makerere/uvri infection and immunity research training ... report 6.pdf · a full report of our...

Version 1.0, December 2013

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SUMMARY The Makerere – UVRI Research Training Programme in Infection and Immunity was established in 2008 to promote partnership between Uganda’s leading tertiary education and research institutions, in order to foster the development of a world class centre of excellence for Infection and Immunity research in Uganda. A full report of our activities to January 2013 has been compiled and is available on our website (www.muii.org.ug). We here present an update to December 2013. A key event of the past year was the Wellcome Trust review visit in January 2013, following which the Trust awarded further funding (£1,077,037) for a period of two years. Our objectives for the new 2013-2016 funding period are (1) to promote training in bioinformatics and computational biology (BCB), laying the foundations for a new BCB hub that will complement and interact with the immunology hub as a basis for translational Infection and Immunity research in Uganda; (2) to support the development of a new department of immunology and molecular biology at Makerere University College of Health Sciences; (3) to support the best trainees from current schemes to advance their careers and to progress towards leadership and independence in research and capacity building and (4) to extend the development of UVRI as a regional centre for I&I research training. Major events in the past year have been the second Makerere-UVRI Open Day (and its associated afternoon for science teachers) held in July, and the Science Symposium, held in November. Achievements have included the development of a bioinformatics curriculum, and participation of MUII fellows in running a Bioinformatics in the Tropics course in South Africa. The next course in this series is scheduled for Uganda in 2014, along with other workshops. For immunology, a MUII-supported lecturer, Bernard Bagaya, was appointed to the Makerere University College of Health Sciences in November 2013. He is already contributing to the teaching and to the development of the department, and is planning research funding proposals. MUII has now supported six Masters, seven PhD and seven post-doctoral fellows. Fellows are progressing with their training and research, but also increasingly participating in the planning and management of the MUII programme, and in networking and in capacity building in their own right. Among their special achievements, Dr Damalie Nakanjako was selected for the 2013 Merle A. Sande Health Leadership Award and Harriet Mpairwe has been awarded a Wellcome Trust Training Fellowship. Infrastructural developments are in progress at both Makerere (with expansion of basic science laboratory space) and at UVRI (with the construction of a training and resource building, co-funded by MRC UK).

Makerere/UVRI Infection and Immunity Research Training Programme

http://www.muii.org.ug/


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Contents Summary 1

Introduction 3

THEME 1. PARTNERSHIP 4

1.1. Progress on prior objectives 4

1.2. Progress on new objective 1, training in bioinformatics and computational biology (BCB) 5

1.3. Progress on new objective 2, supporting the development of a new department of immunology and molecular biology at Makerere University College of Health Sciences 8

THEME 2. A TRAINING PROGRAMME WITH ACCESS TO WORLD-CLASS RESEARCH AND TRAINING 9

2.1. Undergraduate internship programme 10

2.2. Strategic Internships in Biomathematics 10

2.3. Fast track Masters and PhD fellows 11

2.4. Current PhD fellows 11

2.5. Current and past post-doctoral fellows 12

2.6. New PhD and post-doctoral fellowships, 2013-2016 12

2.7. Progress on new objective 3, supporting the best trainees from current schemes to advance their careers and to progress towards leadership and independence in research and capacity building 13

2.8. Special achievements 13

2.9. Mentorship 14

2.10. Golden Opportunities 14

THEME 3. A SUPPORTIVE, SUSTAINABLE AND UP-TO-DATE RESEARCH AND TRAINING ENVIRONMENT 15

3.1. General progress 15

3.2. Progress on new objective 4, extending the development of UVRI as a regional centre for I&I research training 16

Appendix 1. Progress on key deliverables. 17

Appendix 2. Fellows’ presentations at local and international conferences 19

Appendix 3. Programme publications 22

Appendix 4. Additional funding for capacity building secured by programme staff and fellows 26

Appendix 5. Additional funds for research raised by programme staff and fellows 27


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INTRODUCTION The Makerere University – Uganda Virus Research Institute (UVRI) research training programme in Infection and Immunity (MUII) is a strategic initiative designed to establish a centre of excellence for Infection and Immunity (I&I) research in Uganda. Our vision is of African institutions as full and equal partners in global Infection and Immunity research, and of a critical mass of African scientists in Infection and Immunity empowered to identify and ask scientific questions, to lead international funding initiatives from the perspective of issues they see as critical to Africa, to lead research groups and to establish world-class laboratories, to train students, and to produce scientific results of both local and global significance. Our goal is to contribute to the realisation of this vision in Uganda.

Since its inception in 2008, our work has progressed in three theme areas.

1. Partnership between Makerere University and UVRI in Infection & Immunity research, supported by strong links with international partners

2. A training programme aiming to attract the brightest young Ugandan and regional scientists, from secondary school to post-doctoral level, and to support their career development through access to world class research and training

3. Development of a supportive, sustainable and up-to-date research and training environment

Particular successes have been (1) partnership in immunology, resulting in the development of a vibrant immunology hub linking senior and trainee scientists between the institutions, (2) the establishment of a competitive fellowship scheme and a tight-knit, mutually supportive fellowship of trainees and mentors, (3) the development of an outreach programme designed to attract bright young people to research-related careers through open days and internships, and to extend training in I&I research across the region and (4) the development of some key elements of infrastructure for I&I research and training at Makerere and at UVRI. In January 2013 the programme was reviewed by the Wellcome Trust. A full report of our activities to January 2013 was prepared for that meeting and is available at www.muii.org.ug. Following the review, we were delighted that funding was awarded to extend the programme to early 2016. A total of £1,077,037 was awarded for the forthcoming two years. The specific objectives for the new funding period are as follows:

1. To promote training in bioinformatics and computational biology (BCB), laying the foundations for a

new BCB hub that will complement and interact with the immunology hub as a basis for translational Infection and Immunity research in Uganda

2. To support the development of a new department of immunology and molecular biology at Makerere University College of Health Sciences

3. To support the best trainees from current schemes to advance their careers and to progress towards leadership and independence in research and capacity building

4. To extend the development of UVRI as a regional centre for I&I research training

In this document we provide an update on the January 2013 report, using the three theme headings, with particular attention to the work that has been initiated regarding the new objectives.



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Theme 1. Partnership

By developing partnerships for infection and immunity research in Uganda, we aim to build a critical mass of individuals able to lead in this field, and to ensure efficient use of expertise, equipment and resources between local institutions.

1.1. Progress on prior objectives

Key events during 2013 have been the second Makerere-UVRI Open Day, and the fourth Makerere-UVRI science symposium

Event for science teachers. Based on experience from the 2009 Open Day, the 2013 Open Day was preceded by a meeting with science teachers from schools in the region. This was extremely helpful in planning the agenda for the Open Day and also in obtaining reliable information in advance about schools that would, or would not attend, and the numbers of students to expect. Open Day. The second Makerere – UVRI Open Day was held at UVRI on 18th July 2013. The theme was “Science and You”. About 2000 participants from 30 schools attended the event. Over 60 research groups from Makerere, UVRI and other partners presented their work in a science fair format. Also, laboratories at UVRI were open for participants to visit. The event was graced by the presence of the Minister for Health, Dr Rukahana Rugunda. There was media coverage and a documentary film was prepared. Feedback was positive with calls for more such events, and opportunities for a wider range of students (from primary schools, rural schools, and universities) to be able to attend. A full report of this event is available on line at www.muii.org.ug. Symposium. The fourth Makerere - UVRI Symposium on Infection and Immunity research was held on 7th November 2013. This was the first such event to be held at UVRI, previous symposia having been held at Makerere. It was timed to follow the MRC/UVRI Unit’s Scientific Advisory Committee meeting, allowing the committee members to participate as keynote speakers, or as adjudicators for the young scientists’ competition. Keynote talks were given by Professor Massimo Palmarini from the University of Glasgow, UK, on arbovirology, by Professor Doreen Cantrell of University of Dundee, UK, on T cell signalling, and by Professor Richard Hayes of the London School of Hygiene & Tropical Medicine (LSHTM) on studying population “test and treat” strategies for reducing HIV transmission. Professor Pontiano Kaleebu gave a memorial lecture for the late Anthony Kebba. Young scientists gave oral and poster presentations. Prize winners are listed in Box 1. Evaluations were positive, calling for this to be an annual event – possibly expanded to two days, and with a larger venue and increased publicity.

Box 1. MUII Science Symposium, prize winners.

David Meya, THRiVE PhD fellow, College of Health Sciences, Makerere University. Best oral presentation: “Localized cellular immune responses in cerebrospinal fluid from HIV-infected persons with cryptococcal meningitis and Immune Reconstitution Inflammatory Syndrome”

Harriet Mpairwe, Post-doctoral fellow, Co-infection Studies Programme, MRC/UVRI. 1st runner up oral presentation: “Exposure to hookworm prenatally and to worm infections in early childhood is inversely associated with eczema in childhood: results from a birth cohort in Uganda” Irene Kyomuhangi, MSc graduate, LSHTM. Best poster presentation: “The evolution of anti-malarial antibodies in children in the first 5 years of life and effect of maternal helminth infections”

Yunia Mayanja, Scientist, MRC/UVRI. 1st runner up poster presentation: “Uptake of partner treatment among female sex workers diagnosed with Sexually Transmitted Infections in Southern Kampala, Uganda”

Deogratius Ssemwanga, Post doctoral fellow, MRC/UVRI. 2nd runner up poster presentation: “Incidence of HIV-1 superinfection is similar to primary HIV-1 incidence in a cohort of female sex workers in Uganda”



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1.2. Progress on new objective 1, training in bioinformatics and computational biology (BCB)

Background. As we prepared to apply for extension of MUII funding from the Trust, an important gap in capacity for bioinformatic analyses was noted in Uganda. Initiatives such as the National Institutes of Health (MIH) and Wellcome Trust funded “H3Africa” mean that large sets of genetic data from African populations are likely to become increasingly available. In addition, work on pathogen genetics is on-going in the region and discovery orientated immunological investigations using microarray and multiplex assays are of increasing interest to Ugandan scientists. We therefore resolved to seek funding to support researchers from Makerere and UVRI to develop capacity in these areas. We held a meeting involving scientists known to be interested in this field, from the two institutions, to discuss areas of interest and capacity. Table 1, below, provides a flavour of the areas of interest and capacity that were discussed at the meeting.

