Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia
SARS-CoV-2 has spread throughout the world since its discovery in China, and Malaysia is no exception. WGS has been a crucial approach in studying the evolution and genetic diversity of SARS-CoV-2 in the ongoing pandemic. Despite considerable number of SARS-CoV-2 genome sequences have been submitted...
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| Format: | Article |
| Language: | English |
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Public Library of Science
2022
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| Online Access: | http://umpir.ump.edu.my/id/eprint/33578/1/Whole%20genome%20sequence%20analysis%20showing%20unique%20SARS-CoV-2%20lineages%20of%20B.1.524.pdf |
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| author | Ummu Afeera, Zainulabid Aini Syahida, Mat Yassim Hussain, Mushtaq Ayesha, Aslam Sharmeen Nellisa, Soffian Mohamad Shafiq, Mohd Ibrahim Norhidayah, Kamarudin Mohd Nazli, Kamarulzaman Hin, How Soon Hajar Fauzan, Ahmad |
| author_facet | Ummu Afeera, Zainulabid Aini Syahida, Mat Yassim Hussain, Mushtaq Ayesha, Aslam Sharmeen Nellisa, Soffian Mohamad Shafiq, Mohd Ibrahim Norhidayah, Kamarudin Mohd Nazli, Kamarulzaman Hin, How Soon Hajar Fauzan, Ahmad |
| author_sort | Ummu Afeera, Zainulabid |
| collection | UMP |
| description | SARS-CoV-2 has spread throughout the world since its discovery in China, and Malaysia is no exception. WGS has been a crucial approach in studying the evolution and genetic diversity of SARS-CoV-2 in the ongoing pandemic. Despite considerable number of SARS-CoV-2 genome sequences have been submitted to GISAID and NCBI databases, there is still scarcity of data from Malaysia. This study aims to report new Malaysian lineages of the virus, responsible for the sustained spikes in COVID-19 cases during the third wave of the pandemic. Patients with nasopharyngeal and/or oropharyngeal swabs confirmed COVID-19 positive by real-time RT-PCR with CT value < 25 were chosen for WGS. The selected SARS-CoV-2 isolates were then sequenced, characterized and analyzed along with 986 sequences of the dominant lineages of D614G variants currently circulating throughout Malaysia. The prevalence of clade GH and G formed strong ground for the presence of two Malaysian lineages of AU.2 and B.1.524 that has caused sustained spikes of cases in the country. Statistical analysis on the association of gender and age group with Malaysian lineages revealed a significant association (p <0.05). Phylogenetic analysis revealed dispersion of 41 lineages, of these, 22 lineages are still active. Mutational analysis showed presence of unique G1223C missense mutation in transmembrane domain of the spike protein. For better understanding of the SARS-CoV-2 evolution in Malaysia especially with reference to the reported lineages, large scale studies based on WGS are warranted. |
| first_indexed | 2024-03-06T12:55:46Z |
| format | Article |
| id | UMPir33578 |
| institution | Universiti Malaysia Pahang |
| language | English |
| last_indexed | 2024-03-06T12:55:46Z |
| publishDate | 2022 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | UMPir335782022-04-15T03:31:25Z http://umpir.ump.edu.my/id/eprint/33578/ Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia Ummu Afeera, Zainulabid Aini Syahida, Mat Yassim Hussain, Mushtaq Ayesha, Aslam Sharmeen Nellisa, Soffian Mohamad Shafiq, Mohd Ibrahim Norhidayah, Kamarudin Mohd Nazli, Kamarulzaman Hin, How Soon Hajar Fauzan, Ahmad Q Science (General) QH426 Genetics SB Plant culture T Technology (General) SARS-CoV-2 has spread throughout the world since its discovery in China, and Malaysia is no exception. WGS has been a crucial approach in studying the evolution and genetic diversity of SARS-CoV-2 in the ongoing pandemic. Despite considerable number of SARS-CoV-2 genome sequences have been submitted to GISAID and NCBI databases, there is still scarcity of data from Malaysia. This study aims to report new Malaysian lineages of the virus, responsible for the sustained spikes in COVID-19 cases during the third wave of the pandemic. Patients with nasopharyngeal and/or oropharyngeal swabs confirmed COVID-19 positive by real-time RT-PCR with CT value < 25 were chosen for WGS. The selected SARS-CoV-2 isolates were then sequenced, characterized and analyzed along with 986 sequences of the dominant lineages of D614G variants currently circulating throughout Malaysia. The prevalence of clade GH and G formed strong ground for the presence of two Malaysian lineages of AU.2 and B.1.524 that has caused sustained spikes of cases in the country. Statistical analysis on the association of gender and age group with Malaysian lineages revealed a significant association (p <0.05). Phylogenetic analysis revealed dispersion of 41 lineages, of these, 22 lineages are still active. Mutational analysis showed presence of unique G1223C missense mutation in transmembrane domain of the spike protein. For better understanding of the SARS-CoV-2 evolution in Malaysia especially with reference to the reported lineages, large scale studies based on WGS are warranted. Public Library of Science 2022-02 Article PeerReviewed pdf en cc_by_4 http://umpir.ump.edu.my/id/eprint/33578/1/Whole%20genome%20sequence%20analysis%20showing%20unique%20SARS-CoV-2%20lineages%20of%20B.1.524.pdf Ummu Afeera, Zainulabid and Aini Syahida, Mat Yassim and Hussain, Mushtaq and Ayesha, Aslam and Sharmeen Nellisa, Soffian and Mohamad Shafiq, Mohd Ibrahim and Norhidayah, Kamarudin and Mohd Nazli, Kamarulzaman and Hin, How Soon and Hajar Fauzan, Ahmad (2022) Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. PLoS ONE, 17 (2). pp. 1-16. ISSN 1932-6203. (Published) https://doi.org/10.1371/journal.pone.0263678 https://doi.org/10.1371/journal.pone.0263678 |
| spellingShingle | Q Science (General) QH426 Genetics SB Plant culture T Technology (General) Ummu Afeera, Zainulabid Aini Syahida, Mat Yassim Hussain, Mushtaq Ayesha, Aslam Sharmeen Nellisa, Soffian Mohamad Shafiq, Mohd Ibrahim Norhidayah, Kamarudin Mohd Nazli, Kamarulzaman Hin, How Soon Hajar Fauzan, Ahmad Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia |
| title | Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia |
| title_full | Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia |
| title_fullStr | Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia |
| title_full_unstemmed | Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia |
| title_short | Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia |
| title_sort | whole genome sequence analysis showing unique sars cov 2 lineages of b 1 524 and au 2 in malaysia |
| topic | Q Science (General) QH426 Genetics SB Plant culture T Technology (General) |
| url | http://umpir.ump.edu.my/id/eprint/33578/1/Whole%20genome%20sequence%20analysis%20showing%20unique%20SARS-CoV-2%20lineages%20of%20B.1.524.pdf |
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