DISTRIBUSI DAN DINAMIKA GENOTYPE SERTA ANALISIS GEN VP4, VP7, NSP2, NSP4 DAN NSP5 ROTAVIRUS PENYEBAB DIARE ANAK BALITA DI INDONESIA
Background: Rotavirus is the most frequent cause of severe diarrhea in children under five years of age both in developed and developing countries. The highest incidence of rotavirus infection is found among children by 3-24 months of age. In tropical countries, rotavirus infection occurs throughout...
| Main Authors: | , |
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| Format: | Thesis |
| Published: |
[Yogyakarta] : Universitas Gadjah Mada
2013
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| Subjects: |
| _version_ | 1797034442735222784 |
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| author | , HERA NIRWATI , Prof. dr. S. Yati Soenarto, Sp.A(K), Ph.D |
| author_facet | , HERA NIRWATI , Prof. dr. S. Yati Soenarto, Sp.A(K), Ph.D |
| author_sort | , HERA NIRWATI |
| collection | UGM |
| description | Background: Rotavirus is the most frequent cause of severe diarrhea in
children under five years of age both in developed and developing countries.
The highest incidence of rotavirus infection is found among children by 3-24
months of age. In tropical countries, rotavirus infection occurs throughout the
year with only slight variation across different seasons. Implementation of
diarrhea prevention program by improving hygiene and sanitation
improvements could not reduce the morbidity rate. Therefore, vaccination is
believed to be an alternative to reduce mortality and morbidity of rotavirus
infection. Prior to the introduction of a rotavirus vaccine, initial study is required
to assess the burden of rotavirus infection, to map the genotypes of rotavirus,
as well as the epidemiologic characteristics and virulence of rotavirus within
population. Therefore, this study aims to investigate: (1) the prevalence of
diarrhea due to rotavirus infection in various regions in Indonesia, (2) specific
age group that most frequently suffers from rotavirus related diarrhea, (3) the
variability of rotavirus diarrhea by seasonality, (4) the electropherotype profiles
of Indonesian rotavirus isolates, (5) the distribution of rotavirus genotypes
circulating in various regions in Indonesia, (6) the dynamic changes of rotavirus
genotypes circulating in various regions in Indonesia, (7) the of VP4, VP7,
NSP2, NSP4, and NSP5 genotypes of rotavirus strains circulating in Indonesia
compared to those of other countries using phylogenetic analysis (8) amino acid
variations encoded by VP4, VP7, NSP2, NSP4, and NSP5 genes of rotavirus
strains in Indonesia compared to those in other countries as available in
GenBank, and (9) the variation of amino acid composition at VP7 epitopes in
rotavirus variants in Indonesia in comparison to those targeted by vaccine.
Methods: The study was conducted in 7 hospitals in 6 different cities in
Indonesia. Stool samples and epidemiologic data were collected from children
under five years old who were hospitalized due to diarrhea. Rotavirus in the
stools was detected by enzyme immunoassay and then genotyped using RTPCR.
Rotavirus RNA migration pattern was determined by PAGE
electrophoresis. Sequencing was used to determine the genotypes of VP4,
VP7, NSP2, NSP4, and NSP5. Phylogenetic analysis was performed with
neighbor-joining method by using MEGA 5.1.
Results: During the period from January to December 2006 and between
January 2009 and December 2010, there were 5,013 samples of patients with
diarrhea who were hospitalized in those 7 hospitals. Of those, 2,676 (53.38%)
were rotavirus positive. Of 669 samples, G1P[6], G1P[8], and G2P[4] were
detected as the dominant genotypes circulating in Indonesia. RNA profile
analysis showed that 83% had long pattern and 17% had short pattern (n=70).
Sequencing of VP4 gene was performed in 3 isolates of P[4] and 12 isolates of
P[8]. In addition, sequencing analysis of VP7 gene sequencing was completed
in 6 isolates of G1, 4 isolates of G2 , 8 isolates of G9, and 2 isolates of NSP2
gene, 3 isolates of NSP4 gene, and 1 isolate of NSP5 gene.
