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All Profiles

Dr Deogratius Ssemwanga

Call Career Development Fellowship (CDF)
Programme EDCTP2
Start Date 2017-08-01
End Date 2020-07-31
Project Code TMA2015CDF982
Status Active

Title

Immunological Selection of Recombinants following HIV-1 Superinfection

Objectives

• To determine the recombination rate following superinfection • To determine the role of immune selection on recombination • To determine effect of recombination on viral persistence by immune escape • To determine the effect of recombination on disease progression

Host Organisation

Institution Country
Uganda

Participants

Name Institution Country
Professor Pontiano Kaleebu Uganda Virus Research Institute (UVRI) Uganda

Study Design

Longitudinal cohort study, with a nested matched case-control study

Sites

Entebbe, Uganda

Current Organisation

MRC/UVRI and LSHTM Uganda Research Unit

Current Job Title

Senior Scientist

Students Supervised

Type Name Title University Start Date End Date
MSc Jonah Omooja High Rates of HIV-1 Virological Suppression and Acquired Drug Resistance among Fisher-folk Communities on First-line Antiretroviral Therapy in Uganda Makerere University, Kampala, Uganda 2017 2019
MSc Farouk Segujja Prevalence of Transmitted and Pre-treatment HIV-1 drug resistance, the long term virological outcomes and prevalence of acquired HIV-1 drug resistance in the era of test and treat in a cohort of female sex workers in Uganda Makerere University, Kampala, Uganda 2017 2019
MSc • Maria Gloria Nannyonjo The Frequency and Clinical Significance of Minority Drug Resistance Mutations after 12 Months of Antiretroviral Therapy initiation in an HIV Ugandan Population Makerere University, Kampala, Uganda 2015 2018
PhD Nicholas Bbosa HIV-1 phylogenetics in Lake Victoria fishing communities of Uganda: understanding transmission dynamics and networks Makerere University, Kampala, Uganda 2014 2019

Memberships

Role Committee/board Start Date End Date
Member Executive Committee, Makerere University Uganda Virus Research Institute Infection and Immunity (MUII/Wellcome Trust) Programme 2013
Member Steering Committee, Phylogenetics and Networks for Generalised HIV Epidemics in Africa (PANGEA) 2013
Member Uganda HIV Drug Resistance Working Group 2018

Education

Institution Degree Year
Makerere University, Uganda MSc 2006-11-01
Makerere University, Uganda PhD 2013-01-22

Areas Of Specialisation

Human Immuno-deficiency Virus (HIV)

Grants

Nurturing Genomics and Bioinformatics Research Capacity in Africa” (BRecA)
Grant Code:
1U2RTW010672-01
Source of funding:
NIH
Amount:
1250000
Role:
Other(specify)
Start Date:
2017-09-05
End Date:
2022-08-31
H3ABioNet: informatics solutions for H3Africa
Grant Code:
NIH U24 NHGRI
Source of funding:
NIH
Amount:
55433
Role:
Researcher
Start Date:
2017-08-01
End Date:
2022-07-31
Cross-sectional Survey of HIV Drug Resistance in Adults Initiating and Receiving Antiretroviral Therapy in Uganda
Grant Code:
U2GGH000785-03
Source of funding:
CDC
Amount:
230000
Role:
Researcher
Start Date:
2016-10-01
End Date:
2019-09-30
Cross-sectional Survey of HIV Drug Resistance in Adults and Children Failing Second Line Antiretroviral Therapy in Uganda
Grant Code:
U2GGH000785-04
Source of funding:
CDC
Amount:
200000
Role:
Other(specify)
Start Date:
2016-10-01
End Date:
2019-09-30
Immunological and Viral Factors Associated with HIV-1 Superinfection
Grant Code:
1R01AI118368
Source of funding:
NIH
Amount:
650000
Role:
Researcher
Start Date:
2014-12-01
End Date:
2019-11-30
Genetic clustering methods for real-time molecular surveillance of HIV outbreaks
Grant Code:
INV-031335
Source of funding:
Bill and Melinda Gates Foundation
Amount:
100000
Role:
Principal Investigator
Start Date:
2021-01-01
End Date:
2022-01-01

