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Full-in-House Method (FinHM) for SARS-COV-2 Automated Viral RNA Extraction, Followed by in-House ‘Primer-Probe’ Based RT-qPCR Detection; Low Cost Mass Testing
Khaldoun Al-Romaih,
Ibtihaj Alsharif,
Razan Bakheet,
Lina Mahmoud,
Najla Alharbi,
Sara Bin Judia,
Layla Alharbi,
Abdulaziz Alzayed,
Amjad Jabaan,
Jawahar Alotaibi,
Alaiya Ayodele,
Zakiya Shinwari,
Hani Alhadrami,
Ahmed Albarrag,
Esam Azhar,
Haya Al-Saud,
Tahani Alrahbini,
Maha Al-Mozaini
Issue:
Volume 9, Issue 1, January 2021
Pages:
1-10
Received:
7 December 2020
Accepted:
21 December 2020
Published:
4 January 2021
Abstract: Background: Sever acute respiratory syndrome Coronavirus-2 (SARS-COV-2) spread prompted mass testing. The main method for testing is by any FDA approved kits for RNA extraction followed by One-Step RT-qPCR based on primer-probe assays. Yet, the high demand for these kits created a global bottleneck in the testing capacity. Methods: We developed a Full-In-House Method (FinHM) suitable for automated viral RNA extraction using full in-house solutions utilizing the MagMaxTM beads followed by an In-House RT-qPCR based on the CDC/WHO recommended ‘primer-probe’ assay targeting the following genes; E, RdRp2, and RdRp4. FinHM was validated by an FDA approved kit that targets S, N, and ORF1b genes made by Thermo Fisher Scientific (TF). Results: The sensitivity and specificity of the automated RNA extraction were evaluated on serial dilutions of in-laboratory propagated SARS-COV-2 with a successful detection down to 46 copies in both assays (P>0.05). Moreover, automated FinHM was successful in extraction of SARS-COV-2 RNA in 266 clinical samples, in which the test results replicated the FDA approved test results (>99% similarity, P>0.05). The In-House RT-qPCR assay had low limit of detection (5 RNA templates), with significant negative correlation between the Ct values and RNA titrations as shown by Pearson correlation (-0.8, -0.8 and -0.7 for E, RdRp2 and RdRp4, respectively). Finally, FinHM was also successful in extraction of SARS-COV-2-spiked plasma and patient plasma samples. Conclusion: We report a reliable, reproducible, specific, sensitive and low-cost platform for automated RNA extraction and detection from SARS-COV-2 and other viruses which is suitable for clinical and mass testing.
Abstract: Background: Sever acute respiratory syndrome Coronavirus-2 (SARS-COV-2) spread prompted mass testing. The main method for testing is by any FDA approved kits for RNA extraction followed by One-Step RT-qPCR based on primer-probe assays. Yet, the high demand for these kits created a global bottleneck in the testing capacity. Methods: We developed a F...
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Clinical, Laboratory Characteristics and Pregnancy Outcome of COVID-19 Patients Admitted in the Largest COVID Dedicated Hospital of Bangladesh
S. K. Jakaria Been Sayeed,
Md. Mujibur Rahman,
A. K. M. Humayon Kabir,
Md. Moniruzzaman,
Reaz Mahmud,
Mohammad Abdullah Yusuf,
Sabrina Rahman
Issue:
Volume 9, Issue 1, January 2021
Pages:
11-16
Received:
18 December 2020
Accepted:
30 December 2020
Published:
15 January 2021
Abstract: Background: The 2019 novel corona virus (SARS-CoV-2) has become pandemic, it is of paramount importance to conduct near-real-time surveillance of women who are hospitalized and test positive for COVID-19 during pregnancy. Objective: The purpose of the present study was to evaluate clinical and laboratory characteristics and pregnancy outcome among COVID-19 patients. Methodology: This was a prospective longitudinal study done in COVID dedicated unit of Dhaka Medical College Hospital. All pregnant women admitted with confirmed COVID-19 were included. Result: Among 68 pregnant COVID patients mean (SD) age was 26.58 (4.30) years where gestational age was 25.90 (5.34) weeks. Most common symptoms were fever (94%), cough (79%), sore throat (59%), shortness of breath (44), myalgia (34%). According to severity assessment, 51 (75%) was found to be mild, moderate 9 (13%) and severe 8 (12%) respectively. Regarding overall maternal outcome among 68 patients 64 (94%) recovered and discharged, 2 (3%) of them recovered but abortion occurred and 2 (3%) died. Mean (SD) gestational age during delivery was 37.8 (1.2) weeks. Vaginal delivery was done in 18 (35%), cesarean section in 33 (65%) and 13 (19%) continuing pregnancy. Among fifty one neonate, only 41 (80%) completed RT-PCR test and found negative. Regarding neonatal outcome, 48 (94.2%) term baby, 3 (5.8%) preterm, neonatal pneumonia 1 (1%), neonatal hyperbilirubinemia 3 (6%) were observed. Conclusion: The SARS-CoV-2 infection during pregnancy might not associate with adverse obstetrical and neonatal outcomes. It appears to be unlikely of perinatal transmission of SARS-CoV-2.