Table 1. Makerere – UVRI bioinformatics discussion meeting findings. Institution / department Personnel Areas of interest Capacity

Key collaborations Comments

Makerere Mathematics

– Livingstone Luboobi

– John Kitayimbwa

Broad interest in computational biology, including genomics and genome-wide association studies, functional genomics such as gene expression microarray work, structural biology, systems biology and network biology

Mathematics – Institute of Integrative Biology, ETH, Zurich

– Cambridge – Others

– Keen to develop links with biologists, and joint courses that would demystify maths for biologists and vice versa

– Collaborations developing between MUII fellows on training and HIV drug resistance research

Makerere Medical Microbiology

– Eddie Wampande

– David Kateete

Pathogen genomics, Mycobacterium tuberculosis

Molecular biology – Swiss Tropical Institute

– Others

– Noted that currently training can only be obtained outside Uganda

– Strong interest among Ugandan students

Makerere Biochemistry and Veterinary Medicine

– Pius Alibu – Enock Matovu

Trypanosome pathogen genomics and human genetics; part of Trust-funded TrypanoGEN

Molecular biology Human resources Some computing

– Swiss Tropical Institute

– University of Glasgow, UK

– WT Sanger Institute

– Burkina Faso

– Biochemistry collaborate with vet school on teaching and research in this area

– For TrypanoGEN, Burkina Faso has relative strength in bioinformatics and a senior bioinformatician is to be employed there. TrpanoGEN will support some Masters and PhD fellows. Makerere participants in TrypanoGEN will go to Burkina Faso for training.

UVRI, human genetics

– Rebecca Nsubuga

– Jonathan Kayondo

Current studies on population genetics of cardiovascular and metabolic disease, and on immune response to infant vaccines

Limited computing capacity Individuals being trained

– WT Sanger Institute

– University of Oxford, UK

– need for African scientists to acquire the ability to analyse data from African genetic studies

– collaboration in H3ABionet UVRI virology

– Jonathan Kayondo

– Deo Ssemwanga

Molecular epidemiology and evolution of HIV, and in HIV drug resistance. Currently exploring options for establishing a database for the curation of this data.

Sequencing and molecular biology Limited computing

– UCL, UK – University of

Edinburgh, UK – WT Africa

Centre

– External experts, such as Dr Tulio d’Oliveira (WT Africa Centre) very willing to help build capacity in Uganda

UVRI functional genomics

– Enoch Muyanja – Barbara Nerima

Immunology of the response to vaccines and effects of co-infections

Capacity for multiple gene expression studies and protein analysis

– Vaccine and Gene Therapy Institute, USA

– Oxford

– UVRI scientists would welcome partnerships that would support the analysis of the complex data generated.

We proposed a “bioinformatics and computational biology hub” – analogous to the network that we had fostered for immunology research. The Trust review team felt that this was premature, and advised that we focus, first, on offering training in this field. However, the links initiated in the preliminary meeting will be valuable as we work to develop expertise in Uganda. As one step to fostering supportive external collaborations, specifically in pathogen genomics, a MUII-sponsored group from Uganda visited the Wellcome Trust Africa Centre from 25th to 27th November 2012, to discuss collaboration on research and training with Dr Tulio d’Oliveira. Dr d’Oliveira subsequently visited Uganda for the Wellcome Trust review visit. These visits laid the basis for the “Bioinformatics in the Tropics” course series, which is now in progress (see below). The discussions we held will also contribute to the development of a database of HIV genome sequences for Ugandan samples.


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Other initiatives that are expected to support the development of capacity in bioinformatics in the forthcoming period include the African Partnership for Chronic Disease Research (APCDR) (a Wellcome Trust and MRC supported initiative involving collaboration with the University of Cambridge and the Sanger Institute on the genetics of cardiovascular and metabolic diseases), H3ABionet (in which UVRI is a partner) and TrypanoGEN (in which Makerere University is a partner). Also, the MRC/UVRI Unit, in collaboration with Dr Manjinder Sandhu, have submitted a proposal for a medical informatics centre at UVRI, to be housed in the resource building that has been constructed with Wellcome Trust (MUII) and MRC funding.

Bioinformatics courses. During the MUII extension, 2013-2016, we proposed to deliver at least three Bioinformatics courses. In this regard, the series “Bioinformatics in the Tropics” has been developed with Tulio d’Oliveira and Luiz Carlos Alcantara of the Centro de Pesquiza Gonçalo Muniz, Osvaldo Cruz Foundation (FioCruz), Salvador, Bahia, Brazil. Three UVRI staff attended the second course held between 23rd and 26th September 2013 at the Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa, funded by the Wellcome Trust Africa Centre and MUII. They participated in organisation of the course and in teaching, in preparation for running the Uganda course, now scheduled for April 2014. The South Africa course trained 30 participants. Evaluation found the following. “The Bioinformatics in the Tropics workshop was extremely well received and earned high praise from the majority of the participants. Comments included ‘A job well done,’ with participants agreeing that the organisation and content were excellent. Overall, participants

welcomed the mix of the theory and practical sessions and felt that an appropriate balance had been struck between them. However some would have preferred more time to practice on their own datasets. In addition there were those that felt the course should have focused a little less on the mathematics and statistics behind bioinformatics models. An overwhelming majority wanted a greater focus on tree drawing, annotation and interpretation. Interestingly, there was a suggestion that there be more discussion of publications using phylogenetics and bioinformatics tools indicating that participants would enjoy more discussions on translational research, a trend currently observed in many spheres of science. Also of note was that all presenters scored favourably and were clear, informative and concise in delivering their messages. Of the positive comments, one in particular exemplifies the objectives of both the organisers and instructors: ‘This workshop is like building a house with the aim of generating (the) next level of Bioinformaticians’.” This feedback will contribute to the design of the Uganda course. The group interested in functional genomics propose to develop a workshop on the analysis of microarray data and on the analysis of multiplex gene expression data, tentatively scheduled for May 2014, with faculty from the Vaccine and Gene Therapy Institute of Florida and from Leiden University Medical Centre, and co-funded by MUII and the European Union funded consortium “IDEA” (http://www.idearesearch.eu/). In preparation for this we were advised that potential trainees should familiarise themselves with programming using R. Suitable on-line courses were

http://www.idearesearch.eu/


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recommended, but these proved difficult to follow for novices. Therefore a workshop on R programming has been arranged for the 17th and 18th December. These MUII-sponsored activities have been, or will be, complemented by courses supported by other funders to create a substantial curriculum of bioinformatics training (table 2).

Table 2. Bioinformatics curriculum

Dates Courses Funder/ Organiser MUII contribution 19-28 June Wellcome Trust Advanced Course in Functional

Genomics and Systems Biology, Wellcome Trust Sanger Institute, UK

WT/MUII Support for fellow(s) to attend

7-27 July 2013 H3ABioNet Train-the-trainer course, International Centre of Insect Physiology and Ecology (ICIPE), Nairobi Kenya

WT/ H3ABionet Support for fellow(s) to attend

29 July-2 August 2013 Introduction to Bioinformatics using the eBioKit Platform, ICIPE, Nairobi Kenya

WT/ H3ABionet Support for fellow(s) to attend

25-30 August 2013 18th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology, University of Florida

Support for fellow(s) to attend

15-20 September 2013 Genomic Epidemiology in Africa, UVRI WT/ Sanger Institute 23-26 September 2013 Bioinformatics in the Tropics (HIV), Nelson R

Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa

WT/ MUII and Africa Centre, MRC/UVRI and the Brazilian Scientific Foundation (CNPQ)

Support for fellows and faculty

17-18 December 2013 R programming WT/MUII Support for fellows and faculty

7-10 April 2014 Bioinformatics in the Tropics (HIV and TB), UVRI, Entebbe Uganda


Support for faculty and logistics

May 2014 Microarray and multiplex gene expression analysis

WT/ MUII Support for faculty and logistics

June 2014 Bioinformatics in the Tropics course (advanced), Salvador, Bahia Brazil


Possible travel grants for attendance

Bioinformatics travel fellowships. As well as formal courses, we plan to support training in bioinformatic analyses by funding travel awards that will allow individuals to travel to conduct analyses in collaboration with external partners and, where necessary, using the higher computing capacity available at collaborating institutions. These will be advertised early in 2014. In the interim, several MUII fellows and staff have chosen to use funds from their fellowships, or from their MUII Golden Opportunity awards (see below), to fund such trips. • Deo Ssemwanga will use his MUII Golden Opportunity funds to travel to the Wellcome Trust

Sanger Institute and the University of Edinburgh where he will train in full genome sequencing and analysis of samples from his study participants that were found to have HIV-1 superinfection. This work which is part of his MUII Post-Doctoral fellowship where he confirmed 7 cases of superinfection and 8 more cases with multiple infections at baseline testing. These participants will be analysed to determine the rates of emergence of recombinant viruses. He will train at Sanger for four weeks with Prof. Paul Kellam and thereafter at the University of Edinburgh for two weeks with his mentor Prof. Andrew Leigh Brown.

• John Kitayimbwa will use his MUII Golden Opportunity funds to travel to Oxford, and to the Sanger Institute, to participate in the analysis of a genome wide association study designed to investigate genes associated with the immune response to vaccines given during infancy.

• Damalie Nakanjako will use fellowship funds and Barbara Nerima will use her MUII Golden Opportunity funds to travel to the Vaccine and Gene Institute in Florida to together to learn about gene expression microarray analysis. Damalie’s MUII-funded post-doctoral fellowship has allowed her to collect samples from a well characterised cohort that will be used for this training in microarray Illumina Platform. This trip will also allow them to plan with VGTI colleagues for the microarray workshop in Uganda in May.


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Help desk. Through H3ABionet, we have access to a Help Desk knowledge-base. This is a resource that brings together assembled expertise within H3ABioNet (http://www.h3abionet.org) to provide bioinformatics technical assistance. An online interface allows users to submit questions. Technical advice on the following can be provided: • Analysis - Genotyping arrays • Analysis - NGS data • Analysis - Other (Not arrays or sequence data) • Biostatistics, Data Management (storage, etc) • Software Development / Programming • Technical / System Administration • Website / Mailing List • General Project Administration Data bases. Work on this aspect has not yet been initiated. The virology group plan to set up an HIV drug resistance database for Ugandan samples. The plan is that this will be co-funded by CDC-PEPFAR (the President’s Emergency Plan for AIDS Relief). For this the most appropriate system will be determined in the coming months. The template used by the UK HIV Drug Resistance Database has been offered by the MRC Clinical Trial Unit and Professor Deenan Pillay: some adaptation might be required which could be carried out by a Ugandan programmer. A percentage random sample would be placed on Genbank, in keeping with policies developed for the HIV drug resistance database (www.hivrdb.org) and the Swiss Cohort (http://www.shcs.ch/). Alternatively Dr d’Oliveira has offered partnership in SATuRN (the Southern African Treatment and Resistance Network) with its Drug Resistance Database and associated RegaDB Clinical Management and Drug resistance Database). This is hosted by the South African Medical Research Council, removing the need for local database management and maintenance.

