Bbosa, Nicholas; Ssemwanga, Deogratius; Namagembe, Hamidah; Kiiza, Ronald; Kiconco, Jocelyn; Kayiwa, John; Lutalo, Tom; Lutwama, Julius; Ssekagiri, Alfred; Ssewanyana, Isaac; +13 more... Nabadda, Susan; Kyobe-Bbosa, Henry; Giandhari, Jennifer; Pillay, Sureshnee; Ramphal, Upasana; Ramphal, Yajna; Naidoo, Yeshnee; Tshiabuila, Derek; Tegally, Houriiyah; San, Emmanuel J; Wilkinson, Eduan; de Oliveira, Tulio; Kaleebu, Pontiano; (2022) Rapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021. EMERGING INFECTIOUS DISEASES, 28 (5). pp. 1021-1025. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2805.220121

Grant, Heather E; Roy, Sunando; Williams, Rachel; Tutill, Helena; Ferns, Bridget; Cane, Patricia A; Carswell, J Wilson; Ssemwanga, Deogratius; Kaleebu, Pontiano; Breuer, Judith; +1 more... Leigh Brown, Andrew J; (2022) A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism. Retrovirology, 19 (1). 28-. ISSN 1742-4690 DOI: https://doi.org/10.1186/s12977-022-00612-5

Omooja, Jonah; Bbosa, Nicholas; Lule, Dan Bugembe; Nannyonjo, Maria; Lunkuse, Sandra; Nassolo, Faridah; Nabirye, Stella Esther; Suubi, Hamidah Namagembe; Kaleebu, Pontiano; Ssemwanga, Deogratius; (2022) HIV-1 drug resistance genotyping success rates and correlates of Dried-blood spots and plasma specimen genotyping failure in a resource-limited setting. BMC Infectious Diseases, 22 (1). 474-. ISSN 1471-2334 DOI: https://doi.org/10.1186/s12879-022-07453-9

Pujol-Hodge, Emma; Salazar-Gonzalez, Jesus F; Ssemwanga, Deogratius; Charlebois, Edwin D; Ayieko, James; Grant, Heather E; Liegler, Teri; Atkins, Katherine E; Kaleebu, Pontiano; Kamya, Moses R; +3 more... Petersen, Maya; Havlir, Diane V; Leigh Brown, Andrew J; (2022) Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa. Viruses, 14 (8). p. 1673. ISSN 1999-4915 DOI: https://doi.org/10.3390/v14081673

Ssekagiri, Alfred; Jjingo, Daudi; Lujumba, Ibra; Bbosa, Nicholas; Bugembe, Daniel L; Kateete, David P; Jordan, I King; Kaleebu, Pontiano; Ssemwanga, Deogratius; (2022) QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data. Bioinformatics advances, 2 (1). vbac089-. ISSN 2635-0041 DOI: https://doi.org/10.1093/bioadv/vbac089

