Identification and comparison of RCMV ALL 03 open reading frame (ORF) among several different strains of cytomegalovirus worldwide
Background: Rat cytomegalovirus ALL-03 (Malaysian strain) which was isolated from a placenta and uterus of a house rat, Rattus rattus diardii has the ability to cross the placenta and infecting the fetus. To further elucidate the pathogenesis of the Malaysian strain of Rat Cytomegalovirus ALL-03 (RC...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2017
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| Online Access: | http://psasir.upm.edu.my/id/eprint/62068/ http://psasir.upm.edu.my/id/eprint/62068/1/Identification%20and%20comparison%20of%20RCMV%20ALL%2003%20open%20reading%20frame%20.pdf |
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| author | Balakrishnan, Krishnan Nair Abdullah, Ashwaq Ahmed Bala, Jamilu Abubakar Abba, Yusuf Zainal Abidin, Siti Aimi Sarah Abdullah, Faez Firdaus Jesse Allaudin, Zeenathul Nazariah Mohamed Mustapha, Noordin Mohd Lila, Mohd Azmi |
| author_facet | Balakrishnan, Krishnan Nair Abdullah, Ashwaq Ahmed Bala, Jamilu Abubakar Abba, Yusuf Zainal Abidin, Siti Aimi Sarah Abdullah, Faez Firdaus Jesse Allaudin, Zeenathul Nazariah Mohamed Mustapha, Noordin Mohd Lila, Mohd Azmi |
| author_sort | Balakrishnan, Krishnan Nair |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | Background: Rat cytomegalovirus ALL-03 (Malaysian strain) which was isolated from a placenta and uterus of a house rat, Rattus rattus diardii has the ability to cross the placenta and infecting the fetus. To further elucidate the pathogenesis of the Malaysian strain of Rat Cytomegalovirus ALL-03 (RCMV ALL-03), detailed analysis on the viral genome sequence is crucial. Methods: Genome sequencing of RCMV ALL-03 was carried out in order to identify the open reading frame (ORF), homology comparison of ORF with other strains of CMV, phylogenetic analysis, classifying ORF with its corresponding conserved genes, and determination of functional proteins and grouping of gene families in order to obtain fundamental knowledge of the genome. Results: The present study revealed a total of 123 Coding DNA sequences (CDS) from RCMV ALL-03 with 37 conserved ORF domains as with all herpesvirus genomes. All the CDS possess similar function with RCMV-England followed by RCMV-Berlin, RCMV-Maastricht, and Human CMV. The phylogenetic analysis of RCMV ALL-03 based on conserving genes of herpes virus showed that the Malaysian RCMV isolate is closest to RCMV-English and RCMV-Berlin strains, with 99% and 97% homology, respectively. Similarly, it also demonstrated an evolutionary relationship between RCMV ALL-03 and other strains of herpesviruses from all the three subfamilies. Interestingly, betaherpesvirus subfamily, which has been shown to be more closely related with gammaherpesviruses as compared to alphaherpesviruses, shares some of the functional ORFs. In addition, the arrangement of gene blocks for RCMV ALL-03, which was conserved among herpesvirus family members was also observed in the RCMV ALL-03 genome. Conclusion: Genomic analysis of RCMV ALL-03 provided an overall picture of the whole genome organization and it served as a good platform for further understanding on the divergence in the family of Herpesviridae. |
| first_indexed | 2025-11-15T11:11:40Z |
| format | Article |
| id | upm-62068 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T11:11:40Z |
| publishDate | 2017 |
| publisher | Elsevier |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-620682019-12-03T01:29:16Z http://psasir.upm.edu.my/id/eprint/62068/ Identification and comparison of RCMV ALL 03 open reading frame (ORF) among several different strains of cytomegalovirus worldwide Balakrishnan, Krishnan Nair Abdullah, Ashwaq Ahmed Bala, Jamilu Abubakar Abba, Yusuf Zainal Abidin, Siti Aimi Sarah Abdullah, Faez Firdaus Jesse Allaudin, Zeenathul Nazariah Mohamed Mustapha, Noordin Mohd Lila, Mohd Azmi Background: Rat cytomegalovirus ALL-03 (Malaysian strain) which was isolated from a placenta and uterus of a house rat, Rattus rattus