Investigating the Global Spread of SARS-CoV-2 Leveraging Next-Gen Sequencing and Principal Component Analysis
Christiane Scherer,
James Grover,
Darby Kammeraad,
Gabe Rudy,
Andreas Scherer
Issue:
Volume 6, Issue 4, August 2020
Pages:
49-55
Received:
15 June 2020
Accepted:
3 July 2020
Published:
13 August 2020
Abstract: As COVID-19 has spread from the first reported cases into a global pandemic, there has been a number of efforts to understand the mutations and clusters of genetic lineages of the SARS-CoV-2 virus. The high mutation rate and rapid spread makes this analysis capable of tracking chains of infections as well as putting individual sequences in context. Whole genomes of the SARS-CoV-2 virus are being collected and shared from across the globe. With the advent of affordable and prolific Next Generation Sequencing, this is the first pandemic in which the genomic evolution of the pathogen can be tracked in near real-time. So far, phylogenetic analysis methods have recently found a broader application in this regard. Here we demonstrate that Principal Component Analysis (PCA), used heavily in population genetics, corroborates the existing findings while providing unique new capabilities to understand our public repositories of complete virus sequences. This novel application of PCA is demonstrated on all publicly available SARS-CoV-2 samples from GenBank and other open-access databases until mid-April. We show that PCA is a useful and easy-to-use tool to analyze SARS-CoV-2 genomes in addition to phylogenetic analytics. It offers a previously untapped opportunity to analyze the dynamics of the current SARS-CoV-2 pandemic in a new way.
Abstract: As COVID-19 has spread from the first reported cases into a global pandemic, there has been a number of efforts to understand the mutations and clusters of genetic lineages of the SARS-CoV-2 virus. The high mutation rate and rapid spread makes this analysis capable of tracking chains of infections as well as putting individual sequences in context....
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Asymptomatic Bacteriuria and their Antimicrobial Susceptibility Pattern Among Pregnant Women Attending Antenatal Clinics at Mizan Aman Town, Southwestern Ethiopia
Abera Kumalo,
Mezmur Tadesse
Issue:
Volume 6, Issue 4, August 2020
Pages:
56-62
Received:
4 August 2020
Accepted:
20 August 2020
Published:
3 September 2020
Abstract: Introduction: Failure to identify asymptomatic bacteriuria (ASB) is responsible for its improper clinical management. This may lead to severe health complications during pregnancy. However, little is known about antimicrobial susceptibility of ASB in Ethiopian pregnant women. Therefore, the study was conducted to assess the prevalence of ASB and its antimicrobial susceptibility pattern in the target population. Methods: A cross-sectional study was conducted during September-December of 2017 at Mizan-Aman town, south-western Ethiopia among pregnant women (n=260) attending antenatal clinics. 10ml of clean- catch midstream urine was collected and cultured on Cysteine Lactose Electrolyte Deficient agar. Bacterial isolates were identified using Gram staining, colony morphology, and biochemical analysis. Antibiotic susceptibility was assessed by Kirby-Bauer disc-diffusion method. Logistic regression was employed for association analysis. Results: The prevalence of urinary tract infection was 10.3%. ASB was significantly associated with second trimester (AOR=5.61 [1.40-22.45]; p<0.05) and history of urinary tract infection (AOR=12.47 [3.91-39.82]; p<0.001). Escherichia coli were most prevalent pathogen and gram positive bacteria comprised majority of the overall isolates (63%). The Gram-negatives were more resistant with susceptibility rates of 11.8%, 29.4%, and 35.3% for ampicillin, nalidixic acid and chloramphenicol respectively. The susceptibility rates of Gram-positives were 100%, 80%, 70% for ciprofloxacin and kanamycin, co-trimoxazol and ceftriaxone and gentamycin respectively. Multidrug resistance (≥2 drugs) was seen in 81.5% of isolates. Conclusion: In generally, pregnant women with ASB may have serious consequences on both mother and fetus. Since in this study the locale specific heterogeneity in ASB prevalence, type and number of bacterial species, dominant bacterial species, antibiotic susceptibility pattern and multidrug resistance was observed. Therefore, it is important to screen all antenatal women for asymptomatic bacteriuria at their first prenatal visit; preferably in first trimester as well as antimicrobial susceptibility testing should be performed for management of ASB among pregnant women.
Abstract: Introduction: Failure to identify asymptomatic bacteriuria (ASB) is responsible for its improper clinical management. This may lead to severe health complications during pregnancy. However, little is known about antimicrobial susceptibility of ASB in Ethiopian pregnant women. Therefore, the study was conducted to assess the prevalence of ASB and it...
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Metabolic Syndrome and Associated Factors Among HIV-infected Patients at Bafoussam Regional Hospital, Cameroon
Joel Martial Diesse,
Cyril Wilfried Missinga,
Aude Ngueguim Dougue,
Emeline Zogning Makemjio,
Stephen Tamekou Lacmata,
Jean Paul Dzoyem,
Jules-Roger Kuiate
Issue:
Volume 6, Issue 4, August 2020
Pages:
63-70
Received:
12 August 2020
Accepted:
22 August 2020
Published:
7 September 2020
Abstract: The use of highly active antiretroviral therapy (HAART) transformed HIV infection to a chronic disease, and the complexity of the physiological disorders generated leads to the disruption of body fat distribution and insulin resistance. The resulting metabolic syndrome has rarely been investigated among people living with HIV/AIDS in Cameroon. The aim of the current work was to determine the prevalence of metabolic syndrome and associated factors among people living with HIV/AIDS under HAART at the Bafoussam Regional Hospital in Cameroon. A retrospective, cross-sectional study was conducted to collect demographic, clinical and therapeutic data from 371 people living with HIV/AIDS and who are under HAART at the Bafoussam Regional Hospital from November 2017 to February 2019. Abbott Real-time HIV-1 system, FACSCOUNT cytometer and FULLYSMART automates were used to determine HIV RNA level, CD4 cell count and biochemical parameters respectively. The metabolic syndrome was defined according to the International Diabetes Federation (IDF) and the National Cholesterol Education Program -Adult Treatment Panel III (NCEP-ATPIII) criteria. The overall prevalence of metabolic syndrome was 37.74% by IDF and 28.84% by ATPIII. Among patients with metabolic syndrome, HDL-hypocholesterolemia was the most prevalent feature (92.14%). We found that aging (OR, 1.05; p, 0.005), HIV RNA level (OR, 3.42; p, 0.001), family history of metabolic and coronary heart disease (OR, 2.24; P, 0.04), alcohol consumption (OR, 4; P, 0.004) and nutritional supplements (OR, 3.5; P<0.001) were the independent predictors of metabolic syndrome. Male sex (OR, 0.22; p,<0.001), use of traditional medicines (OR, 0.28; P<0.001), Cotrimoxazole prophylaxis (OR, 0.45; p, 0.007) and Lamivudine-Tenofovir-Efavirenz antiretroviral regimen (OR, 0.26; p<0.001) were protective factors. The prevalence of metabolic syndrome is on the increase among people living with HIV/AIDS in our study population. Both HIV related factors and traditional risk factors were associated with metabolic syndrome.
Abstract: The use of highly active antiretroviral therapy (HAART) transformed HIV infection to a chronic disease, and the complexity of the physiological disorders generated leads to the disruption of body fat distribution and insulin resistance. The resulting metabolic syndrome has rarely been investigated among people living with HIV/AIDS in Cameroon. The ...
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