Molecular characterization of rotavirus isolates identified from children under five years with acute gastroenteritis in Kota Kinabalu and Kunak districts, Sabah

Globally, rotavirus is the leading cause of acute gastroenteritis (AGE) in children under five years age. The highest prevalence of rotavirus-positivity was reported in South East Asia. In Malaysia, AGE cases increased exponentially between 1990 and 2017. However, the major etiologic agent was unkno...

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Main Author:	Lia Natasha Amit
Format:	Thesis
Language:	English English
Published:	2022
Subjects:	QR355-502 Virology
Online Access:	https://eprints.ums.edu.my/id/eprint/41477/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/41477/2/FULLTEXT.pdf
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spelling	my-ums-ep.414772024-11-12T02:43:58Z Molecular characterization of rotavirus isolates identified from children under five years with acute gastroenteritis in Kota Kinabalu and Kunak districts, Sabah 2022 Lia Natasha Amit QR355-502 Virology Globally, rotavirus is the leading cause of acute gastroenteritis (AGE) in children under five years age. The highest prevalence of rotavirus-positivity was reported in South East Asia. In Malaysia, AGE cases increased exponentially between 1990 and 2017. However, the major etiologic agent was unknown. The nationwide surveys in 2006 and 2016 showed that Bumiputera children in Borneo were prone to AGE. To date, rotavirus surveillance was conducted between 1977 and 2017 in West Malaysia states and Sarawak. Meanwhile, in Sabah there were two preliminary studies conducted between 2005 and 2018, respectively. This study aimed to determine the burden, distribution of rotavirus G/P genotypes, genomic diversity, and commercial vaccines efficacy towards circulating rotavirus strains. Watery stools were collected from children with AGE under five years old who went to four Sabah government healthcare facilities. Rotavirus was detected by commercially available Rotaclone kit. Viral genomic RNA was extracted from Rotaclone-positive sample. Genotyping was performed by reverse-transcriptase PCR and the result was confirmed by sequencing of outer capsid genes. Genomic diversities were determined by PAGE. Multiple sequence alignment was done by ClustalW. Phylogenetic analyses and amino acid sequence similarity calculations were conducted in MEGA. Between January 2018 and February 2020, 422 watery stool samples were collected at Hospital Likas (n=294), Hospital Kunak (n=104), Klinik Kesihatan Menggatal (n=15), and Klinik Kesihatan Telipok (n=9). The rotaviral-AGE positivity was (96/422) (22.7%). Children aged 12-23 month, male, and Bajau ethnicity were more likely to be infected with rotavirus. Most common G/P genotypes were (n=47)," with "G/P genotypes identified by ELISA in the 69 rotavirus were G3P[8] (n=47), G9P[8] (n=10), G1P[8] (n=7), G12P[6] (n=3), G8P[8] (n=1), and GXP[8] (n=1). Novel rotavirus strains that had never reported in Malaysia before, such as equine-like G3P[8], G12P[6], and bovine-like G8P[8], were identified in this study. Sabahan strains exhibited a large genomic diversity as indicated by the presence of various electrophoretype patterns and G/P genotypes. Phylogenetic analysis showed that Sabahan strains originated from various sources or evolved independently for a long time since then they were introduced to Sabah. Sabahan strains had considerable amino acid variations on VP7 antigenic epitopes, indicating the vaccines would not be effective. Continuous surveillance in all Sabah districts is crucial to capture the overall picture of rotaviral-AGE burden and rotavirus G/P genotype distribution. Whole genome sequencing analysis is required to elucidate the genomic diversity, origin, and evolution of Sabahan strains. Further exploration of sociodemographic and risk factors data is essential to have a better understanding of the rotavirus transmission. 2022 Thesis https://eprints.ums.edu.my/id/eprint/41477/ https://eprints.ums.edu.my/id/eprint/41477/1/24%20PAGES.pdf text en public https://eprints.ums.edu.my/id/eprint/41477/2/FULLTEXT.pdf text en validuser masters Universiti Malaysia Sabah Faculty Of Medicine And Health Sciences
institution	Universiti Malaysia Sabah
collection	UMS Institutional Repository
language	English English
topic	QR355-502 Virology
spellingShingle	QR355-502 Virology Lia Natasha Amit Molecular characterization of rotavirus isolates identified from children under five years with acute gastroenteritis in Kota Kinabalu and Kunak districts, Sabah
