Question

2) Use the NCBI genome database in order to download the complete sequences of the different HBV strains.

3) Use Multiple sequence alignment (MSA) tools to do the following:

a) Construct MSA between the following isolates (LT935660.1/ AB602818.1/ LT717702.1) and discus the results (level of identity/ similarity and explain some obvious mutation/s).

b) Construct MSA for all the HBV genomes that you download.

Answer 1

2. HBV causes significant global health problems despite the presence of a potential vaccine. HBV, a partially double-stranded covalently closed ccc DNA virus belonging to the Hepadnaviridae family, is highly contagious and causes severe liver function in humans. Unlike other DNA viruses , it is genetically diverse, and it includes 10 distinct genotypes and multiple subtypes worldwide. The viral DNA extracted directly from the patients patien using a QIAamp MinElute virus spin kit. Six overlapping amplicons spanning the whole viral genome were generated by PCR and visualised using gel electrophoresis. PCR purification kit and sequenced using a BigDye terminator tersion 3.1 cycle sequencing kit. Analysis of mutations was performed using the Stanford HBVseq database. The genotyping of the sequenced genome was performed using the NCBI genotyping pool.

The assembled genome of isolate NHB17003, which has a length of 3,215bp, comprises four overlapping open reading frames that encode several major proteins. The surface encoded protein with different segments of independent properties. Additionally, isolate NHB17003 was observed to have an amino acid substitution, I126T, which was reported as an HBsAg escape mutation.

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