Abstract: Background: The 2019 novel corona virus (SARS-CoV-2) has become pandemic, it is of paramount importance to conduct near-real-time surveillance of women who are hospitalized and test positive for COVID-19 during pregnancy. Objective: The purpose of the present study was to evaluate clinical and laboratory characteristics and pregnancy outcome among ...
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Acute Jejenal Diverticulitis: Case Report of Uncommon Presentation
Hamza Merza Abdulla,
Ronald Erastus Samuel,
Joseph Marc Shabot
Issue:
Volume 9, Issue 1, January 2021
Pages:
17-20
Received:
27 November 2020
Accepted:
12 January 2021
Published:
22 January 2021
Abstract: Jejunal diverticulitis is a rare condition and often difficult to diagnose. We report a case of 68-year–old man with a history of sigmoid diverticulitis who presented to the emergency room with a one day history of acute abdominal pain of the left lower quadrant. Initial CT of the Abdomen and Pelvis revealed ileus vs early/partial small bowel obstruction mildly distended loops of the small bowel with decompressed loops of small bowel in the right lower quadrant with no distinct transition point. The patient was treated with antibiotics for presumed gastroenteritis. However, given persistent symptoms and unclear etiology a CT enterography was ordered and demonstrated jejunal diverticulitis with microperforation and a significant phlegmon surrounding the inflamed diverticulum. The patient was treated with ciprofloxacin and metronidazole and reported complete resolution of symptoms after the course of antibiotics. Jejunal diverticula are extremely rare with an incidence of 0.06% to 1.3%. Prior case reports described some of its complications including bleeding, perforation and ulceration. Jejunal diverticulitis should be in the differential diagnosis of acute abdomen especially in patients with unclear etiology. This condition can be missed by contrasted CT of the abdomen and dedicated small bowel imaging such as CT Enterography can assist making the diagnosis.
Abstract: Jejunal diverticulitis is a rare condition and often difficult to diagnose. We report a case of 68-year–old man with a history of sigmoid diverticulitis who presented to the emergency room with a one day history of acute abdominal pain of the left lower quadrant. Initial CT of the Abdomen and Pelvis revealed ileus vs early/partial small bowel obstr...
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Frequency of Refractory Hypertension in Turkish Patients and Evaluation of the Factors Affecting Refractory Hypertension
Mustafa Temizel,
Ugur Dilek Calap,
Murtaza Cit,
Mansur Azermir,
Yucel Arman
Issue:
Volume 9, Issue 1, January 2021
Pages:
21-25
Received:
15 December 2020
Accepted:
15 January 2021
Published:
22 January 2021
Abstract: Background: This study aimed to determine the frequency of refractory hypertension (RH) and investigate the factors affecting RH in Turkish hypertensive patients. Materials and methods: Totally 400 hypertensive patients (114 males and 286 females) were enrolled. Blood pressure (BP) was measured by patients at home two times a day. The patients were called for controlling in every four weeks, and those who had BP <140/90 mmHg were not followed-up. In patients with BP >140/90 mmHg drug doses were increased or another antihypertensive drug was added and the patients were continued to be followed-up. The total follow-up period was 36 weeks. Patients with persisting BP >140/90 mmHg despite triple medication administration including a diuretic form at least for 3 months at adequate doses were considered to have RH. Results: A total of 63 patients (15.8%), including 14 males and 49 females, were considered to have RH. Body Mass Index (BMI) values of patients with and without RH were 32.16±3.56 and 29.71±3.42, respectively (t=2.92; p=0.005). The rate of obese and morbidly obese patients was higher in the RH group (p<0.005). Duration of hypertension was longer in the RH group (9.7±5.6 vs 7.0±5.7 years, p<0.001). Conclusion: We found the frequency of RH as 15.8%. There’s a significant correlation between BMI and RH. Duration of hypertension increases the prevalence of RH, and should be considered one of the risks for RH.
Abstract: Background: This study aimed to determine the frequency of refractory hypertension (RH) and investigate the factors affecting RH in Turkish hypertensive patients. Materials and methods: Totally 400 hypertensive patients (114 males and 286 females) were enrolled. Blood pressure (BP) was measured by patients at home two times a day. The patients were...
