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7. Global and regional epidemiology of HIV-1 recombinants in 1990–2015: a systematic review and global survey

Author

Abimiku, Alash'le G, Agwale, Simon, Archibald, Chris, Avidor, Boaz, Barbás, María Gabriela, Barre-Sinoussi, Francoise, Barugahare, Banson, Belabbes, El Hadj, Bertagnolio, Silvia, Birx, Deborah, Bobkov, Aleksei F, Brandful, James, Bredell, Helba, Brennan, Catherine A, Brooks, James, Bruckova, Marie, Buonaguro, Luigi, Buonaguro, Franco, Buttò, Stefano, Buvé, Anne, Campbell, Mary, Carr, Jean, Carrera, Alex, Carrillo, Manuel Gómez, Celum, Connie, Chaplin, Beth, Charles, Macarthur, Chatzidimitriou, Dimitrios, Chen, Zhiwei, Chijiwa, Katsumi, Cooper, David, Cunningham, Philip, Dagnra, Anoumou, de Gascun, Cillian F, Del Amo, Julia, Delgado, Elena, Dietrich, Ursula, Dwyer, Dominic, Ellenberger, Dennis, Ensoli, Barbara, Essex, Max, Gao, Feng, Fleury, Hervé, Fonjungo, Peter N, Foulongne, Vincent, Gadkari, Deepak A, García, Federico, Garsia, Roger, Gershy-Damet, Guy Michel, Glynn, Judith R, Goodall, Ruth, Grossman, Zehava, Lindenmeyer-Guimarães, Monick, Hahn, Beatrice, Hamers, Raph L, Hamouda, Osamah, Handema, Ray, He, Xiang, Herbeck, Joshua, Ho, David D, Holguin, Africa, Hosseinipour, Mina, Hunt, Gillian, Ito, Masahiko, Bel Hadj Kacem, Mohamed Ali, Kahle, Erin, Kaleebu, Pontiano, Kalish, Marcia, Kamarulzaman, Adeeba, Kang, Chun, Kanki, Phyllis, Karamov, Edward, Karasi, Jean-Claude, Kayitenkore, Kayitesi, Kelleher, Tony, Kitayaporn, Dwip, Kostrikis, Leondios G, Kucherer, Claudia, Lara, Claudia, Leitner, Thomas, Liitsola, Kirsi, Lingappa, Jai, Linka, Marek, Lorenzana de Rivera, Ivette, Lukashov, Vladimir, Maayan, Shlomo, Mayr, Luzia, McCutchan, Francine, Meda, Nicolas, Menu, Elisabeth, Mhalu, Fred, Mloka, Doreen, Mokili, John L, Montes, Brigitte, Mor, Orna, Morgado, Mariza, Mosha, Fausta, Moussi, Awatef, Mullins, James, Najera, Rafael, Nasr, Mejda, Ndembi, Nicaise, Neilson, Joel R, Nerurkar, Vivek R, Neuhann, Florian, Nolte, Claudine, Novitsky, Vlad, Nyambi, Philippe, Ofner, Marianna, Paladin, Fem J, Papa, Anna, Pape, Jean, Parkin, Neil, Parry, Chris, Peeters, Martine, Pelletier, Alexandra, Pérez-Álvarez, Lucía, Pillay, Deenan, Pinto, Angie, Quang, Trinh Duy, Rademeyer, Cecilia, Raikanikoda, Filimone, Rayfield, Mark A, Reynes, Jean-Marc, Rinke de Wit, Tobias, Robbins, Kenneth E, Rolland, Morgane, Rousseau, Christine, Salazar-Gonzales, Jesus, Salem, Hanan, Salminen, Mika, Salomon, Horacio, Sandstrom, Paul, Santiago, Mario L, Sarr, Abdoulaye D, Schroeder, Bryan, Segondy, Michel, Selhorst, Philippe, Sempala, Sylvester, Servais, Jean, Shaik, Ansari, Shao, Yiming, Slim, Amine, Soares, Marcelo A, Songok, Elijah, Stewart, Debbie, Stokes, Julie, Subbarao, Shambavi, Sutthent, Ruengpung, Takehisa, Jun, Tanuri, Amilcar, Tee, Kok Keng, Thapa, Kiran, Thomson, Michael, Tran, Tyna, Urassa, Willy, Ushijima, Hiroshi, van de Perre, Philippe, van der Groen, Guido, van Laethem, Kristel, van Oosterhout, Joep, van Sighem, Ard, van Wijngaerden, Eric, Vandamme, Anne-Mieke, Vercauteren, Jurgen, Vidal, Nicole, Wallace, Lesley, Williamson, Carolyn, Wolday, Dawit, Xu, Jianqing, Yang, Chunfu, Zhang, Linqi, Zhang, Rong, Hemelaar, Joris, Elangovan, Ramyiadarsini, Yun, Jason, Dickson-Tetteh, Leslie, Kirtley, Shona, Gouws-Williams, Eleanor, and Ghys, Peter D

Published
2020
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11. Global and regional molecular epidemiology of HIV-1, 1990–2015: a systematic review, global survey, and trend analysis