Tegally, Houriiyah; San, James E; Cotten, Matthew; Moir, Monika; Tegomoh, Bryan; Mboowa, Gerald; Martin, Darren P; Baxter, Cheryl; Lambisia, Arnold W; Diallo, Amadou; +392 more... Amoako, Daniel G; Diagne, Moussa M; Sisay, Abay; Zekri, Abdel-Rahman N; Gueye, Abdou Salam; Sangare, Abdoul K; Ouedraogo, Abdoul-Salam; Sow, Abdourahmane; Musa, Abdualmoniem O; Sesay, Abdul K; Abias, Abe G; Elzagheid, Adam I; Lagare, Adamou; Kemi, Adedotun-Sulaiman; Abar, Aden Elmi; Johnson, Adeniji A; Fowotade, Adeola; Oluwapelumi, Adeyemi O; Amuri, Adrienne A; Juru, Agnes; Kandeil, Ahmed; Mostafa, Ahmed; Rebai, Ahmed; Sayed, Ahmed; Kazeem, Akano; Balde, Aladje; Christoffels, Alan; Trotter, Alexander J; Campbell, Allan; Keita, Alpha K; Kone, Amadou; Bouzid, Amal; Souissi, Amal; Agweyu, Ambrose; Naguib, Amel; Gutierrez, Ana V; Nkeshimana, Anatole; Page, Andrew J; Yadouleton, Anges; Vinze, Anika; Happi, Anise N; Chouikha, Anissa; Iranzadeh, Arash; Maharaj, Arisha; Batchi-Bouyou, Armel L; Ismail, Arshad; Sylverken, Augustina A; Goba, Augustine; Femi, Ayoade; Sijuwola, Ayotunde E; Marycelin, Baba; Salako, Babatunde L; Oderinde, Bamidele S; Bolajoko, Bankole; Diarra, Bassirou; Herring, Belinda L; Tsofa, Benjamin; Lekana-Douki, Bernard; Mvula, Bernard; Njanpop-Lafourcade, Berthe-Marie; Marondera, Blessing T; Khaireh, Bouh Abdi; Kouriba, Bourema; Adu, Bright; Pool, Brigitte; McInnis, Bronwyn; Brook, Cara; Williamson, Carolyn; Nduwimana, Cassien; Anscombe, Catherine; Pratt, Catherine B; Scheepers, Cathrine; Akoua-Koffi, Chantal G; Agoti, Charles N; Mapanguy, Chastel M; Loucoubar, Cheikh; Onwuamah, Chika K; Ihekweazu, Chikwe; Malaka, Christian N; Peyrefitte, Christophe; Grace, Chukwa; Omoruyi, Chukwuma E; Rafaï, Clotaire D; Morang'a, Collins M; Erameh, Cyril; Lule, Daniel B; Bridges, Daniel J; Mukadi-Bamuleka, Daniel; Park, Danny; Rasmussen, David A; Baker, David; Nokes, David J; Ssemwanga, Deogratius; Tshiabuila, Derek; Amuzu, Dominic SY; Goedhals, Dominique; Grant, Donald S; Omuoyo, Donwilliams O; Maruapula, Dorcas; Wanjohi, Dorcas W; Foster-Nyarko, Ebenezer; Lusamaki, Eddy K; Simulundu, Edgar; Ong'era, Edidah M; Ngabana, Edith N; Abworo, Edward O; Otieno, Edward; Shumba, Edwin; Barasa, Edwine; Ahmed, El Bara; Ahmed, Elhadi A; Lokilo, Emmanuel; Mukantwari, Enatha; Philomena, Eromon; Belarbi, Essia; Simon-Loriere, Etienne; Anoh, Etilé A; Manuel, Eusebio; Leendertz, Fabian; Taweh, Fahn M; Wasfi, Fares; Abdelmoula, Fatma; Takawira, Faustinos T; Derrar, Fawzi; Ajogbasile, Fehintola V; Treurnicht, Florette; Onikepe, Folarin; Ntoumi, Francine; Muyembe, Francisca M; Ragomzingba, Frank EZ; Dratibi, Fred A; Iyanu, Fred-Akintunwa; Mbunsu, Gabriel K; Thilliez, Gaetan; Kay, Gemma L; Akpede, George O; van Zyl, Gert U; Awandare, Gordon A; Kpeli, Grace S; Schubert, Grit; Maphalala, Gugu P; Ranaivoson, Hafaliana C; Omunakwe, Hannah E; Onywera, Harris; Abe, Haruka; Karray, Hela; Nansumba, Hellen; Triki, Henda; Kadjo, Herve Albéric Adje; Elgahzaly, Hesham; Gumbo, Hlanai; Mathieu, Hota; Kavunga-Membo, Hugo; Smeti, Ibtihel; Olawoye, Idowu B; Adetifa, Ifedayo MO; Odia, Ikponmwosa; Ben Boubaker, Ilhem Boutiba; Muhammad, Iluoreh Ahmed; Ssewanyana, Isaac; Wurie, Isatta; Konstantinus, Iyaloo S; Halatoko, Jacqueline Wemboo Afiwa; Ayei, James; Sonoo, Janaki; Makangara, Jean-Claude C; Tamfum, Jean-Jacques M; Heraud, Jean-Michel; Shaffer, Jeffrey G; Giandhari, Jennifer; Musyoki, Jennifer; Nkurunziza, Jerome; Uwanibe, Jessica N; Bhiman, Jinal N; Yasuda, Jiro; Morais, Joana; Kiconco, Jocelyn; Sandi, John D; Huddleston, John; Odoom, John K; Morobe, John M; Gyapong, John O; Kayiwa, John T; Okolie, Johnson C; Xavier, Joicymara S; Gyamfi, Jones; Wamala, Joseph F; Bonney, Joseph HK; Nyandwi, Joseph; Everatt, Josie; Nakaseegu, Joweria; Ngoi, Joyce M; Namulondo, Joyce; Oguzie, Judith U; Andeko, Julia C; Lutwama, Julius J; Mogga, Juma JH; O'Grady, Justin; Siddle, Katherine J; Victoir, Kathleen; Adeyemi, Kayode T; Tumedi, Kefentse A; Carvalho, Kevin S; Mohammed, Khadija Said; Dellagi, Koussay; Musonda, Kunda G; Duedu, Kwabena O; Fki-Berrajah, Lamia; Singh, Lavanya; Kepler, Lenora M; Biscornet, Leon; de Oliveira Martins, Leonardo; Chabuka, Lucious; Olubayo, Luicer; Ojok, Lul Deng; Deng, Lul Lojok; Ochola-Oyier, Lynette I; Tyers, Lynn; Mine, Madisa; Ramuth, Magalutcheemee; Mastouri, Maha; ElHefnawi, Mahmoud; Mbanne, Maimouna; Matsheka, Maitshwarelo I; Kebabonye, Malebogo; Diop, Mamadou; Momoh, Mambu; Lima Mendonça, Maria da Luz; Venter, Marietjie; Paye, Marietou F; Faye, Martin; Nyaga, Martin M; Mareka, Mathabo; Damaris, Matoke-Muhia; Mburu, Maureen W; Mpina, Maximillian G; Owusu, Michael; Wiley, Michael R; Tatfeng, Mirabeau Y; Ayekaba, Mitoha Ondo'o; Abouelhoda, Mohamed; Beloufa, Mohamed Amine; Seadawy, Mohamed G; Khalifa, Mohamed K; Matobo, Mooko Marethabile; Kane, Mouhamed; Salou, Mounerou; Mbulawa, Mphaphi B; Mwenda, Mulenga; Allam, Mushal; Phan, My VT; Abid, Nabil; Rujeni, Nadine; Abuzaid, Nadir; Ismael, Nalia; Elguindy, Nancy; Top, Ndeye Marieme; Dia, Ndongo; Mabunda, Nédio; Hsiao, Nei-Yuan; Silochi, Nelson Boricó; Francisco, Ngiambudulu M; Saasa, Ngonda; Bbosa, Nicholas; Murunga, Nickson; Gumede, Nicksy; Wolter, Nicole; Sitharam, Nikita; Ndodo, Nnaemeka; Ajayi, Nnennaya A; Tordo, Noël; Mbhele, Nokuzola; Razanajatovo, Norosoa H; Iguosadolo, Nosamiefan; Mba, Nwando; Kingsley, Ojide C; Sylvanus, Okogbenin; Femi, Oladiji; Adewumi, Olubusuyi M; Testimony, Olumade; Ogunsanya, Olusola A; Fakayode, Oluwatosin; Ogah, Onwe E; Oludayo, Ope-Ewe; Faye, Ousmane; Smith-Lawrence, Pamela; Ondoa, Pascale; Combe, Patrice; Nabisubi, Patricia; Semanda, Patrick; Oluniyi, Paul E; Arnaldo, Paulo; Quashie, Peter Kojo; Okokhere, Peter O; Bejon, Philip; Dussart, Philippe; Bester, Phillip A; Mbala, Placide K; Kaleebu, Pontiano; Abechi, Priscilla; El-Shesheny, Rabeh; Joseph, Rageema; Aziz, Ramy Karam; Essomba, René G; Ayivor-Djanie, Reuben; Njouom, Richard; Phillips, Richard O; Gorman, Richmond; Kingsley, Robert A; Neto Rodrigues, Rosa Maria DESA; Audu, Rosemary A; Carr, Rosina AA; Gargouri, Saba; Masmoudi, Saber; Bootsma, Sacha; Sankhe, Safietou; Mohamed, Sahra Isse; Femi, Saibu; Mhalla, Salma; Hosch, Salome; Kassim, Samar Kamal; Metha, Samar; Trabelsi, Sameh; Agwa, Sara Hassan; Mwangi, Sarah Wambui; Doumbia, Seydou; Makiala-Mandanda, Sheila; Aryeetey, Sherihane; Ahmed, Shymaa S; Ahmed, Side Mohamed; Elhamoumi, Siham; Moyo, Sikhulile; Lutucuta, Silvia; Gaseitsiwe, Simani; Jalloh, Simbirie; Andriamandimby, Soa Fy; Oguntope, Sobajo; Grayo, Solène; Lekana-Douki, Sonia; Prosolek, Sophie; Ouangraoua, Soumeya; van Wyk, Stephanie; Schaffner, Stephen F; Kanyerezi, Stephen; Ahuka-Mundeke, Steve; Rudder, Steven; Pillay, Sureshnee; Nabadda, Susan; Behillil, Sylvie; Budiaki, Sylvie L; van der Werf, Sylvie; Mashe, Tapfumanei; Mohale, Thabo; Le-Viet, Thanh; Velavan, Thirumalaisamy P; Schindler, Tobias; Maponga, Tongai G; Bedford, Trevor; Anyaneji, Ugochukwu J; Chinedu, Ugwu; Ramphal, Upasana; George, Uwem E; Enouf, Vincent; Nene, Vishvanath; Gorova, Vivianne; Roshdy, Wael H; Karim, Wasim Abdul; Ampofo, William K; Preiser, Wolfgang; Choga, Wonderful T; Ahmed, Yahaya Ali; Ramphal, Yajna; Bediako, Yaw; Naidoo, Yeshnee; Butera, Yvan; de Laurent, Zaydah R; Africa Pathogen Genomics Initiative (Africa PGI)‡; Ouma, Ahmed EO; von Gottberg, Anne; Githinji, George; Moeti, Matshidiso; Tomori, Oyewale; Sabeti, Pardis C; Sall, Amadou A; Oyola, Samuel O; Tebeje, Yenew K; Tessema, Sofonias K; de Oliveira, Tulio; Happi, Christian; Lessells, Richard; Nkengasong, John; Wilkinson, Eduan; (2022) The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. 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Bbosa, Nicholas; Ssemwanga, Deogratius; Nsubuga, Rebecca N; Kiwanuka, Noah; Bagaya, Bernard S; Kitayimbwa, John M; Ssekagiri, Alfred; Yebra, Gonzalo; Kaleebu, Pontiano; Leigh-Brown, Andrew; (2021) Phylogenetic Networks and Parameters Inferred from HIV Nucleotide Sequences of High-Risk and General Population Groups in Uganda: Implications for Epidemic Control. Viruses, 13 (6). p. 970. ISSN 1999-4915 DOI: https://doi.org/10.3390/v13060970

