Low-cost SYBR Green-based RT-qPCR assay for detecting SARS-CoV-2 in an Indonesian setting using WHO-recommended primers.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for the ongoing coronavirus disease 2019 (COVID-19) pandemic. For laboratory diagnosis, low-cost detection of SARS-CoV-2 is urgently needed, particularly in developing countries with limited resources. Probe- or TaqMan-based real-time reverse transcription polymerase chain reaction (RT-qPCR) is currently the gold standard for diagnosing infected individuals, as recommended by the World Health Organization (WHO). However, this assay is expensive, making it difficult to use for diagnosis on a large scale. Therefore, in this study, we develop and validate an alternative approach for RT-qPCR diagnosis by employing the DNA intercalating dye SYBR Green. We evaluate and use two WHO-recommended primers, namely CCDC-N and HKU-ORF1b-nsp14. The compatibility of the two primers was tested in silico with Indonesian SARS-CoV-2 genome sequences retrieved from the GISAID database and using bioinformatic tools. Using in vitro-transcribed RNA, optimization, sensitivity, and linearity of the two assays targeting the N and Nsp-14 genes were carried out. For further evaluation, we used clinical samples from patients and performed the SYBR Green-based RT-qPCR assay protocol in parallel with TaqMan-based commercial assay. Our results show that our methodology performs similarly to the broadly used TaqMan-based detection method in terms of specificity and sensitivity and thus offers an alternative assay for the detection of SARS-CoV-2 RNA for diagnostic purposes.

Bronchoscopy Findings of Severe and Critical COVID-19 Patients Treated in ICU: A Year of Experience in a Developing Country.

Background: Bronchoscopy procedure in patients with COVID-19 poses significant challenges, especially in a developing country with limited resources. Objectives: We aim to describe the clinical characteristics of severe and critical COVID-19 patients treated in an intensive care unit (ICU) and their bronchoscopy findings. Methods: We performed a retrospective analysis of clinical data of ICU patients with COVID-19 treated and received bronchoscopy procedures. This study retrospectively included all consecutive patients who underwent bronchoscopy at a teaching hospital in Depok, Indonesia, from May, 2020, until May, 2021. Results: A total of 57 bronchoscopy procedures in 54 patients were performed in this study. Primary procedure indications were retained mucus (68.4%) and ventilatory support weaning failure (15.8%). Bronchoscopic findings were mostly hyperaemic mucosa (95.00%) and purulent secretion (50.90%). Microbiological findings from bronchoalveolar samples were Acinetobacter baumanii, Klebsiella pneumoniae, and Candida albicans (33.3%, 26.6%, and 10.5%, respectively). The most common fungal isolated were Candida albicans (28%), followed by Candida tropicalis (16%) and Aspergillus sp. (8%). The overall length of hospital stay was 24 days, and the in-ICU stay was 22.06 ± 10.99 days. The patients' survival of 28-days postprocedural outcome was 25.9% (14 subjects). Follow-up found that 20.4% of patients survived after sixty days of hospitalization. Conclusion: Diagnostic and therapeutic bronchoscopy in ICU patients with COVID-19 was safe and feasible to perform in developing countries with limited resources. It could help bronchial mucous clearance and confirm microbiological infection. The procedures should be strictly performed for patients with indications and comply with safety standards.

Tinjauan etik pembukaan rahasia medis dan identitas pasien pada situasi wabah pandemi COVID-19 dan kaitannya dengan upaya melawan stigma pasien positif

Surveilans kesehatan masyarakat merupakan hal dasar yang perlu dilaksanakan pada kejadian wabah penyakit menular. Akan tetapi pembukaan rahasia medis yang dikumpulkan pada kondisi wabah (termasuk nama alamat diagnosis riwayat keluarga dan sebagainya) tanpa persetujuan pasien dapat berisiko bagi individu yang bersangkutan. Penanganan data tersebut perlu dilakukan secara hati-hati karena individu terkait dapat menghadapi stigmatisasi maupun diskriminasi bila informasi terkait dirinya terutama data dengan hasil tes positif bocor ke publik. Maka dari itu pengaturan dan panduan penggunaan pembukaan rahasia medis dalam kondisi wabah penyakit menular memerlukan pendalaman etik yang baik. Terdapat beberapa peraturan dan panduan yang mengatur kerahasiaan pasien dalam kondisi wabah. Regulasi hukum serupa pun juga ditemukan pada negara lainnya seperti Amerika Serikat dan Inggris.

The effect of repeated education using live demonstrations and videos of how to use inhalation drugs on quality of life for COPD patients.

Repeated education regarding the proper use of inhalers can reduce the error rate in inhaler-using patients and improve COPD patients' quality of life. This study investigates the effect of repeated education on the quality of life of COPD patients during the pandemic of COVID-19 from February to June 2020. Repeated education is provided using direct demonstrations to patients through educational media in the form of short videos made by the researchers for each inhaler type. This is a pre-experimental study design which was carried out prospectively at Grha Permata Ibu Hospital, Depok. The quality of life of 22 subjects was examined using the COPD assessment test (CAT) questionnaire. Each patient was given a direct verbal demonstration of the appropriate use of the inhaler. One month later, each patient was provided further education using less than 2 min of video sent to them online via the WhatsApp application. Final quality-of-life examination and assessment of inhaler technique were carried out three months after the initial examination. Assessment of proper inhaler technique was carried out using a specific checklist regarding the use of inhaler translated by the researcher. Before and after delivery of repeated education, the mean CAT score showed a decrease of two points, i.e., 12.8 ± 1.3 and 10.8 ± 2.0, respectively. This indicated that quality of life of the patients had significant improvement. However, as many as 63.6% of patients still made mistakes in using inhaler even though they had been educated. For DPI-type inhalers, mistake mostly happened at step "breath out gently, away from inhaler". For pMDI-type inhalers, mistake mostly happened at step "while holding breath, remove inhaler from mouth". It can be concluded that repeated education regarding proper inhaler technique with direct demonstrations and further maintained by videos can improve the quality of life in COPD patients.

Factors Associated with Death in COVID-19 Patients in Jakarta, Indonesia: An Epidemiological Study.

BACKGROUND: Coronavirus Disease 2019 is an emerging respiratory disease that is now a pandemic. Indonesia is experiencing a rapid surge of cases but the local data are scarce. METHODS: this is an analysis using data from the ongoing recapitulation of Epidemiological Surveillance (ES) by the Provincial Health Office of Jakarta from March 2nd to April 27th 2020. We evaluated demographic and clinical characteristics of all confirmed cases in association with death. RESULTS: of the 4,052 patients, 381 (9.4%) patients were deceased. Multivariable analysis showed that death was associated with older age (odds ratio [OR] 1.03; 95% confidence interval [CI] 1.02, 1.05, per year increase; p<0.001), dyspnea (OR 4.83; 95% CI 3.20, 7.29; p<0.001), pneumonia (OR 2.46; 95%CI 1.56, 3.88; p<0.001), and pre-existing hypertension (OR 1.86; 95% CI 1.24, 2.78; p=0.003). Death was highest in the week of April 6th 2020 and declined in the subsequent weeks, after a large-scale social restriction commenced. CONCLUSION: older age, dyspnea, pneumonia, and pre-existing hypertension were associated with death. Mortality was high, but may be reduced by lockdown.