Molecular characterization and methylation status of torque teno virus isolation among hepatitis patients in a public hospital in Pahang, Malaysia
Hepatitis diseases also known as asymptomatic at the early stage of infection. There are viruses classified as commensal yet opportunistic pathogens with a high infection rate, including anellovirus. Torque teno virus (TTV) is a small, nonenveloped and circular single-stranded DNA anellovirus tha...
Saved in:
| Main Author: | |
|---|---|
| Format: | Thesis |
| Language: | English |
| Published: |
2020
|
| Subjects: | |
| Online Access: | http://psasir.upm.edu.my/id/eprint/103864/1/SITI%20NURZULAIKHA%20BINTI%20%20-%20IR.pdf http://psasir.upm.edu.my/id/eprint/103864/ |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Summary: | Hepatitis diseases also known as asymptomatic at the early stage of infection.
There are viruses classified as commensal yet opportunistic pathogens with a high
infection rate, including anellovirus. Torque teno virus (TTV) is a small, nonenveloped
and circular single-stranded DNA anellovirus that infects the human
population worldwide, especially hepatitis patients. A high prevalence of TTV was
reported from various countries to include within the Asian continent. However,
there is no information regarding the TTV prevalence among hepatitis patients in
Malaysia. Hence, this study decided to determine the genotype of TTV as well as
to construct the phylogeny tree of TTV isolated among the hepatitis community in
Hospital Tengku Ampuan Afzan (HTAA) Kuantan. Other than that, this study aims
to determine the mutation by DNA methylation in the CpG distribution of TTV
isolates. The sample subject selected is hepatitis patients who attended HTAA for
a medical appointment. A total of 137 hepatitis patients have been recruited and
the plasma DNA was tested with three sets of primers by using the standard PCR
method to amplify the coding and noncoding region of TTV. It was discovered that
87.5% and 73.7% of the subjects showed the presence of the noncoding region of
TTV when two different sets of primers were used (UTR(a) and UTR(b)).
Meanwhile, for the presence of the N22 region which is the selected coding region
located in ORF1 specifically among Group 1 TTV, 20% of positivity were shown.
The other 80% of positively detected TTV isolates without N22 region could not be
classified into any groups as it is require further sequence analysis. Out of 101
positive UTR(b) samples which have been subjected for sequencing, only 41
samples produce complete readable sequences which belong to TTV genome.
Low concentration amplicon and samples presented with multiple bands which
have the possibility of co-infection were excluded from the analysis. By the
construction of the phylogeny tree, conserved TTV isolates in hepatitis patients
were identified in Clade A with the majority of numbers. Despite that, TTVMY02 is
the first TTV Malaysian isolate from hepatitis patients with partial whole genome
sequence of 3,265 kb and was determined by phylogeny relation to have a high identity percentage with KAV isolate, which grouped in Group 2. The protein
translated region for all ORFs in TTVMY02 isolates were well described on its
physiochemical properties; and ORF1 and ORF2 appeared to be more
hydrophobic while ORF3 more hydrophilic. Lastly, the selected TTV Malaysian
isolate was further investigated for the methylation properties in the region consist
of the highest CG percentage among a few CpG island by bisulfite sequencing
and methylation-specific PCR. The result showed the CpG methylation in the TTV
genome with 80% proved to be methylated in the selected island. Although the
methylation of CpGs which is an addition of methyl group at cytosine base is
considered as mutation, the alteration could be the way for the TTV virus to escape
from the immune cells. Besides, there is no further investigation on the effect of
TTV DNA methylation towards a cell line, but the postulation could be made based
on PPV genome structure due to the similarity shared between both viruses. In
conclusion, the characteristics of the TTV genome described in the study could be
suggested that the virus is a non-pathogenic virus yet potentially leading to latent
infection without any outbreak or disease outcome. |
|---|