Kayondo, Hassan W; Ssekagiri, Alfred; Nabakooza, Grace; Bbosa, Nicholas; Ssemwanga, Deogratius; Kaleebu, Pontiano; Mwalili, Samuel; Mango, John M; Leigh Brown, Andrew J; Saenz, Roberto A; +2 more... Galiwango, Ronald; Kitayimbwa, John M; (2021) Employing phylogenetic tree shape statistics to resolve the underlying host population structure. BMC bioinformatics, 22 (1). 546-. ISSN 1471-2105 DOI: https://doi.org/10.1186/s12859-021-04465-1

Lutalo, Tom; Nalumansi, Aminah; Olara, Denis; Kayiwa, John; Ogwang, Bernard; Odwilo, Emmanuel; Watera, Christine; Balinandi, Stephen; Kiconco, Jocelyn; Nakaseegu, Joweria; +10 more... Serwanga, Jennifer; Kikaire, Bernard; Ssemwanga, Deogratius; Abiko, Brendah; Nsereko, Christopher; Cotten, Matthew; Buule, Joshua; Lutwama, Julius; Downing, Robert; Kaleebu, Pontiano; (2021) Evaluation of the performance of 25 SARS-CoV-2 serological rapid diagnostic tests using a reference panel of plasma specimens at the Uganda Virus Research Institute. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 112. pp. 281-287. ISSN 1201-9712 DOI: https://doi.org/10.1016/j.ijid.2021.09.020

