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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Autores principales:	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
Formato:	article
Lenguaje:	EN
Publicado:	PeerJ Inc. 2021
Materias:	SARS-CoV-2 Genetic diversity Lineages Mutations Linkage disequilibrium Medicine R
Acceso en línea:	https://doaj.org/article/48e78b8a86674e1db26d885301b2676e
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spelling	oai:doaj.org-article:48e78b8a86674e1db26d885301b2676e2021-11-05T15:05:48ZGenomic diversity of SARS-CoV-2 in Malaysia10.7717/peerj.124492167-8359https://doaj.org/article/48e78b8a86674e1db26d885301b2676e2021-11-01T00:00:00Zhttps://peerj.com/articles/12449.pdfhttps://peerj.com/articles/12449/https://doaj.org/toc/2167-8359Background 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.Noorliza Mohamad NoordinJoon Liang TanChee Kheong ChongYu Kie ChemNorazimah TajudinRehan Shuhada Abu BakarSelvanesan SengolHannah Yik Phing PhoonNurul Aina Murni Che AzidW Nur Afiza W Mohd ArifinZirwatul Adilah AzizHani HussinNurul Syahida IbrahimAziyati OmarUshananthiny RaviKamal Hisham Kamarul ZamanMohd Asri YaminYun Fong NgeowPeerJ Inc.articleSARS-CoV-2Genetic diversityLineagesMutationsLinkage disequilibriumMedicineRENPeerJ, Vol 9, p e12449 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	SARS-CoV-2 Genetic diversity Lineages Mutations Linkage disequilibrium Medicine R
spellingShingle	SARS-CoV-2 Genetic diversity Lineages Mutations Linkage disequilibrium Medicine R 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
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.
format	article
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
title	Genomic diversity of SARS-CoV-2 in Malaysia
title_short	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_sort	genomic diversity of sars-cov-2 in malaysia
publisher	PeerJ Inc.
publishDate	2021
url	https://doaj.org/article/48e78b8a86674e1db26d885301b2676e
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Genomic diversity of SARS-CoV-2 in Malaysia

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