Genomic analysis of three SARS-CoV-2 waves in west Sumatra: Evolutionary dynamics and variant clustering.

Background: The Severe Acute Respiratory Syndrome Coronavirus 2 virus (SARS-CoV-2) has been undergoing evolutionary changes to improve its ability to thrive within human hosts, leading to the emergence of specific variants associated with subsequent waves of the coronavirus diseases 2019 (COVID-19) pandemic. Indonesia has grappled with the effects of this pandemic and subsequent waves affecting various regions, including West Sumatra. Although located outside Java island epicenter, West Sumatra experienced significant COVID-19 transmission, especially during the third wave in early 2022. Objective: This study aimed to investigate the genetic evolution and epidemiological dynamics of SARS-CoV-2 variants in West Sumatra throughout the three pandemic waves. Methods: We conducted a genotyping study retrospectively using 278 COVID-19 patient samples from 2020 to 2022. The Real-Time Quantitative Reverse Transcription PCR (RT-qPCR) was used for screening, and whole-genome sequence analysis was conducted through the Illumina MiSeq instrument. Result: The analysis revealed distinct patterns in the prevalence of viral lineages across the waves. The initial wave was predominated by clade 20A (77,4 %) especially lineage B.1.466.2 (50 %). The second wave was marked by a significant emergence of the Delta variant (72,5 %), particularly lineage AY.23 (81,1 %), originating from India, with subsequent local evolution leading to the formation of distinct clusters. We found that about 96,7 % of the third wave variant was dominated by Omicron variants, especially the generation of lineages BA.1 and BA.2, demonstrating widespread global dissemination and local variant development. Phylogenetic analysis indicated a close relatedness of West Sumatra variants to those from Malaysia and other parts of Indonesia, highlighting regional transmission dynamics and potential sources of variant introductions. Conclusion: This study has identified unique variant clusters within each wave, suggesting distinct evolutionary pathways and local adaptations. These findings provide valuable insights into the genomic landscape of SARS-CoV-2 in West Sumatra and emphasize the crucial role of ongoing genomic surveillance in tracking viral changes and guiding public health measures.

Dynamic Evolution of SARS-CoV-2 in West Sumatra: Analyzing S Gene Mutations Across Variants and Their Impact on Public Health and Vaccine Strategies.

<b>Background and Objective:</b> The global SARS-CoV-2 pandemic highlights the importance of tracking virus evolution through genomic surveillance, especially concerning mutations in the SARS-CoV-2 spike protein, crucial for vaccine development. Despite global concern over variants, regions like West Sumatra, Indonesia, lack thorough genomic analysis, prompting this study to analyze S gene mutations across three pandemic waves in West Sumatra. <b>Materials and Methods:</b> Next-generation sequencing was conducted through the Illumina MiSeq instrument to leverage a dataset of 352 anonymized samples collected between March, 2020 and November, 2022 and rigorous analysis of S gene mutation using CLC Genomics Workbench^® 21 version 21.0.3 were employed. Statistical analyses assessed mutation prevalence over time, exploring associations with clinical outcomes. <b>Results:</b> The findings revealed significant variability in mutation profiles across different variants. Notably, the Omicron variant (21K) exhibited a high mutation rate, suggesting enhanced immune evasion capabilities. Comparative analysis highlighted evolutionary trends, from early variants with fewer mutations to highly adapted forms like Delta (21I) and Omicron. The dynamic nature of SARS-CoV-2 evolution underscores the importance of continuous surveillance, rapid public health response and vaccine adaptation. <b>Conclusion:</b> This study contributes valuable insights into the virus's evolving landscape, emphasizing the need for ongoing research, global collaboration and adaptable vaccine strategies to manage the evolving threat of COVID-19 effectively.

Effect of multicomponent crystal of piperine-nicotinic acid on antihyperlipidemic activity in rats.

The alkaloid piperine is the main bioactive compound in black pepper (Piper nigrum L) and exhibits antihyperlipidemic activity. Piperine is a Biopharmaceutical Classification System (BCS) Class II compound, which has low water solubility, resulting in low bioavailability. This study aims to examine the effects of multicomponent nicotinic acid-piperine crystals on antihyperlipidemic activity in rats fed a high-fat diet. To increase the effectiveness of piperine, we prepared multicomponent crystals by the solvent-drop grinding method, using nicotinic acid as a co-former. The antihyperlipidemic activity of the preparation was estimated by measuring total cholesterol (TC), total triglycerides (TG), low-density lipoprotein cholesterol (LDLc) and high-density lipoprotein cholesterol (HDLc), using the enzymatic colorimetric method. Rats fed a high-fat diet exhibited an increase in plasma lipid levels. However, rats administered the multicomponent piperine-nicotinic acid crystals at a dose of 40 mg/kg/BW showed significantly (p<0.050) reduced plasma lipid levels. Compared with hyperlipidemic rats, multicomponent crystals of piperine-nicotinic acid decreased TC from 237.8±8.02 mg/dL to 174.53±7.07mg/dL, TG levels from 208.33±5.79 to 85.95±7.41mg/dL and LDLc levels from 144.225±15.99 mg/dL to 88.55±10.83mg/dL but increased HDLc levels from 51.93±10.92mg/dL to 68.78±2.56 mg/dL. Thus, the results demonstrate that the multicomponent piperine-nicotinic acid crystals lowered TC, TG and LDLc but increased HDLc.