Whole genome sequencing analysis of Spike D614G mutation reveals unique SARS-CoV-2 Lineages of B.1.524 and AU.2 in Malaysia

Zainulabid, Ummu Afeera and Mat Yassim, Aini Syahida and Hussain, Mushtaq and Aslam, Ayesha and Soffian, Sharmeen Nellisa and Mohd Ibrahim, Mohamad Shafiq and Kamarudin, Norhidayah and Kamarulzaman, Mohd Nazli and How, Soon Hin and Ahmad, Hajar Fauzan (2022) Whole genome sequencing analysis of Spike D614G mutation reveals unique SARS-CoV-2 Lineages of B.1.524 and AU.2 in Malaysia. PLOS ONE, 17 (2). pp. 1-16. E-ISSN 1932-6203

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Abstract

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.

Item Type:	Article (Journal)
Additional Information:	7459/92611
Uncontrolled Keywords:	SARS-CoV-2; Mutation; D614G; Spike Protein; G1223C; Clade; Malaysia; Pahang
Subjects:	R Medicine > RC Internal medicine > RC111 Infectious and Parasitic Diseases
Kulliyyahs/Centres/Divisions/Institutes (Can select more than one option. Press CONTROL button):	Kulliyyah of Medicine > Department of Internal Medicine Kulliyyah of Dentistry Kulliyyah of Dentistry > Department of Paediatric Dentistry and Dental Public Health Kulliyyah of Medicine Kulliyyah of Medicine > Department of Surgery Kulliyyah of Medicine > Department of Pathology & Lab Medicine
Depositing User:	Asst. Dr. Ummu Afeera Zainulabid
Date Deposited:	26 Oct 2021 15:56
Last Modified:	30 May 2023 13:56
URI:	http://irep.iium.edu.my/id/eprint/92611

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