description	Globally, rotavirus is the leading cause of acute gastroenteritis (AGE) in children under five years age. The highest prevalence of rotavirus-positivity was reported in South East Asia. In Malaysia, AGE cases increased exponentially between 1990 and 2017. However, the major etiologic agent was unknown. The nationwide surveys in 2006 and 2016 showed that Bumiputera children in Borneo were prone to AGE. To date, rotavirus surveillance was conducted between 1977 and 2017 in West Malaysia states and Sarawak. Meanwhile, in Sabah there were two preliminary studies conducted between 2005 and 2018, respectively. This study aimed to determine the burden, distribution of rotavirus G/P genotypes, genomic diversity, and commercial vaccines efficacy towards circulating rotavirus strains. Watery stools were collected from children with AGE under five years old who went to four Sabah government healthcare facilities. Rotavirus was detected by commercially available Rotaclone kit. Viral genomic RNA was extracted from Rotaclone-positive sample. Genotyping was performed by reverse-transcriptase PCR and the result was confirmed by sequencing of outer capsid genes. Genomic diversities were determined by PAGE. Multiple sequence alignment was done by ClustalW. Phylogenetic analyses and amino acid sequence similarity calculations were conducted in MEGA. Between January 2018 and February 2020, 422 watery stool samples were collected at Hospital Likas (n=294), Hospital Kunak (n=104), Klinik Kesihatan Menggatal (n=15), and Klinik Kesihatan Telipok (n=9). The rotaviral-AGE positivity was (96/422) (22.7%). Children aged 12-23 month, male, and Bajau ethnicity were more likely to be infected with rotavirus. Most common G/P genotypes were (n=47)," with "G/P genotypes identified by ELISA in the 69 rotavirus were G3P[8] (n=47), G9P[8] (n=10), G1P[8] (n=7), G12P[6] (n=3), G8P[8] (n=1), and GXP[8] (n=1). Novel rotavirus strains that had never reported in Malaysia before, such as equine-like G3P[8], G12P[6], and bovine-like G8P[8], were identified in this study. Sabahan strains exhibited a large genomic diversity as indicated by the presence of various electrophoretype patterns and G/P genotypes. Phylogenetic analysis showed that Sabahan strains originated from various sources or evolved independently for a long time since then they were introduced to Sabah. Sabahan strains had considerable amino acid variations on VP7 antigenic epitopes, indicating the vaccines would not be effective. Continuous surveillance in all Sabah districts is crucial to capture the overall picture of rotaviral-AGE burden and rotavirus G/P genotype distribution. Whole genome sequencing analysis is required to elucidate the genomic diversity, origin, and evolution of Sabahan strains. Further exploration of sociodemographic and risk factors data is essential to have a better understanding of the rotavirus transmission.
format	Thesis
qualification_level	Master's degree
author	Lia Natasha Amit
author_facet	Lia Natasha Amit
author_sort	Lia Natasha Amit
title	Molecular characterization of rotavirus isolates identified from children under five years with acute gastroenteritis in Kota Kinabalu and Kunak districts, Sabah
title_short	Molecular characterization of rotavirus isolates identified from children under five years with acute gastroenteritis in Kota Kinabalu and Kunak districts, Sabah
title_full	Molecular characterization of rotavirus isolates identified from children under five years with acute gastroenteritis in Kota Kinabalu and Kunak districts, Sabah
title_fullStr	Molecular characterization of rotavirus isolates identified from children under five years with acute gastroenteritis in Kota Kinabalu and Kunak districts, Sabah
title_full_unstemmed	Molecular characterization of rotavirus isolates identified from children under five years with acute gastroenteritis in Kota Kinabalu and Kunak districts, Sabah
title_sort	molecular characterization of rotavirus isolates identified from children under five years with acute gastroenteritis in kota kinabalu and kunak districts, sabah
granting_institution	Universiti Malaysia Sabah
granting_department	Faculty Of Medicine And Health Sciences
publishDate	2022
url	https://eprints.ums.edu.my/id/eprint/41477/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/41477/2/FULLTEXT.pdf
_version_	1818611410070929408

Molecular characterization of rotavirus isolates identified from children under five years with acute gastroenteritis in Kota Kinabalu and Kunak districts, Sabah

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