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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

                  1 条回复 最后回复 回复 引用 0
                  • 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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                          • A
                            anneng 最后由 编辑

                            https://www.niid.go.jp/niid/images/JJID/58/244.pdf
                            Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences

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                            • A
                              anneng 最后由 anneng 编辑

                              https://www.sciencedirect.com/science/article/pii/S1567134821004846#bb0040
                              Analysis of entire hepatitis B virus genomes reveals reversion of mutations to wild type in natural infection, a 15 year follow-up study

                              2.6. NGS data preprocessing and sample genotyping
                              Quality control and preprocessing of each sample's raw NGS short reads was performed by fastp v0.20.1 (Chen et al., 2018). The adapter sequences were removed and 15 bases of each read were trimmed from the 5’end. Any reads with an average quality score lower than 30, or length shorter than 50 nt, were filtered further. The remaining high quality reads from each sample were then mapped to a common reference sequence (accession no. X02763) using bowtie2 v2.3.4.1 (Langmead and Salzberg, 2012). After sorting and removing the duplications using Samtools v1.7 (Li et al., 2009), the consensus sequence was generated using CliqueSNV v1.5.3 (Knyazev et al., 2021). Consensus sequences of all samples were then multi-aligned with the reference sequences from HBVdb (Hayer et al., 2013) and three additional sequences, including FJ023664 of genotype I, AB486012 of genotype J, and AM117397 from Africa chimpanzees as the outgroup. A maximum-likelihood tree was then constructed using MEGA 7 (Kumar et al., 2016) and each sample was genotyped accordingly.

                              这个文章里面做consensus序列的时候 用的是 cliqueSNV 该软件和samtools consensus 的对比需要研究下：
                              48ce066a-c93b-45f1-8f55-f569eb742f4d-image.png

                              2.7. Haplotype construction and diversity analysis
                              分型完毕后 每个样本对应的参考序列就可以更具体 然后进行突变分析
                              bowtie2's very-sensitive-local 比对
                              Sambamba 去重
                              CliqueSNV haplotype reconstruction
                              haplotypes with a minimum abundance of 1%

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                              • A
                                anneng 最后由 anneng 编辑

                                二代数据分析过程
                                对比分型
                                使用比对 直接将reads比对到参考基因组上 然后进行统计

                                blast分型
                                使用blast直接和hdvdb进行对比查询（ncbi自己的分型工具对查询序列进行了分段 类似kmer 我们一般拿到的reads双端文件 感觉和这种分段很类似 可以直接查询 也不用组装了）ncbi宣称好处是可以找出“重组”过的病毒类型 即一个病毒由多个病毒拼接而成 这种情况很难和混合样本（一个样本有多个分型的感染）区分开
                                e76e0106-c88e-4c78-80c6-d707708cc59b-image.png
                                直接使用reads 来分型 可以参考这个文章
                                https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC4382110/
                                进化树方式进行分型：
                                1.fastp ：质控和预处理
                                2.去接头（可选）
                                3.过滤：碱基质量
                                4.比对：bowtie2、bwa-mem 和通用株X02763
                                5.排序、去重：Samtools
                                6.生成一致性序列：CliqueSNV
                                7.多序列比对：和hdvdb数据库进行多序列比对（blast方法不需要这个步骤 由于病毒的变化很多 很可能在多序列比对时无法有效对齐）
                                8.构建进化树：MEGA 7 maximum-likelihood方法 该步骤就可以得到每个样本的分型

                                构建单倍型 Haplotype construction
                                1.比对：和该样本的对应分型参考序列进行比对
                                bowtie2's very-sensitive-local
                                2.去重：Sambamba
                                3.构建单倍型：CliqueSNV

                                diversity analysis
                                香农商Shannon entropy (Sn)：
                                S = −pilnpi, where pi is the frequency of each haplotype in the viral quasispecies population
                                genetic diversity (D) ：MEGA X v10.1.8 genetic distance of the haplotypes
                                病毒进化率 viral evolutionary rates：MEGA 7 HKY substitution model 、BEAST v2.6.3、Tracer

                                统计分析
                                SPSS

                                突变分析
                                Samtools mpileup：

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                                • A
                                  anneng 最后由 编辑

                                  https://www.rivm.nl/mpf/typingtool/hev/introduction
                                  一个在线的hev的分型工具 有参考报告

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                                  • A
                                    anneng 最后由 编辑

                                    https://livedataoxford.shinyapps.io/1510659619-3Xkoe2NKkKJ7Drg/
                                    一个shinyapps 展示了非洲的HBV耐药性
                                    https://github.com/martinjhnhadley/hbv-alignment-viz

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                                    • A
                                      anneng 最后由 编辑

                                      https://pubmed.ncbi.nlm.nih.gov/11230757/
                                      Nomenclature for antiviral-resistant human hepatitis B virus mutations in the polymerase region
                                      HBV耐药性突变的命名规则 rtL180M

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                                      • A
                                        anneng 最后由 编辑

                                        https://sci-hub.st/10.1053/j.gastro.2009.08.063

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                                        • A
                                          anneng 最后由 anneng 编辑

                                          https://jbiomedsci.biomedcentral.com/articles/10.1186/s12929-018-0442-4
                                          Applications of next-generation sequencing analysis for the detection of hepatocellular carcinoma-associated hepatitis B virus mutations
                                          这篇文章分析了HBV突变和肝癌的相关性
                                          1.对于组装 文章提到有参组装更好 相对de novo 组装而言 毕竟illumina的reads比较短

                                          2.文章里面提到了一个sample-specific 参考序列、同基因型的参考序列、其他不兼容参考序列对假阳性的影响。
                                          0b892b14-29b7-4e7f-8349-f0a7309cc54e-image.png
                                          这个文章很水 没有提到生信是怎么做的

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                                          • A
                                            anneng 最后由 编辑

                                            https://hivdb.stanford.edu/HBV/releaseNotes/

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