SARS-CoV-2 lineages circulating during the first wave of the pandemic in North Sumatra, Indonesia.

Objectives: To determine the lineage distribution of the virus during the first wave of the pandemic in North Sumatra, Indonesia. Methods: A total of 20 samples with positive results based on reverse transcription-polymerase chain reaction were selected for virus culture and then performed whole-genome sequence analysis using next-generation sequencing which was applied by the Illumina MiSeq instrument. Results: Whole-genome sequence analysis revealed that the majority of our samples belong to lineages B.1.468 (n = 10), B.1 (n = 5), B.1.1 (n = 2), B.1.1.398 (n = 2), and B.6 (n = 1). Other unique amino acid mutations found in our samples were present in A58T on non-structural protein (NSP3) (70%), P323L on NSP12 (95%), Q57H on NS3 protein (75%), and D614G on S (100%). Conclusion: The SARS-CoV-2 lineage B.1.468 may be the main virus variant circulating in North Sumatra at the beginning of the emergence of COVID-19 cases in this province.

Cytotoxic T-lymphocyte-associated protein 4 +49A/G polymorphism in Down syndrome children with Hashimoto's thyroiditis.

Thyroid dysfunction is the most common endocrine disorder in Down syndrome (DS) children. Cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) is one of the immune regulatory genes that correlates with Hashimoto's thyroiditis (HT). However, studies on CTLA-4 +49A/G in DS children with HT are still limited. We aimed to evaluate CTLA-4 +49A/G gene polymorphism in DS children with HT. This case-control study, conducted from February 2020 to February 2022 at Dr. Soetomo General Hospital, Surabaya, enrolled 40 DS children with HT and 50 healthy children. The DNA sequencing was performed to identify the polymorphism (Sanger sequencing). Thyroid peroxidase antibodies (TPOAb), thyroglobulin antibodies (TgAb), thyroid-stimulating hormone (TSH), and free thyroxine (FT4) levels were analyzed by enzyme-linked immunosorbent assay (ELISA). The mean age of DS children with HT was 1.78 years. Males predominated in the study population. Subjects with GG genotype were diagnosed earliest with hypothyroidism (8 months) compared with other studies. The most common thyroid dysfunction was central hypothyroidism, with TgAb positivity present in all patients. The AA genotype (odds ratio [OR] 0.265, 95% confidence interval [CI] 0.094-0.746; P = 0.012) and A allele (OR 0.472, 95% CI 0.309-0.721; P = 0.0002) were significantly more frequent in the control group. The AG genotype (OR 2.65, 95% CI 0.094-0.746; P = 0.003) and G allele (OR 2.116, 95% CI 1.386-3.23; P = 0.003) were more frequent in the DS with HT group. The age of the subjects in this study was younger than in previous studies. The AG genotype and the G allele were more prevalent in the DS with HT group and may be a risk factor in HT development in DS children. Furthermore, the AA genotype may act as a protective factor against HT in DS children.

Protein tyrosine phosphatase non-receptor type 22 C1858T gene polymorphism in children with down syndrome and autoimmune thyroid diseases.

Autoimmune Thyroid Disease (AIT) is a frequent comorbidity in Down Syndrome (DS). Protein Tyrosine Phosphatase Non- Receptor Type 22 C1858T (PTPN-22 C1858T) gene polymorphisms have a role in the progression of AIT. The study on PTPN- 22 C1858T gene polymorphism as the risk factor of AIT in DS children is still limited. This study aims to evaluate PTPN-22 C1858T polymorphism in Indonesian DS children. A cross-sectional study involving 31 DS children with hypothyroidism (19 boys/12 girls) was conducted for ten months from February to November 2020 at Dr. Soetomo General Hospital Surabaya. The PTPN-22 C1858T gene polymorphism was analyzed using Polymerase Chain Reaction-Restriction-Fragment-Length Polymorphism (PCR-RFLP). Anti-Thyroid Peroxidase (Anti- TPO) and Anti-Thyroglobulin (Anti-TG), FT4, T3, and TSH levels were analyzed using Enzyme-Linked-Immunosorbent-Assay (ELISA). The mean age of the subjects was 19.45±17.3 months. The CT variant of PTPN-22 C1858T was observed in all subjects. The mean level of T3, FT4, and TSH were 1.59±0.45 ng/mL, 0.81±0.57 ng/mL, 0.22±0.21 µU/mL, respectively. Around 83.9% of patients suffered from central hypothyroidism, 12.9% from primary hypothyroidism, and 3.2% from subclinical hypothyroidism. The positive anti-TG and anti-TPO were observed in 96.8% and 58.1%, respectively. CT variant was observed in Indonesian DS children who suffered from hypothyroidism.