Author

Abimiku, Alash'le G, Agwale, Simon, Archibald, Chris, Avidor, Boaz, Barbás, María Gabriela, Barre-Sinoussi, Francoise, Barugahare, Banson, Belabbes, El Hadj, Bertagnolio, Silvia, Birx, Deborah, Bobkov, Aleksei F, Brandful, James, Bredell, Helba, Brennan, Catherine A, Brooks, James, Bruckova, Marie, Buonaguro, Luigi, Buonaguro, Franco, Buttò, Stefano, Buve, Anne, Campbell, Mary, Carr, Jean, Carrera, Alex, Carrillo, Manuel Gómez, Celum, Connie, Chaplin, Beth, Charles, Macarthur, Chatzidimitriou, Dimitrios, Chen, Zhiwei, Chijiwa, Katsumi, Cooper, David, Cunningham, Philip, Dagnra, Anoumou, de Gascun, Cillian F, Del Amo, Julia, Delgado, Elena, Dietrich, Ursula, Dwyer, Dominic, Ellenberger, Dennis, Ensoli, Barbara, Essex, Max, Gao, Feng, Fleury, Herve, Fonjungo, Peter N, Foulongne, Vincent, Gadkari, Deepak A, García, Federico, Garsia, Roger, Gershy-Damet, Guy Michel, Glynn, Judith R, Goodall, Ruth, Grossman, Zehava, Lindenmeyer-Guimarães, Monick, Hahn, Beatrice, Hamers, Raph L, Hamouda, Osamah, Handema, Ray, He, Xiang, Herbeck, Joshua, Ho, David D, Holguin, Africa, Hosseinipour, Mina, Hunt, Gillian, Ito, Masahiko, Bel Hadj Kacem, Mohamed Ali, Kahle, Erin, Kaleebu, Pontiano Kaleebu, Kalish, Marcia, Kamarulzaman, Adeeba, Kang, Chun, Kanki, Phyllis, Karamov, Edward, Karasi, Jean-Claude, Kayitenkore, Kayitesi, Kelleher, Tony, Kitayaporn, Dwip, Kostrikis, Leondios G, Kucherer, Claudia, Lara, Claudia, Leitner, Thomas, Liitsola, Kirsi, Lingappa, Jai, Linka, Marek, Lorenzana de Rivera, Ivette, Lukashov, Vladimir, Maayan, Shlomo, Mayr, Luzia, McCutchan, Francine, Meda, Nicolas, Menu, Elisabeth, Mhalu, Fred, Mloka, Doreen, Mokili, John L, Montes, Brigitte, Mor, Orna, Morgado, Mariza, Mosha, Fausta, Moussi, Awatef, Mullins, James, Najera, Rafael, Nasr, Mejda, Ndembi, Nicaise, Neilson, Joel R, Nerurkar, Vivek R, Neuhann, Florian, Nolte, Claudine, Novitsky, Vlad, Nyambi, Philippe, Ofner, Marianna, Paladin, Fem J, Papa, Anna, Pape, Jean, Parkin, Neil, Parry, Chris, Peeters, Martine, Pelletier, Alexandra, Pérez-Álvarez, Lucía, Pillay, Deenan, Pinto, Angie, Quang, Trinh Duy, Rademeyer, Cecilia, Raikanikoda, Filimone, Rayfield, Mark A, Reynes, Jean-Marc, Rinke de Wit, Tobias, Robbins, Kenneth E, Rolland, Morgane, Rousseau, Christine, Salazar-Gonzales, Jesus, Salem, Hanan, Salminen, Mika, Salomon, Horacio, Sandstrom, Paul, Santiago, Mario L, Sarr, Abdoulaye D, Schroeder, Bryan, Segondy, Michel, Selhorst, Philippe, Sempala, Sylvester, Servais, Jean, Shaik, Ansari, Shao, Yiming, Slim, Amine, Soares, Marcelo A, Songok, Elijah, Stewart, Debbie, Stokes, Julie, Subbarao, Shambavi, Sutthent, Ruengpung, Takehisa, Jun, Tanuri, Amilcar, Tee, Kok Keng, Thapa, Kiran, Thomson, Michael, Tran, Tyna, Urassa, Willy, Ushijima, Hiroshi, van de Perre, Philippe, van der Groen, Guido, van Laethem, Kristel, van Oosterhout, Joep, van Sighem, Ard, van Wijngaerden, Eric, Vandamme, Anne-Mieke, Vercauteren, Jurgen, Vidal, Nicole, Wallace, Lesley, Williamson, Carolyn, Wolday, Dawit, Xu, Jianqing, Yang, Chunfu, Zhang, Linqi, Zhang, Rong, Hemelaar, Joris, Elangovan, Ramyiadarsini, Yun, Jason, Dickson-Tetteh, Leslie, Fleminger, Isabella, Kirtley, Shona, Williams, Brian, Gouws-Williams, Eleanor, and Ghys, Peter D

Published
2019
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15. The interaction between HTLV-1 Tax protein and the proteasome

Author

Hemelaar, Joris and McMichael, Andrew J.

Subjects
616.9, HTLV-I (Virus), Cellular immunity, Cytokines
Abstract

This thesis presents studies on the interaction between the human T cell lymphotropic virus type 1 (HTLV-1) Tax protein and the 20S proteasome and the role of the interaction in cellular processes and the cytotoxic T cell (CTL) response against HTLV-1. The rapid translocation of Tax into the nucleus is described. Tax accumulates in the nucleus and forms unique bodies involved in transcriptional activation. It was further found that Tax associated with assembled nuclear 20S proteasomes and stimulated the chymotryptic and tryptic activities of the 20S proteasome, independent of the induction of the LMP2 and LMP7 proteasome subunits. Confocal microscopy revealed a partial colocalisation of Tax with nuclear proteasomes. A panel of Tax mutants was generated and their subcellular localisation and association with the 20S proteasome analysed. This analysis revealed that both the N- and C-terminus of Tax play a role in proteasome binding of Tax and further showed that proteasome binding was not sufficient for nuclear localisation of Tax. Therefore, Tax probably translocates into the nucleus prior to and independent of proteasome association. Tax specific CTL clones were generated and characterised using tetrameric MHC class I/peptide complexes. These CTL clones were used to investigate the requirements for processing and presentation of Tax for recognition by CTL. It was found that Tax was a metabolically very stable protein and that the presentation of the immunodominant Tax 11-19 epitope was dependent on the transporter associated with antigen presentation (TAP), independent of the expression of LMP2 and LMP7 proteasome subunits and resistant to treatment with the proteasome inhibitor lactacystin. It is proposed that the interaction between Tax and the 20S proteasome plays a role in Tax mediated transcriptional activation, leading to cellular activation and proliferation, and may not determine the immunodominance of Tax in the CTL response against HTLV-1.

Published
2001

30. Adverse perinatal outcomes associated with timing of initiation of antiretroviral therapy: Systematic review and meta‐analysis.

Author

Sexton, Harriet, Kumarendran, Mary, Brandon, Zoe, Shi, Christine, Kirtley, Shona, and Hemelaar, Joris

Subjects
HIV infections, HIV-positive persons, ONLINE information services, CINAHL database, RELATIVE medical risk, META-analysis, MEDICAL information storage & retrieval systems, PREMATURE infants, CONFIDENCE intervals, SYSTEMATIC reviews, ANTIRETROVIRAL agents, GESTATIONAL age, RETROSPECTIVE studies, PREGNANCY outcomes, LOW birth weight, PERINATAL death, COMPARATIVE studies, MEDLINE, LONGITUDINAL method, PREGNANCY
Abstract