diardii has the ability to cross the placenta and infecting the fetus. To further elucidate the pathogenesis of the Malaysian strain of Rat Cytomegalovirus ALL-03 (RCMV ALL-03), detailed analysis on the viral genome sequence is crucial. Methods: Genome sequencing of RCMV ALL-03 was carried out in order to identify the open reading frame (ORF), homology comparison of ORF with other strains of CMV, phylogenetic analysis, classifying ORF with its corresponding conserved genes, and determination of functional proteins and grouping of gene families in order to obtain fundamental knowledge of the genome. Results: The present study revealed a total of 123 Coding DNA sequences (CDS) from RCMV ALL-03 with 37 conserved ORF domains as with all herpesvirus genomes. All the CDS possess similar function with RCMV-England followed by RCMV-Berlin, RCMV-Maastricht, and Human CMV. The phylogenetic analysis of RCMV ALL-03 based on conserving genes of herpes virus showed that the Malaysian RCMV isolate is closest to RCMV-English and RCMV-Berlin strains, with 99% and 97% homology, respectively. Similarly, it also demonstrated an evolutionary relationship between RCMV ALL-03 and other strains of herpesviruses from all the three subfamilies. Interestingly, betaherpesvirus subfamily, which has been shown to be more closely related with gammaherpesviruses as compared to alphaherpesviruses, shares some of the functional ORFs. In addition, the arrangement of gene blocks for RCMV ALL-03, which was conserved among herpesvirus family members was also observed in the RCMV ALL-03 genome. Conclusion: Genomic analysis of RCMV ALL-03 provided an overall picture of the whole genome organization and it served as a good platform for further understanding on the divergence in the family of Herpesviridae. Elsevier 2017-10 Article PeerReviewed text en http://psasir.upm.edu.my/id/eprint/62068/1/Identification%20and%20comparison%20of%20RCMV%20ALL%2003%20open%20reading%20frame%20.pdf Balakrishnan, Krishnan Nair and Abdullah, Ashwaq Ahmed and Bala, Jamilu Abubakar and Abba, Yusuf and Zainal Abidin, Siti Aimi Sarah and Abdullah, Faez Firdaus Jesse and Allaudin, Zeenathul Nazariah and Mohamed Mustapha, Noordin and Mohd Lila, Mohd Azmi (2017) Identification and comparison of RCMV ALL 03 open reading frame (ORF) among several different strains of cytomegalovirus worldwide. Infection, Genetics and Evolution, 54. pp. 81-90. ISSN 1567-1348; ESSN: 1567-7257 https://www.sciencedirect.com/science/article/pii/S1567134817302071?via%3Dihub#! 10.1016/j.meegid.2017.06.020 |
| spellingShingle | Balakrishnan, Krishnan Nair Abdullah, Ashwaq Ahmed Bala, Jamilu Abubakar Abba, Yusuf Zainal Abidin, Siti Aimi Sarah Abdullah, Faez Firdaus Jesse Allaudin, Zeenathul Nazariah Mohamed Mustapha, Noordin Mohd Lila, Mohd Azmi Identification and comparison of RCMV ALL 03 open reading frame (ORF) among several different strains of cytomegalovirus worldwide |
| title | Identification and comparison of RCMV ALL 03 open reading frame (ORF) among several different strains of cytomegalovirus worldwide |
| title_full | Identification and comparison of RCMV ALL 03 open reading frame (ORF) among several different strains of cytomegalovirus worldwide |
| title_fullStr | Identification and comparison of RCMV ALL 03 open reading frame (ORF) among several different strains of cytomegalovirus worldwide |
| title_full_unstemmed | Identification and comparison of RCMV ALL 03 open reading frame (ORF) among several different strains of cytomegalovirus worldwide |
| title_short | Identification and comparison of RCMV ALL 03 open reading frame (ORF) among several different strains of cytomegalovirus worldwide |
| title_sort | identification and comparison of rcmv all 03 open reading frame (orf) among several different strains of cytomegalovirus worldwide |
| url | http://psasir.upm.edu.my/id/eprint/62068/ http://psasir.upm.edu.my/id/eprint/62068/ http://psasir.upm.edu.my/id/eprint/62068/ http://psasir.upm.edu.my/id/eprint/62068/1/Identification%20and%20comparison%20of%20RCMV%20ALL%2003%20open%20reading%20frame%20.pdf |