Watera, Christine; Ssemwanga, Deogratius; Namayanja, Grace; Asio, Juliet; Lutalo, Tom; Namale, Alice; Sanyu, Grace; Ssewanyana, Isaac; Gonzalez-Salazar, Jesus Fidel; Nazziwa, Jamirah; +9 more... Nanyonjo, Maria; Raizes, Elliot; Kabuga, Usher; Mwangi, Christina; Kirungi, Wilford; Musinguzi, Joshua; Mugagga, Kaggwa; Mbidde, Edward Katongole; Kaleebu, Pontiano; (2021) HIV drug resistance among adults initiating antiretroviral therapy in Uganda. The Journal of antimicrobial chemotherapy, 76 (9). pp. 2407-2414. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkab159

Wilkinson, Eduan; Giovanetti, Marta; Tegally, Houriiyah; San, James E; Lessells, Richard; Cuadros, Diego; Martin, Darren P; Rasmussen, David A; Zekri, Abdel-Rahman N; Sangare, Abdoul K; +292 more... Ouedraogo, Abdoul-Salam; Sesay, Abdul K; Priscilla, Abechi; Kemi, Adedotun-Sulaiman; Olubusuyi, Adewunmi M; Oluwapelumi, Adeyemi OO; Hammami, Adnène; Amuri, Adrienne A; Sayed, Ahmad; Ouma, Ahmed EO; Elargoubi, Aida; Ajayi, Nnennaya A; Victoria, Ajogbasile F; Kazeem, Akano; George, Akpede; Trotter, Alexander J; Yahaya, Ali A; Keita, Alpha K; Diallo, Amadou; Kone, Amadou; Souissi, Amal; Chtourou, Amel; Gutierrez, Ana V; Page, Andrew J; Vinze, Anika; Iranzadeh, Arash; Lambisia, Arnold; Ismail, Arshad; Rosemary, Audu; Sylverken, Augustina; Femi, Ayoade; Ibrahimi, Azeddine; Marycelin, Baba; Oderinde, Bamidele S; Bolajoko, Bankole; Dhaala, Beatrice; Herring, Belinda L; Njanpop-Lafourcade, Berthe-Marie; Kleinhans, Bronwyn; McInnis, Bronwyn; Tegomoh, Bryan; Brook, Cara; Pratt, Catherine B; Scheepers, Cathrine; Akoua-Koffi, Chantal G; Agoti, Charles N; Peyrefitte, Christophe; Daubenberger, Claudia; Morang'a, Collins M; Nokes, D James; Amoako, Daniel G; Bugembe, Daniel L; Park, Danny; Baker, David; Doolabh, Deelan; Ssemwanga, Deogratius; Tshiabuila, Derek; Bassirou, Diarra; Amuzu, Dominic SY; Goedhals, Dominique; Omuoyo, Donwilliams O; Maruapula, Dorcas; Foster-Nyarko, Ebenezer; Lusamaki, Eddy K; Simulundu, Edgar; Ong'era, Edidah M; Ngabana, Edith N; Shumba, Edwin; El Fahime, Elmostafa; Lokilo, Emmanuel; Mukantwari, Enatha; Philomena, Eromon; Belarbi, Essia; Simon-Loriere, Etienne; Anoh, Etilé A; Leendertz, Fabian; Ajili, Faida; Enoch, Fakayode O; Wasfi, Fares; Abdelmoula, Fatma; Mosha, Fausta S; Takawira, Faustinos T; Derrar, Fawzi; Bouzid, Feriel; Onikepe, Folarin; Adeola, Fowotade; Muyembe, Francisca M; Tanser, Frank; Dratibi, Fred A; Mbunsu, Gabriel K; Thilliez, Gaetan; Kay, Gemma L; Githinji, George; van Zyl, Gert; Awandare, Gordon A; Schubert, Grit; Maphalala, Gugu P; Ranaivoson, Hafaliana C; Lemriss, Hajar; Anise, Happi; Abe, Haruka; Karray, Hela H; Nansumba, Hellen; Elgahzaly, Hesham A; Gumbo, Hlanai; Smeti, Ibtihel; Ayed, Ikhlas B; Odia, Ikponmwosa; Ben Boubaker, Ilhem Boutiba; Gaaloul, Imed; Gazy, Inbal; Mudau, Innocent; Ssewanyana, Isaac; Konstantinus, Iyaloo; Lekana-Douk, Jean B; Makangara, Jean-Claude C; Tamfum, Jean-Jacques M; Heraud, Jean-Michel; Shaffer, Jeffrey G; Giandhari, Jennifer; Li, Jingjing; Yasuda, Jiro; Mends, Joana Q; Kiconco, Jocelyn; Morobe, John M; Gyapong, John O; Okolie, Johnson C; Kayiwa, John T; Edwards, Johnathan A; Gyamfi, Jones; Farah, Jouali; Nakaseegu, Joweria; Ngoi, Joyce M; Namulondo, Joyce; Andeko, Julia C; Lutwama, Julius J; O'Grady, Justin; Siddle, Katherine; Adeyemi, Kayode T; Tumedi, Kefentse A; Said, Khadija M; Hae-Young, Kim; Duedu, Kwabena O; Belyamani, Lahcen; Fki-Berrajah, Lamia; Singh, Lavanya; Martins, Leonardo de O; Tyers, Lynn; Ramuth, Magalutcheemee; Mastouri, Maha; Aouni, Mahjoub; El Hefnawi, Mahmoud; Matsheka, Maitshwarelo I; Kebabonye, Malebogo; Diop, Mamadou; Turki, Manel; Paye, Marietou; Nyaga, Martin M; Mareka, Mathabo; Damaris, Matoke-Muhia; Mburu, Maureen W; Mpina, Maximillian; Nwando, Mba; Owusu, Michael; Wiley, Michael R; Youtchou, Mirabeau T; Ayekaba, Mitoha O; Abouelhoda, Mohamed; Seadawy, Mohamed G; Khalifa, Mohamed K; Sekhele, Mooko; Ouadghiri, Mouna; Diagne, Moussa M; Mwenda, Mulenga; Allam, Mushal; Phan, My VT; Abid, Nabil; Touil, Nadia; Rujeni, Nadine; Kharrat, Najla; Ismael, Nalia; Dia, Ndongo; Mabunda, Nedio; Hsiao, Nei-Yuan; Silochi, Nelson B; Nsenga, Ngoy; Gumede, Nicksy; Mulder, Nicola; Ndodo, Nnaemeka; Razanajatovo, Norosoa H; Iguosadolo, Nosamiefan; Judith, Oguzie; Kingsley, Ojide C; Sylvanus, Okogbenin; Peter, Okokhere; Femi, Oladiji; Idowu, Olawoye; Testimony, Olumade; Chukwuma, Omoruyi E; Ogah, Onwe E; Onwuamah, Chika K; Cyril, Oshomah; Faye, Ousmane; Tomori, Oyewale; Ondoa, Pascale; Combe, Patrice; Semanda, Patrick; Oluniyi, Paul E; Arnaldo, Paulo; Quashie, Peter K; Dussart, Philippe; Bester, Phillip A; Mbala, Placide K; Ayivor-Djanie, Reuben; Njouom, Richard; Phillips, Richard O; Gorman, Richmond; Kingsley, Robert A; Carr, Rosina AA; El Kabbaj, Saâd; Gargouri, Saba; Masmoudi, Saber; Sankhe, Safietou; Lawal, Salako B; Kassim, Samar; Trabelsi, Sameh; Metha, Samar; Kammoun, Sami; Lemriss, Sanaâ; Agwa, Sara HA; Calvignac-Spencer, Sébastien; Schaffner, Stephen F; Doumbia, Seydou; Mandanda, Sheila M; Aryeetey, Sherihane; Ahmed, Shymaa S; Elhamoumi, Siham; Andriamandimby, Soafy; Tope, Sobajo; Lekana-Douki, Sonia; Prosolek, Sophie; Ouangraoua, Soumeya; Mundeke, Steve A; Rudder, Steven; Panji, Sumir; Pillay, Sureshnee; Engelbrecht, Susan; Nabadda, Susan; Behillil, Sylvie; Budiaki, Sylvie L; van der Werf, Sylvie; Mashe, Tapfumanei; Aanniz, Tarik; Mohale, Thabo; Le-Viet, Thanh; Schindler, Tobias; Anyaneji, Ugochukwu J; Chinedu, Ugwu; Ramphal, Upasana; Jessica, Uwanibe; George, Uwem; Fonseca, Vagner; Enouf, Vincent; Gorova, Vivianne; Roshdy, Wael H; Ampofo, William K; Preiser, Wolfgang; Choga, Wonderful T; Bediako, Yaw; Naidoo, Yeshnee; Butera, Yvan; de Laurent, Zaydah R; Sall, Amadou A; Rebai, Ahmed; von Gottberg, Anne; Kouriba, Bourema; Williamson, Carolyn; Bridges, Daniel J; Chikwe, Ihekweazu; Bhiman, Jinal N; Mine, Madisa; Cotten, Matthew; Moyo, Sikhulile; Gaseitsiwe, Simani; Saasa, Ngonda; Sabeti, Pardis C; Kaleebu, Pontiano; Tebeje, Yenew K; Tessema, Sofonias K; Happi, Christian; Nkengasong, John; de Oliveira, Tulio; (2021) A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science, 374 (6566). pp. 423-431. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.abj4336

