Evaluation of different deoxyribonucleic acid (DNA) extraction methods using dried blood spot for early infant diagnosis of HIV1 in Sub-Saharan Africa

2012 ◽  
Vol 6 (27) ◽  
Author(s):  
Ceffa Susanna
2018 ◽  
Author(s):  
Charles Chiku ◽  
Maria Zolfo ◽  
Mbazi Senkoro ◽  
Mzwandile Mabhala ◽  
Hannock Tweya ◽  
...  

Background: Early infant diagnosis (EID) of HIV in infants provides an opportunity for early detection of the infection and early access to Antiretroviral treatment (ART). Dried Blood Spot (DBS) samples are used for EID of HIV-exposed infants, born from HIV positive mothers. However, DBS rejection rates have been exceeding in Zimbabwe the target of less than 2% per month set by the National Microbiology Reference Laboratory (NMRL). The aim of this study was to determine the DBS samples rejection rate, the reasons for rejection and the possible associations between rejection and level of health facility where the sample was collected. Methods: Analytic cross-sectional study using routine DBS samples data from the NMRL in Harare, Zimbabwe, between January and December 2017. Results: A total of 34.950 DBS samples were received at the NMRL. Of these, 1291(4%) were rejected and reasons for rejections were: insufficient specimen volume (72%), missing request form (11%), missing sample (6%), cross contamination (6%), mismatch information (4%) and clotted sample (1%). Samples collected from clinics/rural health facilities had five times likelihood to be rejected compared to those from a central hospital. Conclusion: Rejection rates were above the set target of 2%. The reasons for rejection were 'pre-analytical' errors including labeling errors, sample damage, missing or inconsistent data, and insufficient volume. Samples collected at primary healthcare facilities had higher rejection rates. Key words: Operational Research, SORT IT, Early Infant Diagnosis, Dried Blood Spot


2016 ◽  
Vol 18 (3) ◽  
Author(s):  
Veneranda M. Bwana ◽  
Christiana Frimpong ◽  
Edgar Simulundu ◽  
Sayoki G. Mfinanga ◽  
Leonard E.G. Mboera ◽  
...  

Background: Early Infant Diagnosis (EID) of Human Immunodeficiency Virus (HIV) is one of the major interventions for HIV and AIDS in sub-Saharan Africa. However, the coverage is still lower than the recommended levels. The objective of this review was to systematically assess factors associated with accessibility of EID services in sub-Saharan Africa.Methods: Scientific engines were searched from library catalogues and public databases. The review included free full text articles in English published from 1996 to 2015 and fitting to the objectives of the study.Results: A total of 1,039,715 results appeared on the databases after initial searching. Of these, 48 eligible articles were identified and reviewed. From 2004 to 2014, the proportion of HIV exposed infants who received a virological test within the first 2 months of life in sub-Saharan Africa varied from 3 to 58%, far below the 80% recommended level by the World Health Organization. EID services were not available in more than 30% of health facilities in most sub-Saharan African countries. Factors associated with accessibility of EID services included parents with low formal education level, maternal unemployment, geographical relocation, religious beliefs, lack of paternal support, insufficient awareness of HIV control and prevention services, poor compliance to prevention of mother to child transmission services, lack of general knowledge of HIV transmission, stigma and discrimination, inadequate human resource for health, weak infrastructure, inadequate supplies of laboratory materials and late feedback of HIV test results.Conclusion: Availability and accessibility of EID services in sub-Saharan Africa is still low despite the investment made during the past decade. Both individual and institutional factors affect the availability and accessibility of the services. It is important that these factors are urgently addressed to improve EID services.


2017 ◽  
Vol 65 (6) ◽  
pp. 1479-1493 ◽  
Author(s):  
Jónas Oddur Jónasson ◽  
Sarang Deo ◽  
Jérémie Gallien

2016 ◽  
Vol 52 ◽  
pp. 171-176
Author(s):  
M. Palkina ◽  
O. Metlitska

The aim of the research – adaptation, optimization and using of existing DNA extraction methods from bees’ biological material with the reagent «Chelex-100" under complex economic conditions of native laboratories, which will optimize labour costs and improve the economic performance of DNA extraction protocol. Materials and methods. In order to conduct the research the samples of honey bees’ biological material: queen pupae exuviae, larvae of drone brood, some adult bees’ bodies (head and thorax) were selected. Bowl and drone brood were obtained from the experimental bee hives of Institute of Apiculture nd. a. P. I. Prokopovich of NAAS. DNA extraction from biosamples of Apis mellifera ssp. was carried out using «Chelex-100®» ion exchange resin in different concentrations and combinations. Before setting tests for determination of quantitative and quality indexes, dilution of DNA samples of the probed object was conducted in ratio 1:40. The degree of contamination with protein and polysaccharide fractions (OD 260/230), quantitative content of DNA (OD 260/280) in the extracted tests were conducted using spectrophotometer of «Biospec – nano» at the terms of sample volume in 2 µl and length of optical way in 0,7 mm [7]. Verification of DNA samples from biological material of bees, isolated by «Chelex-100®», was conducted after cold keeping during 24 hours at 20°C using PСR with primaries to the fragment of gene of quantitative trait locus (QTL) Sting-2 of next structure [8]:  3' – CTC GAC GAG ACG ACC AAC TTG – 5’; 3' – AAC CAG AGT ATC GCG AGT GTT AC – 5’ Program of amplification: 94 °C – 5 minutes – 1 cycle; 94 °C – 1 minute, 57°C – 1 minute, 72 °C – 2 minutes – 30 cycles; elongation after 72°C during 2 minutes – 1 cycle. The division of obtained amplicons was conducted by gel electrophoresis at a low current – 7 µÀ, in 1,5 % agarose gel (Sigma ®) in TAE buffer [7]. The results. At the time of optimization of DNA isolation methods, according to existing methods of foreign experts, it was found optimal volume of ion exchange resin solution was in the proposed concentration: instead of 60 µl of solution used 120 µl of «Chelex-100®», time of incubation was also amended from 30 minutes to 180 minutes [9]. The use of the author's combination of method «Chelex-100®» with lysis enzymes, proteinase K and detergents (1M dithiothreitol), as time of incubation was also amended, which was reduced to 180 minutes instead of the proposed 12 hours [10]. Changes in quality characteristics of obtained DNA in samples after reduction in incubation time were not found. Conclusions. The most economical method of DNA isolation from bees’ biological material is 20% solution of «Chelex-100» ion exchange resin with the duration of the incubation period of 180 minutes. It should also be noted that the best results can be obtained from exuviae, selected immediately after the queen’s exit from bowl, that reduces the likelihood of DNA molecules destruction under the influence of nucleases activation, but not later than 12 hours from release using the technology of isolated obtain of queens.


Molecules ◽  
2021 ◽  
Vol 26 (7) ◽  
pp. 1989
Author(s):  
Laura Téblick ◽  
Severien Van Keer ◽  
Annemie De Smet ◽  
Pierre Van Damme ◽  
Michelle Laeremans ◽  
...  

The potential of first-void (FV) urine as a non-invasive liquid biopsy for detection of human papillomavirus (HPV) DNA and other biomarkers has been increasingly recognized over the past decade. In this study, we investigated whether the volume of this initial urine stream has an impact on the analytical performance of biomarkers. In parallel, we evaluated different DNA extraction protocols and introduced an internal control in the urine preservative. Twenty-five women, diagnosed with high-risk HPV, provided three home-collected FV urine samples using three FV urine collection devices (Colli-Pee) with collector tubes that differ in volume (4, 10, 20 mL). Each collector tube was prefilled with Urine Conservation Medium spiked with phocine herpesvirus 1 (PhHV-1) DNA as internal control. Five different DNA extraction protocols were compared, followed by PCR for GAPDH and PhHV-1 (qPCR), HPV DNA, and HBB (HPV-Risk Assay), and ACTB (methylation-specific qPCR). Results showed limited effects of collection volume on human and HPV DNA endpoints. In contrast, significant variations in yield for human endpoints were observed for different DNA extraction methods (p < 0.05). Additionally, the potential of PhHV-1 as internal control to monitor FV urine collection, storage, and processing was demonstrated.


2018 ◽  
Vol 1 (3) ◽  
pp. 27 ◽  
Author(s):  
Džiuginta Jakočiūnė ◽  
Arshnee Moodley

Bacteriophages (phages) are intensely investigated as non-antibiotic alternatives to circumvent antibiotic resistance development as well as last resort therapeutic options against antibiotic resistant bacteria. As part of gaining a better understanding of phages and to determine if phages harbor putative virulence factors, whole genome sequencing is used, for which good quality phage DNA is needed. Traditional phage DNA extraction methods are tedious and time consuming, requiring specialized equipment e.g., an ultra-centrifuge. Here, we describe a quick and simple method (under four hours) to extract DNA from double stranded DNA (dsDNA) phages at titers above 1.0 × 1010 plaque-forming units (PFU)/mL. This DNA was suitable for library preparation using the Nextera XT kit and sequencing on the Illumina MiSeq platform.


2007 ◽  
Vol 68 (1) ◽  
pp. S80
Author(s):  
Victoriano J. Leon ◽  
Alberto J. Leon ◽  
Juan Luis Garcia

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