How Effective is Angiotensin II in Decreasing Mortality of Vasodilatory Shock? A Systematic Review.

Background: Patients with severe vasodilation accompanied by refractory hypotension despite high doses of vasopressors were associated with a high mortality rate. The Ang-2 for the Treatment of High-Output Shock (ATHOS) 3 trial demonstrated that angiotensin 2 (Ang-2) could effectively increase MAP and blood pressure in vasodilatory shock patients. This systematic review aims to summarize the impact of Ang-2 for the treatment of vasodilatory shock on clinical outcomes, including length of stay, MAP level (before and after), and mortality also Ang-2 dose needed. Methods: A systematic search in PubMed, Sage, ScienceDirect, Scopus and Gray literature was conducted to obtain studies about the use of Ang-2 in vasodilatory shock patients. Results: In all of the studies that we obtained, there were different results regarding mortality in patients with vasodilatory shock with Ang-2. Mortality was significantly lower when Ang-2 was administered to patients with elevated renin. The initial dose of Ang-2 can be started at 10-20 ng/kg/min, but there is no agreement on the maximum dose. Ang-2 may be considered a third-line vasopressor if the targeted MAP has not been achieved after administration of norepinephrine >200 ng/kg/min for more than 6 hours. Although not statistically significant, the use of Ang-2 can reduce the length of stay in the ICU and in the hospital when compared to patients without Ang-2 therapy, in addition to reducing the dose of vasopressor. Conclusion: Overall, the use of Ang-2 has potential to be a regimen for patients with vasodilatory shock. Further study is needed to obtain more data.

The Correlations of Human Atrial Natriuretic Peptide on Cardiac Function and Hemodynamics in Pediatric Septic Shock.

Purpose: We aimed to determine the correlations of human Atrial Natriuretic Peptide (ANP) on cardiac function and hemodynamics in pediatric septic shock. Patients and Methods: We conducted an observational and prospective study on 30 children with septic shock. Measurement of the level of human atrial natriuretic peptide was determined in the serum of patients. Cardiac power (CP) is a cardiac function parameter measured with cardiac output (cardiovascular flow) and mean arterial (intravascular) pressure. Cardiac output and mean arterial pressure were monitored using pressure recording analytical methods (PRAM). Hemodynamic status was represented by a vasoactive inotropic score. Results: Thirty pediatric septic shock patients fulfilled the eligibility criteria. The human ANP level was not significantly different in pediatric septic shock on three days of examination. Cardiac power was significantly different in pediatric septic shock on three days of examination. There was a correlation between human ANP and cardiac power on day 3 and human ANP and VIS on day 2. Conclusion: There was a significant correlation between human ANP level and cardiac power on day 3 and ANP level and VIS on day 2. The cardiac power on day 3 and VIS on 48 hours can be alternatives to evaluate the hemodynamic status and cardiac function concerning human ANP in pediatric septic shock.

Osteoblast iron genes: real time PCR and microarray hybridization approach under hyperoxia.

