Background Transmission within families and multiple spike protein mutations have been associated with the rapid transmission of SARS-CoV-2. We aimed to: (1) describe full genome characterization of SARS-CoV-2 and correlate the sequences with epidemiological data within family clusters, and (2) conduct phylogenetic analysis of all samples from Yogyakarta and Central Java, Indonesia and other countries. Methods The study involved 17 patients with COVID-19, including two family clusters. We determined the full-genome sequences of SARS-CoV-2 using the Illumina MiSeq next-generation sequencer. Phylogenetic analysis was performed using a dataset of 142 full-genomes of SARS-CoV-2 from different regions. Results Ninety-four SNPs were detected throughout the open reading frame (ORF) of SARS-CoV-2 samples with 58% (54/94) of the nucleic acid changes resulting in amino acid mutations. About 94% (16/17) of the virus samples showed D614G on spike protein and 56% of these (9/16) showed other various amino acid mutations on this protein, including L5F, V83L, V213A, W258R, Q677H, and N811I. The virus samples from family cluster-1 (n = 3) belong to the same clade GH, in which two were collected from deceased patients, and the other from the survived patient. All samples from this family cluster revealed a combination of spike protein mutations of D614G and V213A. Virus samples from family cluster-2 (n = 3) also belonged to the clade GH and showed other spike protein mutations of L5F alongside the D614G mutation. Conclusions Our study is the first comprehensive report associating the full-genome sequences of SARS-CoV-2 with the epidemiological data within family clusters. Phylogenetic analysis revealed that the three viruses from family cluster-1 formed a monophyletic group, whereas viruses from family cluster-2 formed a polyphyletic group indicating there is the possibility of different sources of infection. This study highlights how the same spike protein mutations among members of the same family might show different disease outcomes.

Wegener's granulomatosis adalah suatu vaskulitis yang mengenai pembuluh darah kecil hingga sedang, yang umumnya terjadi pada usia 64-75 tahun dengan kejadian 8-10/1.000.000 orang. Manifestasi meningoensefalitis jarang ditemukan pada WG dengan angka kejadian hanya berkisar 0-7%. Anti-neutrophil cytoplasmic antibody (ANCA) sering digunakan dalam mendiagnosis Wegener's granulomatosis, namun ANCA negatif dapat ditemukan pada 10-20% kasus. Seorang laki-laki usia 30 tahun datang dengan penurunan kesadaran. Dari hasil anamnesis dan pemeriksaan fisik didapatkan tanda-tanda yang mengarah kepada Wegener's granulomatosis, walaupun hasil pemeriksaan ANCA negatif. Setelah mendapatkan terapi sesuai tata laksana Wegener's granulomatosis, terdapat perbaikan secara klinis pada pasien. Kasus ini diangkat karena merupakan kasus jarang dan perlu ketajaman dalam penegakan diagnosis. Wegener's granulomatosis dapat menyebabkan progresivitas yang sangat buruk, namun jika ditangani secara tepat, maka remisi komplit dapat tercapai.

Background. Under the National Comprehensive Cancer Network (NCCN) guidelines for non-small-cell lung carcinoma (NSCLC), anaplastic lymphoma kinase (ALK) gene rearrangement is required to be assessed. However, data showing the prevalence of the ALK rearrangement is still deficient and is not yet available in Indonesia. This study used direct smear preparation from transthoracic needle specimens that are minimally invasive. The main objective of the study is to identify the prevalence of the ALK fusion rearrangement gene in cytological specimens. Materials and Methods. A total of 35 direct smear preparations diagnosed as lung adenocarcinoma and EGFR mutation negative were involved in this study. The samples were taken between 2017 and 2019. These samples were examined for EML4-ALK fusion rearrangement gene using qRT-PCR. The EML4-ALK rearrangement status was determined by qRT-PCR with high-resolution melting (HRM) analysis. Results. A total of 28 (80%) samples were from males, and 7 samples were from females. Seven (20% 95% CI: 8.4%-36.9%) samples were EML4-ALK rearrangement positive. The average age of the patients was 63.5 years old. The most common sites of metastasis in this study were pleural cavity, bone, liver, and CNS. Conclusions. qRT-PCR successfully identified EML4-ALK fusion rearrangement in direct smear preparations of lung adenocarcinoma. Direct smear samples can be used for EML4-ALK rearrangement detection using qRT-PCR. The EML4-ALK rearrangement gene has high prevalence in selected lung adenocarcinoma and EGFR mutation-negative populations. ALK inhibitors in lung cancer can be openly considered for use in Indonesian patients to improve the outcome of this subset of patients.

Background Hydroxychloroquine/chloroquine (HCQ/CQ) treatment for COVID‐19 was associated with QT interval prolongation and arrhythmia risks. This study aimed to investigate QTc interval and ventricular repolarization dispersion changes, as markers of arrhythmia risks, after HCQ/CQ administration with/without azithromycin (AZT) during COVID‐19 pandemic. Methods A prospective observational study was performed in two academic hospitals in Indonesia. Adult patients who received HCQ/CQ alone and HCQ/CQ + AZT concomitant treatments for COVID‐19 infection were enrolled. Baseline and post HCQ/CQ treatment electrocardiograms were obtained. Baseline and post HCQ/CQ treatment QT interval by Bazett (B‐QTc) and Fridericia (F‐QTc) formulas and ventricular repolarization dispersion indices by Tpeak‐Tend (Tp‐e) interval and Tpeak‐Tend/QT (Tp‐e/QT) ratio were calculated and analyzed. Results The study enrolled 55 (HCQ/CQ alone) and 77 subjects (HCQ/CQ + AZT concomitant). F‐QTc interval significantly lengthened in subjects with HCQ/CQ + AZT (mean difference 11.89 ms [P = .028]). The incidences of severe B‐QTc and F‐QTc lengthening were 13.1% and 12.3%, B‐QTc and F‐QTc prolongation were 25.4% and 12.3%, and severe B‐QTc and F‐QTc prolongation were 6.2% and 3.2%. Tp‐e interval lengthened significantly from baseline to posttreatment in HCQ/CQ alone and HCQ/CQ + AZT (mean difference 10.83 ms [P = .006] and 18.73 ms [P < .001], respectively). Tp‐e/QT ratio increased significantly from baseline to posttreatment in HCQ/CQ + AZT concomitant (mean difference 0.035 [P < .001]). No fatal arrhytmia occurred. Conclusions During COVID‐19 pandemic, HCQ/CQ + AZT concomitant treatment caused significant F‐QTc lengthening, significantly increased Tp‐e interval and increased Tp‐e/QT ratio. HCQ/CQ alone only caused significant increase of Tp‐e interval. Incidences of severe QTc lengthening and prolongation were low in both HCQ/CQ alone and HCQ/CQ + AZT concomitant.