Sains Malaysiana 53(8)(2024): 1767-1776

http://doi.org/10.17576/jsm-2024-5308-04

Genome Sequencing and Phylogenetic Analysis of SARS-CoV-2 Isolated from Patients with COVID-19 in Hospital Canselor Tuanku Muhriz (HCTM), Malaysia

(Penjujukan Genom dan Analisis Filogenetik SARS-CoV-2 Dipencilkan daripada Pesakit COVID-19 di Hospital Canselor Tuanku Muhriz (HCTM), Malaysia)

KON KEN WONG¹, NOOR ZETTI ZAINOL RASHID¹, UMI KALSOM ALI¹, NUR HAZLIN CHONG², SHAIRAH ABDUL RAZAK², NAJMA KORI³, PETRICK PERIYASAMY³ & ALFIZAH HANAFIAH¹

¹Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, Malaysia

²Department of Biological Sciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia

³Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, Malaysia

Received: 18 March 2024/Accepted: 26 June 2024

Abstract

SARS-CoV-2 infection has reached pandemic status in numerous countries worldwide, including Malaysia. Monitoring the genetic diversity of SARS-CoV-2 is essential for identifying the emergence and prevalence of novel variants in different geographical areas. From May to October 2021, this research endeavor analyzed the SARS-CoV-2 genome of 40 COVID-19 patients diagnosed using real-time RT-PCR at the local hospital HCTM-UKM. The process involved extracting RNA from these patients, which was subsequently subjected to whole genome sequencing. Our discovery underscores the primary strains responsible for the fourth wave of the COVID-19 pandemic in Malaysia in May 2021 were the Beta variant, primarily associated with the B.1.351 lineage. However, by October 2021, the Delta variant had become predominant and was categorized within the AV.59 and AV.79 lineages. Genomic epidemiological analysis showed about 19 amino acid mutations in the spike protein that were prevalent during the Beta variant outbreak. Among these, the N501Y mutation is particularly noteworthy as it significantly enhances the virus's ability to bind to the ACE2 receptor. Additionally, 32 amino acid mutations were identified during the Delta variant outbreak, with the T478K mutation being linked to increased viral infectivity and affecting the virus's affinity for human cells. Throughout our research, we consistently noted the presence of Spike D614G mutations in all the strains we collected which is known to reduce S1 shedding and increase infectivity. These findings could contribute significantly to our understanding of specific variants due to their clinical implications and rapid spread within the community.

Keywords: COVID-19; genome sequencing; phylogenetic; spike protein mutations; variant

Abstrak

Jangkitan SARS-CoV-2 telah mencapai status pandemik di hampir semua negara di seluruh dunia, termasuk Malaysia. Pemantauan kepelbagaian genetik SARS-CoV-2 adalah penting untuk mengenal pasti penemuan dan prevalen varian baharu di kawasan geografi yang berbeza. Dari Mei hingga Oktober 2021, kami menganalisis genom SARS-CoV-2 bagi 40 pesakit COVID-19 dengan menggunakan kaedah ‘realtime RT-PCR’ di hospital tempatan HCTM-UKM. Proses ini melibatkan pengekstrakan RNA daripada sampel pesakit ini dan dikaji dengan teknik jujukan lengkap genom. Penemuan utama kami adalah strain SARS-CoV-2 yang berleluasa semasa pandemik COVID-19 gelombang keempat di Malaysia pada Mei 2021 adalah varian Beta dengan garis keturunan B.1.351. Namun demikian, varian Delta telah menjadi dominan pada Oktober 2021, dan dikategorikan dalam garis keturunan AV.59 dan AV.79. Analisis epidemiologi genom menunjukkan kira-kira 19 mutasi asid amino dalam protein spike yang mendominasi semasa wabak varian Beta. Antara ini, mutasi N501Y adalah perlu diperhatikan kerana ia akan meningkatkan keupayaan virus untuk berikatan dengan reseptor ACE2 secara signifikan. Tambahan pula, sebanyak 32 mutasi asid amino dikenal pasti semasa wabak varian Delta dengan mutasi T478K dikaitkan dengan peningkatan jangkitan virus dan mempengaruhi keupayaan virus untuk berikatan dengan sel manusia. Sepanjang penyelidikan kami, mutasi Spike D614G dijumpai dalam semua strain yang kami kumpulkan. Mutasi ini dapat mengurangkan pembuangan S1 dan meningkatkan jangkitan virus. Dapatan kajian ini boleh memberi sumbangan yang signifikan kepada pemahaman kita mengenai varian tertentu disebabkan implikasi klinikal dan penyebaran yang pesat dalam komuniti.

Kata kunci: COVID-19; filogenetik; mutasi protein Spike; penjujukan genom; varian

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*Corresponding author; email: alfizah@ppukm.ukm.edu.my