Background: The World Health Organization (WHO) recommends immediate initiation of lifelong antiretroviral therapy (ART) for all people living with HIV, including pregnant women. As a result, an increasing number of women living with HIV conceive while taking ART, the vast majority of whom reside in low‐ and middle‐income countries (LMICs). We aimed to assess the association between timing of ART initiation and perinatal outcomes. Methods: We conducted a systematic literature review by searching PubMed, CINAHL (EBSCOhost), Global Health (Ovid), EMBASE (Ovid), and the Cochrane Central Register of Controlled Trials and four clinical trial databases (WHO International Clinical Trials Registry Platform, the Pan African Clinical Trials Registry, the ClinicalTrials.gov database, and the ISRCTN Registry) from 1 January 1980 to 28 April 2018. We identified studies reporting specific perinatal outcomes among pregnant women living with HIV according to timing of ART initiation and extracted data. Perinatal outcomes assessed were preterm birth (<37 weeks), very preterm birth (<32 weeks), low birthweight (<2500 g), very low birthweight (<1500 g), small for gestational age (<10th centile), very small for gestational age (<3rd centile) and neonatal death (<29 days). Random‐effects meta‐analyses examined perinatal outcomes associated with preconception and antenatal ART initiation as well as according to trimesters of antenatal initiation. We performed quality assessments and subgroup and sensitivity analyses, and assessed the effect of adjustment for confounders. This systematic review and meta‐analyses is registered with PROSPERO, number CRD42021248987. Results: Of 51 874 unique citations, 25 studies (eight prospective and 17 retrospective cohort studies) were eligible for analysis, including 40 920 women living with HIV. Preconception ART initiation was associated with a significantly increased risk of preterm birth (relative risk 1.16; 95% confidence interval [CI] 1.03–1.31) compared with antenatal ART initiation. Preconception ART initiation was not significantly associated with very preterm birth, low birthweight, very low birthweight, small for gestational age, very small for gestational age, or neonatal death. First trimester exposure (i.e. preconception or first trimester initiation) was not significantly associated with any increased risk of adverse perinatal outcomes. No significant association between timing of ART initiation and adverse perinatal outcomes was found in the studies of higher quality and those conducted in LMICs. Conclusion: Preconception ART initiation is associated with preterm birth but no other adverse perinatal outcomes. In LMICs, where most pregnant women living with HIV reside, the timing of ART initiation was not associated with any adverse perinatal outcomes. [ABSTRACT FROM AUTHOR]

Published
2023
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33. Country Level Diversity of the HIV-1 Pandemic between 1990 and 2015

Author

Hemelaar, Joris, Loganathan, Shanghavie, Elangovan, Ramyiadarsini, Yun, Jason, Dickson-Tetteh, Leslie, Kirtley, Shona, Abimiku, Alash’le G., Agwale, Simon, Archibald, Chris, Avidor, Boaz, Barbás, María Gabriela, Barre-Sinoussi, Francoise, Barugahare, Banson, Belabbes, El Hadj, Bertagnolio, Silvia, Birx, Deborah, Bobkov, Aleksei F., Brandful, James, Bredell, Helba, Brennan, Catherine A., Brooks, James, Bruckova, Marie, Buonaguro, Luigi, Buonaguro, Franco, Buttò, Stefano, Buvé, Anne, Campbell, Mary, Carr, Jean, Carrera, Alex, Carrillo, Manuel G. mez, Celum, Connie, Chaplin, Beth, Charles, Macarthur, Chatzidimitriou, Dimitrios, Chen, Zhiwei, Chijiwa, Katsumi, Cooper, David, Cunningham, Philip, Dagnra, Anoumou, de Gascun, Cillian F., del Amo, Julia, Delgado, Elena, Dietrich, Ursula, Dwyer, Dominic, Ellenberger, Dennis, Ensoli, Barbara, Essex, Max, Hamers, Raph L., Loukachov, Vladimir, Rinke de Wit, Tobias, Global Health, AII - Infectious diseases, APH - Personalized Medicine, APH - Quality of Care, Graduate School, and Experimental Immunology

Subjects
medicine.medical_specialty, Unique recombinant form, Genotype, URF, Immunology, HIV Infections, Drug resistance, Biology, Global Health, Microbiology, Circulating recombinant form, 03 medical and health sciences, Diversity index, 0302 clinical medicine, Virology, Pandemic, Epidemiology, Global health, medicine, Humans, 030212 general & internal medicine, HIV vaccine, Pandemics, 030304 developmental biology, Recombination, Genetic, Diversity, 0303 health sciences, Recombinant, Molecular epidemiology, Genetic Variation, HIV, virus diseases, CRF, Cross-Sectional Studies, Genetic Diversity and Evolution, Insect Science, HIV-1, Viral load, Demography
Abstract

Background: The global diversity of HIV forms a major challenge to the development of an HIV vaccine, as well as diagnostic, drug resistance, and viral load assays, which are essential to reaching the UNAIDS 90:90:90 targets. We sought to determine country-level HIV-1 diversity globally during 1990-2015.Methods: We assembled a global HIV-1 molecular epidemiology database through a systematic literature search and a global survey. We searched PubMed, EMBASE (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) for HIV-1 subtyping studies published from Jan 1, 1990, to Dec 31, 2015. We collected additional unpublished data through a global survey of experts. Prevalence studies with original HIV-1 subtyping data collected during 1990-2015 were included. This resulted in a database with 383 519 subtyped HIV-1 samples from 116 countries over four time periods (1990-99, 2000-04, 2005-09 and 2010-15). We analysed country-specific numbers of distinct HIV-1 subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) in each time period. We also analysed country-specific proportions of infections due to HIV-1 recombinants, CRFs, and URFs and calculated the Shannon Diversity Index for each country. Finally, we analysed global temporal trends in each of these measures of HIV-1 diversity.Results: We found extremely wide variation in complexity of country-level HIV diversity around the world. Central African countries such as Chad, Democratic Republic of the Congo, Angola and Republic of the Congo have the most diverse HIV epidemics. The number of distinct HIV-1 subtypes and recombinants was greatest in Western Europe (Spain and France) and North America (USA) (up to 39 distinct HIV-1 variants in Spain). The proportion of HIV-1 infections due to recombinants was highest in South-East Asia (>95% of infections in Viet Nam, Cambodia, and Thailand), China and West and Central Africa, mainly due to high proportions of CRF01_AE and CRF02_AG. Other CRFs played major roles (>75% of HIV-1 infections) in Estonia (CRF06_cpx), Iran (CRF35_AD), and Algeria (CRF06_cpx). The highest proportions of URFs (>30%) were found in Myanmar, Republic of the Congo and Argentina. Global temporal analysis showed consistent increases over time in country-level numbers of distinct HIV-1 variants and proportions of CRFs and URFs, leading to increases in country-level HIV-1 diversity.Conclusion: Our study provides epidemiological evidence that the HIV pandemic is diversifying at country-level and highlights the increasing challenge to prevention and treatment efforts. HIV-1 molecular epidemiological surveillance needs to be continued and improved.IMPORTANCE Global HIV diversity forms a major challenge to the development of an HIV vaccine, as well as diagnostic, drug resistance, and viral load assays, which are essential to reaching the UNAIDS 90:90:90 targets. This is the first study to analyse global country-level HIV-1 diversity during 1990-2015. We found extremely wide variation in complexity of country-level HIV diversity around the world. Central African countries have the most diverse HIV epidemics. The number of distinct HIV-1 subtypes and recombinants was greatest in Western Europe and North America. The proportion of HIV-1 infections due to recombinants was highest in South-East Asia, China and West and Central Africa. The highest proportions of URFs were found in Myanmar, Republic of the Congo and Argentina. Our study provides epidemiological evidence that the HIV pandemic is diversifying at country-level and highlights the increasing challenge to HIV vaccine development, and diagnostic, drug resistance, and viral load assays.