Publications

Rates of HIV-1 superinfection and primary HIV-1 infection are similar in female sex workers in Uganda
Authors:
Redd AD, Ssemwanga D, Vandepitte J, Wendel SK, Ndembi N, Bukenya J, Nakubulwa S, Grosskurth H, Parry CM, Martens C, Bruno D, Porcella SF, Quinn TC, Kaleebu P , 28(14):2147-52. doi: 10.1097/QAD.0000000000000365
Date:
2014-09-10
Journal:
AIDS
Content:
Transmitted Antiretroviral Drug Resistance among drug-naïve Female Sex Workers with recent infection in Kampala, Uganda
Authors:
Deogratius Ssemwanga, Nicaise Ndembi, Frederick Lyagoba, Brian Magambo, Anne Kapaata, Justine Bukenya, George W. Lubega, Silvia Bertagnolio, Judith Vandepitte, Heiner Grosskurth, Pontiano Kaleebu , 2012 May;54 Suppl 4:S339-42
Date:
2012-05-01
Journal:
Clin Infect Dis
Content:
Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic
Authors:
Yebra G, Hodcroft EB, Ragonnet-Cronin ML, Pillay D, Brown AJ; PANGEA_HIV Consortium; ICONIC Project , 6:39489. doi: 10.1038/srep39489. PMID: 28008945
Date:
2016-12-23
Journal:
Sci Rep
Content:
Deciphering the complex distribution of Human Immunodeficiency Virus Type 1 subtypes among different risk populations in northern Tanzania
Authors:
Harr F Njai, Fiona M Ewings, Eric Lyimo, Vincent Foulongne, Dhamira Ngerageza, Deogratius Ssemwanga, Aura Andreasen, Balthazar Nyombi, Tony Ao, Aika Mongi, Denna Michael, Mark Urassa, Jim Todd, Basia Zaba, John Changalucha, Richard Hayes and Saidi Kapiga , 8(12):e81848. doi: 10.1371/journal.pone.0081848. eCollection 2013
Date:
2013-12-11
Journal:
PLoS One
Content:
HIV-1 superinfection can occur in the presence of broadly neutralizing antibodies. Vaccine.
Authors:
1. Serwanga J, Ssemwanga D, Muganga M, Nakiboneka R, Nakubulwa S, Kiwuwa-Muyingo S, Morris L, Redd AD, Quinn TC, Kaleebu P; HIV Superinfection Study Group , pii: S0264-410X(17)31718-8. doi:
Date:
2017-12-20
Journal:
Vaccine
Content:
Molecular identification, cloning and characterization of transmitted/founder HIV-1 subtype A, D and AD infectious molecular clones
Authors:
Joshua Baalwa, Shuyi Wang, Nicholas Parrish, Julie M. Decker, Brandon F. Keele, Gerald H. Learn, Ling Yue, Eugene Ruzagira, Deogratius Ssemwanga, Anatoli Kamali, John C. Kappes, Etienne Karita, Pontiano Kaleebu, Eduard Sanders, Patricia Fast, Jill Gilmour, Susan Allen, Eric Hunter, Barton F. Haynes, Emmanuel Cormier, Beatrice H. Hahn and George M. Shaw , 436(1):33-48. doi: 10.1016/j.virol.2012.10.009. Epub 2012 Nov 1
Date:
2013-02-05
Journal:
Virology
Content:
Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic. . 2016 Dec 23
Authors:
Yebra G, Hodcroft EB, Ragonnet-Cronin ML, Pillay D, Brown AJ; PANGEA_HIV Consortium; ICONIC Project. Collaborators (Fraser C, Kellam P, de Oliveira T, Denis A, Hoppe A, Kityo C, Frampton D, Ssemwanga D, Tanser F, Keshani J, Lingappa J, Herbeck J, Wawer M, Essex M, Cohen MS, Paton N, Ratmann O, Kaleebu P, Hayes R, Fidler S, Quinn T, Novitsky V, Haywards A, Nastouli E, Morris S, Clark D, Kozlakidis Z) , 6:39489. doi: 10.1038/srep39489
Date:
2016-12-23
Journal:
Sci Rep
Content:
Low Drug Resistance Levels Among Drug-Naive Individuals with Recent HIV Type 1 Infection in a Rural Clinical Cohort in Southwestern Uganda
Authors:
Deogratius Ssemwanga, Anne Kapaata, Frederick Lyagoba, Brian Magambo, Maria Nannyonjo, Billy N. Mayanja, Chris M. Parry and Pontiano Kaleebu , 28(12):1784-7. doi: 10.1089/AID.2012.0090
Date:
2012-08-03
Journal:
AIDS Res Hum Retroviruses
Content:
Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis
Authors:
Rhee SY, Blanco JL, Jordan MR, Taylor J, Lemey P, Varghese V, Hamers RL, Bertagnolio S, de Wit TF, Aghokeng AF, Albert J, Avi R, Avila-Rios S, Bessong PO, Brooks JI, Boucher CA, Brumme ZL, Busch MP, Bussmann H, Chaix ML, Chin BS, D'Aquin TT, De Gascun CF, Derache A, Descamps D, Deshpande AK, Djoko CF, Eshleman SH, Fleury H, Frange P, Fujisaki S, Harrigan PR, Hattori J, Holguin A, Hunt GM, Ichimura H, Kaleebu P, Katzenstein D, Kiertiburanakul S, Kim JH, Kim SS, Li Y, Lutsar I, Morris L, Ndembi N, Ng KP, Paranjape RS, Peeters M, Poljak M, Price MA, Ragonnet-Cronin ML, Reyes-Terán G, Rolland M, Sirivichayakul S, Smith DM, Soares MA, Soriano VV, Ssemwanga D, Stanojevic M, Stefani MA, Sugiura W, Sungkanuparph S, Tanuri A, Tee KK, Truong HH, van de Vijver DA, Vidal N, Yang C, Yang R, Yebra G, Ioannidis JP, Vandamme AM, Shafer RW , 12(4):e1001810. doi: 10.1371/journal.pmed.1001810. eCollection 2015 Apr
