Thesis

The Utilization of Next Generation Sequencing in Analyzing HIV Whole Genome

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Human Immunodeficiency Virus (HIV) is a retrovirus responsible for causing acquired
immunodeficiency syndrome (AIDS). The pol gene of the HIV genome encodes protease and reverse
transcriptase, and integrase region which is responsible for viral infection and survival inside the host
cell. Antiretroviral Therapy is usually administered to target these regions due to their significance in
virus survival, however, due to HIV’s high mutation rate mutations in these regions have been
frequently reported reducing ART effectiveness. To improve treatment outcome, daily sequencing of
HIV people living with HIV should be performed. The current gold standard of HIV drug resistance
analysis is sanger sequencing however, next generation sequencing (NGS) isstarting to show potential
in replacing sanger sequencing as the gold standard because of the high accuracy that has been
reported in these platforms. This study aims to compare the efficiency and accuracy of Illumina,
MinION, and PacBio in analyzing HIV whole genome. Using Bioinformatic tools such as PBAA, vSearch,
and IVA the whole genome assembly was then analyzed and compared to sanger sequencing results
acting as a reference sequence. It was found that both PacBio and Illumina have the highest accuracy
while MinION is the most efficient out of the three. From this experiment it can be concluded that no
significant difference was observed between these platforms. For future outcomes, it can be said that
PacBio is best suited for HIV whole genome analysis as Illumina is still considered a short-read
sequencing platform while MinION still has a high error rate.

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Detail Information

Series Title

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Call Number

BM 24-012

Publisher

i3L, Jakarta : i3L Press., 2024

Collation

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Language

English

ISBN/ISSN

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Classification

NONE

Content Type

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Media Type

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Carrier Type

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Edition

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Subject(s)

Next Generation Sequencing
Human Immunodeficiency Virus
Protease and Reverse

Specific Detail Info

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Statement of Responsibility

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