Conclusion: Our present data suggest that (1) the prevalence of diarrhea due
to rotavirus in children under five years of age in Indonesia ranges between 29-
67%, (2) rotavirus most often affects children by the age of 6-23 months, (3)
rotavirus diarrhea in Indonesia occurs throughout the year, and does not
depend on seasonality, (4) Indonesian rotavirus isolates demonstrate
electropherotype-specific pattern of Rotavirus A and 83% of isolates have longpattern,
(5) the dominant rotavirus genotypes circulating in Indonesia are
G1P[6], G1P[8], and G2P[4], (6) rotavirus genotypes circulating in various
regions in Indonesia always change in proportions, (7) based on the results of
phylogenetic analysis of the VP7 gene, Indonesian G1 isolates are included in
lineage I, G2 isolates are included in lineage II and G9 isolates are included in
lineage III. While based on phylogenetic analysis of the gene VP4, it is known
that Indonesian P[4] isolates are included in lineage V and P[8] isolates are
included in lineage III, (8) there are variations in the amino acid composition of
the Indonesian VP4, VP7, and NSP4 genes when compared with other
countries� isolates published in GenBank, and (9) there are variations in the
amino acid composition of the Indonesian VP7 gene when compared with the
vaccine strains. |
| first_indexed | 2024-03-13T23:11:48Z |
| format | Thesis |
| id | oai:generic.eprints.org:125800 |
| institution | Universiti Gadjah Mada |
| last_indexed | 2024-03-13T23:11:48Z |
| publishDate | 2013 |
| publisher | [Yogyakarta] : Universitas Gadjah Mada |
| record_format | dspace |
| spelling | oai:generic.eprints.org:1258002016-03-04T08:38:31Z https://repository.ugm.ac.id/125800/ DISTRIBUSI DAN DINAMIKA GENOTYPE SERTA ANALISIS GEN VP4, VP7, NSP2, NSP4 DAN NSP5 ROTAVIRUS PENYEBAB DIARE ANAK BALITA DI INDONESIA , HERA NIRWATI , Prof. dr. S. Yati Soenarto, Sp.A(K), Ph.D ETD Background: Rotavirus is the most frequent cause of severe diarrhea in children under five years of age both in developed and developing countries. The highest incidence of rotavirus infection is found among children by 3-24 months of age. In tropical countries, rotavirus infection occurs throughout the year with only slight variation across different seasons. Implementation of diarrhea prevention program by improving hygiene and sanitation improvements could not reduce the morbidity rate. Therefore, vaccination is believed to be an alternative to reduce mortality and morbidity of rotavirus infection. Prior to the introduction of a rotavirus vaccine, initial study is required to assess the burden of rotavirus infection, to map the genotypes of rotavirus, as well as the epidemiologic characteristics and virulence of rotavirus within population. Therefore, this study aims to investigate: (1) the prevalence of diarrhea due to rotavirus infection in various regions in Indonesia, (2) specific age group that most frequently suffers from rotavirus related diarrhea, (3) the variability of rotavirus diarrhea by seasonality, (4) the electropherotype profiles of Indonesian rotavirus isolates, (5) the distribution of rotavirus genotypes circulating in various regions in Indonesia, (6) the dynamic changes of rotavirus genotypes circulating in various regions in Indonesia, (7) the of VP4, VP7, NSP2, NSP4, and NSP5 genotypes of rotavirus strains circulating in Indonesia compared to those of other countries using phylogenetic analysis (8) amino acid variations encoded by VP4, VP7, NSP2, NSP4, and NSP5 genes of rotavirus strains in Indonesia compared to those in other countries as available in GenBank, and (9) the variation of amino acid composition at VP7 epitopes in rotavirus variants in Indonesia in comparison to those targeted by vaccine. Methods: The study was conducted in 7 hospitals in 6 different cities in Indonesia. Stool samples and epidemiologic data were collected from children under five years old who were hospitalized due to diarrhea. Rotavirus in the stools was detected by enzyme immunoassay and then genotyped using RTPCR. Rotavirus RNA migration pattern