The quasispecies of EV-A71 in Hand, Foot and Mouth Disease (HFMD) patients during the 2003 Sibu, Sarawak outbreak

Hand, Foot and Mouth Disease (HFMD) is a common childhood illness. Viruses from the enterovirus genus, in particular enterovirus 71 (EV-A71) and other species A enteroviruses, are the most common viruses responsible for HFMD infection. Similar to other RNA viruses, EV-A71 also exist as quasispecies...

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Main Author:	Fauzziah Dahlan, Sarkawi
Format:	Thesis
Language:	English
Published:	2015
Subjects:	RA Public aspects of medicine
Online Access:	http://ir.unimas.my/id/eprint/9419/1/FAUZZIAH.pdf
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spelling	my-unimas-ir.94192023-03-24T02:01:36Z The quasispecies of EV-A71 in Hand, Foot and Mouth Disease (HFMD) patients during the 2003 Sibu, Sarawak outbreak 2015 Fauzziah Dahlan, Sarkawi RA Public aspects of medicine Hand, Foot and Mouth Disease (HFMD) is a common childhood illness. Viruses from the enterovirus genus, in particular enterovirus 71 (EV-A71) and other species A enteroviruses, are the most common viruses responsible for HFMD infection. Similar to other RNA viruses, EV-A71 also exist as quasispecies. Quasispecies describe a cloud of viral population in which mutation and selection pressures are at a balance. This occurs when viruses are adapting to environmental changes. In this study, we determined the quasispecies population of EV-A71 genogroup B5 viruses, obtained during a HFMD outbreak in Sibu, Sarawak in 2003. Ten patients with multiple swabs sample with confirmed EV-A71 genogroup B5 were selected for the study. Partial VP1 gene sequence from two separate swab samples from each of the selected patients were cloned. A total of twenty randomly selected colonies with the correct inserts were selected from each sample and subjected to sequencing. These cloned sequences were then compared to a parental consensus sequence generated directly from PCR of the primary clinical sample. Sequence differences observed between cloned product and parental PCR product suggest quasispecies diversity of EV-A71 for that sample. The three sample types studied included throat, rectal and vesicle swab samples. Ten percent of the cloned-derived colonies were identified with nucleotide change. About a third of the nucleotide changes led to a silent mutation during protein translation. No correlation was observed between quasispecies diversity and the phenotype of the virus as determined by ough the cloned-derived colonies in the vesicles swab samples are variants instead of clonal, the percentage of the cloned-derived colonies with amino acid change is only 6.7% which is the lowest compared to the other two sample types Universiti Malaysia Sarawak (UNIMAS) 2015 Thesis http://ir.unimas.my/id/eprint/9419/ http://ir.unimas.my/id/eprint/9419/1/FAUZZIAH.pdf text en validuser masters University Malaysia Sarawak, UNIMAS Institute of Health and Community Medicine
institution	Universiti Malaysia Sarawak
collection	UNIMAS Institutional Repository
language	English
topic	RA Public aspects of medicine
spellingShingle	RA Public aspects of medicine Fauzziah Dahlan, Sarkawi The quasispecies of EV-A71 in Hand, Foot and Mouth Disease (HFMD) patients during the 2003 Sibu, Sarawak outbreak
description	Hand, Foot and Mouth Disease (HFMD) is a common childhood illness. Viruses from the enterovirus genus, in particular enterovirus 71 (EV-A71) and other species A enteroviruses, are the most common viruses responsible for HFMD infection. Similar to other RNA viruses, EV-A71 also exist as quasispecies. Quasispecies describe a cloud of viral population in which mutation and selection pressures are at a balance. This occurs when viruses are adapting to environmental changes. In this study, we determined the quasispecies population of EV-A71 genogroup B5 viruses, obtained during a HFMD outbreak in Sibu, Sarawak in 2003. Ten patients with multiple swabs sample with confirmed EV-A71 genogroup B5 were selected for the study. Partial VP1 gene sequence from two separate swab samples from each of the selected patients were cloned. A total of twenty randomly selected colonies with the correct inserts were selected from each sample and subjected to sequencing. These cloned sequences were then compared to a parental consensus sequence generated directly from PCR of the primary clinical sample. Sequence differences observed between cloned product and parental PCR product suggest quasispecies diversity of EV-A71 for that sample. The three sample types studied included throat, rectal and vesicle swab samples. Ten percent of the cloned-derived colonies were identified with nucleotide change. About a third of the nucleotide changes led to a silent mutation during protein translation. No correlation was observed between quasispecies diversity and the phenotype of the virus as determined by ough the cloned-derived colonies in the vesicles swab samples are variants instead of clonal, the percentage of the cloned-derived colonies with amino acid change is only 6.7% which is the lowest compared to the other two sample types
format	Thesis
qualification_level	Master's degree
author	Fauzziah Dahlan, Sarkawi
author_facet	Fauzziah Dahlan, Sarkawi
author_sort	Fauzziah Dahlan, Sarkawi
title	The quasispecies of EV-A71 in Hand, Foot and Mouth Disease (HFMD) patients during the 2003 Sibu, Sarawak outbreak
title_short	The quasispecies of EV-A71 in Hand, Foot and Mouth Disease (HFMD) patients during the 2003 Sibu, Sarawak outbreak
title_full	The quasispecies of EV-A71 in Hand, Foot and Mouth Disease (HFMD) patients during the 2003 Sibu, Sarawak outbreak
title_fullStr	The quasispecies of EV-A71 in Hand, Foot and Mouth Disease (HFMD) patients during the 2003 Sibu, Sarawak outbreak
title_full_unstemmed	The quasispecies of EV-A71 in Hand, Foot and Mouth Disease (HFMD) patients during the 2003 Sibu, Sarawak outbreak
title_sort	quasispecies of ev-a71 in hand, foot and mouth disease (hfmd) patients during the 2003 sibu, sarawak outbreak
granting_institution	University Malaysia Sarawak, UNIMAS
granting_department	Institute of Health and Community Medicine
publishDate	2015
url	http://ir.unimas.my/id/eprint/9419/1/FAUZZIAH.pdf
_version_	1783728061024305152

The quasispecies of EV-A71 in Hand, Foot and Mouth Disease (HFMD) patients during the 2003 Sibu, Sarawak outbreak

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