OBJECTIVES: Iron is essential for cell growth, differentiation, electron transfer, and oxygen transport. Hyperoxia may increase the turnover of bone matrix components with a net effect of accelerated bone growth. Although hyperoxia was claimed could increase osteoblast activity, but expression level in possible genes which play role in proliferation is still unclear. This research aims to prove the differences of expression level of transferrin receptor gene and iron regulated transporter and other genes of 7F2 under 24 h normoxia, 24 h hyperoxia, and 48 h hyperoxia and the effect of hyperoxia by using osteoblast cell culture 7F2. METHODS: Reverse transcriptase, real time Polymerase Chain Reaction (PCR), and microarray is used to qualitatively detect gene expression. The computer softwares such as National Center for Biotechnology Information (NCBI) data base, Software Affymetrix, DNA Strider program, Genomatix - DiAlign program, Oligo 5.0 program (Software primer design) from Wojciech & Piotr Rychlik, and Genetyx-Mac version 8.0 have been used to analyze the PCR result. RESULTS: Under 24 h hyperoxia, there were 3,884 copies of transferrin receptor mRNA per 1,000,000 copies of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) mRNA. After 24 h hyperoxia, 8,325 copies of transferrin receptor mRNA per 1,000,000 GAPDH mRNA copies were found showing 2.1-fold up regulation. After 48 h hyperoxia, there was no significant increase at the level of expression of transferrin receptor mRNA, 8,079 mRNA copies per 1,000,000 copies of mRNA were found (2.0-fold up regulation compared with 24 h normoxia). CONCLUSIONS: It can be concluded that hyperoxia might have an effect on upregulating the expression of some osteoblast genes which might have an impact on osteoblast activity.

Meta-analysis: Association between hepatitis B virus preS mutation and hepatocellular carcinoma risk.

Previous observational studies suggested that hepatitis B virus (HBV) preS mutation plays an important role in the existence of HBV-related hepatocellular carcinoma (HCC). However, the results are still debatable. With an increasing number of studies about this topic, this study employed a meta-analysis to identify the association between HBV preS mutation and HCC risk. We searched for eligible studies from PubMed, ProQuest, CINAHL, ScienceDirect and Springer databases to assess the association between HBV mutation and HCC risk. This meta-analysis was conducted using RevMan 5.3 to provide pooled estimate for odds ratio (ORs) with 95% confidence intervals (95% CIs). Twenty-one clinical studies were included in this meta-analysis study which consisted of 1738 participants with HBV-related HCC and 3740 HBsAg-positive patients without HCC. All studies used samples of Asian population. PreS deletion was the most common mutation found in all studies. We found that ORs of HBV overall preS deletion was associated with HCC (OR = 3.28; 95% CI = 2.32-4.65; P < .00001; random-effects model). Each preS1 and preS2 deletion was associated with increased risk of HCC, with OR 2.42 (95% CI = 1.25-4.68, P = .008) and 3.36 (95% CI = 2.04-5.55, P < .00001), respectively. PreS2 start codon mutation was also significantly associated with HCC risk (OR = 2.47; 95% CI: 1.15-5.27; P = .02; random-effect model). The result of this meta-analysis suggested that HBV preS deletion (all, preS1 and preS2) and preS2 start codon mutation might contribute to the increased risk of HBV-related HCC.

Isolation and identification of a flavonoid compound and in vivo lipid-lowering properties of Imperata cylindrica.

Cogon grass (Imperata cylindrica/I. cylindrica) of the Gramineae family is found abundantly in nature, and the roots of this plant possess several beneficial biological properties. The present study aimed to isolate and identify flavonoid compounds from cogon grass roots and examine their potential as hypocholesterolemic agents. The flavonoid compound was isolated using a maceration method, followed by gravity column chromatography until a pure compound was obtained. The molecular structure of the isolated compound was determined using 1H-nuclear magnetic resonance (NMR) and 13C-NMR spectroscopy. An in vivo lipid-lowering test used a randomized post-test only control group experimental design in rats with hypercholesterolemia. The animals were divided into four groups: K0, negative control; K1, positive control; K2, ethanol extract treated group; and K3, ethyl acetate fraction treated group, and the lipid profiles were examined at the end of the study. The isolated compound, 7,3',5'-trimethoxyflavonol, was collected in yellow powder form; was shown to be a flavonoids and was comprised of 18 carbon atoms and 16 hydrogen atoms. In vivo tests demonstrated that 15 mg/200 g body weight (BW) of an ethanol extract significantly lowered total cholesterol levels (P=0.001) but did not lower low-density lipoprotein (LDL) (P=0.109) and high-density lipoprotein (HDL) levels (P=0.003). The fraction of ethyl acetate administered at 15 mg/200 g BW was capable of lowering the total cholesterol levels significantly (P=0.002) and lowered LDL levels (P=0.006) but was unable to increase HDL levels (P=0.190). The in vivo tests showed that the ethyl acetate fraction of I. cylindrica reduced total cholesterol and LDL levels more effectively than the ethanol extract, but did not affect HDL levels in rats with hypercholesterolemia.