Bioinformatics challenges, reflection and learning. Much has been learnt in the past year but the principal challenge remains the lack of an experienced bioinformatician in Uganda to provide day-to-day advice. This will improve as trainees acquire experience, and already local networking (including amongst MUII fellows) has been beneficial. Development of strong international partnerships will also be extremely valuable.

1.3. Progress on new objective 2, supporting the development of a new department of immunology and molecular biology at Makerere University College of Health Sciences MUII partnership activities on immunology are already active between Makerere University and UVRI. In the forthcoming period our goal is to support the development of a new department of immunology and molecular biology within the College of Health Sciences (CHS). Lecturer in Immunology. To this end, the position of lecturer in Immunology was advertised by MUII and the CHS. Six applications were received, and five individuals were short-listed and four interviewed. Four of the five shortlisted were based overseas at the time and these were offered interviews by Skype. One of these did not receive the information e-mailed and so failed to attend the interview. This unfortunate mistake highlighted the need to follow up and ensure that such messages are received. Candidates were interviewed by Moses Joloba, head of the CHS department of microbiology (within which the post would be based), together with Steve Cose and Damalie Nakanjako. Of the candidates interviewed Bernard Bagaya was first choice, and was offered and accepted the position. Bernard has just completed a PhD at Case Western Reserve University on the design of vaccines against HIV and the induction of neutralising antibodies. He is the winner of the 2013 Krampitz Prize, awarded by Case Western Reserve University to the outstanding Graduate Student the year. Bernard returned to Uganda to take up the position at the beginning of November 2013.

http://www.h3abionet.org/

http://www.hivrdb.org/

http://www.shcs.ch/


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He has already submitted the proposal for creation of the department of Immunology and Molecular Biology to the University senate and it is under review by the directorate of quality assurance. Bernard is also preparing to employ a technician and is developing research funding proposals. Immunology at Makerere. MUII has continued to support the Immunology at Makerere University College of Health Sciences (CHS). With the Infectious Diseases Institute (IDI) and the department of microbiology, we established a flow cytometry core based in the MUII-funded immunology laboratory, where Damalie Nakanjako (MUII post-doctoral fellow) has done most of her flow cytometry work using the FacsCanto II. Several MUII fellows and staff have participated in training and mentoring of masters' students in MSc Immunology and Clinical Microbiology, in order to build capacity of scientists for the upcoming immunology department. Damalie has also encouraged multidiciplinary utilisation of basic immunology to improve patient care: she has had three flow cytometry projects from Internal Medicine (Immune recovery during HAART) and two projects in collaboration with Surgery-Opthalmology (Immunology of cataracts among adults aging with HIV/AIDS). Expansion of basic science laboratory space at Makerere. In conjunction with the MUII extension, CHS, together with the IDI, planned to contribute by extending the laboratory space available for immunology and related basic science, because the MUII-funded immunology laboratory, developed in 2009, had become overcrowded. Plans for space in the department of pharmacology have fallen through, but IDI is now working with the department of Obstetrics and Gynaecology (including MUII fellow Annettee Nakimuli) to develop the laboratory immediately below the current immunology laboratory, in the medical school building. This is likely to be a better option, allowing the expanding group of scientists interested in this field to keep in close touch and readily share equipment in the two laboratories. Immunology in the Tropics, our four-week, six-module course, continues to be run regularly and now recovers approximately half of its costs. During the New Year, plans are to pursue accreditation of the course at Makerere, and, or, as part of a Master’s degree programme at LSHTM. Immunology challenges, reflection and learning. There is still lack of some critical instrumentation such as a multilabel (including fluorescence) plate reader, ultraspeed centrifuge, immunofluorescent microscopes and, indeed, a cell sorter. Development of a shared Immunology core is a medium - long term objective and solution for critical instrumentation that may be expensive for single units within the CHS and Makerere University, or for UVRI.

Theme 2. A training programme with access to world-class research and training

By promoting access to world-class science and training, we aim to ensure that young African scientists are empowered to develop research proposals and conduct research that is at the cutting edge in the field. During the 2013-2016 period our key goal is to help our trainees and alumni, and our Ugandan programme staff, to progress towards leadership and independence. As well, the extended funding allowed for the recruitment of four new fellows: two fast-track PhD fellows and two post-doctoral fellows. Given the limited length of the extension, the idea of the fast-track PhD fellowships is to allow candidates at Makerere who have completed an excellent Masters project to convert this to a PhD project.


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2.1. Undergraduate internship programme The undergraduate internship programme has continued to expand in 2013. A total of 360 applications were received in 2013, with 105 placements so far, compared to 300 applications with 100 placements in 2012. Nine interns from 2013 and 10 from 2012 have been taken on in employment at UVRI. Among success stories, one former intern, Gyaviira Nkurunungi, who was subsequently employed at UVRI, won a Commonwealth Scholarship allowing him now to undertake a Masters in the Immunology of Infectious Diseases at the London School of Hygiene & Tropical Medicine. Innovations in 2012-2013 were the development of a document on general conditions for students and visiting workers at UVRI, which is provided to all interns, together with the safety code, which all interns are required to read and sign. Also, on induction day at the peak intern intake in June, students are required to take the Oath of Secrecy of the Public Health Service. This has been administered by the UVRI director, who is not a available for students taken on at other times. The UVRI training committee is pursuing arrangements such that this can be administered by other, more readily available, staff members. Induction Day evaluations were good (Box 1), and usefully indentified additional areas that had been under-represented, but would be of interest to students on future occasions – particularly administration and social science.

Box 1: Feedback on students’ induction day

The induction was educating, helpful, full of practical skills and interactive. So it improved on my capability and capacity as well as widening my knowledge base.

The Induction was fantastic, welfare was so rewarding and even a good start for progression and orientation of training at Uganda Virus Institute.

The day has been good and can be maintained for the future induction day.

All the lectures have been so good and I appreciated it except with social science was too brief i.e. not detailed enough.

To have the UVRI administration in future.

Social work students felt left out because mostly it was about science students (Laboratory) so please look into that section in future.

Internship challenges, reflections and learning. In general the programme is running well, is strongly appreciated and increasingly well-organised. It is helping to support the progression of the best alumni into employment in research-related positions. Tracking alumni has been challenging, but we hope that the improved MUII website (with facebook and twitter pages, see below) will improve this for the 2014 intake. A bad experience came with the gross misuse of printing equipment by one intern. This intern was dismissed and the University concerned was informed that he had not completed his internship satisfactorily. It has not been possible, so far, to obtain feedback from the University as to any measures that were taken. Additional measures will be taken at UVRI, for future interns, to emphasise the need for appropriate, professional conduct and respect for programme equipment.

2.2. Strategic Internships in Biomathematics Early in 2013, MUII mathematics PhD fellow, John Kitayimbwa, identified two exceptional maths students in their final year: Ronald Galiwango and Ronald Katende. These students were interested in computational biology, and expected to obtain first class degrees (which they subsequently did). In line with our goal of promoting training in bioinformatics, these two


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individuals were offered internship placements at UVRI, to experience something of biomedical research. They performed well and the MUII executive then decided to use some remaining undergraduate internship funds to support them further, and to mentor them as they prepare Masters fellowship applications. Currently they have submitted applications for appropriate Masters degree fellowships at European Universities including Cambridge, Berlin and Hasselt. Ronald Galiwango has been put forward by the Wellcome Trust for a Commonwealth fellowship. They plan to submit Masters training fellowship proposals to the Trust, with appropriate bioinformatic projects.

2.3. Fast track Masters and PhD fellows

All of the four MUII fast-track Masters fellows have completed their courses and projects, as well as the two additional Masters fellows sponsored by European Union funded consortium “The SchistoVac” and mentored within the MUII programme. Two of these six fellows (Simon Kimuda and Moses Egesa) were the successful candidates for MUII fast-track PhD fellowships (despite external competition) and are now developing their extended research proposals; they, together with Harriet Namanya, have defended their Masters theses and submitted corrections, and are awaiting the final response from the examiners. Justine Bukirwa is making corrections to her thesis following her defence. Two other Masters fellows are facing significant challenges regarding completion. In one case, this is because the School of Public Health has delayed the thesis defence for all students in the current cohort for administrative reasons relating to the appointment of external examiners. In the other case, for a degree in Molecular Biology and Biotechnology, the fellow has travelled to Belgium for further post-graduate training, but reports that he is awaiting feedback from his supervisors before he can submit his Makerere Masters dissertation. In terms of career progression, two fellows have gone on to the MUII PhD programme and one to a further Masters programme (as mentioned above). One has obtained a contract with a project at the School of Public Health. Two are seeking further employment or training. Masters fellows, challenges, reflections and learning. Disappointing administrative and supervision delays remain challenging hurdles for post-graduate students at Makerere.

2.4. Current PhD fellows MUII has fully supported four PhD fellows as well as providing peer support and mentorship for one PhD fellow sponsored by the European Union funded consortium, IDEA. Three of the MUII fellows (Annettee Nakimuli, John Kitayimbwa and Agnes Kiragga) are close to completion and Annettee plans to submit her thesis during the week of 16th December. The fourth, Irene Biraro, was given an extension because of maternity leave and illness and she expects to submit her thesis by June 2014. The IDEA fellow, Andrew Obuku, has one more year to go. Annettee Nakimuli has been awarded a MUII post-doctoral fellowship and expects to take this up in January 2014. John and Agnes are currently seeking post-doctoral funding. Some bridging funding will be available for John, Agnes and Irene from the MUII 2013-16 budget. PhD fellows, challenges, reflections and learning. All the PhD fellows are substantially behind schedule. Contributing factors include the Makerere change in policy regarding publications which was introduced about two years after the MUII fellows commenced their programme. There has been lack of clarity on this policy but, in essence, it has been taken to mean that two papers must be published before the thesis can be submitted. This has delayed fellows who had aimed to produce a monograph and to work on publications at the end of their programme. Another


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contributing factor has been that none of the fellows has focussed entirely on their PhD, despite the expectation that they would do so. Full focus may be difficult to achieve for older PhD fellows who are already in employment and have major family commitments. Time away for writing up, for example at the external partner institution, should be considered s a possible requirement in the planning of such PhD programmes.