Bbosa, Nicholas; Ssemwanga, Deogratius; Kaleebu, Pontiano; (2020) Short Communication: Choosing the Right Program for the Identification of HIV-1 Transmission Networks from Nucleotide Sequences Sampled from Different Populations. AIDS research and human retroviruses, 36 (11). pp. 948-951. ISSN 0889-2229 DOI: https://doi.org/10.1089/AID.2020.0033

Bbosa, Nicholas; Ssemwanga, Deogratius; Ssekagiri, Alfred; Xi, Xiaoyue; Mayanja, Yunia; Bahemuka, Ubaldo; Seeley, Janet; Pillay, Deenan; Abeler-Dörner, Lucie; Golubchik, Tanya; +3 more... Fraser, Christophe; Kaleebu, Pontiano; Ratmann, Oliver; (2020) Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda. Viruses, 12 (3). p. 331. DOI: https://doi.org/10.3390/v12030331

Bugembe, Daniel Lule; Kayiwa, John; Phan, My VT; Tushabe, Phiona; Balinandi, Stephen; Dhaala, Beatrice; Lexow, Jonas; Mwebesa, Henry; Aceng, Jane; Kyobe, Henry; +4 more... Ssemwanga, Deogratius; Lutwama, Julius; Kaleebu, Pontiano; Cotten, Matthew; (2020) Main Routes of Entry and Genomic Diversity of SARS-CoV-2, Uganda. EMERGING INFECTIOUS DISEASES, 26 (10). pp. 2411-2415. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2610.202575