was determined by PAGE electrophoresis. Sequencing was used to determine the genotypes of VP4, VP7, NSP2, NSP4, and NSP5. Phylogenetic analysis was performed with neighbor-joining method by using MEGA 5.1. Results: During the period from January to December 2006 and between January 2009 and December 2010, there were 5,013 samples of patients with diarrhea who were hospitalized in those 7 hospitals. Of those, 2,676 (53.38%) were rotavirus positive. Of 669 samples, G1P[6], G1P[8], and G2P[4] were detected as the dominant genotypes circulating in Indonesia. RNA profile analysis showed that 83% had long pattern and 17% had short pattern (n=70). Sequencing of VP4 gene was performed in 3 isolates of P[4] and 12 isolates of P[8]. In addition, sequencing analysis of VP7 gene sequencing was completed in 6 isolates of G1, 4 isolates of G2 , 8 isolates of G9, and 2 isolates of NSP2 gene, 3 isolates of NSP4 gene, and 1 isolate of NSP5 gene. Conclusion: Our present data suggest that (1) the prevalence of diarrhea due to rotavirus in children under five years of age in Indonesia ranges between 29- 67%, (2) rotavirus most often affects children by the age of 6-23 months, (3) rotavirus diarrhea in Indonesia occurs throughout the year, and does not depend on seasonality, (4) Indonesian rotavirus isolates demonstrate electropherotype-specific pattern of Rotavirus A and 83% of isolates have longpattern, (5) the dominant rotavirus genotypes circulating in Indonesia are G1P[6], G1P[8], and G2P[4], (6) rotavirus genotypes circulating in various regions in Indonesia always change in proportions, (7) based on the results of phylogenetic analysis of the VP7 gene, Indonesian G1 isolates are included in lineage I, G2 isolates are included in lineage II and G9 isolates are included in lineage III. While based on phylogenetic analysis of the gene VP4, it is known that Indonesian P[4] isolates are included in lineage V and P[8] isolates are included in lineage III, (8) there are variations in the amino acid composition of the Indonesian VP4, VP7, and NSP4 genes when compared with other countries� isolates published in GenBank, and (9) there are variations in the amino acid composition of the Indonesian VP7 gene when compared with the vaccine strains. [Yogyakarta] : Universitas Gadjah Mada 2013 Thesis NonPeerReviewed , HERA NIRWATI and , Prof. dr. S. Yati Soenarto, Sp.A(K), Ph.D (2013) DISTRIBUSI DAN DINAMIKA GENOTYPE SERTA ANALISIS GEN VP4, VP7, NSP2, NSP4 DAN NSP5 ROTAVIRUS PENYEBAB DIARE ANAK BALITA DI INDONESIA. UNSPECIFIED thesis, UNSPECIFIED. http://etd.ugm.ac.id/index.php?mod=penelitian_detail&sub=PenelitianDetail&act=view&typ=html&buku_id=65978 |
| spellingShingle | ETD , HERA NIRWATI , Prof. dr. S. Yati Soenarto, Sp.A(K), Ph.D DISTRIBUSI DAN DINAMIKA GENOTYPE SERTA ANALISIS GEN VP4, VP7, NSP2, NSP4 DAN NSP5 ROTAVIRUS PENYEBAB DIARE ANAK BALITA DI INDONESIA |
| title | DISTRIBUSI DAN DINAMIKA GENOTYPE SERTA ANALISIS GEN VP4, VP7, NSP2, NSP4 DAN NSP5 ROTAVIRUS PENYEBAB DIARE ANAK BALITA DI INDONESIA |
| title_full | DISTRIBUSI DAN DINAMIKA GENOTYPE SERTA ANALISIS GEN VP4, VP7, NSP2, NSP4 DAN NSP5 ROTAVIRUS PENYEBAB DIARE ANAK BALITA DI INDONESIA |
| title_fullStr | DISTRIBUSI DAN DINAMIKA GENOTYPE SERTA ANALISIS GEN VP4, VP7, NSP2, NSP4 DAN NSP5 ROTAVIRUS PENYEBAB DIARE ANAK BALITA DI INDONESIA |
| title_full_unstemmed | DISTRIBUSI DAN DINAMIKA GENOTYPE SERTA ANALISIS GEN VP4, VP7, NSP2, NSP4 DAN NSP5 ROTAVIRUS PENYEBAB DIARE ANAK BALITA DI INDONESIA |
| title_short | DISTRIBUSI DAN DINAMIKA GENOTYPE SERTA ANALISIS GEN VP4, VP7, NSP2, NSP4 DAN NSP5 ROTAVIRUS PENYEBAB DIARE ANAK BALITA DI INDONESIA |
| title_sort | distribusi dan dinamika genotype serta analisis gen vp4 vp7 nsp2 nsp4 dan nsp5 rotavirus penyebab diare anak balita di indonesia |
| topic | ETD |
| work_keys_str_mv | AT heranirwati distribusidandinamikagenotypesertaanalisisgenvp4vp7nsp2nsp4dannsp5rotaviruspenyebabdiareanakbalitadiindonesia AT profdrsyatisoenartospakphd distribusidandinamikagenotypesertaanalisisgenvp4vp7nsp2nsp4dannsp5rotaviruspenyebabdiareanakbalitadiindonesia |