Genomic diversity of SARS-CoV-2 in Malaysia
Background More than a year after its first appearance in December 2019, the COVID-19 pandemic is still on a rampage in many parts of the world. Although several vaccines have been approved for emergency use, the emergence and rapid spread of new SARS-CoV-2 variants have sparked fears of vaccine fai...
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| Format: | Article |
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PeerJ Inc.
2021-11-01
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| Online Access: | https://peerj.com/articles/12449.pdf |
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| author | Noorliza Mohamad Noordin Joon Liang Tan Chee Kheong Chong Yu Kie Chem Norazimah Tajudin Rehan Shuhada Abu Bakar Selvanesan Sengol Hannah Yik Phing Phoon Nurul Aina Murni Che Azid W Nur Afiza W Mohd Arifin Zirwatul Adilah Aziz Hani Hussin Nurul Syahida Ibrahim Aziyati Omar Ushananthiny Ravi Kamal Hisham Kamarul Zaman Mohd Asri Yamin Yun Fong Ngeow |
| author_facet | Noorliza Mohamad Noordin Joon Liang Tan Chee Kheong Chong Yu Kie Chem Norazimah Tajudin Rehan Shuhada Abu Bakar Selvanesan Sengol Hannah Yik Phing Phoon Nurul Aina Murni Che Azid W Nur Afiza W Mohd Arifin Zirwatul Adilah Aziz Hani Hussin Nurul Syahida Ibrahim Aziyati Omar Ushananthiny Ravi Kamal Hisham Kamarul Zaman Mohd Asri Yamin Yun Fong Ngeow |
| author_sort | Noorliza Mohamad Noordin |
| collection | DOAJ |
| description | Background More than a year after its first appearance in December 2019, the COVID-19 pandemic is still on a rampage in many parts of the world. Although several vaccines have been approved for emergency use, the emergence and rapid spread of new SARS-CoV-2 variants have sparked fears of vaccine failure due to immune evasion. Massive viral genome sequencing has been recommended to track the genetic changes that could lead to adverse consequences. Methods We sequenced SARS-CoV-2 respiratory isolates from the National Public Health Laboratory, Malaysia and examined them together with viral genomes deposited in GISAID by other Malaysian researchers, to understand the evolutionary trend of the virus circulating in the country. We studied the distribution of virus lineages and site-wise mutations, analysed genetic clustering with the goeBURST full Minimum Spanning Tree algorithm, examined the trend of viral nucleotide diversity over time and performed nucleotide substitution association analyses. Results We identified 22 sub-lineages, 13 clonal complexes, 178 sequence types and seven sites of linkage disequilibrium in 277 SARS-CoV-2 genomes sequenced between January and December 2020. B.1.524 was the largest lineage group. The number of mutations per genome ranged from 0 to 19. The mean genomic diversity value over 12 months was 3.26 × 10−4. Of 359 mutations detected, 60.5% of which were non-synonymous, the most frequent were in the ORF1ab (P4715L), S (D614G and A701V) and N (S194L) genes. Conclusion The SARS-CoV-2 virus accumulated an abundance of mutations in the first year of the COVID-19 pandemic in Malaysia. Its overall genetic diversity, however, is relatively low compared to other Asian countries with larger populations. Continuous genomic and epidemiological surveillance will help to clarify the evolutionary processes determining viral diversity and impacting on human health. |
| first_indexed | 2024-03-09T07:22:44Z |
| format | Article |
| id | doaj.art-48e78b8a86674e1db26d885301b2676e |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:22:44Z |
| publishDate | 2021-11-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-48e78b8a86674e1db26d885301b2676e2023-12-03T07:14:01ZengPeerJ Inc.PeerJ2167-83592021-11-019e1244910.7717/peerj.12449Genomic diversity of SARS-CoV-2 in MalaysiaNoorliza Mohamad Noordin0Joon Liang Tan1Chee Kheong Chong2Yu Kie Chem3Norazimah Tajudin4Rehan Shuhada Abu Bakar5Selvanesan Sengol6Hannah Yik Phing Phoon7Nurul Aina Murni Che Azid8W Nur Afiza W Mohd Arifin9Zirwatul Adilah Aziz10Hani Hussin11Nurul Syahida Ibrahim12Aziyati Omar13Ushananthiny Ravi14Kamal Hisham Kamarul Zaman15Mohd Asri Yamin16Yun Fong Ngeow17National Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, MalaysiaFaculty of Information Science and Technology, Multimedia