Published
2020
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37. Global and regional epidemiology of HIV-1 recombinants in 1990–2015: a systematic review and global survey

Author

Hemelaar, Joris, primary, Elangovan, Ramyiadarsini, additional, Yun, Jason, additional, Dickson-Tetteh, Leslie, additional, Kirtley, Shona, additional, Gouws-Williams, Eleanor, additional, Ghys, Peter D, additional, Abimiku, Alash'le G, additional, Agwale, Simon, additional, Archibald, Chris, additional, Avidor, Boaz, additional, Barbás, María Gabriela, additional, Barre-Sinoussi, Francoise, additional, Barugahare, Banson, additional, Belabbes, El Hadj, additional, Bertagnolio, Silvia, additional, Birx, Deborah, additional, Bobkov, Aleksei F, additional, Brandful, James, additional, Bredell, Helba, additional, Brennan, Catherine A, additional, Brooks, James, additional, Bruckova, Marie, additional, Buonaguro, Luigi, additional, Buonaguro, Franco, additional, Buttò, Stefano, additional, Buvé, Anne, additional, Campbell, Mary, additional, Carr, Jean, additional, Carrera, Alex, additional, Carrillo, Manuel Gómez, additional, Celum, Connie, additional, Chaplin, Beth, additional, Charles, Macarthur, additional, Chatzidimitriou, Dimitrios, additional, Chen, Zhiwei, additional, Chijiwa, Katsumi, additional, Cooper, David, additional, Cunningham, Philip, additional, Dagnra, Anoumou, additional, de Gascun, Cillian F, additional, Del Amo, Julia, additional, Delgado, Elena, additional, Dietrich, Ursula, additional, Dwyer, Dominic, additional, Ellenberger, Dennis, additional, Ensoli, Barbara, additional, Essex, Max, additional, Gao, Feng, additional, Fleury, Hervé, additional, Fonjungo, Peter N, additional, Foulongne, Vincent, additional, Gadkari, Deepak A, additional, García, Federico, additional, Garsia, Roger, additional, Gershy-Damet, Guy Michel, additional, Glynn, Judith R, additional, Goodall, Ruth, additional, Grossman, Zehava, additional, Lindenmeyer-Guimarães, Monick, additional, Hahn, Beatrice, additional, Hamers, Raph L, additional, Hamouda, Osamah, additional, Handema, Ray, additional, He, Xiang, additional, Herbeck, Joshua, additional, Ho, David D, additional, Holguin, Africa, additional, Hosseinipour, Mina, additional, Hunt, Gillian, additional, Ito, Masahiko, additional, Bel Hadj Kacem, Mohamed Ali, additional, Kahle, Erin, additional, Kaleebu, Pontiano, additional, Kalish, Marcia, additional, Kamarulzaman, Adeeba, additional, Kang, Chun, additional, Kanki, Phyllis, additional, Karamov, Edward, additional, Karasi, Jean-Claude, additional, Kayitenkore, Kayitesi, additional, Kelleher, Tony, additional, Kitayaporn, Dwip, additional, Kostrikis, Leondios G, additional, Kucherer, Claudia, additional, Lara, Claudia, additional, Leitner, Thomas, additional, Liitsola, Kirsi, additional, Lingappa, Jai, additional, Linka, Marek, additional, Lorenzana de Rivera, Ivette, additional, Lukashov, Vladimir, additional, Maayan, Shlomo, additional, Mayr, Luzia, additional, McCutchan, Francine, additional, Meda, Nicolas, additional, Menu, Elisabeth, additional, Mhalu, Fred, additional, Mloka, Doreen, additional, Mokili, John L, additional, Montes, Brigitte, additional, Mor, Orna, additional, Morgado, Mariza, additional, Mosha, Fausta, additional, Moussi, Awatef, additional, Mullins, James, additional, Najera, Rafael, additional, Nasr, Mejda, additional, Ndembi, Nicaise, additional, Neilson, Joel R, additional, Nerurkar, Vivek R, additional, Neuhann, Florian, additional, Nolte, Claudine, additional, Novitsky, Vlad, additional, Nyambi, Philippe, additional, Ofner, Marianna, additional, Paladin, Fem J, additional, Papa, Anna, additional, Pape, Jean, additional, Parkin, Neil, additional, Parry, Chris, additional, Peeters, Martine, additional, Pelletier, Alexandra, additional, Pérez-Álvarez, Lucía, additional, Pillay, Deenan, additional, Pinto, Angie, additional, Quang, Trinh Duy, additional, Rademeyer, Cecilia, additional, Raikanikoda, Filimone, additional, Rayfield, Mark A, additional, Reynes, Jean-Marc, additional, Rinke de Wit, Tobias, additional, Robbins, Kenneth E, additional, Rolland, Morgane, additional, Rousseau, Christine, additional, Salazar-Gonzales, Jesus, additional, Salem, Hanan, additional, Salminen, Mika, additional, Salomon, Horacio, additional, Sandstrom, Paul, additional, Santiago, Mario L, additional, Sarr, Abdoulaye D, additional, Schroeder, Bryan, additional, Segondy, Michel, additional, Selhorst, Philippe, additional, Sempala, Sylvester, additional, Servais, Jean, additional, Shaik, Ansari, additional, Shao, Yiming, additional, Slim, Amine, additional, Soares, Marcelo A, additional, Songok, Elijah, additional, Stewart, Debbie, additional, Stokes, Julie, additional, Subbarao, Shambavi, additional, Sutthent, Ruengpung, additional, Takehisa, Jun, additional, Tanuri, Amilcar, additional, Tee, Kok Keng, additional, Thapa, Kiran, additional, Thomson, Michael, additional, Tran, Tyna, additional, Urassa, Willy, additional, Ushijima, Hiroshi, additional, van de Perre, Philippe, additional, van der Groen, Guido, additional, van Laethem, Kristel, additional, van Oosterhout, Joep, additional, van Sighem, Ard, additional, van Wijngaerden, Eric, additional, Vandamme, Anne-Mieke, additional, Vercauteren, Jurgen, additional, Vidal, Nicole, additional, Wallace, Lesley, additional, Williamson, Carolyn, additional, Wolday, Dawit, additional, Xu, Jianqing, additional, Yang, Chunfu, additional, Zhang, Linqi, additional, and Zhang, Rong, additional

Published
2020
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44. Global and regional molecular epidemiology of HIV-1, 1990–2015: a systematic review, global survey, and trend analysis

