Background Recently, SARS-CoV-2 virus with the D614G mutation has become a public concern due to rapid dissemination of this variant across many countries. Our study aims were (1) to report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central Java provinces, Indonesia; (2) to compare the clade distribution of full-length genome sequences from Indonesia (n = 60) from March to September 2020 and (3) to perform phylogenetic analysis of SARS-CoV-2 complete genomes from different countries, including Indonesia. Methods Whole genome sequencing (WGS) was performed using next-generation sequencing (NGS) applied in the Illumina MiSeq instrument. Full-length virus genomes were annotated using the reference genome of hCoV-19/Wuhan/Hu-1/2019 (NC_045512.2) and then visualized in UGENE v. 1.30. For phylogenetic analysis, a dataset of 88 available SARS-CoV-2 complete genomes from different countries, including Indonesia, was retrieved from GISAID. Results All patients were hospitalized with various severities of COVID-19. Phylogenetic analysis revealed that one and three virus samples belong to clade L and GH. These three clade GH virus samples (EPI_ISL_525492, EPI_ISL_516800 and EPI_ISL_516829) were not only located in a cluster with SARS-CoV-2 genomes from Asia but also those from Europe, whereas the clade L virus sample (EPI_ISL_516806) was located amongst SARS-CoV-2 genomes from Asia. Using full-length sequences available in the GISAID EpiCoV Database, 39 of 60 SARS-CoV-2 (65%) from Indonesia harbor the D614G mutation. Conclusion These findings indicate that SARS-CoV-2 with the D614G mutation appears to become the major circulating virus in Indonesia, concurrent with the COVID-19 situation worldwide.

Hemodialysis patients are at an increased risk of acquiring hepatitis B virus (HBV) and hepatitis C virus (HCV) infection. However, the prevalence of hepatitis viral infection and its genotype distribution among hemodialysis patients in Indonesia are unclear. In order to investigate these issues and the possibility of nosocomial transmission, 161 hemodialysis patients and 35 staff members at one of the hemodialysis unit in Yogyakarta, Indonesia, were tested for serological and virological markers of both viruses. HBV surface antigen (HBsAg) was detected in 18 patients (11.2%) and in two staff members (5.7%). Anti-HCV was detected in 130 patients (80.7%) but not in any staff members. Occult HBV and HCV infection were detected in 21 (14.7%) and 4 (12.9%) patients, respectively. The overall prevalence rates of HBV and HCV infection among patients were 24.2% and 83.2%, respectively. HCV infection was independently associated with hemodialysis duration and the number of blood transfusions. Phylogenetic analysis revealed that 23 of 39 tested HBV strains (59%) were genotype B, 11 (28.2%) were genotype C, and 5 (12.8%) were genotype A. HCV genotype 1a was dominant (95%) among 100 tested HCV strains. Nosocomial transmission was suspected because the genotype distribution differed from that of the general population in Indonesia, and because the viral genomes of several strains were identical. These findings suggest that HBV and HCV infection is common among hemodialysis patients in Yogyakarta, and probably occurs through nosocomial infection. Implementation of strict infection-control programs is necessary in hemodialysis units in Indonesia.

Kidney ischemic/reperfusion (I/R) injury is the main cause of acute kidney injury (AKI) involving renal function deterioration, renal architecture damage, and inflammation. This condition may lead to kidney fibrosis with epithelial to mesenchymal transition (EMT) and myofibroblast formation. Inhibition of chronic effects of kidney I/R injury may provide effective strategies for treating AKI and chronic kidney diseases (CKDs). Chlorogenic acid (CGA) is recognized as a powerful antioxidant, with anti-inflammatory and antifibrotic properties in many conditions. However, the effect of CGA on kidney I/R injury has not been elucidated yet. Kidney I/R injury was performed on male Swiss background mice (I/R group, n = 5, 3-4 months, 30–40 g) which underwent bilateral renal pedicles clamping for 30 minutes and then were euthanized on day three after operation. Three groups of I/R were treated with 3 different doses of CGA intraperitoneally for 2 days: 3.5 (I/R + CGA1 group), 7 (I/R + CGA2 group), and 14 (I/R + CGA3 group) mg/kg of body weight. Tubular injury was quantified based on Periodic Acid-Schiff staining, while reverse transcriptase PCR (RT-PCR) was performed to quantify mRNA expression of TGF-β1, vimentin, SOD-1, TLR-4, TNF-α, NF-κB and MCP-1. Immunohistochemical staining was done to quantify proliferating cell nuclear antigen (PCNA), myofibroblast (α-SMA), SOD-1 and macrophage (CD68) number. Kidney I/R demonstrated tubular injury and increased inflammatory mediator expression, macrophage number, and myofibroblast expansion. Meanwhile, histological analysis showed lower tubular injury with higher epithelial cell proliferation in CGA-treated groups compared to the I/R group. RT-PCR also revealed significantly lower TGF-β1 and vimentin mRNA expressions with higher SOD-1 mRNA expression. CGA-treated groups also demonstrated a significantly lower macrophage and myofibroblast number compared to the I/R group. These findings associated with lower mRNA expression of TLR-4, TNF-α, NF-κB, and MCP-1 as inflammatory mediators in CGA groups. I/R + CGA3 represented the highest amelioration effect among other CGA-treated groups. CGA treatment attenuates kidney I/R injury through reducing inflammation, decreasing myofibroblast expansion, and inducing epithelial cells proliferation.

Pregenomic RNA (pgRNA) is generated from covalently closed circular DNA (cccDNA) and plays important roles in viral genome amplification and replication. Hepatic pgRNA and cccDNA expression levels indicate viral persistence and replication activity. This study was aimed to measure hepatic pgRNA and cccDNA expression levels in various states of hepatitis B virus (HBV) infection. Thirty-eight hepatocellular carcinoma (HCC) patients, including 14 positive for hepatitis B surface antigen (HBsAg) and 24 negative for HBsAg but positive for anti-hepatitis B core (anti-HBc) antibody, were enrolled in this study. In HBsAg-negative but anti-HBc-positive group, HBV-DNA was detected in 20 of 24 (83%) noncancerous liver tissues for at least two genomic regions based on polymerase chain reaction (PCR) analysis. pgRNA and cccDNA expression levels in occult HBV-infected patients were significantly lower than those in HBsAg-positive patients (P < 0.001). pgRNA and cccDNA in cancerous tissues were also detected without significant difference from those in noncancerous tissues. In conclusion, cccDNA and pgRNA are detected and represented HBV replication not only in noncancerous but also in cancerous liver tissues. In addition, the replication is shown in not only patients with HBsAg-positive but also occult HBV-infected patients, suggesting the contribution to HCC development.