The role of Mycobacterium tuberculosis complex species on apoptosis and necroptosis state of macrophages derived from active pulmonary tuberculosis patients.

OBJECTIVE: The role of Mycobacterium tuberculosis complex (MTBC) species in tuberculosis (TB) infection in human is still questioned. The aim of this study was to determine whether M. tuberculosis and M. bovis is associated with apoptosis and necroptosis by measuring the expression of specific signaling pathways components (Fas-associated protein with death domain (FADD) and receptor interacting protein 3 (RIP3)), and the level of apoptosis. RESULTS: We recruited 30 patients with pulmonary TB; 24 patients were infected with M. tuberculosis Beijing strain and six patients with M. bovis BCG strain. M. tuberculosis-infected patients were more likely to have severe lung damage compared to those infected with M. bovis (odds ratio [OR] 7.60; 95% confidence interval [CI] 1.07-54.09). M. tuberculosis infection was associated with lower expression of FADD and lower apoptosis level of macrophages compared to M. bovis. No significant different of RIP3 between MTBC species groups. In conclusion, M. tuberculosis Beijing strain was associated with severe pulmonary damage, inhibited FADD expression and reduced apoptosis level of macrophages derived from pulmonary TB patients. This suggests that the M. tuberculosis Beijing strain is potentially to be used as determinant of disease progressivity and tissue damage in TB cases.

Molecular epidemiology of hepatitis A outbreaks in two districts in Indonesia in 2018: Same subtype, but different strains.

The present study aimed to analyse molecular epidemiological data from hepatitis A virus (HAV) outbreaks in two affected areas. The association between the knowledge of hepatitis A and incidence of infection was also determined. Serum samples were obtained from 88 individuals with clinical manifestations of acute hepatitis in Lamongan (n=54) in January 2018 and Bangkalan (n=34) in March 2018. The outbreak investigation was started one day after the outbreaks were reported by the Public Health Offices in Lamongan and Bangkalan. Anti-HAV immunoglobulin M (IgM) and PCR amplification products of the VP1 capsid protein-P2A protease and VP1-VP3 junctions were analysed. Positive PCR products were sequenced, and a phylogenetic tree was constructed using Molecular Evolutionary Genetics Analysis X software. The control group comprised healthy students and staff members from the two affected areas. Thus, 172 responses from the control and hepatitis A case groups were analysed to assess the association between the students' knowledge level and the incidence of HAV infection. A total of 32 (59.25%) of the 54 individuals from Lamongan and 19 (55.9%) of the 34 participants from Bangkalan were positive for anti-HAV IgM; 26 PCR tests were positive in the VP3-VP1 and/or VP1-P2A junction, which were identified as HAV subgenotype IA. The subtype of HAV in the two areas was IA, similar to those identified previously, but the viruses did not originate from the same strain, as identified by multiple alignment. The knowledge level of the students and staff members in Lamongan studying and working at a half-day school exhibited a significant association with the incidence; however, no association was observed among the students in Bangkalan studying at a full-day school with a dormitory.

The Emergence of HIV-1 Transmitted Drug Resistance Mutations Among Antiretroviral Therapy-naive Individuals in Buleleng, Bali, Indonesia.