Author

Hemelaar, Joris, Elangovan, Ramyiadarsini, Yun, Jason, Dickson-Tetteh, Leslie, Fleminger, Isabella, Kirtley, Shona, Williams, Brian, Gouws-Williams, Eleanor, Ghys, Peter D, Abimiku, Alash'le G, Agwale, Simon, Archibald, Chris, Avidor, Boaz, Barbás, María Gabriela, Barre-Sinoussi, Francoise, Barugahare, Banson, Belabbes, El Hadj, Bertagnolio, Silvia, Birx, Deborah, Bobkov, Aleksei F, Brandful, James, Bredell, Helba, Brennan, Catherine A, Brooks, James, Bruckova, Marie, Buonaguro, Luigi, Buonaguro, Franco, Buttò, Stefano, Buve, Anne, Campbell, Mary, Carr, Jean, Carrera, Alex, Carrillo, Manuel Gómez, Celum, Connie, Chaplin, Beth, Charles, Macarthur, Chatzidimitriou, Dimitrios, Chen, Zhiwei, Chijiwa, Katsumi, Cooper, David, Cunningham, Philip, Dagnra, Anoumou, de Gascun, Cillian F, Del Amo, Julia, Delgado, Elena, Dietrich, Ursula, Dwyer, Dominic, Ellenberger, Dennis, Ensoli, Barbara, Essex, Max, Gao, Feng, Fleury, Herve, Fonjungo, Peter N, Foulongne, Vincent, Gadkari, Deepak A, García, Federico, Garsia, Roger, Gershy-Damet, Guy Michel, Glynn, Judith R, Goodall, Ruth, Grossman, Zehava, Lindenmeyer-Guimarães, Monick, Hahn, Beatrice, Hamers, Raph L, Hamouda, Osamah, Handema, Ray, He, Xiang, Herbeck, Joshua, Ho, David D, Holguin, Africa, Hosseinipour, Mina, Hunt, Gillian, Ito, Masahiko, Bel Hadj Kacem, Mohamed Ali, Kahle, Erin, Kaleebu, Pontiano Kaleebu, Kalish, Marcia, Kamarulzaman, Adeeba, Kang, Chun, Kanki, Phyllis, Karamov, Edward, Karasi, Jean-Claude, Kayitenkore, Kayitesi, Kelleher, Tony, Kitayaporn, Dwip, Kostrikis, Leondios G, Kucherer, Claudia, Lara, Claudia, Leitner, Thomas, Liitsola, Kirsi, Lingappa, Jai, Linka, Marek, Lorenzana de Rivera, Ivette, Lukashov, Vladimir, Maayan, Shlomo, Mayr, Luzia, McCutchan, Francine, Meda, Nicolas, Menu, Elisabeth, Mhalu, Fred, Mloka, Doreen, Mokili, John L, Montes, Brigitte, Mor, Orna, Morgado, Mariza, Mosha, Fausta, Moussi, Awatef, Mullins, James, Najera, Rafael, Nasr, Mejda, Ndembi, Nicaise, Neilson, Joel R, Nerurkar, Vivek R, Neuhann, Florian, Nolte, Claudine, Novitsky, Vlad, Nyambi, Philippe, Ofner, Marianna, Paladin, Fem J, Papa, Anna, Pape, Jean, Parkin, Neil, Parry, Chris, Peeters, Martine, Pelletier, Alexandra, Pérez-Álvarez, Lucía, Pillay, Deenan, Pinto, Angie, Quang, Trinh Duy, Rademeyer, Cecilia, Raikanikoda, Filimone, Rayfield, Mark A, Reynes, Jean-Marc, Rinke de Wit, Tobias, Robbins, Kenneth E, Rolland, Morgane, Rousseau, Christine, Salazar-Gonzales, Jesus, Salem, Hanan, Salminen, Mika, Salomon, Horacio, Sandstrom, Paul, Santiago, Mario L, Sarr, Abdoulaye D, Schroeder, Bryan, Segondy, Michel, Selhorst, Philippe, Sempala, Sylvester, Servais, Jean, Shaik, Ansari, Shao, Yiming, Slim, Amine, Soares, Marcelo A, Songok, Elijah, Stewart, Debbie, Stokes, Julie, Subbarao, Shambavi, Sutthent, Ruengpung, Takehisa, Jun, Tanuri, Amilcar, Tee, Kok Keng, Thapa, Kiran, Thomson, Michael, Tran, Tyna, Urassa, Willy, Ushijima, Hiroshi, van de Perre, Philippe, van der Groen, Guido, van Laethem, Kristel, van Oosterhout, Joep, van Sighem, Ard, van Wijngaerden, Eric, Vandamme, Anne-Mieke, Vercauteren, Jurgen, Vidal, Nicole, Wallace, Lesley, Williamson, Carolyn, Wolday, Dawit, Xu, Jianqing, Yang, Chunfu, Zhang, Linqi, Zhang, Rong, John Radcliffe Hospital [Oxford University Hospital], Centre for Statistics in Medicine, University of Oxford [Oxford], Stellenbosch University, UNAIDS [Genève, Suisse] (ONUSIDA), Institut Pasteur [Paris], Noguchi Memorial Institute for Medical Research [Accra, Ghana] (NMIMR), University of Ghana, Institute of Tropical Medicine [Antwerp] (ITM), State Key Laboratory of Silkworm Genome Biology, Southwest University, Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Georg-Speyer-Haus, The University of Sydney, National AIDS Centre, Istituto Superiore di Sanita [Rome], Harvard School of Public Health, Digital Enterprise Research Institute (DERI-NUIG), National University of Ireland [Galway] (NUI Galway), Microbiologie cellulaire et moléculaire et pathogénicité (MCMP), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Virologie, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Pathogénèse et contrôle des infections chroniques (PCCI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), Departments of Medicine and Microbiology, University of Alabama at Birmingham [ Birmingham] (UAB), Robert Koch Institute [Berlin] (RKI), Beihang University (BUAA), Statens Serum Institut [Copenhagen], Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), SANTE/SIDA [Bobo-Dioulasso, Burkina Faso], Institut de Recherche en Sciences de la Santé (IRSS) / Centre Muraz, Department of Microbiology, University of Washington School of Medicine, Department of Microbiology, Medical School, University of Thessaly [Volos] (UTH), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Africa Centre for Health and Population Studies, University of KwaZulu-Natal (UKZN)-Medical Research Council