University, Melaka, Melaka, MalaysiaPublic Health Department, Ministry of Health, Putrajaya, MalaysiaNational Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, MalaysiaNational Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, MalaysiaNational Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, MalaysiaNational Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, MalaysiaNational Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, MalaysiaNational Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, MalaysiaNational Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, MalaysiaNational Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, MalaysiaNational Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, MalaysiaNational Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, MalaysiaNational Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, MalaysiaNational Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, MalaysiaNational Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, MalaysiaNational Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Selangor, MalaysiaFaculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Bandar Sungai Long, Selangor, MalaysiaBackground More than a year after its first appearance in December 2019, the COVID-19 pandemic is still on a rampage in many parts of the world. Although several vaccines have been approved for emergency use, the emergence and rapid spread of new SARS-CoV-2 variants have sparked fears of vaccine failure due to immune evasion. Massive viral genome sequencing has been recommended to track the genetic changes that could lead to adverse consequences. Methods We sequenced SARS-CoV-2 respiratory isolates from the National Public Health Laboratory, Malaysia and examined them together with viral genomes deposited in GISAID by other Malaysian researchers, to understand the evolutionary trend of the virus circulating in the country. We studied the distribution of virus lineages and site-wise mutations, analysed genetic clustering with the goeBURST full Minimum Spanning Tree algorithm, examined the trend of viral nucleotide diversity over time and performed nucleotide substitution association analyses. Results We identified 22 sub-lineages, 13 clonal complexes, 178 sequence types and seven sites of linkage disequilibrium in 277 SARS-CoV-2 genomes sequenced between January and December 2020. B.1.524 was the largest lineage group. The number of mutations per genome ranged from 0 to 19. The mean genomic diversity value over 12 months was 3.26 × 10−4. Of 359 mutations detected, 60.5% of which were non-synonymous, the most frequent were in the ORF1ab (P4715L), S (D614G and A701V) and N (S194L) genes. Conclusion The SARS-CoV-2 virus accumulated an abundance of mutations in the first year of the COVID-19 pandemic in Malaysia. Its overall genetic diversity, however, is relatively low compared to other Asian countries with larger populations. Continuous genomic and epidemiological surveillance will help to clarify the evolutionary processes determining viral diversity and impacting on human health.https://peerj.com/articles/12449.pdfSARS-CoV-2Genetic diversityLineagesMutationsLinkage disequilibrium |
| spellingShingle | Noorliza Mohamad Noordin Joon Liang Tan Chee Kheong Chong Yu Kie Chem Norazimah Tajudin Rehan Shuhada Abu Bakar Selvanesan Sengol Hannah Yik Phing Phoon Nurul Aina Murni Che Azid W Nur Afiza W Mohd Arifin Zirwatul Adilah Aziz Hani Hussin Nurul Syahida Ibrahim Aziyati Omar Ushananthiny Ravi Kamal Hisham Kamarul Zaman Mohd Asri Yamin Yun Fong Ngeow Genomic diversity of SARS-CoV-2 in Malaysia PeerJ SARS-CoV-2 Genetic diversity Lineages Mutations Linkage disequilibrium |
| title | Genomic diversity of SARS-CoV-2 in Malaysia |
| title_full | Genomic diversity of SARS-CoV-2 in Malaysia |
| title_fullStr | Genomic diversity of SARS-CoV-2 in Malaysia |
| title_full_unstemmed | Genomic diversity of SARS-CoV-2 in Malaysia |
| title_short | Genomic diversity of SARS-CoV-2 in Malaysia |
| title_sort | genomic diversity of sars cov 2 in malaysia |
| topic | SARS-CoV-2 Genetic diversity Lineages Mutations Linkage disequilibrium |
| url | https://peerj.com/articles/12449.pdf |
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