2.5. Current and past post-doctoral fellows The two original post-doctoral fellows, Jonathan Kayondo and Robert Tweyongere, have completed their fellowships and are continuing as researchers based at UVRI and Makerere, Jonathan with funding from the Wellcome Trust through THRiVE and H3ABionet, with funding also from EDCTP and TWAS; Robert with funding from the European Foundations Initiative for Neglected Tropical Diseases. The three current post-doctoral fellows, Harriet Mpairwe, Deo Ssemwanga and Damalie Nakanjako are close to completion of their fellowships. All have achieved additional funding: Harriet and Deo won MRC Centenary Awards while Damalie won a Canadian Grand Challenges rising star award as well as additional funding from the Centers for AIDS Research (CFAR; an International Mentored Science Award) and from the University of California Global Health Institute (UCGHI; a GloCal Health Fellowship). Harriet Mpairwe has won a Wellcome Trust Research Training Fellowship in Public Health and Tropical Medicine which will allow her to conduct a case control study on risk factors for asthma in Uganda. Deo plans to apply for a Wellcome Research Training Fellowship in the next round. Post-doctoral fellows, challenges, reflections and learning. The fellows have been successful in achieving recognition for their work, and further funding, but the latter remains a major challenge as options for funding are few and highly competitive.

2.6. New PhD and post-doctoral fellowships, 2013-2016

The new fellowships were advertised in June 2013 for a single step application process (given the limited time available), based on procedures developed for previous rounds, and with a deadline at the end of July. Short-listed candidates were interviewed by a panel composed as set out by our Advisory Board, chaired by Professor Akiiki. Ten applications for fast-track PhD fellowships and five applications for post-doctoral fellowships were received. Six PhD candidates and four post-doctoral fellowship candidates were short-listed and their applications were sent for expert review. All short-listed candidates were offered the opportunity to practice for the interview with senior scientific staff of the MUII executive (as part of the training and mentorship process; these staff did not participate in the subsequent selection process). The following candidates were successful, and accepted the fellowship offers: Simon Kimuda. MUII fast-track Masters fellow, for a fast track PhD fellowship on the effects of Mycobacterium tuberculosis infection and disease on antibody responses. Moses Egesa. The SchistoVac Masters fellow, for a fast-track PhD fellowship on immune responses to larval stage antigens of Schistosoma mansoni. Annettee Nakimuli. MUII PhD fellow, for a post-doctoral fellowship taking forward her work on KIR genes in pre-eclampsia. Maggie Nampijja. A clinician with a PhD in developmental psychology, for post-doctoral studies on the effects of Schistosoma mansoni and its treatment on cognitive function in young children.


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2.7. Progress on new objective 3, supporting the best trainees from current schemes to

advance their careers and to progress towards leadership and independence in research and capacity building We have taken steps towards this goal by encouraging our trainees and alumni, and our Ugandan programme staff, to undertake positions of responsibility in the programme, with support and mentorship from senior staff. Barbara Nerima (the post-doctoral scientists who was employed in 2011 as deputy coordinator) has been appointed chair of the MUII executive committee and of the regular fellows meetings, and she is leading in the monitoring and evaluation of the programme. She has also taken a key role in several events and processes including the interns’ selection, induction day and competition, and in the MUII science symposium. She is working with John Kitayimbwa to arrange the R programming workshop to be held in December. Representatives of the fellows at different stages of their careers have also been appointed to the executive committee (Doreen Tuhebwe, Masters fellows; Annettee Nakimuli, PhD fellows; Deo Ssemwanga, post-doctoral fellows). The Makerere-UVRI Open Day was chaired by Jonathan Kayondo, post-doctoral fellowship alumnus. A Bioinformatics and Computational Biology sub-committee has been formed comprising Deo Ssemwanga, together with Jonathan Kayondo, John Kitayimbwa and Barbara Nerima, driving the development of the BCB curriculum and training. Deo will lead the Uganda “Bioinformatics in the Tropics” workshop in April 2014 with support from Tulio d’Oliveira, as well as from local senior staff. Barbara will lead the microarray workshop planned for May 2014. The interview panel for new PhD and post-doctoral fellows included two current post-doctoral fellows, Deo Ssemwanga and Damalie Nakanjako, to give them experience of the “other side” of decision making on funding proposals. In addition to these mentored responsibilities, we are developing a curriculum of leadership training workshops, which will be tailored to the fellows’ needs.

2.8. Special achievements

In addition to the achievements described above, our fellows and staff have now contributed to over 30 presentations at international conferences and to over 50 publications (Appendices 2 and 3). They are contributing to capacity building by mentoring more junior MUII fellows, as well as Masters and PhD students of their own, and by their increasing contribution to running this programme. As discussed in the January 2013 report, they have established and fostered important international collaborations as well as developing collaborations within and between Makerere and UVRI, and between themselves. Their key research findings will be presented at the forthcoming Advisory Board meeting. Fellows and programme staff have contributed to raising further research capacity building and research funding. To date a total of over £2,400,000 has been raised for capacity building and over £1,700,000 for research (appendix 4). Special congratulations go to Damalie Nakanjako who received the 2013 Merle A. Sande Health Leadership Award recognising “African Leaders in Infectious Disease Research, Teaching, and


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Clinical Science”. Also, she has been promoted to Associate Professor in the Makerere College of Health Sciences. Congratulations, too, to Harriet Mpairwe who achieved recognition at the European Academy for Allergy and Clinical Immunology meeting in Milan in June 2013, where her abstract on the effects of prenatal exposure to hookworm on eczema in pre-school children was selected as among the best 10 from over 2000 presented at the meeting. Also to Simon Kimuda, Peter Naniima and Doreen Tuhebwe who achieved first class grade point averages in the taught components of their Masters degrees.

2.9. Mentorship

A mentorship and peer support day was organised on 4th October 2013. Senior staff of the programme (Alison Elliott, Steve Cose and Barbara Nerima) contributed and had mentor meetings with the post-doctoral fellows. The post-doctoral fellows then paired with the senior staff and with each other to hold meetings with more junior members of the team. The day was evaluated and appreciation was expressed by the fellows. They liked the format and felt that having a variety of mentors available was good. The main limitation was time: at least an hour was needed for each fellow, and it was not possible to keep to the schedule that had been planned for theday.. Formal training in mentorship and supervision is expected to form part of the professional development curriculum to be developed during 2014.

2.10. Golden Opportunities

Some funding remained in the fellowship budget of 2008-2013, so PhD and post-doctoral fellows, and members of the executive, were offered “Golden Opportunity” Awards. A written application was required and the application was reviewed and approved by members of the executive (not including the person concerned, if applicable). Awards made to date, and achievements, are listed in Table 3.

Table 3. Achievements and plans for Golden Opportunity Awards

Fellow Designation Approximate date of activities Activities for which funds were/ will be used

Agnes Kiragga PhD fellow September 2013 1. A short course on systematic review and meta-analysis at the LSHTM (September 2013) 2. Attended a short course on grants writing 3. Carry out a pilot study on tracing patients who are lost to follow-up in Kiboga district.

Harriet Mpairwe Post-doctoral fellow October 2013 A trip to Cambridge to discuss plans for her Wellcome Trust training fellowship proposal, which was successful

Damalie Nakanjako Post-doctoral fellow October 2013 Consumables and bench fees Jonathan Kayondo Post-doctoral fellow October 2013 Consumables Irene Biraro PhD fellow October 2013 Consumables

Robert Tweyongyere Post-doctoral fellow November 2013 Attended the meeting of the American Society for Tropical Medicine and presented the work on eosinophils that had been undertaken as part of the MUII fellowship

Steve Cose Senior Immunologist December 2013

1. Attended 2013 British Society for Immunology in Liverpool 2. Made contact with a B-cell immunologist with a view to begin a new collaboration 3. Many good sessions, learnt quite a lot, particularly on innate function of the immune

system - the focus of the meeting this year. Also interesting ideas to put towards granuloma biology for TB. These would be incorporated into new applications to continue the post mortem study.

4. Attended Patrice Mawa’s PhD upgrading at LSHTM - I am a co-supervisor. He passed his upgrading and is now officially a PhD student.

Moses Kizza Administrator December 2013 1. Attended a one-week training for managers in London by Reed Learning. 2. Visited fellow administrators at the LSHTM

Barbara Nerima Deputy coordinator January 2014 Planning to visit VGTI Florida to learn about analysing microarrays

Deo Ssemwanga Post-doctoral fellow January 2014 Planning to visit the Wellcome Trust Sanger Institute and the University of Edinburgh to work on data analyses

John Kitayimbwa PhD fellow January 2014 Planning to visit the Wellcome Trust Sanger Institute and the University of Oxford to work on analyses of the genetics of the infant immune response to vaccines


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Theme 3. A supportive, sustainable and up-to-date research and training environment

By providing a supportive, sustainable and up-to-date training environment, we aim to facilitate the work of Makerere University and UVRI in attracting bright young Ugandans to research, and supporting their career development.

3.1. General progress

MUII has contributed to several elements of research infrastructure including the Makerere Immunology laboratory (discussed above), the e-library at UVRI, video-conferencing facilities at UVRI, Makerere Department of Microbiology, and Makerere College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB). MUII has also contributed to the construction of the new resource building at UVRI which is being co-funded by the MRC, UK. These activities are described in the January 2013 report. MUII also seeks to provide good administrative facilitation to fellows and for training and outreach activities. As part of the MUII 2013-2016 extension we have been able to take on an additional administrator, Martha Nakiganda, to work with Moses Kizza and Godfrey Mukalazi (the financial officer). Martha has particularly assisted in work on the resource building, in developing the MUII website and on video-conferencing. The improved website can be viewed at www.muii.org.ug. It features additional content on planned and current courses, as well as relevant application forms and news about past events. It also links to facebook and twitter pages, which we hope will improve outreach and feedback through social networking. Throughout the programme, efforts have been made to evaluate the activities undertaken and to learn from the experience we have gained. To help us with this, and to help us with planning for the future, we have engaged a consultant, Dr Tom Barton. We have held two useful workshops with him – one in preparation for the Wellcome Trust review visit, and one at the start of the 2013-2016 extension. We are in the process of developing an evaluation framework with him. Challenges, learning and reflection. Challenges for use of the UVRI library by staff, students and visitors have resulted from its being regularly occupied for meetings. This should be mitigated by the opening of the new building. However, the computer and wireless access have also, already, made the library a useful facility for courses such as Genetic Epidemiology, statistical workshops, the Uganda Intensive Course in Statistics and Epidemiology (held in November 2013), and the R programming workshop scheduled for December 17th and 18th 2013. The use of the video-conference facility at UVRI has commenced, with some extremely successful meetings with Cambridge and with LSHTM – for example, for the interviews for new MUII fellows. Optimising the use of available bandwidth at UVRI is critical and can cause some inconvenience to other internet users. However, regular communication with colleagues that were equipped for video-conferencing at the Makerere CHS and at COVAB has not yet been established. This will be a key goal in the New Year but internet bandwidth is expected to be a challenge at these sites also. Limited internet bandwidth is also expected to be an important constraint in bioinformatic work. However, the Research and Education Network of Uganda (RENU) is working to provide a high capacity internet service to institutes for higher education and research. UVRI and Makerere are participants, and expect to benefit with marked improvements in internet speed in the next year or two.



