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Comparative genetic analyses of Human Rhinovirus C (HRV-C) complete genome from Malaysia

Human rhinovirus-C (HRV-C) has been implicated in more severe illnesses than HRV-A and HRV-B, however, the limited number of HRV-C complete genomes (complete 5' and 3' non-coding region and open reading frame sequences) has hindered the in-depth genetic study of this virus. This study aime...

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Main Authors: Yam, Sim Khaw, Yoke, Fun Chan, Jafar, Faizatul Lela, Othman, Norlijah, Hui, Yee Chee
Format: Article
Language:English
Published: Frontiers 2016
Online Access:http://psasir.upm.edu.my/id/eprint/55324/1/Comparative%20Genetic%20Analyses%20of%20Human%20Rhinovirus%20C%20%28HRV-C%29%20Complete%20Genome%20from%20Malaysia.pdf
http://psasir.upm.edu.my/id/eprint/55324/
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spelling my.upm.eprints.553242017-11-07T02:32:48Z http://psasir.upm.edu.my/id/eprint/55324/ Comparative genetic analyses of Human Rhinovirus C (HRV-C) complete genome from Malaysia Yam, Sim Khaw Yoke, Fun Chan Jafar, Faizatul Lela Othman, Norlijah Hui, Yee Chee Human rhinovirus-C (HRV-C) has been implicated in more severe illnesses than HRV-A and HRV-B, however, the limited number of HRV-C complete genomes (complete 5' and 3' non-coding region and open reading frame sequences) has hindered the in-depth genetic study of this virus. This study aimed to sequence seven complete HRV-C genomes from Malaysia and compare their genetic characteristics with the 18 published HRV-Cs. Seven Malaysian HRV-C complete genomes were obtained with newly redesigned primers. The seven genomes were classified as HRV-C6, C12, C22, C23, C26, C42, and pat16 based on the VP4/VP2 and VP1 pairwise distance threshold classification. Five of the seven Malaysian isolates, namely, 3430-MY-10/C22, 8713-MY-10/C23, 8097-MY-11/C26, 1570-MY-10/C42, and 7383-MY-10/pat16 are the first newly sequenced complete HRV-C genomes. All seven Malaysian isolates genomes displayed nucleotide similarity of 63-81% among themselves and 63-96% with other HRV-Cs. Malaysian HRV-Cs had similar putative immunogenic sites, putative receptor utilization and potential antiviral sites as other HRV-Cs. The genomic features of Malaysian isolates were similar to those of other HRV-Cs. Negative selections were frequently detected in HRV-Cs complete coding sequences indicating that these sequences were under functional constraint. The present study showed that HRV-Cs from Malaysia have diverse genetic sequences but share conserved genomic features with other HRV-Cs. This genetic information could provide further aid in the understanding of HRV-C infection. Frontiers 2016 Article PeerReviewed application/pdf en http://psasir.upm.edu.my/id/eprint/55324/1/Comparative%20Genetic%20Analyses%20of%20Human%20Rhinovirus%20C%20%28HRV-C%29%20Complete%20Genome%20from%20Malaysia.pdf Yam, Sim Khaw and Yoke, Fun Chan and Jafar, Faizatul Lela and Othman, Norlijah and Hui, Yee Chee (2016) Comparative genetic analyses of Human Rhinovirus C (HRV-C) complete genome from Malaysia. Frontiers in Microbiology , 7. art. no. 543. pp. 1-13. ISSN 1664-302X; ESSN: 1664-302X 10.3389/fmicb.2016.00543
institution Universiti Putra Malaysia
building UPM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Putra Malaysia
content_source UPM Institutional Repository
url_provider http://psasir.upm.edu.my/
language English
description Human rhinovirus-C (HRV-C) has been implicated in more severe illnesses than HRV-A and HRV-B, however, the limited number of HRV-C complete genomes (complete 5' and 3' non-coding region and open reading frame sequences) has hindered the in-depth genetic study of this virus. This study aimed to sequence seven complete HRV-C genomes from Malaysia and compare their genetic characteristics with the 18 published HRV-Cs. Seven Malaysian HRV-C complete genomes were obtained with newly redesigned primers. The seven genomes were classified as HRV-C6, C12, C22, C23, C26, C42, and pat16 based on the VP4/VP2 and VP1 pairwise distance threshold classification. Five of the seven Malaysian isolates, namely, 3430-MY-10/C22, 8713-MY-10/C23, 8097-MY-11/C26, 1570-MY-10/C42, and 7383-MY-10/pat16 are the first newly sequenced complete HRV-C genomes. All seven Malaysian isolates genomes displayed nucleotide similarity of 63-81% among themselves and 63-96% with other HRV-Cs. Malaysian HRV-Cs had similar putative immunogenic sites, putative receptor utilization and potential antiviral sites as other HRV-Cs. The genomic features of Malaysian isolates were similar to those of other HRV-Cs. Negative selections were frequently detected in HRV-Cs complete coding sequences indicating that these sequences were under functional constraint. The present study showed that HRV-Cs from Malaysia have diverse genetic sequences but share conserved genomic features with other HRV-Cs. This genetic information could provide further aid in the understanding of HRV-C infection.
format Article
author Yam, Sim Khaw
Yoke, Fun Chan
Jafar, Faizatul Lela
Othman, Norlijah
Hui, Yee Chee
spellingShingle Yam, Sim Khaw
Yoke, Fun Chan
Jafar, Faizatul Lela
Othman, Norlijah
Hui, Yee Chee
Comparative genetic analyses of Human Rhinovirus C (HRV-C) complete genome from Malaysia
author_facet Yam, Sim Khaw
Yoke, Fun Chan
Jafar, Faizatul Lela
Othman, Norlijah
Hui, Yee Chee
author_sort Yam, Sim Khaw
title Comparative genetic analyses of Human Rhinovirus C (HRV-C) complete genome from Malaysia
title_short Comparative genetic analyses of Human Rhinovirus C (HRV-C) complete genome from Malaysia
title_full Comparative genetic analyses of Human Rhinovirus C (HRV-C) complete genome from Malaysia
title_fullStr Comparative genetic analyses of Human Rhinovirus C (HRV-C) complete genome from Malaysia
title_full_unstemmed Comparative genetic analyses of Human Rhinovirus C (HRV-C) complete genome from Malaysia
title_sort comparative genetic analyses of human rhinovirus c (hrv-c) complete genome from malaysia
publisher Frontiers
publishDate 2016
url http://psasir.upm.edu.my/id/eprint/55324/1/Comparative%20Genetic%20Analyses%20of%20Human%20Rhinovirus%20C%20%28HRV-C%29%20Complete%20Genome%20from%20Malaysia.pdf
http://psasir.upm.edu.my/id/eprint/55324/
_version_ 1643835861055307776
score 13.211869

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