Non-Synonymous Mutation Analysis of SARS-CoV-2 ORF3a in Indonesia

Yuliawuri, Hartiyowidi; Christian, Jeanne Elvia; Steven, Nathanael

doi:10.21705/mcbs.v6i1.221

Cited by 7 publications

(7 citation statements)

References 10 publications

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“…This is most likely related to high mutation rate in SARS-CoV-2 genome. [16][17][18] In this study, the first neutralizing antibody titer examination was carried out on day 14 after administration of the first vaccine dose. The second antibody titer examination was also carried out 14 days after the second dose administration to equalize the time of the first and second examinations.…”

Section: Discussionmentioning

confidence: 99%

Neutralizing Antibody Response by Inactivated SARS-CoV-2 Vaccine on Healthcare Workers

Tandirogang

Fitriany

Mardania

et al. 2023

Mol Cell Biomed Sci

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Background: Currently, the key to combat coronavirus disease 2019 (COVID-19) as a global pandemic is relying mainly on vaccination, and several factors might affect the level of protection. This study aimed to determine the quantitative increase of neutralizing antibody titer against COVID-19 and the influence of gender, body mass index (BMI), routine consumption of vitamin C, D, and E towards the neutralizing antibodies after vaccination.Materials and methods: One hundred nine health workers from various health facilities were recruited. Sinovac inactivated severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) vaccine was used in this study. Antibody titer measurements were carried out quantitatively using electrochemiluminescence immunoassay (ECLIA) on day 14 after the first and second doses administration of the vaccine.Results: The average of antibody titers after the first and second doses were 109.1 and 191.6 U/mL, respectively. Antibody titer significantly increased (p=0.000) as much as 82.5 U/mL from the first to the second dose. There was a significant difference in the increase in antibody titer between respondents who consumed vitamin E regularly and those who did not (p=0.036). Routine consumption of vitamin C and D, gender, and BMI did not affect the increase in neutralizing antibody titer with p-values of 0.983, 0.337, 0.186, and 0.424, respectively.Conclusion: Routine consumption of vitamin E is associated with post-SARS-CoV-2 vaccination neutralizing antibody response. Gender, BMI, and the routine consumption of vitamin C and D have no association with the immune response.Keywords: COVID-19, neutralizing antibody, inactivated SARS-CoV-2 vaccine

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Section: Discussionmentioning

confidence: 99%

Neutralizing Antibody Response by Inactivated SARS-CoV-2 Vaccine on Healthcare Workers

Tandirogang

Fitriany

Mardania

et al. 2023

Mol Cell Biomed Sci

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“…Those highest mutations did not occur in the functional domain. 14,15 So, the purpose of this study is to look for other nonsynonymous mutations, which were found in Indonesia samples that occur in the functional domains of ORF3a SARS-CoV-2. Furthermore, we analyze the unique truncated protein of ORF3a SARS-CoV-2.…”

Section: Introductionmentioning

confidence: 99%

Unique truncated and non-synonymous mutations in functional domains of ORF3a SARS-CoV-2

Christian¹,

Yuliawuri²

2023

JMedScie

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Previous studies showed that mutations in the SARS-CoV-2 ORF3a protein can influence viral pathogenesis. Therefore, it is necessary to observe mutations, especially in the functional domain of the protein. We observed the presence of mutations in the ORF3a protein by analyzing 5,131 samples from the GISAID database since it was first discovered in March 2020 until November 2021. The sequence was aligned using Clustal Omega Multiple Sequence Alignment from EMBL-EBI and analyzed using BioEdit version 7.2.5 software using reference sequences NC045512. Samples having the letter N were omitted from the analysis. The effect of point mutations on proteins was analyzed using the Protein Variation Effect Analyzer (PROVEAN) v1.1.3 software. The functional domains of the ORF3a protein were visualized using RasWin software. We identified 312 mutations in the SARS-CoV-2 ORF3a protein. In addition, from 5,131 samples, 915 samples were found to be truncated in the C-terminal region of the protein. These non-synonymous mutations data in functional domains and truncated sequences indicate that amino acid changes in the ORF3a protein require further studies to determine the effect of viral pathogenicity in humans.

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“…Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which is the cause of the coronavirus disease 2019 (COVID-19), continues to mutate until it becomes a new variant 1 , such as omicron which is currently found in many countries. Although not as many as when there was delta variant, COVID-19 cases are still being reported.…”

Section: Introductionmentioning

confidence: 99%

Association between 25(OH)D3 Levels and the Presence of COVID-19 Symptoms

Hermawan

Aryastuti

Muhani

et al. 2023

Mol Cell Biomed Sci

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Background: Recently, there have been studies reporting a relationship between vitamin D levels in the blood and the immune system. This study aimed to analyze the association between vitamin D levels and symptoms of coronavirus disease 2019 (COVID-19).Materials and methods: This study was an analytical survey study with a cross-sectional approach, with lecturers at Universitas Malahayati that have been infected with COVID-19 in 2022 as subjects. Total 47 subjects were included. Subjects were fasted overnight, then blood samples were taken from subjects in the next morning. The blood was centrifuged, then the serum was separated for examination by the direct competitive chemiluminescence immunoassay (CLIA) method using Architect 25-OH Vitamin D Reagent. Data was analyzed using logistic regression.Results: None of the subjects had normal blood levels of 25(OH)D3 and almost half (48.9%) of the subjects had symptoms when infected with COVID-19. There was a significant relationship between the level of 25(OH)D3 (p=0.001) and the status of the COVID-19 vaccine (p=0.013) with the presence of symptoms in COVID-19 patients.Conclusion: The lower the level of 25(OH)D3 in the blood and the more incomplete the COVID-19 vaccine, the greater the onset potential of COVID-19 symptoms. It is necessary to maintain vitamin D intake and increase the coverage of the COVID-19 vaccine, especially at booster doses.Keywords: vitamin D, COVID-19, vaccination, health protocol

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Non-Synonymous Mutation Analysis of SARS-CoV-2 ORF3a in Indonesia

Cited by 7 publications

References 10 publications

Neutralizing Antibody Response by Inactivated SARS-CoV-2 Vaccine on Healthcare Workers

Neutralizing Antibody Response by Inactivated SARS-CoV-2 Vaccine on Healthcare Workers

Unique truncated and non-synonymous mutations in functional domains of ORF3a SARS-CoV-2

Association between 25(OH)D3 Levels and the Presence of COVID-19 Symptoms

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