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3.2. Progress on new objective 4, extending the development of UVRI as a regional centre for I&I research training The specific contribution to this objective expected from MUII 2013-2016 is to complete the research training building at UVRI and to develop the facilities to be provided there – a core flow cytometry laboratory, a teaching laboratory and a bioinformatics facility. Currently civil works are nearly complete after prolonged challenges with the main contractor involving delays and poor workmanship on the finishes. This contractor has now left and other contractors will be employed to complete the finishes. However, progress has been made in parallel on purchasing required furnishings and the United States Centers for Disease Control has contributed equipment for the teaching laboratory which will contribute to the development of the Ugandan Centre for Integrated Laboratory Training. As noted above, a funding application has been submitted to MRC for a bioinformatics resource centre that would be housed in the building, greatly strengthening this aspect of the work.


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APPENDIX 1. PROGRESS ON KEY DELIVERABLES.

Achievements Achievements Deliverables Objectives 2008-2010 2011-12 2013-15 Theme 1. Academic partnership between Uganda Virus Research Institute & Makerere University Shared supervision and teaching In progress In progress In progress Makerere students study at UVRI In progress In progress In progress UVRI staff study at Makerere In progress In progress In progress Joint seminars and workshops In progress In progress In progress Symposia Two held Two held 1 to be held Open Days 1 held 1 held Event for science teachers 1 held New aim 1 BCB travel fellowships 8 trips to be taken New aim 1 Bioinformatics course 3 courses to be conducted New aim 1 Databases To be set up and in use Senior Immunologist Appointed and in post In post Mentoring lecturer for leadership New aim 2 Immunology lecturer at Makerere To be appointed and in post

New aim 2 Immunology laboratory at Makerere Renovated, equipped and in use In use Expansion by College of Health Sciences/ Infectious Diseases Inst

Immunology course Initiated 2009; 2 courses per year 2 courses per year 2 courses per year Theme 2. UVRI-Makerere training programme, with access to world-class science and training

Undergraduate internships Over 60 in 2008, 98 in 2009, over 100 in 2010 80-100 per year 80-100 per year

Fast-track Masters fellows 4 appointed, plus 2 EU funded; completion pending Upgrade best to PhD

New aim 3 Fast-track PhD fellowships Appoint & complete 2

PhD fellowships 4 appointed, preliminary results available

1 EU funded PhD fellow added; 4 completion pending

Hub support for PhD fellows funded by others

New aim 3 Post-PhD bridging year fellowships 4 one-year writing grants awarded and completed

Post-doctoral training fellowships 2 appointed 3 appointed; completion Appoint & complete 2

Supervision and mentorship Guidelines developed, a supervision workshop held One-one mentorship on-going Supervision training for fellows;

formalised mentorship scheme

Fellows achieve independent funding 4 additional grants or funding awarded 7 additional grants awarded Mentor to obtain independent

funding


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Theme 3. Infrastructure and administration

High speed internet and video-conferencing Facilities in place In use for MUII and other activities

UVRI library renovated and equipped for internet and e-library Renovated, equipped and in use In use for MUII and other activities

Research training resource building Building in progress In use for MUII and other activities New aim 4 Core flow-cytometry facility Development in progress In use for MUII and other activities New aim 4 Core bioinformatics resources centre Developed and in use

New aim 4 Deputy PI mentored to participate in research capacity building Appointed and mentored Contributing to future proposal

design and writing Research training administrator Appointed In post

MUII website Set up and in use In use Upgraded to serve both BCB and immunology hubs

Grey shaded areas indicate that activities do not apply to the period indicated

Blue shaded areas indicate activities that are new to the extended funding period


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APPENDIX 2. FELLOWS’ PRESENTATIONS AT LOCAL AND INTERNATIONAL CONFERENCES Jonathan Kayondo 1. Kayondo JK. Mbidde EK, Grosskurth H and Kaleebu P. Uganda Virus Research Institute (UVRI), EDCTP,

IANPHI and MRC (UK): A successful example of capacity development through an international Partnership. Poster Number: CE 05. The 5th EDCTP forum, Arusha, Tanzania, October 2009. Poster presentation.

2. Kayondo JK, Ndembi N, Cane PA, Kityo C, Chirara M, Hué S, Goodall R, Dunn D, Kaleebu P, Pillay D and Mbisa JL on behalf of the DART Virology Committee. Evolution of resistance rncovered by single-genome sequencing (SGS) during continuous or interrupted antiretroviral therapy . Abstract/Poster Number: 113. The International HIV & Hepatitis Drug Resistance Workshop meet in Croatia, June 2010. Poster presentation.

Simon Kimuda 3. Simon Kimuda, Irene Andia-Biraro, Jonathan Levin, Angela Nalwoga, Alison Elliott and Stephen Cose.

Effect of Mycobacterium tuberculosis Infection on Levels of Antibodies to Tetanus Toxoid. Oral presentation at the Makerere/UVRI Infection and Immunity Research Training Programme Science Symposium, UVRI, Entebbe, 7th November 2013 .

Agnes Kiragga 4. Kiragga A, Castelnuovo B, Mambule I, Kambugu A, Manabe Y. Clinical and immunological outcomes of

patients on Second Line treatment delivered in a routine clinical setting in Uganda.. MOPEB068- International AIDS Society-2009, CapeTown, South Africa.

5. Kiragga AN, Castelnuovo B, Kamya MR, Moore R, Manabe YC. WHO Immunologic criteria are more predictive of treatment failure in patients from a Western Cohort compared to a cohort in Resource Limited Settings. Poster No.115, International Workshop of HIV Observational Databases, March 2010, Barcelona, Spain

6. Kiragga AN, Castelnuovo B, Sempa JB, Manabe YC. Trends and frequency of CD4+ cell count among patients on ART in a large HIV observational database in resource limited settings. International Workshop of HIV Observational Databases, March 2011, Prague, Czech Republic

7. Kiragga AN, Musick B, Bosch R, Mwangi A, Yiannoutsos CT. CD4 trajectory among HIV positive patients receiving HAART in a large East African HIV care centre. International Workshop of HIV Observational Databases, March 2012, Athens, Greece

John Kitayimbwa 8. Kitayimbwa JM, Mugisha JYT, Saenz RA. Within-host dynamics of HIV during structured treatment

interruptions. Abstract Number: P2.62. Epidemics3 conference in Boston, USA 9. Kitayimbwa JM, Mugisha JYT, Saenz RA. The role of backward mutations on the within-host dynamics

of HIV. 10th Anniversary of the Eastern Africa Universities Mathematics Programme Conference, Arusha, Tanzania, 22nd- 25th of August.

Harriet Mpairwe 10. Harriet Mpairwe, Emily L. Webb, Lawrence Muhangi, Juliet Ndibazza, Denise Akishule, Margaret

Nampijja, Sophy Ngom-wegi, Josephine Tumusime, Frances M. Jones, Colin Fitzsimmons, David W. Dunne, Moses Muwanga, Laura C. Rodrigues, Alison M. Elliott. Impact of maternal helminth infections on childhood allergy-related conditions in Uganda. Oral presentation at the first East African DTM&H academic open day; 6th October 2012 at Kilimanjaro Christian Medical Centre, Moshi, Tanzania.

11. Harriet Mpairwe, Emily L. Webb, Lawrence Muhangi, Juliet Ndibazza, Denise Akishule, Margaret Nampijja, Sophy Ngom-wegi, Josephine Tumusime, Frances M. Jones, Colin Fitzsimmons, David W. Dunne, Moses Muwanga, Laura C. Rodrigues, Alison M. Elliott. Impact of maternal helminth infections on childhood allergy-related conditions in Uganda. Oral presentation at the first annual conference for the Uganda Thoracic society; 14th November 2012 in Kampala, Uganda.

12. Harriet Mpairwe, Ndibazza Juliet, Emily L. Webb, Lawrence Muhangi, Swaibu Lule, Barbra Apule, Alison M. Elliott. Exposure to hookworm prenatally and to worm infections in early childhood is inversely


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associated with eczema in childhood: results from a birth cohort in Uganda. Oral presentation at the Uganda Society of Health Scientists Conference; 29-30 May 2013 in Kampala, Uganda.

13. Harriet Mpairwe, Ndibazza Juliet, Emily L. Webb, Lawrence Muhangi, Swaibu Lule, Barbra Apule, Alison M. Elliott. Exposure to hookworm prenatally and to worm infections in early childhood is inversely associated with eczema in childhood: results from a birth cohort in Uganda. Oral presentation at the European Academy of Allergy and Clinical Immunology-World Allergy Organization (EAACI-WAO) Congress; 21-26th July 2013 in Milan, Italy.