of South Africa, Lab-STICC_UBO_CID_IHSEV, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Laboratory of Virology, CHU Rouen, Normandie Université (NU)-Normandie Université (NU), Universidade Federal do Rio de Janeiro (UFRJ), Departements of Medicine and Microbiology, University of Alabama [Tuscaloosa] (UA), Stichting HIV Monitoring [Amsterdam], Universiteit van Amsterdam (UvA), Département Génétique Internal Médecine, Hôpital Universitaire Leuven, Department of Chemical and Biomolecular Engineering [Baltimore], Johns Hopkins University (JHU), Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, China Academy of Chinese Medical Sciences, Chatzidimitriou, Dimitrios [0000-0001-9656-5898], University of Oxford, Institut Pasteur [Paris] (IP), Istituto Superiore di Sanità (ISS), Microbiologie Fondamentale et Pathogénicité (MFP), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), University of KwaZulu-Natal [Durban, Afrique du Sud] (UKZN)-Medical Research Council of South Africa, Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), UNAIDS, Noguchi Memorial Institute for Medical Research, University of Ghana, Laboratoire d'Electronique et des Technologies de l'Information (CEA-LETI), Université Grenoble Alpes (UGA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Beihang University, Recherches Translationnelles sur le VIH et les maladies infectieuses (TransVIHMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 1 (UM1)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Universtié Yaoundé 1 [Cameroun]-Université de Montpellier (UM), Universidade Federal do Rio de Janeiro [Rio de Janeiro] (UFRJ), Nuffield Department of Women's and Reproductive Health (NDWRH), University of Oxford- John Radcliffe Hospital [Oxford University Hospital], South African Centre for Epidemiological Modelling and Analysis, JH is supported by the Oxford University Clinical Academic Graduate School (Oxford, UK) and Linacre College, Oxford University (Oxford, UK)., WHO–UNAIDS Network for HIV Isolation Characterisation : Alash'le G Abimiku, Simon Agwale, Chris Archibald, Boaz Avidor, María Gabriela Barbás, Francoise Barre-Sinoussi, Banson Barugahare, El Hadj Belabbes, Silvia Bertagnolio, Deborah Birx, Aleksei F Bobkov, James Brandful, Helba Bredell, Catherine A Brennan, James Brooks, Marie Bruckova, Luigi Buonaguro, Franco Buonaguro, Stefano Buttò, Anne Buve, Mary Campbell, Jean Carr, Alex Carrera, Manuel Gómez Carrillo, Connie Celum, Beth Chaplin, Macarthur Charles, Dimitrios Chatzidimitriou, Zhiwei Chen, Katsumi Chijiwa, David Cooper, Philip Cunningham, Anoumou Dagnra, Cillian F de Gascun, Julia Del Amo, Elena Delgado, Ursula Dietrich, Dominic Dwyer, Dennis Ellenberger, Barbara Ensoli, Max Essex, Feng Gao, Herve Fleury, Peter N Fonjungo, Vincent Foulongne, Deepak A Gadkari, Federico García, Roger Garsia, Guy Michel Gershy-Damet, Judith R Glynn, Ruth Goodall, Zehava Grossman, Monick Lindenmeyer-Guimarães, Beatrice Hahn, Raph L Hamers, Osamah Hamouda, Ray Handema, Xiang He, Joshua Herbeck, David D Ho, Africa Holguin, Mina Hosseinipour, Gillian Hunt, Masahiko Ito, Mohamed Ali Bel Hadj Kacem, Erin Kahle, Pontiano Kaleebu Kaleebu, Marcia Kalish, Adeeba Kamarulzaman, Chun Kang, Phyllis Kanki, Edward Karamov, Jean-Claude Karasi, Kayitesi Kayitenkore, Tony Kelleher, Dwip Kitayaporn, Leondios G Kostrikis, Claudia Kucherer, Claudia Lara, Thomas Leitner, Kirsi Liitsola, Jai Lingappa, Marek Linka, Ivette Lorenzana de Rivera, Vladimir Lukashov, Shlomo Maayan, Luzia Mayr, Francine McCutchan, Nicolas Meda, Elisabeth Menu, Fred Mhalu, Doreen Mloka, John L Mokili, Brigitte Montes, Orna Mor, Mariza Morgado, Fausta Mosha, Awatef Moussi, James Mullins, Rafael Najera, Mejda Nasr, Nicaise Ndembi, Joel R Neilson, Vivek R Nerurkar, Florian Neuhann, Claudine Nolte, Vlad Novitsky, Philippe Nyambi, Marianna Ofner, Fem J Paladin, Anna Papa, Jean Pape, Neil Parkin, Chris Parry, Martine Peeters, Alexandra Pelletier, Lucía Pérez-Álvarez, Deenan Pillay, Angie Pinto, Trinh Duy Quang, Cecilia Rademeyer, Filimone Raikanikoda, Mark A Rayfield, Jean-Marc Reynes, Tobias Rinke de Wit, Kenneth E Robbins, Morgane Rolland, Christine Rousseau, Jesus Salazar-Gonzales, Hanan Salem, Mika Salminen, Horacio Salomon, Paul Sandstrom, Mario L Santiago, Abdoulaye D Sarr, Bryan Schroeder, Michel Segondy, Philippe Selhorst, Sylvester Sempala, Jean Servais, Ansari Shaik, Yiming Shao, Amine Slim, Marcelo A Soares, Elijah Songok, Debbie Stewart, Julie Stokes, Shambavi Subbarao, Ruengpung Sutthent, Jun Takehisa, Amilcar Tanuri, Kok Keng Tee, Kiran Thapa, Michael Thomson, Tyna Tran, Willy Urassa, Hiroshi Ushijima, Philippevan de Perre, Guidovan der Groen, Kristel van Laethem, Joep van Oosterhout, Ard van Sighem, Eric van Wijngaerden, Anne-Mieke Vandamme, Jurgen Vercauteren, Nicole Vidal, Lesley Wallace, Carolyn Williamson, Dawit Wolday, Jianqing Xu, Chunfu Yang, Linqi Zhang, and Rong Zhang

