Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia Article Swipe
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· 2022
· Open Access
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· DOI: https://doi.org/10.1371/journal.pone.0263678
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 C T 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.
Related Topics
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1371/journal.pone.0263678
- https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0263678&type=printable
- OA Status
- gold
- Cited By
- 15
- References
- 64
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4214602185
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4214602185Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1371/journal.pone.0263678Digital Object Identifier
- Title
-
Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in MalaysiaWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2022Year of publication
- Publication date
-
2022-02-25Full publication date if available
- Authors
-
Ummu Afeera Zainulabid, Aini Syahida Mat Yassim, Mushtaq Hussain, Ayesha Aslam, Sharmeen Nellisa Soffian, Mohamad Shafiq Mohd Ibrahim, Norhidayah Kamarudin, Mohd Nazli Kamarulzaman, How Soon Hin, Hajar Fauzan AhmadList of authors in order
- Landing page
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https://doi.org/10.1371/journal.pone.0263678Publisher landing page
- PDF URL
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https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0263678&type=printableDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0263678&type=printableDirect OA link when available
- Concepts
-
Phylogenetic tree, Biology, Clade, Genetics, Pandemic, Phylogenetics, Genome, Missense mutation, Whole genome sequencing, Genetic diversity, Sequence analysis, Evolutionary biology, Mutation, Coronavirus disease 2019 (COVID-19), Virology, Gene, Population, Medicine, Infectious disease (medical specialty), Disease, Environmental health, PathologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
15Total citation count in OpenAlex
- Citations by year (recent)
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2025: 2, 2024: 5, 2023: 6, 2022: 2Per-year citation counts (last 5 years)
- References (count)
-
64Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.caused | 154 |
| abstract_inverted_index.chosen | 103 |
| abstract_inverted_index.domain | 207 |
| abstract_inverted_index.during | 77 |
| abstract_inverted_index.formed | 138 |
| abstract_inverted_index.gender | 168 |
| abstract_inverted_index.genome | 40 |
| abstract_inverted_index.ground | 140 |
| abstract_inverted_index.number | 37 |
| abstract_inverted_index.report | 62 |
| abstract_inverted_index.showed | 198 |
| abstract_inverted_index.spikes | 73, 156 |
| abstract_inverted_index.spread | 2 |
| abstract_inverted_index.strong | 139 |
| abstract_inverted_index.these, | 190 |
| abstract_inverted_index.unique | 201 |
| abstract_inverted_index.virus, | 68 |
| abstract_inverted_index.B.1.524 | 151 |
| abstract_inverted_index.Despite | 35 |
| abstract_inverted_index.active. | 195 |
| abstract_inverted_index.crucial | 20 |
| abstract_inverted_index.genetic | 27 |
| abstract_inverted_index.ongoing | 33 |
| abstract_inverted_index.studies | 230 |
| abstract_inverted_index.COVID-19 | 75, 91 |
| abstract_inverted_index.Malaysia | 12, 220 |
| abstract_inverted_index.Patients | 84 |
| abstract_inverted_index.analysis | 163, 183, 197 |
| abstract_inverted_index.analyzed | 115 |
| abstract_inverted_index.approach | 21 |
| abstract_inverted_index.country. | 161 |
| abstract_inverted_index.dominant | 122 |
| abstract_inverted_index.isolates | 109 |
| abstract_inverted_index.lineages | 65, 123, 147, 174, 192 |
| abstract_inverted_index.missense | 203 |
| abstract_inverted_index.mutation | 204 |
| abstract_inverted_index.positive | 92 |
| abstract_inverted_index.presence | 143, 199 |
| abstract_inverted_index.protein. | 211 |
| abstract_inverted_index.reported | 226 |
| abstract_inverted_index.revealed | 175, 184 |
| abstract_inverted_index.scarcity | 53 |
| abstract_inverted_index.selected | 107 |
| abstract_inverted_index.studying | 23 |
| abstract_inverted_index.variants | 126 |
| abstract_inverted_index.Malaysia. | 57, 130 |
| abstract_inverted_index.Malaysian | 64, 146, 173 |
| abstract_inverted_index.confirmed | 90 |
| abstract_inverted_index.currently | 127 |
| abstract_inverted_index.discovery | 8 |
| abstract_inverted_index.diversity | 28 |
| abstract_inverted_index.evolution | 25, 218 |
| abstract_inverted_index.lineages, | 188, 227 |
| abstract_inverted_index.pandemic. | 34, 83 |
| abstract_inverted_index.real-time | 94 |
| abstract_inverted_index.reference | 223 |
| abstract_inverted_index.sequences | 41, 119 |
| abstract_inverted_index.submitted | 44 |
| abstract_inverted_index.sustained | 72, 155 |
| abstract_inverted_index.<0.05). | 181 |
| abstract_inverted_index.Mutational | 196 |
| abstract_inverted_index.SARS-CoV-2 | 0, 30, 39, 108, 217 |
| abstract_inverted_index.databases, | 49 |
| abstract_inverted_index.dispersion | 185 |
| abstract_inverted_index.especially | 221 |
| abstract_inverted_index.exception. | 15 |
| abstract_inverted_index.prevalence | 132 |
| abstract_inverted_index.sequenced, | 112 |
| abstract_inverted_index.throughout | 3, 129 |
| abstract_inverted_index.warranted. | 235 |
| abstract_inverted_index.Statistical | 162 |
| abstract_inverted_index.association | 166, 178 |
| abstract_inverted_index.circulating | 128 |
| abstract_inverted_index.responsible | 69 |
| abstract_inverted_index.significant | 177 |
| abstract_inverted_index.Phylogenetic | 182 |
| abstract_inverted_index.considerable | 36 |
| abstract_inverted_index.characterized | 113 |
| abstract_inverted_index.oropharyngeal | 88 |
| abstract_inverted_index.transmembrane | 206 |
| abstract_inverted_index.understanding | 214 |
| abstract_inverted_index.nasopharyngeal | 86 |
| cited_by_percentile_year.max | 98 |
| cited_by_percentile_year.min | 94 |
| corresponding_author_ids | https://openalex.org/A5070064693, https://openalex.org/A5013708153, https://openalex.org/A5030391747, https://openalex.org/A5106182393, https://openalex.org/A5022622478, https://openalex.org/A5070384787, https://openalex.org/A5018518758, https://openalex.org/A5013584193, https://openalex.org/A5109834708, https://openalex.org/A5038635899 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 10 |
| corresponding_institution_ids | https://openalex.org/I102913810, https://openalex.org/I39727005, https://openalex.org/I4164984 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/3 |
| sustainable_development_goals[0].score | 0.8399999737739563 |
| sustainable_development_goals[0].display_name | Good health and well-being |
| citation_normalized_percentile.value | 0.84429703 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |