KRISP NEWS
KRISP is running a Sanger Sequencing promotion to celebrate the launch of two new Sanger Sequencers (ABI 3730xl and 3500). Unbelievable prices for the first 6 months. Capillary electrophoresis only – R 25 (per sample well). Sequencing of PCR purified amplicons – R 45 (per primer). Sequencing of PCR unpurified amplicons – R 75 (per primer).
UKZN African Health Flagship Grants Support Unit discuss about new funding opportunities: AAS and Royal Society FLAIR Fellowship & SAMRC-NIH Calls 2019. Wednesday, 24 April 2019 (1:00pm - 2:00pm), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!
The IndabaX is a means with which to experiment with the ways in which we strengthen African machine learning, artificial intelligence and its local communities. KRISP is a sponsor of the Deep Learning IndabaX 2019, 14 to 17 April, South Africa.
Radio interview by Dr. Astrid Treffry-Goatley about the use of story telling of our BMJ Medical Humanities 2019 paper entitled: Community engagement with HIV drug adherence in rural South Africa: a transdisciplinary approach.
KRISP Team Leader Dr. Veron Ramsuran is one of 30 leading scientists to receive the prestigious AAS and UK Royal Society FLAIR Fellowship. The 2019 FLAIR funded scientists were selected from a competitive pool of more than 700 applicants. Their research is diverse, ranging from providing renewable energy solutions and addressing climate change, to tackling food security and targeting health and environmental problems that are most acute for people living in African countries.
This month, we focused our newsletter on the new services and technologies available at KRISP. The newsletter also highlights our educational events (Talks, Wet-Lab and Dry-Lab workshops) and publications, including a paper on the increase of HIV-1 drug resistance in South Africa and another on the use of deep-sequence phylogenies to infer HIV-1 transmission networks
KRISP has invested in two new Sanger DNA sequencers, including the ABI3730xl, which is the largest and most automated Sanger machine in the world. This equipment has 96 capillaries and it is able to produce over 1,500 sequences a day.
KRISP has invested in a new Illumina DNA sequencer, providing access to NGS services using Miseq, NextSeq and HiSeq DNA sequencers. We are now in the position to generate NGS sequencing data at similar price, quality and speed as the international leading genomics centres.
KRISP has invested in two high-throughput qPCR equipment (QuantStudio 7 Flex Real Time PCR Systems. We have validated qPCR TaqMan Array Card for many common pathogens and pathogens including panels for Gastrointestinal Panel (38 pathogens), Sexually Transmitted Infections (STI) Panel (12 pathogens) and Respiratory Diagnostic Panel (34 pathogens).
KRISP partner with Thermo Fisher Scientific on an educational program in Africa. As part of this program we organized 5 training workshops on STEM subjects in 2018 and 2019, ranging from PCR, qPCR, DNA sequencing and bioinformatics techniques.
KRISP PAPERS
Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.
Ratmann O, Grabowski KM, Hall M, Golubchik T, Wymant C, Abeler-Dorner L, Bonsall D, Hoppe A, Leigh Brown A, de Oliveira T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C, PANGEA Consortium and Rakai Health Sciences Program
, Nature Communications (2019), 10:1411:https://doi.org/10.1038/s41467-019-09139-4.
Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000–2016: A Pooled Sequence Analysis.
Chimukangara B, Lessells RJ, Rhee S-Y, Giandhari J, Kharsany ABM, Naidoo K, Lewis L, Cawood C, Khanyile D, Ayalew KA, Diallo K, Samuel R, Hunt G, Vandormael A, Stray-Pedersen B, Gordon M, Makadzange T, Kiepiela P, Ramjee G, Ledwaba J, Kalimashe M, Morris L, Parikh UM, Mellors JW, Shafer RW, Katzenstein D, Moodley P, Gupta RK, Pillay D, Karim SSA, de Oliveira T, EClinicalMedicine (Lancet) (2019), DOI:https://doi.org/10.1016/j.eclinm.2019.03.006:.
Effects of Migration on Risky Sexual Behavior and HIV Acquisition in South Africa: A Systematic Review and Meta-analysis, 2000-2017..
Dzomba A, Tomita A, Govender K, Tanser F, AIDS Behav. (2019), doi: 10.1007/s10461-018-2367-z:.
Major depression and household food insecurity among individuals with multidrug-resistant tuberculosis (MDR-TB) in South Africa..
Tomita A, Ramlall S, Naidu T, Mthembu SS, Padayatchi N, Burns JK, Soc Psychiatry Psychiatr Epidemiol. (2019), doi: 10.1007/s00127-019-01669-y:.
Effect of ART scale-up and female migration intensity on risk of HIV acquisition: results from a population-based cohort in KwaZulu-Natal, South Africa.
Dzomba A, Tomita A, Vandormael A, Govender K, Tanser F, BMC Public Health (2019), 19(1):196:doi: 10.1186/s12889-019-6494-x.
Effects of genetic variability on rifampicin and isoniazid pharmacokinetics in South African patients with recurrent tuberculosis.
Naidoo A, Chirehwa M, Ramsuran V, McIlleron H, Naidoo K, Yende-Zuma N, Singh R, Ncgapu S, Adamson J, Govender K, Denti P, Padayatchi N, Pharmacogenomics (2019), doi: 10.2217/pgs-2018-0166:.
Estimating trends in the incidence rate with interval censored data and time-dependent covariates.
Vandormael A, Tanser F, Cuadros D, Dobra A, Stat Methods Med Res (2019), 962280219829892. doi: 10.1177/0962280219829892:.
KRISP VIDEOS
Human Genome, S5Ion Sequencing & Women in Science in Africa
By: Maryam Fish
KRISP TEAM
KRISP BLOGS
KRISP TOOLS
2019-02-12
REGA HIV Subtyping Tool V3 - Belgium Mirror
Phylogenetic tool to identify the HIV-1 subtypes and recombinants. Query sequences are analysed for recombination using bootscanning methods. The version 3 contains new CRFs (CRF01_AE to CRF47_BF).
2018-12-05
Booster: a new bootstrap method for construction of large trees
A new version of the phylogenetic bootstrap in which the presence of inferred branches in replications is measured using a gradual 'transfer' distance rather than the binary presence or absence index used in Felsenstein's original version. The resulting supports are higher and do not induce falsely supported branches.
2016-08-21
REGA HIV Subtyping Tool V3 - South African mirror
This tool is designed to use phylogenetic methods in order to identify the HIV-1 subtype of a specific sequence. The sequence is analysed for recombination using bootscanning methods. The version 3 contains new CRFs (CRF01_AE to CRF47_BF).
2016-08-20
This is the first version of the Zika typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.
2016-08-20
This is the first version of our Arbovirus typing tool for Chikungunya, Dengue, Yellow Fever and Zika
2016-08-20
This is the first version of the Chikungunya typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.