HBV分析

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1.去宿主
2.组装
3.找出最接近的参考基因组

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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

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https://www.ablsa.com/laboratory-applications/deepchek-hbv-software-ce-ivd/

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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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https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC7564258/

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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https://www.news-medical.net/health/Hepatitis-B-Structure-Capsid-Flexibility-and-Function.aspx
表达的抗原

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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

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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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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

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：

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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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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

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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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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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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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.