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    • A
      anneng 最后由 编辑

      https://www.intechopen.com/chapters/43243
      Hepatitis B Virus Genetic Diversity: Disease Pathogenesis
      7f3e7a63-2e37-43c2-bc2e-3c6d8bad6332-image.png
      c0861f1d-a0f7-4066-b775-25f728ff6531-image.png

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      • A
        anneng 最后由 编辑

        1.去宿主
        2.组装
        3.找出最接近的参考基因组

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        • A
          anneng 最后由 编辑

          https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC4448583/
          Hepatitis B Virus Genotypes and Variants
          HBV 基因型、血清型、亚型的地理分布
          ec2b53eb-132a-4380-a9c0-69a046258090-image.png

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          • A
            anneng 最后由 编辑

            https://www.ablsa.com/laboratory-applications/deepchek-hbv-software-ce-ivd/
            0d63d973-527d-49ea-b98f-0b3bbe3f5c16-image.png
            28afe20c-103a-40a8-952f-b55b4d1ce005-image.png
            d47e8b6a-ce26-4e97-b34b-c4b764d3dc54-image.png

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            • A
              anneng 最后由 编辑

              https://www.nature.com/articles/srep28274
              A fast and low-cost genotyping method for hepatitis B virus based on pattern recognition in point-of-care settings

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              • A
                anneng 最后由 anneng 编辑

                https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC7564258/
                9e3c2efc-187d-41c6-80e7-0894c75be13a-image.png
                分型的方法：
                Sanger sequencing：
                Sanger sequencing is often restricted to analyzing the S gene and is inaccurate for detecting minority genetic variants
                reverse hybridization：
                reverse hybridization detects only known mutations

                这个文档提到的分型方法
                The analyzed data was deposited in the NCBI SRA database under the bioproject number PRJNA659786 and the accession numbers SRR12535947, SRR12535946, SRR12535938, SRR12535937 and SRR12535936. The read quality was accessed using FastQC and reads of <150 nt were excluded using Trimmomaticv0.36 [22]; the latter program was also used to filter the reads (Illuminaclip, Headcrop = 14, Leading = 3, Trailing = 3, Slidingwindow = 4:30, Minlen = 18).

                The high-quality reads (all samples with minimum Q-Score = 30) were mapped, independently, over all genomes of all eight HBV genotypes obtained from HBVdb [21] using Bowtie2 v2.3.2. [23] with stringent parameters (–very-sensitive, –no-discordant –N 0 –L 4, –gbar 10). The aligned read counting was performed using Bed tools multiBamCov v2.25.0 [24] (default) and was loaded into an in-house Python script for mean coverage plot and genotype determination; moreover, genomic coverage throughout the A, D, and G genomes was compared using Circos plot [25].

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                • A
                  anneng 最后由 编辑

                  https://www.news-medical.net/health/Hepatitis-B-Structure-Capsid-Flexibility-and-Function.aspx
                  表达的抗原
                  2e17c577-2f17-4507-8619-e3cdd7f547af-image.png

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                  • A
                    anneng 最后由 anneng 编辑

                    https://www.ncbi.nlm.nih.gov/nuccore/AB981583.1
                    参考基因组

                    https://hbvdb.lyon.inserm.fr/HBVdb/
                    HBV数据库 可以找到各种分型好的序列
                    https://academic.oup.com/nar/article/41/D1/D566/1051781
                    HBVdb: a knowledge database for Hepatitis B Virus

                    dfbfa074-495d-4f7e-87c7-411930e98eba-image.png

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                    • A
                      anneng 最后由 编辑

                      https://pubmed.ncbi.nlm.nih.gov/25034481/
                      Genotypes and genetic variability of hepatitis B virus
                      Based on an intergroup divergence of greater than 7.5%
                      across the complete genome, HBV has been classified phylogenetically into 9 genotypes, A–I, with a putative 10th genotype ‘J’, isolated from a single individual.
                      基因组之间差异7.5%作为分类的边界值

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                      • A
                        anneng 最后由 anneng 编辑

                        https://github.com/DrTrevorBell/CCT

                        http://hbv-glue.cvr.gla.ac.uk/#/home
                        GLUE
                        http://hbv-glue.cvr.gla.ac.uk/#/aboutGlueProject

                        https://github.com/LosicLab/ViralMine
                        A pipeline tool that mines unmapped RNA/DNA reads for viral sequences and predicts viral genotype (built for HBV)

