Whole-genome sequencing analysis of the Chikungunya virus during 2021 outbreak in Malaysia Article Swipe
Jeevanathan Kalyanasundram
,
Zarina Mohd Zawawi
,
Khayri Azizi Kamel
,
Emmanuel Tiagaraj Aroidoss
,
Kavithambigai Ellan
,
Mohd Ishtiaq Anasir
,
Muhammad Afif Azizan
,
Murni Maya Sari Zulkifli
,
Rozainanee Mohd Zain
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-4877663/v1
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-4877663/v1
Background Chikungunya cases was reported to be on the rise in Malaysia from 2019 to 2021. Although potential endemicity was described previously, genotype shift during 2008 outbreak originating from the 2004 Indian Ocean Islands outbreak presents the probability of current CHIKV spread from neighboring countries. This is due to the prevalence of the new IOL sub-lineage which consists of E1-226A wildtype or reverted strains that are circulating in the Indian subcontinent before spreading to neighboring Thailand during 2018-2019 outbreak. Method In this study, samples received mostly from the Tangkak, Johor were analyzed. A total 56 CHIKV positive serum samples received in 2021 by Institute of Medical Research Malaysia (IMR), were collected based on sample selection criteria. Selected samples were subjected to total RNA extraction, whole-genome sequencing as well as bioinformatic analysis such as phylogenetic, variant and mutation analysis. Results Based on the genomic and phylogenetic analysis, the CHIKV samples from 2021 outbreak were of ECSA-IOL genotype. Genome similarity analysis also revealed that these CHIKVs are highly similar to 2018-2019 outbreak strain from Thailand. In comparison to the 2008 outbreak CHIKV isolate, the current CHIKVs lacked the E1-A226V mutation and harbored the new E1-K211E/E2-V264A sub-linage mutation. Since the E1-K211E/E2-V264A mutation facilitates adaptation to Ae. aegypti as opposed to the E1-A226V mutation which improves adaptation to Ae. albopictus, the emergence 2021 CHIKV outbreak in Malaysia can be postulated due to vector shift. Interestingly, a novel nsP3-T441A/V mutation detected in this study, may also play a role in virus transmission, pathogenicity, fitness and vector adaptation Conclusion In summary, the current CHIKV outbreak are strains originated from the Indian subcontinent through Thailand which may have capitalized on vector shifting by adapting to Ae. aegypti. The presence of novel nsP3-T441A/V mutation may also contribute to the spread of this virus across peninsular Malaysia.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- http://doi.org/10.21203/rs.3.rs-4877663/v1
- OA Status
- gold
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4402561490
All OpenAlex metadata
Raw OpenAlex JSON
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https://openalex.org/W4402561490Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.21203/rs.3.rs-4877663/v1Digital Object Identifier
- Title
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Whole-genome sequencing analysis of the Chikungunya virus during 2021 outbreak in MalaysiaWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
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2024-09-18Full publication date if available
- Authors
-
Jeevanathan Kalyanasundram, Zarina Mohd Zawawi, Khayri Azizi Kamel, Emmanuel Tiagaraj Aroidoss, Kavithambigai Ellan, Mohd Ishtiaq Anasir, Muhammad Afif Azizan, Murni Maya Sari Zulkifli, Rozainanee Mohd ZainList of authors in order
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https://doi.org/10.21203/rs.3.rs-4877663/v1Publisher landing page
- Open access
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://doi.org/10.21203/rs.3.rs-4877663/v1Direct OA link when available
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Chikungunya, Outbreak, Virology, Virus, Genome, Whole genome sequencing, Biology, Chikungunya fever, Genetics, GeneTop concepts (fields/topics) attached by OpenAlex
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0Total citation count in OpenAlex
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.postulated | 226 |
| abstract_inverted_index.prevalence | 51 |
| abstract_inverted_index.sequencing | 126 |
| abstract_inverted_index.similarity | 158 |
| abstract_inverted_index.sub-linage | 194 |
| abstract_inverted_index.<italic>Ae. | 203, 215, 279 |
| abstract_inverted_index.Chikungunya | 2 |
| abstract_inverted_index.capitalized | 272 |
| abstract_inverted_index.circulating | 67 |
| abstract_inverted_index.extraction, | 124 |
| abstract_inverted_index.facilitates | 200 |
| abstract_inverted_index.neighboring | 44, 75 |
| abstract_inverted_index.originating | 28 |
| abstract_inverted_index.previously, | 22 |
| abstract_inverted_index.probability | 38 |
| abstract_inverted_index.sub-lineage | 56 |
| abstract_inverted_index.nsP3-T441A/V | 234, 285 |
| abstract_inverted_index.phylogenetic | 145 |
| abstract_inverted_index.subcontinent | 71, 266 |
| abstract_inverted_index.whole-genome | 125 |
| abstract_inverted_index.bioinformatic | 130 |
| abstract_inverted_index.phylogenetic, | 134 |
| abstract_inverted_index.transmission, | 247 |
| abstract_inverted_index.Interestingly, | 231 |
| abstract_inverted_index.pathogenicity, | 248 |
| abstract_inverted_index.aegypti</italic> | 204 |
| abstract_inverted_index.E1-K211E/E2-V264A | 193, 198 |
| abstract_inverted_index.aegypti</italic>. | 280 |
| abstract_inverted_index.albopictus</italic>, | 216 |
| abstract_inverted_index.<title>Abstract</title> | 0 |
| cited_by_percentile_year | |
| countries_distinct_count | 0 |
| institutions_distinct_count | 9 |
| citation_normalized_percentile.value | 0.26359195 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |