 and R129 in ORF-S that may cause immune/vaccine/diagnostic escape and N128 in ORF-P, implicated as compensatory Lamivudine resistance mutation. CONCLUSIONS: IndD4 has potential to undermine vaccination programs or anti-viral therapy and its introduction to North-East India is believed to be linked with the settlement of ancient Tibeto-Burman migrants from East-Asia

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Not AvailableSoil plays a critical role in earth's biosphere by supporting the production of food, fodder and fiber. However, rapid land use changes in recent times in different parts of the world led to increasing concern on soil health. It has been realized that changes in land use systems significantly affect soil properties. Therefore, we studied the impact of land use systems on soil physicochemical properties in the Thar Desert of India. Surface soil samples (0-30 cm) from four land use systems: (1) sand dunes, (2) grazing lands, (3) rainfed croplands and (4) irrigated croplands have been collected and analyzed in laboratory to determine soil pH, electrical conductivity (EC), CaCO3 content, organic carbon content, available P content, available K content and micronutrients (Zn, Fe, Mn, and Cu) content. We observed higher clay, organic carbon and nutrient contents and lower bulk density values in irrigated croplands than in other land use systems. Soil pH and EC were higher in irrigated croplands than in the other land use systems. Principal component analysis of soil physicochemical properties revealed two major soil factors, the clay-carbon factor and salinity factor, which were able to significantly differentiate the land use systems. For irrigated croplands, the clay-carbon factor was found to be higher than the rest of the land uses; however, the salinity factor was the lowest. Higher values of these two factors will lead to a favorable soil physicochemical environment for plant growth or better soil health. These two factors may further be used for assessing the impact of land use systems on soil quality in other regions.Not Availabl

Not Available

Not AvailableSoil plays a critical role in earth’s biosphere by supporting the production of food, fodder and fiber. However, rapid land use changes in recent times in different parts of the world led to increasing concern on soil health. It has been realized that changes in land use systems significantly affect soil properties. Therefore, we studied the impact of land use systems on soil physico-chemical properties in the Thar Desert of India. Surface soil samples (0-30 cm) from four land use systems; (i) sand dunes, (ii) grazing lands, (iii) rainfed croplands and (iv) irrigated croplands have been collected and analyzed in laboratory to determine soil pH, electrical conductivity (EC), CaCO3 content, organic carbon (OC) content, available P content, available K content and micronutrients (Zn, Fe, Mn, and Cu) content. We observed higher clay, organic carbon and nutrient contents and lower bulk density values in irrigated croplands than in other land use systems. Soil pH and EC were higher in irrigated croplands than in the other land use systems. Principal component analysis of soil physico-chemical properties revealed two major soil factors, the clay-carbon factor and salinity factor, which were able to significantly differentiate the land use systems. For irrigated croplands, the clay-carbon factor was found to be higher than the rest of the land uses, however, the salinity factor was the lowest. Higher values of these two factors will lead to a favourable soil physico-chemical environment for plant growth or better soil health. These two factors may further be used for assessing the impact of land use systems on soil quality in other regions.ICAR-CAZR

Distinct distribution pattern of hepatitis B virus genotype C and D in liver tissue and serum of dual genotype infected liver cirrhosis and hepatocellular carcinoma patients.

The impact of co-infection of several hepatitis B virus (HBV) genotypes on the clinical outcome remains controversial. This study has for the first time investigated the distribution of HBV genotypes in the serum and in the intrahepatic tissue of liver cirrhotic (LC) and hepatocellular carcinoma (HCC) patients from India. In addition, the genotype-genotype interplay and plausible mechanism of development of HCC has also been explored.The assessment of HBV genotypes was performed by nested PCR using either surface or HBx specific primers from both the circulating virus in the serum and replicative virus that includes covalently closed circular DNA (cccDNA) and relaxed circular DNA (rcDNA) of HBV from the intrahepatic tissue. The integrated virus within the host chromosome was genotyped by Alu-PCR method. Each PCR products were cloned and sequences of five randomly selected clones were subsequently analysed.HBV/genotype D was detected in the serum of all LC and HCC patients whereas the sequences of the replicative HBV DNA (cccDNA and rcDNA) from the intrahepatic tissue of the same patients revealed the presence of both HBV/genotype C and D. The sequences of the integrated viruses exhibited the solo presence of HBV/genotype C in the majority of LC and HCC tissues while both HBV/genotype C and D clones were found in few patients in which HBV/genotype C was predominated. Moreover, compared to HBV/genotype D, genotype C had higher propensity to generate double strand breaks, ER stress and reactive oxygen species and it had also showed higher cellular homologous-recombination efficiency that engendered more chromosomal rearrangements, which ultimately led to development of HCC.Our study highlights the necessity of routine analysis of HBV genotype from the liver tissue of each chronic HBV infected patient in clinical practice to understand the disease prognosis and also to select therapeutic strategy

Nucleic Acid Sequence Analysis of Basal Core Promoter/Precore/Core Region of Hepatitis B Virus Isolated from Chronic Carriers of the Virus from Kolkata, Eastern India: Low Frequency of Mutation in the Precore Region

The aim of the present study was to characterize the predominant hepatitis B virus (HBV) strains and their molecular variants present in the HBV isolates of the different genotypes found among the chronic carriers of the virus in our community. Methods: Precore/core and core promoter regions of HBV DNA were amplifi ed by polymerase chain reaction and then subjected to direct sequencing. Of the 64 hepatitis B surface antigen (HBsAg)-positive chronic HBV carriers investigated, 44 were HBeAg negative and 20 were HBeAg positive. Results: In addition to genotype D, which was the predominant ge notype, 12 genotype C (18.7%) and 6 genotype A (9.4%) were also detected. Presence of T at nt 1858 has often been related to the development of precore stop mutation at nt 1896, while that of C has been related to the development of 1762–1764 double mutation. In ou

Estimates of Evolutionary Divergence over Sequence Pairs between HBV/D subgenotypes (D1–D9) and Indian HBV/D4 (IndD4).

<p>Genetic distances of Indian HBV/D4 (IndD4) with other subgenotypes of D are indicated in bold and the genetic distance between IndD4 and reported D4 is enclosed within a box.</p><p>Estimates of Evolutionary Divergence over Sequence Pairs between HBV/D subgenotypes (D1–D9) and Indian HBV/D4 (IndD4).</p

Primers used in this study.

<p>**  =  nucleotide [nt] positions are given according to HBV sequence with accession no. AF121242 obtained from GenBank.</p>ψ<p>Gunther S <i>et al</i>. J. Virol. 1995; 69: 5437–44.</p><p>Primers used in this study.</p

Conserved amino acid residues in four open reading frames of Indian HBV/D4 (IndD4) isolates compared with the previously reported residues at the same position in different subgenotypes of D (D1–D9).

<p>Unique residues of IndD4 are underlined. The major amino acids are indicated in <b>bold</b>. ^aThe conserved domains of the open reading frame of HBV polymerase are indicated as follows: tp, terminal protein domain; sp, spacer region; rt, reverse transcriptase domain; rh, RNase H region. *, ** the overlapping surface and polymerase mutations</p><p>Conserved amino acid residues in four open reading frames of Indian HBV/D4 (IndD4) isolates compared with the previously reported residues at the same position in different subgenotypes of D (D1–D9).</p

Estimation of divergence times of non-recombinant HBV subgenotypes D1–D7 including Indian HBV/D4 (IndD4).

<p>The tree was constructed by the DNAMLK program of the PHYLIP package, using indel-free HBV sequences of different subgenotypes of D, derived from GenBank, along with 12 IndD4 sequences. Reference sequences are indicated by their specific subgenotypes followed by accession numbers and the IndD4 sequences are indicated by respective isolate numbers beginning with “TP.”</p