Subjects
0301 basic medicine, Serotype, Genotype, Genotyping Techniques, 030106 microbiology, DIVERSITY, MULTICENTER, VACCINE, HIV Infections, Genome, Viral, Biology, Global Health, Serogroup, SUBTYPES, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Surveys and Questionnaires, INFECTION, Genetic variation, Global health, Humans, HIV vaccine, Serotyping, AIDS Vaccines, Science & Technology, Molecular epidemiology, Genetic Variation, Subtyping, 3. Good health, Trend analysis, 030104 developmental biology, Infectious Diseases, 13. Climate action, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, HIV-1, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Life Sciences & Biomedicine, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Demography
Abstract

BACKGROUND: Global genetic diversity of HIV-1 is a major challenge to the development of HIV vaccines. We aimed to estimate the regional and global distribution of HIV-1 subtypes and recombinants during 1990-2015. METHODS: We searched PubMed, EMBASE (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) for HIV-1 subtyping studies published between Jan 1, 1990, and Dec 31, 2015. We collected additional unpublished HIV-1 subtyping data through a global survey. We included prevalence studies with HIV-1 subtyping data collected during 1990-2015. We grouped countries into 14 regions and analysed data for four time periods (1990-99, 2000-04, 2005-09, and 2010-15). The distribution of HIV-1 subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) in individual countries was weighted according to the UNAIDS estimates of the number of people living with HIV (PLHIV) in each country to generate regional and global estimates of HIV-1 diversity in each time period. The primary outcome was the number of samples designated as HIV-1 subtypes A, B, C, D, F, G, H, J, K, CRFs, and URFs. The systematic review is registered with PROSPERO, number CRD42017067164. FINDINGS: This systematic review and global survey yielded 2203 datasets with 383 519 samples from 116 countries in 1990-2015. Globally, subtype C accounted for 46·6% (16 280 897/34 921 639 of PLHIV) of all HIV-1 infections in 2010-15. Subtype B was responsible for 12·1% (4 235 299/34 921 639) of infections, followed by subtype A (10·3%; 3 587 003/34 921 639), CRF02_AG (7·7%; 2 705 110/34 921 639), CRF01_AE (5·3%; 1 840 982/34 921 639), subtype G (4·6%; 1 591 276/34 921 639), and subtype D (2·7%; 926 255/34 921 639). Subtypes F, H, J, and K combined accounted for 0·9% (311 332/34 921 639) of infections. Other CRFs accounted for 3·7% (1 309 082/34 921 639), bringing the proportion of all CRFs to 16·7% (5 844 113/34 921 639). URFs constituted 6·1% (2 134 405/34 921 639), resulting in recombinants accounting for 22·8% (7 978 517/34 921 639) of all global HIV-1 infections. The distribution of HIV-1 subtypes and recombinants changed over time in countries, regions, and globally. At a global level during 2005-15, subtype B increased, subtypes A and D were stable, and subtypes C and G and CRF02_AG decreased. CRF01_AE, other CRFs, and URFs increased, leading to a consistent increase in the global proportion of recombinants over time. INTERPRETATION: Global and regional HIV diversity is complex and evolving, and is a major challenge to HIV vaccine development. Surveillance of the global molecular epidemiology of HIV-1 remains crucial for the design, testing, and implementation of HIV vaccines. FUNDING: None. ispartof: LANCET INFECTIOUS DISEASES vol:19 issue:2 pages:143-155 ispartof: location:United States status: published

Published
2018
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45. Global and regional molecular epidemiology of HIV-1, 1990–2015: a systematic review, global survey, and trend analysis

Author

Hemelaar, Joris, primary, Elangovan, Ramyiadarsini, additional, Yun, Jason, additional, Dickson-Tetteh, Leslie, additional, Fleminger, Isabella, additional, Kirtley, Shona, additional, Williams, Brian, additional, Gouws-Williams, Eleanor, additional, Ghys, Peter D, additional, Abimiku, Alash'le G, additional, Agwale, Simon, additional, Archibald, Chris, additional, Avidor, Boaz, additional, Barbás, María Gabriela, additional, Barre-Sinoussi, Francoise, additional, Barugahare, Banson, additional, Belabbes, El Hadj, additional, Bertagnolio, Silvia, additional, Birx, Deborah, additional, Bobkov, Aleksei F, additional, Brandful, James, additional, Bredell, Helba, additional, Brennan, Catherine A, additional, Brooks, James, additional, Bruckova, Marie, additional, Buonaguro, Luigi, additional, Buonaguro, Franco, additional, Buttò, Stefano, additional, Buve, Anne, additional, Campbell, Mary, additional, Carr, Jean, additional, Carrera, Alex, additional, Carrillo, Manuel Gómez, additional, Celum, Connie, additional, Chaplin, Beth, additional, Charles, Macarthur, additional, Chatzidimitriou, Dimitrios, additional, Chen, Zhiwei, additional, Chijiwa, Katsumi, additional, Cooper, David, additional, Cunningham, Philip, additional, Dagnra, Anoumou, additional, de Gascun, Cillian F, additional, Del Amo, Julia, additional, Delgado, Elena, additional, Dietrich, Ursula, additional, Dwyer, Dominic, additional, Ellenberger, Dennis, additional, Ensoli, Barbara, additional, Essex, Max, additional, Gao, Feng, additional, Fleury, Herve, additional, Fonjungo, Peter N, additional, Foulongne, Vincent, additional, Gadkari, Deepak A, additional, García, Federico, additional, Garsia, Roger, additional, Gershy-Damet, Guy Michel, additional, Glynn, Judith R, additional, Goodall, Ruth, additional, Grossman, Zehava, additional, Lindenmeyer-Guimarães, Monick, additional, Hahn, Beatrice, additional, Hamers, Raph L, additional, Hamouda, Osamah, additional, Handema, Ray, additional, He, Xiang, additional, Herbeck, Joshua, additional, Ho, David D, additional, Holguin, Africa, additional, Hosseinipour, Mina, additional, Hunt, Gillian, additional, Ito, Masahiko, additional, Bel Hadj Kacem, Mohamed Ali, additional, Kahle, Erin, additional, Kaleebu, Pontiano Kaleebu, additional, Kalish, Marcia, additional, Kamarulzaman, Adeeba, additional, Kang, Chun, additional, Kanki, Phyllis, additional, Karamov, Edward, additional, Karasi, Jean-Claude, additional, Kayitenkore, Kayitesi, additional, Kelleher, Tony, additional, Kitayaporn, Dwip, additional, Kostrikis, Leondios G, additional, Kucherer, Claudia, additional, Lara, Claudia, additional, Leitner, Thomas, additional, Liitsola, Kirsi, additional, Lingappa, Jai, additional, Linka, Marek, additional, Lorenzana de Rivera, Ivette, additional, Lukashov, Vladimir, additional, Maayan, Shlomo, additional, Mayr, Luzia, additional, McCutchan, Francine, additional, Meda, Nicolas, additional, Menu, Elisabeth, additional, Mhalu, Fred, additional, Mloka, Doreen, additional, Mokili, John L, additional, Montes, Brigitte, additional, Mor, Orna, additional, Morgado, Mariza, additional, Mosha, Fausta, additional, Moussi, Awatef, additional, Mullins, James, additional, Najera, Rafael, additional, Nasr, Mejda, additional, Ndembi, Nicaise, additional, Neilson, Joel R, additional, Nerurkar, Vivek R, additional, Neuhann, Florian, additional, Nolte, Claudine, additional, Novitsky, Vlad, additional, Nyambi, Philippe, additional, Ofner, Marianna, additional, Paladin, Fem J, additional, Papa, Anna, additional, Pape, Jean, additional, Parkin, Neil, additional, Parry, Chris, additional, Peeters, Martine, additional, Pelletier, Alexandra, additional, Pérez-Álvarez, Lucía, additional, Pillay, Deenan, additional, Pinto, Angie, additional, Quang, Trinh Duy, additional, Rademeyer, Cecilia, additional, Raikanikoda, Filimone, additional, Rayfield, Mark A, additional, Reynes, Jean-Marc, additional, Rinke de Wit, Tobias, additional, Robbins, Kenneth E, additional, Rolland, Morgane, additional, Rousseau, Christine, additional, Salazar-Gonzales, Jesus, additional, Salem, Hanan, additional, Salminen, Mika, additional, Salomon, Horacio, additional, Sandstrom, Paul, additional, Santiago, Mario L, additional, Sarr, Abdoulaye D, additional, Schroeder, Bryan, additional, Segondy, Michel, additional, Selhorst, Philippe, additional, Sempala, Sylvester, additional, Servais, Jean, additional, Shaik, Ansari, additional, Shao, Yiming, additional, Slim, Amine, additional, Soares, Marcelo A, additional, Songok, Elijah, additional, Stewart, Debbie, additional, Stokes, Julie, additional, Subbarao, Shambavi, additional, Sutthent, Ruengpung, additional, Takehisa, Jun, additional, Tanuri, Amilcar, additional, Tee, Kok Keng, additional, Thapa, Kiran, additional, Thomson, Michael, additional, Tran, Tyna, additional, Urassa, Willy, additional, Ushijima, Hiroshi, additional, van de Perre, Philippe, additional, van der Groen, Guido, additional, van Laethem, Kristel, additional, van Oosterhout, Joep, additional, van Sighem, Ard, additional, van Wijngaerden, Eric, additional, Vandamme, Anne-Mieke, additional, Vercauteren, Jurgen, additional, Vidal, Nicole, additional, Wallace, Lesley, additional, Williamson, Carolyn, additional, Wolday, Dawit, additional, Xu, Jianqing, additional, Yang, Chunfu, additional, Zhang, Linqi, additional, and Zhang, Rong, additional

