Prognostic factors for the outcomes of COVID-19 patients infected with SARS-CoV-2 Omicron and Delta variants

Differential gene expression of immune response in COVID-19 and its relationship with progression of COVID-19

Human immune response evolved in virus clearance and gene expression levels of immune response may be associated with progression of Coronavirus disease 2019 (COVID-19). Our current study aims to investigate the relationship between differential gene expression of immune response and progression of COVID-19. A total of 50 participants of COVID-19 group were studied, compared with 39 participants of healthy control group. There were different gene expression profiles in pathways of activation of neutrophil, defense response and adaptive immune response for COVID-19 group before treatment compared to the healthy control group. Distinct gene expression profiles showed that pathways of chemotaxis, immune response and antibacterial humoral response involved in rehabilitation of severe COVID-19 group while pathways of immune system process, defense response to virus and negative regulation of viral genome replication involved in rehabilitation of moderate COVID-19 group. Both protein expression of ATP-binding cassette transporter A1 levels and protein expression of low affinity Fc-receptor FcγRIIIb levels were significantly and positively correlated with COVID-19-IgM levels and might be suitable as biomarkers for monitoring of COVID-19. This study showed that differential gene expression of immune response predicted onset and rehabilitation of COVID-19.

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.