Grant, Heather E; Hodcroft, Emma B; Ssemwanga, Deogratius; Kitayimbwa, John M; Yebra, Gonzalo; Esquivel Gomez, Luis Roger; Frampton, Dan; Gall, Astrid; Kellam, Paul; de Oliveira, Tulio; +12 more... Bbosa, Nicholas; Nsubuga, Rebecca N; Kibengo, Freddie; Kwan, Tsz Ho; Lycett, Samantha; Kao, Rowland; Robertson, David L; Ratmann, Oliver; Fraser, Christophe; Pillay, Deenan; Kaleebu, Pontiano; Leigh Brown, Andrew J; (2020) Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus evolution, 6 (1). veaa004-. ISSN 2057-1577 DOI: https://doi.org/10.1093/ve/veaa004

Nalumansi, Aminah; Lutalo, Tom; Kayiwa, John; Watera, Christine; Balinandi, Stephen; Kiconco, Jocelyn; Nakaseegu, Joweria; Olara, Denis; Odwilo, Emmanuel; Serwanga, Jennifer; +12 more... Kikaire, Bernard; Ssemwanga, Deogratius; Nabadda, Susan; Ssewanyana, Isaac; Atwine, Diane; Mwebesa, Henry; Bosa, Henry Kyobe; Nsereko, Christopher; Cotten, Matthew; Downing, Robert; Lutwama, Julius; Kaleebu, Pontiano; (2020) Field evaluation of the performance of a SARS-CoV-2 antigen rapid diagnostic test in Uganda using nasopharyngeal samples. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 104. pp. 282-286. ISSN 1201-9712 DOI: https://doi.org/10.1016/j.ijid.2020.10.073

Segujja, Farouk; Omooja, Jonah; Lunkuse, Sandra; Nanyonjo, Maria; Nabirye, Stella E; Nassolo, Faridah; Bugembe, Daniel L; Bbosa, Nicholas; Kateete, David P; Ssenyonga, William; +5 more... Mayanja, Yunia; Nsubuga, Rebecca N; Seeley, Janet; Kaleebu, Pontiano; Ssemwanga, Deogratius; (2020) High Levels of Acquired HIV Drug Resistance Following Virological Nonsuppression in HIV-Infected Women from a High-Risk Cohort in Uganda. AIDS research and human retroviruses, 36 (9). pp. 782-791. ISSN 0889-2229 DOI: https://doi.org/10.1089/AID.2019.0279

Ssemwanga, Deogratius; Asio, Juliet; Watera, Christine; Nannyonjo, Maria; Nassolo, Faridah; Lunkuse, Sandra; Salazar-Gonzalez, Jesus F; Salazar, Maria G; Sanyu, Grace; Lutalo, Tom; +12 more... Kabuga, Usher; Ssewanyana, Isaac; Namatovu, Faridah; Namayanja, Grace; Namale, Alice; Raizes, Elliot; Kaggwa, Mugagga; Namuwenge, Norah; Kirungi, Wilford; Katongole-Mbidde, Edward; Kaleebu, Pontiano; Uganda HIV Drug Resistance Technical Working Group; (2020) Prevalence of viral load suppression, predictors of virological failure and patterns of HIV drug resistance after 12 and 48 months on first-line antiretroviral therapy: a national cross-sectional survey in Uganda. The Journal of antimicrobial chemotherapy, 75 (5). pp. 1280-1289. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkz561

Ssemwanga, Deogratius; Bbosa, Nicholas; Nsubuga, Rebecca N; Ssekagiri, Alfred; Kapaata, Anne; Nannyonjo, Maria; Nassolo, Faridah; Karabarinde, Alex; Mugisha, Joseph; Seeley, Janet; +3 more... Yebra, Gonzalo; Leigh Brown, Andrew; Kaleebu, Pontiano; (2020) The Molecular Epidemiology and Transmission Dynamics of HIV Type 1 in a General Population Cohort in Uganda. Viruses, 12 (11). p. 1283. DOI: https://doi.org/10.3390/v12111283

Bbosa, Nicholas; Kaleebu, Pontiano; Ssemwanga, Deogratius; (2019) HIV subtype diversity worldwide. Current opinion in HIV and AIDS, 14 (3). pp. 153-160. ISSN 1746-630X DOI: https://doi.org/10.1097/COH.0000000000000534

Bbosa, Nicholas; Ssemwanga, Deogratius; Nsubuga, Rebecca N; Salazar-Gonzalez, Jesus F; Salazar, Maria G; Nanyonjo, Maria; Kuteesa, Monica; Seeley, Janet; Kiwanuka, Noah; Bagaya, Bernard S; +3 more... Yebra, Gonzalo; Leigh-Brown, Andrew; Kaleebu, Pontiano; (2019) Phylogeography of HIV-1 suggests that Ugandan fishing communities are a sink for, not a source of, virus from general populations. Scientific reports, 9 (1). 1051-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-018-37458-x

Namale, Gertrude; Kamacooko, Onesmus; Bagiire, Daniel; Mayanja, Yunia; Abaasa, Andrew; Kilembe, William; Price, Matt; Ssemwanga, Deogratius; Lunkuse, Sandra; Nanyonjo, Maria; +5 more... Ssenyonga, William; Mayaud, Philippe; Newton, Rob; Kaleebu, Pontiano; Seeley, Janet; (2019) Sustained virological response and drug resistance among female sex workers living with HIV on antiretroviral therapy in Kampala, Uganda: a cross-sectional study. Sexually Transmitted Infections, 95 (6). pp. 405-411. ISSN 1368-4973 DOI: https://doi.org/10.1136/sextrans-2018-053854

