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Genome Sequences and Phylogeny of Two Duck Hepatitis B Viruses.

ABSTRACT: Duck hepatitis B virus (DHBV) infection in Pekin ducks is a model for human hepatitis B. Sequence variations may contribute to host therapy responses against the virus. We provide full genome sequences of two DHBVs from France, their phylogenetic classification, and their sequence variability.

SUBMITTER: Apolonio Silva de Oliveira D

PROVIDER: S-EPMC7892665 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Genome Sequences and Phylogeny of Two Duck Hepatitis B Viruses.

Apolônio Silva de Oliveira Daniel D Debing Yannick Y Dieryck Ines I Lyimu Wilfred Michael WM Paeshuyse Jan J

Microbiology resource announcements 20210218 7

Duck hepatitis B virus (DHBV) infection in Pekin ducks is a model for human hepatitis B. Sequence variations may contribute to host therapy responses against the virus. We provide full genome sequences of two DHBVs from France, their phylogenetic classification, and their sequence variability. ...[more]

PMID: 33602732

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Project description:Background & objectivesSince December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally affected 195 countries. In India, suspected cases were screened for SARS-CoV-2 as per the advisory of the Ministry of Health and Family Welfare. The objective of this study was to characterize SARS-CoV-2 sequences from three identified positive cases as on February 29, 2020.MethodsThroat swab/nasal swab specimens for a total of 881 suspected cases were screened by E gene and confirmed by RdRp (1), RdRp (2) and N gene real-time reverse transcription-polymerase chain reactions and next-generation sequencing. Phylogenetic analysis, molecular characterization and prediction of B- and T-cell epitopes for Indian SARS-CoV-2 sequences were undertaken.ResultsThree cases with a travel history from Wuhan, China, were confirmed positive for SARS-CoV-2. Almost complete (29,851 nucleotides) genomes of case 1, case 3 and a fragmented genome for case 2 were obtained. The sequences of Indian SARS-CoV-2 though not identical showed high (~99.98%) identity with Wuhan seafood market pneumonia virus (accession number: NC 045512). Phylogenetic analysis showed that the Indian sequences belonged to different clusters. Predicted linear B-cell epitopes were found to be concentrated in the S1 domain of spike protein, and a conformational epitope was identified in the receptor-binding domain. The predicted T-cell epitopes showed broad human leucocyte antigen allele coverage of A and B supertypes predominant in the Indian population.Interpretation & conclusionsThe two SARS-CoV-2 sequences obtained from India represent two different introductions into the country. The genetic heterogeneity is as noted globally. The identified B- and T-cell epitopes may be considered suitable for future experiments towards the design of vaccines and diagnostics. Continuous monitoring and analysis of the sequences of new cases from India and the other affected countries would be vital to understand the genetic evolution and rates of substitution of the SARS-CoV-2.

Dataset Information

Genome Sequences and Phylogeny of Two Duck Hepatitis B Viruses.

Publications

Genome Sequences and Phylogeny of Two Duck Hepatitis B Viruses.

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