Damalie Nakanjako 14. Nakanjako Damalie, Otiti-Sengeri Juliet , Ssewanyana Isaac, Nabatanzi Rose , Bayigga Lois, Colebunders

Robert , Mayanja-Kizza Harriet High immune activation and immune senescence are associated with early development of cataracts among HIV-infected adults in Uganda, Poster presentation at the 2013 Keystone meeting on immune Activation in HIV Infection: Basic Mechanisms and Clinical Implications (D2), April 3 - April 8, 2013 at Beaver Run Resort • Breckenridge, Colorado USA

15. Nakanjako Damalie, Agnes Kiragga, Beverly Musick, ConstantinYiannoutsos, Andrew Kambugu, Philippa Easterbrook. Increased opportunistic infections among suboptimal immune responders to first-line HAART within the IeDEA-East Africa cohorts. Oral presentation at 7TH IAS Conference on HIV Pathogenesis, Treatment and Prevention 30 June– 3 July 2013; Kuala Lumpur, Malaysia

16. Mugasha Christine, Kigozi Joanita, Muganzi Alex, Kiragga Agnes, Sewankambo Nelson, Coutinho Alex, Nakanjako Damalie Intra-Facility linkage of HIV-positive mothers and exposed infants into HIV chronic care: Rural and urban experience in a resource limited setting. Poster presentation at 7TH IAS Conference on HIV Pathogenesis, Treatment and Prevention; 30 June– 3 July 2013 Kuala Lumpur, Malaysia

17. Elyanu J. P., Nakanjako D., Shellack C.J., Damba D., Namagala E., Kiyaga C., Kekitiinwa A., Mawani N., Sewankambo N. Gaps in linkage to antiretroviral therapy among HIV-infected infants and children in Uganda. Poster presentation at 7TH IAS Conference on HIV Pathogenesis, Treatment and Prevention; 30 June– 3 July 2013 Kuala Lumpur, Malaysia

18. Nakanjako Damalie, Rose Nabatanzi, Lois Bayigga, Olive Mbabazi, Lincoln Pac, Stephani Sowinski, Yukari Manabe, Harriet Mayanja-Kizza, Warner Greene Role of regulatory T-cell dysfunction in immune recovery in a Ugandan rural HIV treatment cohort. Oral presentation at the Annual Fogarty Global Health fellows meeting; 8 July -12 July 2013 at the National Institute of Health, Bethesda, Maryland, USA.

Annettee Nakimuli 19. Nakimuli A. Maternal Mortality in Africa: Experiences of a Ugandan Obstetrician . Conference on New

Approaches to Maternal Mortality in Africa conference in Cambridge, 2nd – 3rdJuly 2012. Invited speaker.

20. Nakimuli A. Presentation on preliminary findings of my research project. 16th International HLA and Immunogenetics workshop in Liverpool, 28th-30th May 2012.

21. Nalimuli A. A presentation about my experience as a PhD student in a capacity building training grant at a symposium organised by the Wellcome Trust. The Annual General Meeting of the American Society of Tropical Medicine and Hygiene (ASTMH) at Philadelphia, USA, December 2011. Oral presentation.

22. Nakimuli A. A presentation on measures useful in prevention and management of post partum haemorrhage. Annual Scientific Conference for the Association of Obstetricians and Gynaecologists of Uganda, August 2010.

Margaret Nampijja 23. Margaret Nampijja, Kizindo R., Lule S., Apule B., Akurut H., Muhangi L., Alcock K.J., Elliott A.M.

Associations between the home environment and cognitive performance of rural and semi-urban Ugandan children. Oral presentation at the Eastern African Regional Conference on Psychology; 6-8th November 2013 at Silver Springs Hotel, Kampala.

Deogratius Ssemwanga 24. Deogratius Ssemwanga, Andrew D. Redd, Sarah K. Wendel, Nicaise Ndembi, Judith Vandepitte, Heiner

Grosskurth, Chris M. Parry, Craig Martens, Daniel Bruno, Stephen F. Porcella, Thomas C. Quinn, Pontiano Kaleebu. Incidence of HIV-1 Superinfection is Similar to Primary HIV-1 Inc idence in a Cohort of Female Sex Workers in Uganda. 18th International BioInformatics Workshop on Virus Evolution and


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Molecular Epidemiology August 25th - August 30th, 2013, University of Florida, Emerging Pathogens Institute Gainesville, Florida, USA. Poster presentation.

25. Andrew D. Redd, Deogratius Ssemwanga, Sarah K. Wendel, Nicaise Ndembi, Judith Vandepitte, Heiner Grosskurth, Chris M. Parry, Craig Martens, Daniel Bruno, Stephen F. Porcella, Thomas C. Quinn, Pontiano Kaleebu. Incidence of HIV-1 Superinfection is Similar to Primary HIV-1 Incidence in a Cohort of Female Sex Workers in Uganda. AIDS Vaccine 2013, 7 – 10 October 2013, Barcelona, Spain. Poster No. P05.06.

26. Deogratius Ssemwanga, Andrew D. Redd, Sarah K. Wendel, Yunia Mayanja, Nicaise Ndembi, Judith Vandepitte, Heiner Grosskurth, Chris M. Parry, Jonathan Levin, Craig Martens, Daniel Bruno, Stephen F. Porcella, Thomas C. Quinn, Pontiano Kaleebu.HIV-1 superinfection and disease progression in a cohort of female sex workers in Uganda. Seventh EDCTP Forum, 21st – 24th October 2013 Dakar, Senegal. Oral presentation.

27. Ssemwanga D, Lyagoba F, Ndembi N, Vanderpaal L, Grosskurth H, Williamson C, Kaleebu P. HIV-1 Mixed Infections, Viral Recombination and Disease Progression in Sexual Partners in a Rural Clinical Cohort in Uganda. 15th International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology at Erasmus Medical Center, Rotterdam The Netherlands. 7th-11th September 2009. Poster presentation.

28. Ssemwanga D, Nicaise N, Lyagoba F, Bukenya J, Seeley J, Vandepitte J, Grosskurth H, Kaleebu P. HIV-1 Subtype Distribution, Multiple Infections, Sexual Networks And Partnership Histories In Female Sex Workers In Kampala, Uganda. Sixth EDCTP Forum Addis Ababa Ethiopia 9th -12th October 2011. Oral Presentation.

Doreen Tuhebwe 29. Tuhebwe D, Elizabeth Ekirapa Kiracho, Adoke Yeka. Factors associated with uptake of Mass Drug

Administration for Schistosomiasis Control in Koome Island, Central Uganda at the 2013 62nd ASTMH meeting in Washington Dc, United States of America. Late Breaker 2099. Poster presentation.

30. Tuhebwe D, Tumushabe E, Leontsini E, Wanyenze RK. Pneumonia among children under five in Uganda: symptom recognition and actions taken by caretakers. AFENET 5th Scientific Conference 2013, Addis Ababa Ethiopia. Theme; Towards and Beyond MDGs. Oral presentation.

31. Tuhebwe D, Elizabeth Ekirapa Kiracho, Adoke Yeka. Factors associated with uptake of Mass Drug Administration for Schistosomiasis Control in Koome Island, Central Uganda. AFENET 5th Scientific Conference, Addis Ababa, Ethiopia. Oral Poster presentation.

32. Tuhebwe D, Tumushabe E, Leontsini E, Wanyenze RK. Pneumonia among children under five in Uganda: symptom recognition and actions taken by caretakers. 2013 Makerere University Joint Annual Scientific Conference at Silver Springs Hotel, Kampala. Abstract No.P06-02 .Oral Presentation

33. Tuhebwe D. Perceived quality of postnatal care among women of reproductive age in Mukono. Global Maternal Health Conference, Arusha, Tanzania, January 2013. Oral presentation.

Robert Tweyongyere 34. Tweyongyere R. Effect of Schistosoma mansoni infection and praziquantel treatment during pregnancy

on immune offspring of affected women. African International conference on immunity (AICI) Victoria Falls, Zimbabwe. Oral and Poster presentation.


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APPENDIX 3. PROGRAMME PUBLICATIONS 1. Sempa JB, Kiragga AN, Castelnuovo B, Kamya MR, Manabe YC. Among patients with sustained viral

suppression in a resource-limited setting, CD4 gains are continuous although gender-based differences occur. PLoS One. 2013 Aug 27;8(8):e73190.

2. Muwanga AN, Katabira E, Kiragga A, Kambugu A, Lubwama EN, Manabe Y, Alamo S, Colebunders R. Factors before enrolment are associated with being removed from a Pharmacy-only Refill Program at a large urban HIV/AIDS clinic, Uganda. Int J STD AIDS. 2013 Jul 19. [Epub ahead of print]

3. Nakanjako D, Ssewanyana I, Nabatanzi R, Kiragga A, Kamya MR, Cao H, Mayanja-Kizza H. Impaired T-cell proliferation among HAART-treated adults with suboptimal CD4 recovery in an African cohort. BMC Immunol. 2013 Jun 20;14:26.

4. Hermans SM, Manabe YC, Kiragga AN, Hoepelman AI, Lange JM, van Leth F. Risk of tuberculosis after antiretroviral treatment initiation: a comparison between efavirenz and nevirapine using inverse probability weighting. Antivir Ther. 2013;18(4):615-22.

5. Castelnuovo B, Kiragga A, Afayo V, Ncube M, Orama R, Magero S, Okwi P, Manabe YC, Kambugu A. Implementation of provider-based electronic medical records and improvement of the quality of data in a large HIV program in Sub-Saharan Africa. PLoS One. 2012;7(12):e51631.

6. Hermans SM, van Leth F, Kiragga AN, Hoepelman AI, Lange JM, Manabe YC. Unrecognised tuberculosis at antiretroviral therapy initiation is associated with lower CD4+ T cell recovery. Trop Med Int Health. 2012 Nov 6. doi: 10.1111/tmi.12001. [Epub ahead of print]

7. Kiragga AN, Castelnuovo B, Kamya MR, Moore R, Manabe YC. Regional differences in predictive accuracy of WHO immunologic failure criteria. AIDS. 2012 Mar 27;26 (6):768-70.

8. Abouyannis M, Menten J, Kiragga A, Lynen L, Robertson G, Castelnuovo B, Manabe YC, Reynolds SJ, Roberts L. Development and validation of systems for rational use of viral load testing in adults receiving first-line ART in sub-Saharan Africa. AIDS. 2011 Aug 24;25 (13):1627-35.

9. Wandera B, Kamya MR, Castelnuovo B, Kiragga A, Kambugu A, Wanyama JN, Easterbrook P, Sethi AK. Sexual behaviors over a 3-year period among individuals with advanced HIV/AIDS receiving antiretroviral therapy in an urban HIV clinic in Kampala, Uganda. J Acquir Immune Defic Syndr. 2011 May; 57(1):62-8.

10. Castelnuovo B, Sempa J, Kiragga AN, Kamya MR, Manabe YC. Evaluation of WHO criteria for Viral Failure on patients on Antiretroviral Treatment in Resource-Limited Settings. AIDS Res Treat. 2011; 2011:736938. Epub 2011 Apr 10.

11. Babigumira JB, Castelnuovo B, Stergachis A, Kiragga A, Shaefer P, Lamorde M, Kambugu A, Muwanga A, Garrison LP. Cost effectiveness of a pharmacy-only refill program in a large urban HIV/AIDS clinic in Uganda. PLoS One. 2011 Mar 28;6(3):e18193.

12. Nakanjako D, Kiragga AN, Castelnuovo B, Kyabayinze DJ, Kamya MR. Low prevalence of Plasmodium falciparum antigenaemia among asymptomatic HAART – treated adults in an urban cohort in Uganda. Malar J. 2011 Mar 22;10:66.

13. Nakanjako D, Ssewanyana I, Mayanja-Kizza H, Kiragga A, Colebunders R, Manabe YC, Nabatanzi R, Kamya MR, Cao H. High T-cell immune activation and immune exhaustion among individuals with suboptimal CD4 recovery after 4 years of antiretroviral therapy in an African cohort. BMC Infect Dis. 2011 Feb 8;11:43.

14. Kiragga AN, Castelnuovo B, Schaefer P, Muwonge T, Easterbrook PJ. Quality of data collection in a large HIV observational clinic database in sub-Saharan Africa: implications for clinical research and audit of care. J Int AIDS Soc. 2011 Jan 20;14:3.

15. Castelnuovo B, Kiragga A, Kamya MR, Manabe Y. Stavudine toxicity in women is the main reason for treatment change in a 3-year prospective cohort of adult patients started on first-line antiretroviral treatment in Uganda. J Acquir Immune Defic Syndr. 2011 Jan; 56(1):59-63.

16. Kiragga AN, Castelnuovo B, Nakanjako D, Manabe YC. Baseline severe anaemia should not preclude use of zidovudine in antiretroviral-eligible patients in resource-limited settings. J Int AIDS Soc. 2010 Nov 3; 13:42.

17. von Dadelszen P, Payne B, Li J, Ansermino JM, Broughton Pipkin F, Côté AM, Douglas MJ, Gruslin A, Hutcheon JA, Joseph KS, Kyle PM, Lee T, Loughna P, Menzies JM, Merialdi M, Millman AL, Moore MP,


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Moutquin JM, Ouellet AB, Smith GN, Walker JJ, Walley KR, Walters BN, Widmer M, Lee SK, Russell JA, Magee LA; Preeclampsia Integrated Estimate of RiSk (PIERS) Study Group Study Group. Prediction of adverse maternal outcomes in pre-eclampsia: development and validation of the full PIERS model. Lancet. 2011 Jan 15;377(9761):219-27. Epub 2010 Dec 23. PMID: 21185591

18. Nakimuli A, Chazara O, Farrell L, Hiby SE, Tukwasibwe S, Elliott AM, Kaleebu P, Moffett A, Mirembe F. Hypertension persisting after pre-eclampsia: A prospective cohort study at Mulago Hospital, Uganda. PLoS One, in press.

19. Nakimuli A, Chazara O, Byamugisha J, Elliott AM, Kaleebu P, Mirembe F, Moffett A. Pregnancy, parturition and preeclampsia in women of African ancestry. Am J Obstet Gynecol. 2013 Oct 30. doi:pii: S0002-9378(13)01989-3.

20. Nakimuli A, Chazara O, Farrell L, Hiby SE, Tukwasibwe S, Knee J, Jayaraman J, Traherne JA, Elliott AM, Kaleebu P, Mirembe F, Moffett A (2013). Killer cell immunoglobulin-like receptor (KIR) genes and their HLA-C ligands in a Ugandan population. Immunogenetics 2013 Nov;65(11):765-75.

21. Busingye P, Nakimuli A, Nabunya E, Mutyaba T. Acceptability of cervical cancer screening via visual inspection with acetic acid or Lugol’s iodine at Mulago Hospital,Uganda. International Journal of Gynecology and Obstetrics 2012, Dec: 119(3): 262-265.

22. Atuhairwe S, Busingye RB, Sekikubo M, Nakimuli A, Mutyaba T. Urologic complications among women with advanced cervical cancer at a tertiary referral hospital in Uganda. Int J Gynaecol Obstet. 2011 Dec;115(3):282-4. Epub 2011 Sep 19. PMID: 21937039

23. Kozic JR, Benton SJ, Hutcheon JA, Payne BA, Magee LA, von Dadelszen P; PIERS Study Group. Abnormal liver function tests as predictors of adverse maternal outcomes in women with preeclampsia. J Obstet Gynaecol Can. 2011 Oct;33(10):995-1004. PMID: 22014776

24. Payne B, Hutcheon JA, Qu Z, Haniff F, Bhutta Z, Biryabarema C, Duan T, Hall DR, Grobman WA, Groen H , Magee LA, Merialdi M, Mirembe F, Nakimuli A, Qureshi R, Sass N, Sikandar R, Steyn W, Widmer M, Zhou V, von Dadelszen P, PIERS Study Group. OS037. Minipiers (pre-eclampsia integrated estimate of risk): Development of a clinical prediction model for use in low and middle income countries (LMIC). Journal of Pregnancy Hypertension. Volume 2, Issue 3 , Pages 195-196, July 2012

25. Busingye P, Nakimuli A, Nabunya E, Mutyaba T. Acceptability of cervical cancer screening via visual inspection with acetic acid or Lugol’s iodine at Mulago Hospital, Uganda. Int J Gynecol Obstet (2012), http://dx.doi.org/10.1016/j.ijgo.2012.06.015 (article in press)

26. Kitayimbwa J, Mugisha JYT, Saenz RA. The role of backward mutations on the within-host dynamics of HIV-1. Journal of Mathematical Biology 2013 Nov;67(5):1111-39.

27. Kizito D, Tweyongyere R, Namatovu A, Webb EL, Muhangi L, Lule SA, Bukenya H, Cose S, Elliott AM. Factors affecting the infant antibody response to measles immunisation in Entebbe-Uganda. BMC Public Health. 2013,13(1):619.

28. Tweyongyere R, Naniima P, Mawa PA, Jones FM, Webb EL, Cose S, Dunne DW, Elliott AM. Effect of maternal Schistosoma mansoni infection and praziquantel treatment during pregnancy on Schistosoma mansoni infection and immune responsiveness among offspring at age five years. PLoS Neglected Tropical Diseases 2013, 7(10): e2501.

29. Tweyongyere R, Mawa PA, Kihembo M, Jones MF, Webb EL, Cose S, Dunne WD, Vennervald JB, and Elliott MA. Effect of praziquantel treatment of Schistosoma mansoni during pregnancy on immune responses to schistosome antigens among the offspring: results of a randomised, placebo-controlled trial. BMC Infect Dis 2011, 11: 234

30. Ndibazza J, Mpairwe H, Webb EL, Mawa PA, Nampijja M, Muhangi L, Kihembo M, Lule SA, Rutebarika D, Apule B, Akello F, Akurut H, Oduru G, Naniima P, Kizito D, Kizza M, Kizindo R, Tweyongyere R, Alcock K, Muwanga M, Elliott AM. Impact of anthelminthic treatment in pregnancy and early childhood on response to immunisation and on the incidence of infectious diseases and eczema in early childhood: results of a randomised, double-blind, placebo-controlled trial. PLoS One 2012, 7:e50325.

31. Elliott AM, Ndibazza J, Mpairwe H, Muhangi L, Webb EL, Kizito D, Mawa P, Tweyongyere R, Muwanga M for the Entebbe Mother and Baby Study Team. Treatment with anthelminthics during pregnancy: what gains and what risks for the mother and child? Parasitology 2011, 1-9.

32. Webb EL, Mawa PA, Ndibazza J, Kizito D, Namatovu A, Kyosiimire-Lugemwa J, Nanteza B, Nampijja M, Muhangi L, Woodburn PW, Akurut H, Mpairwe H, Akello M, Lyadda N, Bukusuba J, Kihembo M, Kizza M, Kizindo R, Nabulime J, Ameke C, Namujju PB, Tweyongyere R, Muwanga M, Whitworth JA, Elliott AM.


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(2011) Effect of single-dose anthelmintic treatment during pregnancy on an infant's response to immunisation and on susceptibility to infectious diseases in infancy: a randomised, double-blind, placebo-controlled trial. Lancet. 2011 Jan 1;377(9759):52-62. Epub 2010 Dec 20

33. Tweyongyere R, Mawa PA, Emojong ON, Mpeirwe H, Jones MF, Trinh Duong, Dunne WD, Vennervald JB, Katunguka-Rwakishaya E, Elliott AM (2009) Effect of praziquantel treatment of Schistosoma mansoni during pregnancy on intensity of infection and antibody responses to schistosome antigens: results of a randomised, placebo-controlled trial. Journal: BioMed Central Infectious Diseases. 2009 Mar 18;9(1):32.

34. Deogratius Ssemwanga, Rebecca Nsubuga, Billy Mayanja, Frederick Lyagoba, Dave Yirrell, Lieve van der Pal, Heiner Grosskurth, Pontiano Kaleebu. Effect of HIV-1 Subtypes on Disease Progression in Rural Uganda: a Prospective Clinical Cohort study. PLoS One. 2013 Aug 12;8(8):e71768.

35. Baalwa J, Wang S, Parrish NF, Decker JM, Keele BF, Learn GH, Yue L, Ruzagira E, Ssemwanga D, Kamali A, Amornkul PN, Price MA, Kappes JC, Karita E, Kaleebu P, Sanders E, Gilmour J, Allen S, Hunter E, Montefiori DC, Haynes BF, Cormier E, Hahn BH, Shaw GM. Molecular identification, cloning and characterization of transmitted/founder HIV-1 subtype A, D and A/D infectious molecular clones. Virology 2013 Feb 5;436(1):33-48.

36. Anne Kapaata, Frederick Lyagoba, Deogratius Ssemwanga, Brian Magambo, Maria Nanyonjo, Jonathan Levin, Billy N. Mayanja, Claire Mugasa, Chris M. Parry and Pontiano Kaleebu. HIV-1 Subtype Distribution Trends and Evidence of Transmission Clusters among Incident Cases in a Rural Clinical Cohort in South-west Uganda. AIDS Res Hum Retroviruses. In press, August 2012.

37. Raphael W. Lihana, Deogratius Ssemwanga, Rita I. Okonkwo, Alash’le Abimiku and Nicaise Ndembi. Evolution and Diversity of HIV-1 in Africa: A Systematic Review 2000 – 2011. AIDS Rev. 2012 Apr-Jun;14(2):83-100. Review.