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Multi-organ Dysfunction Due to SARS-CoV-2 Infection: A Comparative Overview
Moshiul Alam Mishu,
Fairoz Samiha,
Kohinoor Zahan,
Akash Saha,
Shahida Ferdousee
Issue:
Volume 9, Issue 1, January 2021
Pages:
26-35
Received:
26 November 2020
Accepted:
15 December 2020
Published:
22 January 2021
Abstract: SARS-CoV-2 or COVID-19 is a highly transmittable and pathogenic viral disease, which was first reported in the province Wuhan of China in late December 2019. The disease has shown its catastrophic effect in more than 200 countries and territories, causing more than 53.7 million confirmed cases and over 1.3 million deaths since its outbreak. Although the virus was primarily presumed to cause respiratory disease, reports are emerging of the plausible impact of the virus on multiple organs. The multi-organ dysfunction in severe patients of COVID-19 results in high morbidity and mortality rate compared to the other coronavirus family members like SARS and MERS. In this review, we provided a brief overview of the current insights of potential COVID-19 impacts on multiple organ functions. Reports suggest that the virus may exert direct (e.g., using ACE2 receptor) or indirect (e.g., cytokine storm) effects on several organs, including the lung, kidney, heart, liver, and brain. These multi-organ injuries may contribute to poor health outcomes and even may lead to death, especially to those suffering from cardiac disease, diabetes, liver, kidney diseases, etc. However, further investigation is required to know the exact mechanism of the infection. This study will provide valuable information on multi-organ dysfunction due to COVID-19 and thus, help clinicians to combat the disease until an effective vaccine arrives.
Abstract: SARS-CoV-2 or COVID-19 is a highly transmittable and pathogenic viral disease, which was first reported in the province Wuhan of China in late December 2019. The disease has shown its catastrophic effect in more than 200 countries and territories, causing more than 53.7 million confirmed cases and over 1.3 million deaths since its outbreak. Althoug...
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Analysis of the Differentially Expressed Genes and microRNAs and Prediction of miRNA-mRNA negative Regulatory Network in Nasopharyngeal Carcinoma
Ping Ouyang,
Wenyan Wu,
Rang Li,
Xuefeng Zhou,
Tao Li
Issue:
Volume 9, Issue 1, January 2021
Pages:
36-48
Received:
5 January 2021
Accepted:
22 January 2021
Published:
28 January 2021
Abstract: Introduction: Nasopharyngeal carcinoma (NPC) is an endemic cancer in southern China, particularly in Guangdong population, but the prognosis of NPC is poor. Recently microRNA (miR) has been shown to have function in aiding the treatment of cancer. Thus, in this study, miRNAs and genes associated with NPC were analyzed. Methods: mRNA-sequencing and miR-sequencing data were obtained from the Gene Expression Omnibus. The differentially expressed genes (DEGs) and miRNAs (DEMs) were filter out. Then, the gene function annotations about the DEGs were predicted using Gene Ontology (GO) and KEGG pathway. Subsequently, the protein-protein interaction (PPI) network was established based on the STRING database, and function modules were identified using Cytoscape. Finally, DEGs targeted by DEMs were predicted by using the miRDB, miRTarBase, TargetScan and DIANA databases, and the DEM-DEG negative interaction network was built. Results: In all, 704 DEGs (about 49.9% upregulated) were enriched in 234 GO terms and 53 KEGG pathways. Seven hub genes (APP, GNG2, VAV1, RAC2, YES1, EGFR and GNB5) in 6 function modules were found for the PPI network. In addition, 86 DEMs were identified containing 56 upregulated and 30 downregulated miRNAs. There were 538 DEM-DEG pairs, of which miR-93-5p/TGFBR2, miR-455-3p/STK17B and miR-766-5p/ITGAV had functions in other cancers, moreover, these pairs may potentially contributed to NPC pathogenesis. Conclusion: The constructed miRNA-mRNA negetive regulatory network will give help in elucidating the molecular mechanisms of NPC. The important DEGs, DEMs and DEM-DEG pairs associated with NPC may contribute to the diagnosis and treatment of NPC in the future.
Abstract: Introduction: Nasopharyngeal carcinoma (NPC) is an endemic cancer in southern China, particularly in Guangdong population, but the prognosis of NPC is poor. Recently microRNA (miR) has been shown to have function in aiding the treatment of cancer. Thus, in this study, miRNAs and genes associated with NPC were analyzed. Methods: mRNA-sequencing and ...