BACKGROUND: the global scale-up of antiretroviral therapy (ART) is the primary factor contributing to the decline in deaths from acquired immune deficiency syndrome (AIDS)-related illnesses. However, the emergence of transmitted drug resistance (TDR) compromises the effects of ART in treatment-naïve individuals, which may hinder treatment success. The present study aimed to identify the presence of TDR among treatment-naive individuals in Buleleng, Bali, which is currently ranked sixth among Indonesian provinces with the highest cumulative human immunodeficiency virus type 1 (HIV-1) infection cases. METHODS: thirty-nine ART-naive individuals in Buleleng Regency General Hospital were enrolled in the present study. Blood samples from participants were subjected to a genotypic analysis. RESULTS: 28 protease (PR) and 30 reverse transcriptase (RT) genes were successfully amplified and sequenced from 37 samples. HIV-1 subtyping revealed CRF01_AE as the dominant circulating recombinant form in the region. No TDR for PR inhibitors was detected; however, TDR for RT inhibitors was identified in five out of 30 samples (16.7%). CONCLUSION: these results indicate the emergence of TDR among ART-naive individuals in Buleleng, Bali. This issue warrants serious consideration because TDR may hamper treatment success and reduce ART efficacy among newly diagnosed individuals. Continuous surveillance with a larger sample size is necessary to monitor TDR among ART-naive individuals.

Association between host TNF-α, TGF-ß1, p53 polymorphisms, HBV X gene mutation, HBV viral load and the progression of HBV-associated chronic liver disease in Indonesian patients.

In developing countries, including Indonesia, there is a high mortality rate associated with the progression of hepatitis B virus (HBV)-associated chronic liver disease (CLD). The pathogenesis of HBV infection is influenced by viral and host factors. To determine potential associations between these factors, host single nucleotide polymorphisms (SNPs) on TNF-α, TGF-ß1 and p53, HBV X gene mutation and HBV viral load were investigated in patients with HBV-associated CLD in Surabaya, Indonesia. Sera were collected from 87 CLD patients with HBV infection. TNF-α, TGF-ß1 and p53 SNPs were genotyped by PCR restriction fragment length polymorphism. The HBV X gene was sequenced and compared with reference strains to determine mutations and the viral load was measured using reverse transcription-quantitative PCR. In Indonesian patients, no association between TNF-α, TGF-ß1 and p53 SNPs and CLD or X gene mutation were identified. A total of 23% (20/87) of samples had HBV X gene mutations, including ten substitution types, one deletion and one insertion. Multinomial regression analysis revealed that the K130M/V131I mutations were correlated with CLD progression (OR, 7.629; 95% CI, 1.578-36.884). Significant differences in viral load were found in HBV-infected patients who had X gene mutations, such as R87W/G, I127L/T/N/S and K130M/V131I mutations (P<0.05). The presence of K130M and V131I mutations may be predictive for the progression of HBV-associated CLD in Indonesia.

Association between quasispecies variants of hepatitis B virus, as detected by high­throughput sequencing, and progression of advanced liver disease in Indonesian patients.

Mutations in the hepatitis B virus (HBV) X region and truncation of the preS2 region are well­known to affect the progression of liver disease. Recently, it has been observed that an increasing number of S region quasispecies variants are associated with disease progression. However, few studies have analysed quasispecies of the whole genome using high­throughput sequencing methods. Using high­throughput sequencing, whole­genome variations in 12 Indonesian patients infected with HBV (eight with advanced liver disease and four with chronic hepatitis) were examined. Variations with cut­off values of ≥1% of the total viral population were investigated. It was revealed that within the four open reading frames, quasispecies variations of the S and X regions were higher in advanced liver diseases compared with in chronic hepatitis (S region: 89.53 vs. 50.69%, P=0.047; X region: 76.95 vs. 35.88%, P=0.044). Notably, the mutation frequencies in the basal core promoter, B cell epitope, RT Box G, RNAseH and small S region were greater in advanced liver disease. The proportion of quasispecies variants increased for the majority of the mutations, with the exception for W196* in the small S gene, during disease progression. The present study demonstrated that quasispecies in the S and X regions of the HBV genome changed during disease progression and were associated with advanced liver disease development in Indonesian patients with HBV.

Growth differentiation factor 9 concentration in the follicular fluid of infertile women with endometriosis.

This study evaluated the level of growth differentiation factor 9 (GDF-9) in the follicular fluid of infertile women with endometriosis. The presence of GDF-9 in follicular fluid of preovulatory follicle was confirmed by Western blotting method in the band of 53 kDa, and GDF-9 concentration in women with severe endometriosis was lower than in those without.