38. Deogratius Ssemwanga, Anne Kapaata, Frederick Lyagoba, Brian Magambo, Maria Nannyonjo, Billy N. Mayanja, Chris M. Parry and Pontiano Kaleebu. Low Drug Resistance Levels Among Drug-Naïve Individuals with Recent HIV Type 1 Infection in a Rural Clinical Cohort in Southwestern Uganda. AIDS Res Hum Retroviruses. 2012 Aug 3. [Epub ahead of print]

39. Deogratius Ssemwanga, Nicaise Ndembi, Frederick Lyagoba, Brian Magambo, Anne Kapaata, Justine Bukenya, George W. Lubega, Silvia Bertagnolio, Judith Vandepitte, Heiner Grosskurth, Pontiano Kaleebu. Transmitted Antiretroviral Drug Resistance among drug-naïve Female Sex Workers with recent infection in Kampala, Uganda. Clin Infect Dis. 2012 May;54 Suppl 4:S339-42.

40. Deogratius Ssemwanga, Nicaise Ndembi, Fred Lyagoba, Justine Bukenya, Janet Seeley, Judith Vandepitte, Heiner Grosskurth and Pontiano Kaleebu. HIV-1 subtype distribution, multiple infections, sexual networks and partnership histories in Commercial Sex Workers in Kampala, Uganda. AIDS Res Hum Retroviruses. 2012 Apr;28(4):357-65. Epub 2011 Aug 21.

41. Nakiyingi L, Bwanika JM, Kirenga B, Nakanjako D, Katabira C, Lubega G, Sempa J, Nyesiga B, Albert H, Manabe YC. Clinical Predictors and Accuracy of Empiric Tuberculosis Treatment among Sputum Smear-Negative HIV-Infected Adult TB Suspects in Uganda. PLoS One. 2013 Sep 6;8(9):e74023.

42. Tumwesigye BT, Nakanjako D, Wanyenze R, Akol Z, Sewankambo N. Policy development, implementation and evaluation by the AIDS control program in Uganda: a review of the processes. Health Res Policy Syst. 2013 Feb 23;11(1):7.

43. Kyabayinze DJ, Achan J, Nakanjako D, Mpeka B, Mawejje H, Mugizi R, Kalyango JN, D'Alessandro U, Talisuna AO, Van Geertruden JP. Parasite-based malaria diagnosis: Are Health Systems in Uganda equipped enough to implement the policy? BMC Public Health. 2012 Aug 24;12(1):695. [Epub ahead of print]

44. Semeere AS, Nakanjako D, Ddungu H, Kambugu A, Manabe YC, Colebunders R. Sub-optimal vitamin B-12 levels among ART-naïve HIV-positive individuals in an urban cohort in Uganda. PLoS One. 2012;7(7):e40072. Epub 2012 Jul 2.

45. Kyabayinze DJ, Asiimwe C, Nakanjako D, Nabakooza J, Bajabaite M, Strachan C, Tibenderana JK, Van Geetruyden JP. Programme level implementation of malaria rapid diagnostic tests (RDTs) use: outcomes and cost of training health workers at lower level health care facilities in Uganda. BMC Public Health. 2012 Apr 20;12:291.

46. Cose S, Kaleebu P, Elliott AM, Whittle H (2013). The immune response to infection. In: Principles of Medicine in Africa. Parry EHO, Godfrey RC, Mabey DMW, Gill GV (editors). Fourth edition, Cambridge


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University Press. 47. Sebina I, Cliff JM, Smith SG, Nogaro S, Webb EL, Riley EM, Dockrell HM, Elliott AM, Hafalla JCR, Cose S

Long-lived memory B-cell responses following BCG vaccination. PLoS One 2012 7(12): e51381 48. Nkurunungi G, Lutangira EJ, Lule SA, Akurut H, Kizindo R, Fitchett JR, Kizito D, Sebina I, Muhangi L,

Webb EL, Cose S, Elliott AM. Determining Mycobacterium tuberculosis Infection among BCG-immunised Ugandan Children by Interferon Gamma Release Assay and Tuberculin Skin Testing. PLoS One 2012, 7(10): e47340.

49. Inman CF, Zangerle Murray T, Bailey M, Cose S. Most B cells in non-lymphoid tissues are naive. Immunol Cell Biol 2011, 90: 235-42

50. Ndibazza J, Webb EL, Lule S, Mpairwe H, Akello M, Oduru G, Kizza M, Akurut H, Muhangi L, Magnussen P, Vennervald B, Elliott EM. Associations between maternal helminth and malaria infections in pregnancy, and clinical malaria in the offspring: a birth cohort in Entebbe, Uganda. J Infect Dis2013; doi: 10.1093/infdis/jit397.

51. Muhangi L, Lule AS, Mpairwe H, Ndibazza J, Kizza M, Nampijja M, Nakazibwe E, Kihembo M, Webb EL, Elliott AM. Maternal HIV infection and other factors associated with growth outcomes of HIV uninfected infants in Entebbe, Uganda. Public Health Nutrition. 2013;18:1-10.

52. Ndibazza J∗, Mpairwe H∗, Webb EL∗, Mawa AP, Nampijja M, Muhangi L, Kihembo M, Lule AS, Rutebarika D, Apule B, Akello F, Akurut H, Oduru G, Naniima P, Kizito D, Kizza M, Kizindo R, Tweyongere R, Alcock KJ, Muwanga M, Elliott AM. Impact of anthelminthic treatment in pregnancy and childhood on immunisations, infections and eczema in early childhood: a randomised controlled trial. PLoS One 2012;7(12):e50325. *Joint first author.


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APPENDIX 4. ADDITIONAL FUNDING FOR CAPACITY BUILDING SECURED BY PROGRAMME STAFF AND FELLOWS Awardee Project Funding agency Currency Amount Amount, GBP

A. Elliott Extension of MUII Wellcome Trust GBP 980,000 980,000 1,077,037 1,077,037

P.Kaleebu, A.Elliott IDEA consortium, work package 5 European Union Euro 67,200 58,435 P. Kaleebu Contribution to resource building MRC GBP 135,000 135,000 P. Kaleebu Contribution to library refurbishment EDCTP Euro (approx) 5,000 4,348 E. Mbidde Contribution to library refurbishment CDC USD (approx) 15,000 9,375

Contribution to equipping teaching lab CDC USD (approx) 60,000 37,500 John Kitayimbwa (PhD fellow)

Travel awardCarnegie Corporation

USD 8,172 5,108

E. Mbidde, J.Kayondo H3BionetNational Institutes of Health

USD (approx) 250,000 156,250

Open Day contributions in cashCDC, MRC, IAVI, RHSP, UVRI

Ush 11,692,000 3,248

MUII Income from course fees Ush 56,514,550 15,698 2,481,998 Total additional capacity building funds


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APPENDIX 5. ADDITIONAL FUNDS FOR RESEARCH RAISED BY PROGRAMME STAFF AND FELLOWS Awardee Project Funding agency Currency Amount Amount, GBP S. Cose Post mortem studies on tuberculosis Wellcome Trust/ THRiVE GBP 10,000 10,000

S. CoseMasters Training Fellowship for Ismail Sebina: “Circulating B lymphocytes as biomarkers for latent tuberculosis infection status in Uganda”

Wellcome Trust GBP 121,039 121,039

S. Cose, A. ElliottMRC Project grant: The impact of maternal infection with Mycobacterium tuberculosis on the infant response to BCG immunisation

MRC GBP 1,006,738 1,006,738

R. Tweyongyere (post-doctoral fellow)

EFINTD Fellowship: Does praziquantel treatment of schistosomiasis during pregnancy influence immune responses to S. mansoni infection among children born to the treated women?

European Foundations Initiative for Neglected Tropical Diseases

Euro 100,000 86,957

R. Tweyongyere (post-doctoral fellow)

EFINTD Senior Fellowship: Immune modulation in Schistosoma mansoni infections and effects on immune responses to childhood immunisation

European Foundations Initiative for Neglected Tropical Diseases

Euro 155,000 134,783

J. Kayondo (post-doctoral fellow)

EDCTP Fellowship: Investigating the evolution of HIV drug resistance

European - Developing Countries Clinical Trials Partnership

Euro 200,000 173,913

J. Kayondo (post-doctoral fellow)

Post-doctoral Research supplementary funds for development of AS-PCR molecular assays for G190A/S and other common Reverse Transcriptase Inhibitor (RTI) mutations.

The World Academy of Sciences (TWAS)

USD 15,000 9,200

Damalie Nakanjako (post-doctoral fellow)

Additional funding for the trial of atorvastatin asan intervention in suboptimal responders to antiretroviral therapy

Canadian Grand Challenges rising stars programme

Canadian dollars

113,000 70,625


Additional funding from CFAR to study cell death pathways among poor responders to antiretroviral therapy

Centre for AIDS Research at University of California at San Francisco

USD 25,000 15,625


Additional funding from UCSF-Global Health Institute to understand role of Tregs among suboptimal responders to antiretroviral therapy

University of California at San Francisco

USD 55,000 34,375

Harriet Mpairwe (post-doctoral fellow)

Antibody microarray for the analysis of IgE responses to allergens in Ugandans

MRC Centenary Award GBP 16,800 16,800

Harriet Mpairwe (post-doctoral fellow)

Study on parasitic infections and asthma in UgandaWellcome Trust Training Fellowship

GBPnot yet announced

Deogratius Ssemwanga (post-doctoral fellow)

Molecular epidemiology of the early HIV epidemic in Uganda


Annettee Nakimuli (PhD fellow)

Supplementary funds for the investigation of KIR and HLA polymorphisms in pre-eclampsia

Trophoblast Reseach Centre, University of Cambridge

GBP 30,000 30,000


The role of Killer Immunoglobulin-like Receptor (KIR) genes in Placental Malaria among women admitted at MulagoHospital, Uganda.

Wellcome Trust/ THRiVE GBP 9,899 9,899


The role of immune system genes in pre-eclampsia in Uganda

Wellcome Trust Uganda Post-doctoral Fellowship in Infection & Immunity

MUII funds, included above

Irene Andia (PhD fellow)

Supplementary funds for the investigation of the effects of co-infections on the response to infection with Mycobacterium tuberculosis

European Union, IDEA consortium

Euro 38,000 33,043

Andrew ObukuSupplementary funds to establish a neutralising antibody assay for his work at UVRI


Simon KimudaCharacterisation of humoral responses to mycobacteria in tuberculosis infected individuals from Uganda

Wellcome Trust Uganda Fast-track PhD Fellowship in Infection & Immunity

MUII funds, included above

1,781,197 Total research funds

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