Date:
2015-04-07
Journal:
PLoS Med
Content:
Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience
Authors:
Kim T. Gurwitz, Shaun Aron, Sumir Panji, Suresh Maslamoney, Pedro
L. Fernandes, David P. Judge, Amel Ghouila, Jean-Baka Domelevo Entfellner, Fatma Z. Guerfali, Colleen Saunders, Ahmed Mansour Alzohairy, Samson P. Salifu,
Rehab Ahmed, Ruben Cloete, Jonathan Kayondo, Deogratius Ssemwanga, Nicola Mulder, H3ABioNet Consortium’s Education Training and Working Group as members of the H3Africa Consortium , 13(10):e1005715. doi: 10.1371/journal.pcbi.1005715. eCollection 2017 Oct. PMID: 28981516
Date:
2017-10-05
Journal:
PLoS Comput Biol
Content:
HIV-1 Subtype Distribution Trends and Evidence of Transmission Clusters among Incident Cases in a Rural Clinical Cohort in South-west Uganda; 2004-2010
Authors:
Anne Kapaata, Frederick Lyagoba, Deogratius Ssemwanga, Magambo Brian, Nanyonjo Maria, Levin Jonathan, Mayanja Billy Nsubuga, Mugasa Claire, Parry Chris M, Kaleebu Pontiano , 29(3):520-7. doi: 10.1089/AID.2012.0170. Epub
Date:
2012-12-16
Journal:
AIDS Res Hum Retroviruses
Content:
Effect of HIV-1 Subtypes on Disease Progression in Rural Uganda: a Prospective Clinical Cohort study
Authors:
Deogratius Ssemwanga, Rebecca N. Nsubuga, Billy N. Mayanja, Frederick Lyagoba, Brian Magambo, Dave Yirrell, Lieve Van Der Paal, Heiner Grosskurth, Pontiano Kaleebu , 8(8):e71768
Date:
2013-08-12
Journal:
PLoS One
Content:
Update on HIV-1 diversity in Africa: a decade in review
Authors:
Raphael W. Lihana, Deogratius Ssemwanga, Rita I. Okonkwo, Alash’le Abimiku and Nicaise Ndembi , 2012 Apr-Jun;14(2):83-100. Review
Date:
2012-04-01
Journal:
AIDS Rev
Content:
HIV-1 subtype distribution, multiple infections, sexual networks and partnership histories in Commercial Sex Workers in Kampala, Uganda
Authors:
Deogratius Ssemwanga, Nicaise Ndembi, Fred Lyagoba, Justine Bukenya, Janet Seeley, Judith Vandepitte, Heiner Grosskurth and Pontiano Kaleebu , 2012 Apr;28(4):357-65. Epub 2011 Aug 21
Date:
2011-08-21
Journal:
AIDS Res Hum Retroviruses
Content:
Update on HIV-1 Acquired and Transmitted Drug Resistance in Africa
Authors:
Deogratius Ssemwanga, Raphael W. Lihana, Chinenye Ugoji, Alash’le Abimiku John Nkengasong, Patrick Dakum and Nicaise Ndembi , Jan-Mar;17(1):3-20
Date:
2015-01-01
Journal:
AIDS Reviews 2015
Content:
HIV‐1 full‐genome phylogenetics of generalized epidemics in sub‐Saharan Africa: impact of missing nucleotide characters in next‐generation sequences
Authors:
Oliver Ratmann, Chris Wymant, Caroline Colijn, Siva Danaviah, Max Essex, Simon Frost, Astrid Gall, Simani Gaseitsiwe, Mary Grabowski, Ronald Gray, Stephane Guindon, Arndt von Haeseler, Pontiano Kaleebu, Michelle Kendall, Alexey Kozlov, Justen Manasa, Bui Quang Minh, Sikhulile Moyo, Vlad Novitsky, Rebecca Nsubuga, Sureshnee Pillay, Thomas C. Quinn, David Serwadda, Deogratius Ssemwanga, Alexandros Stamatakis, Jana Trifinopoulos, Maria Wawer, Andy Leigh Brown, Tulio de Oliveira, Paul Kellam, Deenan Pillay and Christophe Fraser on behalf of the PANGEA‐HIV Consortium , doi: 10.1089/AID.2017.0061. [Epub ahead of print]
Date:
2017-05-25
Journal:
AIDS Res Hum Retroviruses
Content:
Multiple HIV-1 Infections with evidence of recombination in Heterosexual Partnerships in a low risk Rural Clinical Cohort in Uganda
Authors:
Ssemwanga Deogratius, Lyagoba Frederick, Ndembi Nicaise, Mayanja Billy .N, Larke Natasha, Wang Shuyi, Baalwa Joshua, Williamson Carolyn, Grosskurth Heiner, and Kaleebu Pontiano , 2011 Mar 1;411(1):113-31. Epub 2011 Jan 15
Date:
2011-01-15
Journal:
Virology
Content:
Analysis of the History and Spread of HIV-1 in Uganda using Phylodynamics
Authors:
Yebra G, Ragonnet-Cronin M, Ssemwanga D, Parry CM, Logue CH, Cane PA, Kaleebu P, Leigh-Brown AJ , pii: vir.0.000107. doi: 10.1099/vir.0.000107. [Epub ahead of print]
Date:
2015-02-27
Journal:
J Gen Virol
Content:
HIV-1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach
Authors:
Sylvia Kiwuwa-Muyingo, Jamirah Nazziwa, Deogratius Ssemwanga,
Pauliina Ilmonen, Harr Njai, Nicaise Ndembi, Chris Parry, Paul Kato Kitandwe, Asiki Gershim, Juliet Mpendo, Leslie Neilsen, Janet Seeley, Heikki Seppa ̈la, Fred Lyagoba, Anatoli Kamali, Pontiano Kaleebu , 12(10):e0185818. doi: 10.1371/journal.pone.0185818. eCollection 2017. PMID: 29023474
Date:
2017-10-12
Journal:
PLoS One
Content:

