Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia

Zainulabid, Ummu Afeera; Kamarudin, Norhidayah; Zulkifly, Ahmad Hafiz; Gan, Han Ming; Tay, Darren Dean; Siew, Shing Wei; Yassim, Aini Syahida Mat; Soffian, Sharmeen Nellisa; Faudzi, Ahmad Afif Mohd; Gazali, Ahmad Mahfuz; Maniam, Gaanty Pragas; Ahmad, Hajar Fauzan

doi:10.1128/mra.00657-21

Cited by 8 publications

(7 citation statements)

References 8 publications

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“…The quantity of HCWs increased rapidly with the development of the population, the usage of disposable medical products, and the establishment of new private clinics ( Khan et al, 2019 ). In addition, COVID-19's aftereffects impacted the healthcare system worldwide including Malaysia ( Syahida Mat Yassim et al, 2021 ; Ummu Afeera; Zainulabid et al, 2022 ; Ummu Afeera Zainulabid et al, 2021 ), with the obligatory use of extra personal protective equipment and laboratory materials resulted in an increase in HCW that exceeded the disposal capacity ( Hantoko et al, 2021 ). According to Agamuthu and Barasarathi (2021) , the daily HCW generation in Malaysia is estimated to be 90 metric tonnes (MT), with COVID-19 waste accounting for 27% of the increment (25 MT) during the pandemic.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of pre-treated healthcare wastes during COVID-19 pandemic reveals pathogenic microbiota, antibiotics residues, and antibiotic resistance genes against beta-lactams

Siew

Musa

Sabri

et al. 2023

Environmental Research

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Section: Introductionmentioning

confidence: 99%

Evaluation of pre-treated healthcare wastes during COVID-19 pandemic reveals pathogenic microbiota, antibiotics residues, and antibiotic resistance genes against beta-lactams

Siew

Musa

Sabri

et al. 2023

Environmental Research

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“…Publicly available sequences suggest that these lineages identified in PNG are also commonly observed in other countries in the region, particularly Indonesia ( Cahyani et al. 2022 ; Zainulabid et al. 2021 ) which may explain why the B.1.466.2 and AU lineages are persisting and present in all unrelated clusters, despite multiple introductions into the country.…”

Section: Discussionmentioning

confidence: 87%

Genomic characterisation reveals a dominant lineage of SARS-CoV-2 in Papua New Guinea

et al. 2022

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The COVID-19 pandemic has highlighted the utility of pathogen genomics as a key part of a comprehensive public health response to emerging infectious diseases threats, however the ability to generate, analyses and respond to pathogen genomic data varies around the world. Papua New Guinea (PNG), which has limited in-country capacity for genomics, has experienced significant outbreaks of SARS-CoV-2 with initial genomics data indicating a large proportion of cases were from lineages that are not well-defined within the current nomenclature. Through a partnership between in-country public health agencies and academic organisations, industry, and a public health genomics reference laboratory in Australia a system for routine SARS-CoV-2 genomics from PNG was established. Here we aim to characterise and describe the genomics of PNG’s second wave and examine the sudden expansion of a lineage that is not well defined but very prevalent in the Western Pacific region. We generated 1797 sequences from cases in PNG and performed phylogenetic and phylodynamic analyses to examine the outbreak and characterise the circulating lineages and clusters present. Our results reveal the rapid expansion of the B.1.466.2 and related lineages within PNG, from multiple introductions into the country. We also highlight the difficulties that unstable lineage assignment causes when using genomics to assist with rapid cluster definitions.

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“…Next-generation sequencing (NGS) library was constructed after amplifying full length genome using synthesized cDNA from SuperScriptIV (ThermoFisher Scientific, USA) with some modifications [25,26]. Briefly, 5 μl of the cDNA was used as template for multiplex PCR using Q5 polymerase (NEB, USA) as well as the Artic v3 primer pools during library preparation.…”

Section: Next-generation Sequencing Of the Full-length Viral Genomementioning

confidence: 99%

Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia

Zainulabid

Yassim²,

Hussain

et al. 2022

PLoS ONE

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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.

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Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia

Cited by 8 publications

References 8 publications

Evaluation of pre-treated healthcare wastes during COVID-19 pandemic reveals pathogenic microbiota, antibiotics residues, and antibiotic resistance genes against beta-lactams

Evaluation of pre-treated healthcare wastes during COVID-19 pandemic reveals pathogenic microbiota, antibiotics residues, and antibiotic resistance genes against beta-lactams

Genomic characterisation reveals a dominant lineage of SARS-CoV-2 in Papua New Guinea

Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia

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