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Relapsed Mantle Cell Lymphoma, Allogenic Stem Cell Transplantation and COVID-19
James Dillon,
Elizabeth Higgins,
Carmel-Ann Galligan,
Majella Moran,
Brendan Crowley,
Ciaran Bannan,
Carmel Waldron,
Christopher Larry Bacon,
Elisabeth Vandenberghe
Issue:
Volume 9, Issue 1, January 2021
Pages:
49-51
Received:
11 January 2021
Accepted:
25 January 2021
Published:
30 January 2021
Abstract: The standard of care for fit patients with Mantle Cell Lymphoma (MCL) includes cytarabine containing induction treatment and consolidation with BEAM (Carmustine, Etoposide, Cytarabine and Melphalan). Chemo-refractory cases have a poorer prognosis and are candidates for allogenic stem cell transplantation (allo-SCT). Targeted therapy, such as BTK-inhibitors or BCL-mimetics can be used to bridge patients to SCT. COVID-19, a novel coronavirus has the potential to cause life threatening immune dysregulation and cytokine release syndrome (CRS) resulting in respiratory failure. Haematology patients, particularly post allogenic stem cell transplant, are high risk for developing CRS due to T-lymphopenia. PD, a 55-year-old male, with chemo-refractory MCL tested positive for COVID-19 day + 45 post allo-SCT after presenting with mild gastrointestinal symptoms and remained positive for 70 days. At day + 92 relapse was confirmed by CT and axillary node biopsy. Ibrutinib, a BTK inhibitor, was commenced with resolution of symptoms and a negative test within 20 days. With minimal reduction in adenopathy, Ibrutinib was stopped at day +110, while Cytarabine and Venetoclax (BCL-mimetic) were commenced with Donor lymphocyte infusion at day +145 resulting in complete remission. Ibrutinib’s therapeutic role against COVID-19 is now being investigated in clinical trials.
Abstract: The standard of care for fit patients with Mantle Cell Lymphoma (MCL) includes cytarabine containing induction treatment and consolidation with BEAM (Carmustine, Etoposide, Cytarabine and Melphalan). Chemo-refractory cases have a poorer prognosis and are candidates for allogenic stem cell transplantation (allo-SCT). Targeted therapy, such as BTK-in...
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Outcome of Instrumental Oxygen Therapy in COVID-19: Survivors Versus Non-survivors in Bangladeshi Cohort
Morshed Nasir,
Rawshan Ara Perveen,
Sonia Nasreen Ahmad,
Rumana Nazneen,
Shafi Mohammad Parvez Ahmed
Issue:
Volume 9, Issue 1, January 2021
Pages:
52-57
Received:
27 January 2021
Accepted:
7 February 2021
Published:
23 February 2021
Abstract: Background and objectives: Mortality of critically ill COVID-19 patients in ICU are high around the globe. There are variable reports on the outcome of invasive and non-invasive ventilation, change of oxygen saturation, and clinical characteristics in different countries and hospital set-ups. This study aimed to observe the demographic and clinical characteristics of critical COVID-19 cases, the trend of SpO2 in 10-days, and the mortality outcome of oxygen therapy in a tertiary level hospital in Bangladesh. Methods: In this retrospective study, data obtained from 99 patients admitted in ICU with COVID-19 was confirmed by RT-PCR of the nasopharyngeal swab. The 720-bed Holy Family Red Crescent Medical College Hospital (HFRCMCH), Dhaka, Bangladesh with a 9-bed ICU facility designated as "COVID-dedicated" from May17 to September 9, 2020. Ninety-nine patients were selected for the study, divided into two groups. 39 of them were non-survivors, whereas 60 included in the survivors group. Demographic data, correlation with age groups, clinical symptoms, instrumental oxygen therapy, and mortality were collected from hospital records. Appropriate statistical analysis was done using SPSS version 26.0. Results: Out of 99 patients admitted in ICU with COVID-19, 72 were male and 27 were female. The mean age of the patients was 61.08 years. Most of the ICU patients were in the 60-69 years of age group and the highest mortality rates (35.89%) were observed in this age range. The presenting symptoms of the patients were shortness of breath (85.85%) was the most common symptom followed by fever (66.66%), cough (32.32%), lethargy (12.12%), and others (7.77%). The mean SpO2 of their 10-days ICU stay was also variable between the two groups. A gradual increase of mean SpO2 was observed in the survivors' group. Whereas, the mean SpO2 level of non-survivor had ups and downs from 92% to 83% on day-10, along with the lowest level of mean SpO2 (77%) was on the 7th day. Conclusions: With the constrain of the healthcare support system and limited ICU facilities in a low-middle income country like Bangladesh, the mortality outcome and instrumental oxygen therapy to fight the ARDS caused by COVID-19 is far challenging. The present study clearly showed the highest mortality in patients who required mechanical ventilation, whereas, almost 75% of patients survived with high flow nasal cannula (HFNC). Therefore, the experience advocates the necessity of HFNC at the earliest possible time to avoid invasive ventilation in COVID-19 patients admitted in ICU.
Abstract: Background and objectives: Mortality of critically ill COVID-19 patients in ICU are high around the globe. There are variable reports on the outcome of invasive and non-invasive ventilation, change of oxygen saturation, and clinical characteristics in different countries and hospital set-ups. This study aimed to observe the demographic and clinical...
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