Projects

Immunological Selection of Recombinants following HIV-1 Superinfection
Fellow:
Deogratius Ssemwanga
Collaborators:
Name Country Institution
Prof. Pontiano Kaleebu Uganda MRC/UVRI and LSHTM Uganda Research Unit
Dr. Jesus Salazar Uganda MRC/UVRI and LSHTM Uganda Research Unit
Dr. Rebecca Nsubuga Uganda Dr. Rebecca Nsubuga
Dr. Andrew Redd United States National Institutes of Health
Prof. James Mullins United States Departments of Microbiology, Medicine and Laboratory Medicine University of Washington
Prof. Andrew Leigh Brown United Kingdom University of Edinburgh
Objectives:
• To determine the recombination rate following superinfection • To determine the role of immune selection on recombination • To determine the effect of recombination on viral persistence by immune escape • To determine the effect of recombination on disease progression
Sites:
Entebbe, Uganda
Study Design:
This is a longitudinal cohort study, with a nested matched case-control study
Subjects:
HIV infected patients in Uganda
Linked Grant:
Immunological and Viral Factors Associated with HIV-1 Superinfection
Start Date:
2017-08-01
End Date:
2020-07-31
Immunological Selection of Recombinants following HIV-1 Superinfection
Fellow:
Deogratius Ssemwanga
Collaborators:
Name Country Institution
Prof. Pontiano Kaleebu Uganda MRC/UVRI and LSHTM Uganda Research Unit
Dr. Jesus Salazar Uganda MRC/UVRI and LSHTM Uganda Research Unit
Dr. Rebecca Nsubuga Uganda Dr. Rebecca Nsubuga
Dr. Andrew Redd United States National Institutes of Health
Prof. James Mullins United States Departments of Microbiology, Medicine and Laboratory Medicine University of Washington
Prof. Andrew Leigh Brown United Kingdom University of Edinburgh
Objectives:
• To determine the recombination rate following superinfection • To determine the role of immune selection on recombination • To determine the effect of recombination on viral persistence by immune escape • To determine the effect of recombination on disease progression
Sites:
Entebbe, Uganda
Study Design:
This is a longitudinal cohort study, with a nested matched case-control study
Subjects:
HIV infected patients in Uganda
Linked Grant:
Immunological and Viral Factors Associated with HIV-1 Superinfection
Start Date:
2017-08-01
End Date:
2020-07-31

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