Sequence analysis of SARS-CoV-2 Delta variant isolated from Makassar, South Sulawesi, Indonesia

Sequence analysis of the Spike, RNA-dependent RNA polymerase, and protease genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia

During the Covid-19 pandemic, the resurgence of SARS-CoV-2 was due to the development of novel variants of concern (VOC). Thus, genomic surveillance is essential to monitor continuing evolution of SARS-CoV-2 and to track the emergence of novel variants. In this study, we performed phylogenetic, mutation, and selection pressure analyses of the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 isolates circulating in Yogyakarta and Central Java provinces, Indonesia from May 2021 to February 2022. Various bioinformatics tools were employed to investigate the evolutionary dynamics of distinct SARS-CoV-2 isolates. During the study period, 213 and 139 isolates of Omicron and Delta variants were identified, respectively. Particularly in the Spike gene, mutations were significantly more abundant in Omicron than in Delta variants. Consistently, in all of four genes studied, the substitution rates of Omicron were higher than that of Delta variants, especially in the Spike and nsp12 genes. In addition, selective pressure analysis revealed several sites that were positively selected in particular genes, implying that these sites were functionally essential for virus evolution. In conclusion, our study demonstrated a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia.

Factors related to serum levels of intercellular adhesion molecule-1 in probable COVID-19 patients in surgical treatment: an observational study

Introduction

COVID-19 causes a systemic inflammatory response, involving dysregulation and misexpression of many inflammatory cytokines. The recruitment and activation of inflammatory cells depend on the expression of many classes of inflammatory mediators, with increased expression of endothelial cell adhesion molecules being related to COVID-19 disease severity. With the World Health Organization having recently updated case definitions to suspect, probable, and confirmed, this study aimed to measure the mean value of intercellular adhesion molecule 1 (ICAM-1) and its relation to suspected COVID-19.

Methods

all suspected patients (n=20) were hospitalized and treated following the Indonesian National Guidelines for COVID-19 management. ICAM-1 levels were measured on days 1 and 7, demographic data were recorded, and routine blood count values were measured and additionally considered.

Results

the results showed that the levels of ICAM-1 in the 1st-day group (mean 271.3 ng/ml) were higher than those in the 7th-day group (mean 253.9 ng/ml). This difference was statistically significant (p = 0.00, p ≤ 0.05). All of the patients with suspected COVID-19 were included in this study and tested for COVID-19 by reverse transcription polymerase chain reaction (RT-PCR) testing. A total of 10 patients were confirmed positive with a COVID-19 infection, with elevated ICAM-1 levels compared to the confirmed negative patients (with a mean 1st day 296.8 versus a mean 7th day 279.0 ng/ml). ICAM-1 levels of all patients decreased by the seventh day.

Conclusion

the mean value of ICAM-1 levels for patients with confirmed positive COVID-19 cases was higher than those with suspected COVID-19 cases.