Omooja, Jonah; Nannyonjo, Maria; Sanyu, Grace; Nabirye, Stella E; Nassolo, Faridah; Lunkuse, Sandra; Kapaata, Anne; Segujja, Farouk; Kateete, David Patrick; Ssebaggala, Eric; +5 more... Bbosa, Nicholas; Aling, Emmanuel; Nsubuga, Rebecca N; Kaleebu, Pontiano; Ssemwanga, Deogratius; (2019) Rates of HIV-1 virological suppression and patterns of acquired drug resistance among fisherfolk on first-line antiretroviral therapy in Uganda. The Journal of antimicrobial chemotherapy, 74 (10). pp. 3021-3029. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkz261

Fily, F; Ayikobua, E; Ssemwanga, D; Nicholas, S; Kaleebu, P; Delaugerre, C; Pasquier, E; Amoros Quiles, I; Balkan, S; Schramm, B; (2018) HIV-1 drug resistance testing at second-line regimen failure in Arua, Uganda: avoiding unnecessary switch to an empiric third-line. Tropical medicine & international health, 23 (10). pp. 1075-1083. ISSN 1360-2276 DOI: https://doi.org/10.1111/tmi.13131 Full text not available from this repository.

Ssemwanga, Deogratius; Doria-Rose, Nicole A; Redd, Andrew D; Shiakolas, Andrea R; Longosz, Andrew F; Nsubuga, Rebecca N; Mayanja, Billy N; Asiki, Gershim; Seeley, Janet; Kamali, Anatoli; +10 more... Ransier, Amy; Darko, Samuel; Walker, Michael P; Bruno, Daniel; Martens, Craig; Douek, Daniel; Porcella, Stephen F; Quinn, Thomas C; Mascola, John R; Kaleebu, Pontiano; (2018) Characterization of the Neutralizing Antibody Response in a Case of Genetically Linked HIV Superinfection. The Journal of infectious diseases, 217 (10). pp. 1530-1534. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiy071

von Braun, Amrei; Sekaggya-Wiltshire, Christine; Bachmann, Nadine; Ssemwanga, Deogratius; Scherrer, Alexandra U; Nanyonjo, Maria; Kapaata, Anne; Kaleebu, Pontiano; Günthard, Huldrych F; Castelnuovo, Barbara; +2 more... Fehr, Jan; Kambugu, Andrew; (2018) HIV-1 Drug Resistance Among Ugandan Adults Attending an Urban Out-Patient Clinic. Journal of acquired immune deficiency syndromes, 78 (5). pp. 566-573. ISSN 1525-4135 DOI: https://doi.org/10.1097/QAI.0000000000001717

Kiwuwa-Muyingo, Sylvia; Nazziwa, Jamirah; Ssemwanga, Deogratius; Ilmonen, Pauliina; Njai, Harr; Ndembi, Nicaise; Parry, Chris; Kitandwe, Paul Kato; Gershim, Asiki; Mpendo, Juliet; +6 more... Neilsen, Leslie; Seeley, Janet; Seppälä, Heikki; Lyagoba, Fred; Kamali, Anatoli; Kaleebu, Pontiano; (2017) HIV-1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach. PloS one, 12 (10). e0185818-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0185818

Ratmann, Oliver; Wymant, Chris; Colijn, Caroline; Danaviah, Siva; Essex, M; Frost, Simon DW; Gall, Astrid; Gaiseitsiwe, Simani; Grabowski, Mary; Gray, Ronald; +22 more... Guindon, Stephane; von Haeseler, Arndt; Kaleebu, Pontiano; Kendall, Michelle; Kozlov, Alexey; Manasa, Justen; Minh, Bui Quang; Moyo, Sikhulile; Novitsky, Vladimir; Nsubuga, Rebecca; Pillay, Sureshnee; Quinn, Thomas C; Serwadda, David; Ssemwanga, Deogratius; Stamatakis, Alexandros; Trifinopoulos, Jana; Wawer, Maria; Leigh Brown, Andrew; de Oliveira, Tulio; Kellam, Paul; Pillay, Deenan; Fraser, Christophe; (2017) HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences. AIDS research and human retroviruses, 33 (11). pp. 1083-1098. ISSN 0889-2229 DOI: https://doi.org/10.1089/AID.2017.0061