                        https://www.ncbi.nlm.nih.gov/projects/genotyping/formpagex.cgi
                        b2c14f82-f146-4762-bd98-df3bb39e5f20-image.png
                        https://pubmed.ncbi.nlm.nih.gov/15215470/

                        https://github.com/tacatanach/Hepatitis_B_Virus_alignment
                        NCBI的分型曲线解释：
                        1.矩形是按照窗口作为宽度 每个窗口内步进的各个矩形堆叠展示
                        2.曲线Y是score值 X是每个窗口的起始点坐标
                        这些数据可以下载下来 用excel处理 如下：
                        bb80e687-e881-4e69-a854-64158d0c093a-image.png

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                        • A
                          anneng 最后由 anneng 编辑

                          https://www.frontiersin.org/articles/10.3389/fmicb.2020.616023/full
                          Comprehensive Analysis of Clinically Significant Hepatitis B Virus Mutations in Relation to Genotype, Subgenotype and Geographic Region
                          临床样本的突变分析
                          immune escape,
                          antiviral resistance
                          hepatocellular carcinoma (HCC)

                          该文章提到了一些突变的临床意义
                          https://www.sciencedirect.com/science/article/abs/pii/S001650850901556X

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                          • A
                            anneng 最后由 编辑

                            分型方法研究：
                            https://www.sciencedirect.com/science/article/pii/S1201971210024239

                            https://onlinelibrary.wiley.com/doi/abs/10.1002/rmv.400
                            Hepatitis B virus genotypes: comparison of genotyping methods
                            35b0b9d6-f965-41ee-8204-e75835e9c3e9-image.png

                            https://journals.asm.org/doi/pdf/10.1128/cmr.00009-07
                            Molecular Testing in the Diagnosis and Management of
                            Chronic Hepatitis B

                            https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-020-05269-z
                            Distribution of hepatitis B virus genotypes in the general population of Myanmar via nationwide study

                            https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC4431363/
                            Sequence-based genotyping of hepatitis B virus in general population

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                            • A
                              anneng 最后由 编辑

                              Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)
                              https://www.nature.com/articles/s41598-019-43524-9#Sec11

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                              • A
                                anneng 最后由 编辑

                                https://bmcinfectdis.biomedcentral.com/track/pdf/10.1186/s12879-017-2697-x.pdf
                                Molecular characterization of hepatitis B
                                virus in Vietnam
                                The Illumina fastq sequence files were assembled
                                using Genious 8.0.5, software package (Biomatters
                                Ltd, AK, New Zeland) utilizing a reference-based
                                mapping tool after primer sequence clipping (i.e. the
                                consensus sequence was obtained by mapping individual reads of each sample to a reference sequence).
                                Finally, screening of minor (sub-consensus) variants
                                was performed using the SNP detection tool available
                                in Geneious. A minimum variant frequency of 5% and
                                500-fold coverage were chosen as cut-off values.

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                                • A
                                  anneng 最后由 编辑

                                  https://sci-hub.st/10.1007/978-1-4939-6700-1_17
                                  Deep Sequencing of the Hepatitis B Virus Genome: Analysis
                                  of Multiple Samples by Implementation of the Illumina
                                  Platform
                                  A BLASTN comparison analysis is performed between clean
                                  reads and the HBV genomic reference sequence, to eliminate
                                  non-HBV sequences (anything with similarity<70%). After
                                  this filtering step, the average coverage of HBV sequence site
                                  should be above 2600× (Fig. 1).
                                  6. Shan entropy and Relative entropy calculations are carried out.

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                                  • A
                                    anneng 最后由 编辑

                                    Identification and Comparative Analysis of Hepatitis B Virus Genotype D/E Recombinants in Africa
                                    https://stacks.cdc.gov/view/cdc/50437

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                                    • A
                                      anneng 最后由 编辑

                                      https://sci-hub.st/10.1016/j.jviromet.2013.06.015
                                      08373011-71d4-4b31-9a33-846b89b5eebb-image.png

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                                      • A
                                        anneng 最后由 编辑

                                        https://github.com/hr283

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                                        • A
                                          anneng 最后由 编辑

                                          The Study of Hepatitis B Virus Using Bioinformatics
                                          https://www.intechopen.com/chapters/50624

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                                          • A
                                            anneng 最后由 anneng 编辑

                                            https://hbv.geno2pheno.org/
                                            http://www.hiv-grade.de/hbv_grade/deployed/grade

                                            分型工具和耐药分型

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