Rhee, Soo-Yon; Blanco, Jose Luis; Jordan, Michael R; Taylor, Jonathan; Lemey, Philippe; Varghese, Vici; Hamers, Raph L; Bertagnolio, Silvia; de Wit, Tobias F Rinke; Aghokeng, Avelin F; +63 more... Albert, Jan; Avi, Radko; Avila-Rios, Santiago; Bessong, Pascal O; Brooks, James I; Boucher, Charles AB; Brumme, Zabrina L; Busch, Michael P; Bussmann, Hermann; Chaix, Marie-Laure; Chin, Bum Sik; D'Aquin, Toni T; De Gascun, Cillian F; Derache, Anne; Descamps, Diane; Deshpande, Alaka K; Djoko, Cyrille F; Eshleman, Susan H; Fleury, Herve; Frange, Pierre; Fujisaki, Seiichiro; Harrigan, P Richard; Hattori, Junko; Holguin, Africa; Hunt, Gillian M; Ichimura, Hiroshi; Kaleebu, Pontiano; Katzenstein, David; Kiertiburanakul, Sasisopin; Kim, Jerome H; Kim, Sung Soon; Li, Yanpeng; Lutsar, Irja; Morris, Lynn; Ndembi, Nicaise; Kee, Peng NG; Paranjape, Ramesh S; Peeters, Martine; Poljak, Mario; Price, Matt A; Ragonnet-Cronin, Manon L; Reyes-Terán, Gustavo; Rolland, Morgane; Sirivichayakul, Sunee; Smith, Davey M; Soares, Marcelo A; Soriano, Vincent V; Ssemwanga, Deogratius; Stanojevic, Maja; Stefani, Mariane A; Sugiura, Wataru; Sungkanuparph, Somnuek; Tanuri, Amilcar; Tee, Kok Keng; Truong, Hong-Ha M; van de Vijver, David AMC; Vidal, Nicole; Yang, Chunfu; Yang, Rongge; Yebra, Gonzalo; Ioannidis, John PA; Vandamme, Anne-Mieke; Shafer, Robert W; (2015) Correction: 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. PLoS medicine, 12 (6). e1001845-. ISSN 1549-1277 DOI: https://doi.org/10.1371/journal.pmed.1001845

Yebra, Gonzalo; Ragonnet-Cronin, Manon; Ssemwanga, Deogratius; Parry, Chris M; Logue, Christopher H; Cane, Patricia A; Kaleebu, Pontiano; Brown, Andrew J Leigh; (2015) Analysis of the history and spread of HIV-1 in Uganda using phylodynamics. The Journal of general virology, 96 (Pt 7). pp. 1890-1898. ISSN 0022-1317 DOI: https://doi.org/10.1099/vir.0.000107

Redd, Andrew D; Ssemwanga, Deogratius; Vandepitte, Judith; Wendel, Sarah K; Ndembi, Nicaise; Bukenya, Justine; Nakubulwa, Susan; Grosskurth, Heiner; Parry, Chris M; Martens, Craig; +4 more... Bruno, Daniel; Porcella, Stephen F; Quinn, Thomas C; Kaleebu, Pontiano; (2014) Rates of HIV-1 superinfection and primary HIV-1 infection are similar in female sex workers in Uganda. AIDS (London, England), 28 (14). pp. 2147-2152. ISSN 0269-9370 DOI: https://doi.org/10.1097/QAD.0000000000000365

Njai, Harr F; Ewings, Fiona M; Lyimo, Eric; Foulongne, Vincent; Ngerageza, Dhamira; Mongi, Aika; Ssemwanga, Deogratius; Andreasen, Aura; Nyombi, Balthazar; Ao, Tony; +7 more... Michael, Denna; Urassa, Mark; Todd, Jim; Zaba, Basia; Changalucha, John; Hayes, Richard; Kapiga, Saidi H; (2013) Deciphering the complex distribution of human immunodeficiency virus type 1 subtypes among different cohorts in Northern Tanzania. PloS one, 8 (12). e81848-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0081848

Ssemwanga, Deogratius; Nsubuga, Rebecca N; Mayanja, Billy N; Lyagoba, Frederick; Magambo, Brian; Yirrell, Dave; Van der Paal, Lieve; Grosskurth, Heiner; Kaleebu, Pontiano; (2013) Effect of HIV-1 subtypes on disease progression in rural Uganda: a prospective clinical cohort study. PloS one, 8 (8). e71768-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0071768

Ssemwanga, Deogratius; Kapaata, Anne; Lyagoba, Frederick; Magambo, Brian; Nanyonjo, Maria; Mayanja, Billy N; Parry, Chris M; Kaleebu, Pontiano; (2012) Low drug resistance levels among drug-naive individuals with recent HIV type 1 infection in a rural clinical cohort in southwestern Uganda. AIDS research and human retroviruses, 28 (12). pp. 1784-1787. ISSN 0889-2229 DOI: https://doi.org/10.1089/AID.2012.0090 Full text not available from this repository.

Ssemwanga, Deogratius; Ndembi, Nicaise; Lyagoba, Fred; Bukenya, Justine; Seeley, Janet; Vandepitte, Judith; Grosskurth, Heiner; Kaleebu, Pontiano; (2012) HIV type 1 subtype distribution, multiple infections, sexual networks, and partnership histories in female sex workers in Kampala, Uganda. AIDS research and human retroviruses, 28 (4). pp. 357-365. ISSN 0889-2229 DOI: https://doi.org/10.1089/aid.2011.0024

Ssemwanga, Deogratius; Ndembi, Nicaise; Lyagoba, Frederick; Magambo, Brian; Kapaata, Anne; Bukenya, Justine; Lubega, George W; Bertagnolio, Silvia; Vandepitte, Judith; Grosskurth, Heiner; +1 more... Kaleebu, Pontiano; (2012) Transmitted antiretroviral drug resistance among drug-naive female sex workers with recent infection in Kampala, Uganda. Clinical infectious diseases, 54 Sup (suppl_). S339-S342. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/cir937

Ssemwanga, Deogratius; Lyagoba, Frederick; Ndembi, Nicaise; Mayanja, Billy N; Larke, Natasha; Wang, Shuyi; Baalwa, Joshua; Williamson, Carolyn; Grosskurth, Heiner; Kaleebu, Pontiano; (2011) Multiple HIV-1 infections with evidence of recombination in heterosexual partnerships in a low risk Rural Clinical Cohort in Uganda. Virology, 411 (1). pp. 113-131. ISSN 0042-6822 DOI: https://doi.org/10.1016/j.virol.2010.12.025