Published
2019
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46. Global and Regional Estimates for Subtype-Specific Therapeutic and Prophylactic HIV-1 Vaccines: A Modeling Study.

Author

Elangovan, Ramyiadarsini, Jenks, Michael, Yun, Jason, Dickson-Tetteh, Leslie, Kirtley, Shona, Hemelaar, Joris, Abimiku, Alash'le G, Agwale, Simon, Archibald, Chris, Avidor, Boaz, Barbás, María Gabriela, Barre-Sinoussi, Francoise, Barugahare, Banson, Belabbes, El Hadj, Bertagnolio, Silvia, Birx, Deborah, Bobkov, Aleksei F, Brandful, James, Bredell, Helba, and Brennan, Catherine A

Subjects
HIV, AIDS vaccines, HIV infections, GENETIC variation, VACCINES
Abstract

Global HIV-1 genetic diversity forms a major obstacle to the development of an HIV vaccine. It may be necessary to employ subtype-specific HIV-1 vaccines in individual countries according to their HIV-1 subtype distribution. We estimated the global and regional need for subtype-specific HIV-1 vaccines. We took into account the proportions of different HIV-1 variants circulating in each country, the genetic composition of HIV-1 recombinants, and the different genome segments (gag , pol , env) that may be incorporated into vaccines. We modeled different scenarios according to whether countries would employ subtype-specific HIV-1 vaccines against (1) the most common subtype; (2) subtypes contributing more than 5% of HIV infections; or (3) all circulating subtypes. For therapeutic vaccines targeting the most common HIV-1 subtype in each country, 16.5 million doses of subtype C vaccine were estimated globally, followed by subtypes A (14.3 million) and B (4.2 million). A vaccine based on env required 2.6 million subtype E doses, and a vaccine based on pol required 4.8 million subtype G doses. For prophylactic vaccines targeting the most common HIV-1 subtype in each country, 1.9 billion doses of subtype A vaccine were estimated globally, followed by subtype C (1.1 billion) and subtype B (1.0 billion). A vaccine based on env required 1.2 billion subtype E doses, and a vaccine based on pol required 0.3 billion subtype G doses. If subtype-specific HIV-1 vaccines are also directed against less common subtypes in each country, vaccines targeting subtypes D, F, H, and K are also needed and would require up to five times more vaccine doses in total. We conclude that to provide global coverage, subtype-specific HIV-1 vaccines need to be directed against subtypes A, B, and C. Vaccines targeting env also need to include subtype E and those targeting pol need to include subtype G. [ABSTRACT FROM AUTHOR]

Published
2021
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47. Country Level Diversity of the HIV-1 Pandemic between 1990 and 2015.

Author

Hemelaar, Joris, Loganathan, Shanghavie, Elangovan, Ramyiadarsini, Jason Yun, Dickson-Tetteh, Leslie, and Kirtley, Shona

Subjects
*OVERTIME, *VACCINE development, *AIDS vaccines, *VIRAL load, *ACQUISITION of data, *PANDEMICS, *MOLECULAR epidemiology
Abstract

The global diversity of HIV forms a major challenge to the development of an HIV vaccine, as well as diagnostic, drug resistance, and viral load assays, which are essential to reaching the UNAIDS 90:90:90 targets. We sought to determine country level HIV-1 diversity globally between 1990 and 2015. We assembled a global HIV-1 molecular epidemiology database through a systematic literature search and a global survey. We searched PubMed, EMBASE (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) for HIV-1 subtyping studies published from 1 January 1990 to 31 December 2015. We collected additional unpublished data through a global survey of experts. Prevalence studies with original HIV-1 subtyping data collected between 1990 and 2015 were included. This resulted in a database with 383,519 subtyped HIV-1 samples from 116 countries over four time periods (1990 to 1999, 2000 to 2004, 2005 to 2009, and 2010 to 2015). We analyzed country-specific numbers of distinct HIV-1 subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) in each time period. We also analyzed country-specific proportions of infections due to HIV-1 recombinants, CRFs, and URFs and calculated the Shannon diversity index for each country. Finally, we analyzed global temporal trends in each of these measures of HIV-1 diversity. We found extremely wide variation in complexity of country level HIV diversity around the world. Central African countries such as Chad, Democratic Republic of the Congo, Angola, and Republic of the Congo have the most diverse HIV epidemics. The number of distinct HIV-1 subtypes and recombinants was greatest in Western Europe (Spain and France) and North America (United States) (up to 39 distinct HIV-1 variants in Spain). The proportion of HIV-1 infections due to recombinants was highest in Southeast Asia (-95% of infections in Viet Nam, Cambodia, and Thailand), China, and West and Central Africa, mainly due to high proportions of CRF01_AE and CRF02_AG. Other CRFs played major roles (-75% of HIV-1 infections) in Estonia (CRF06_cpx), Iran (CRF35_AD), and Algeria (CRF06_cpx). The highest proportions of URFs (-30%) were found in Myanmar, Republic of the Congo, and Argentina. Global temporal analysis showed consistent increases over time in country level numbers of distinct HIV-1 variants and proportions of CRFs and URFs, leading to increases in country level HIV-1 diversity. Our study provides epidemiological evidence that the HIV pandemic is diversifying at country level and highlights the increasing challenge to prevention and treatment efforts. HIV-1 molecular epidemiological surveillance needs to be continued and improved. [ABSTRACT FROM AUTHOR]

Published
2021
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48. The interaction between HTLV-1 Tax protein and the proteasome

Author

Hemelaar, J, Hemelaar, Joris, and McMichael, A

Subjects
HTLV-I (Virus), Cytokines, Cellular immunity
Abstract

This thesis presents studies on the interaction between the human T cell lymphotropic virus type 1 (HTLV-1) Tax protein and the 20S proteasome and the role of the interaction in cellular processes and the cytotoxic T cell (CTL) response against HTLV-1. The rapid translocation of Tax into the nucleus is described. Tax accumulates in the nucleus and forms unique bodies involved in transcriptional activation. It was further found that Tax associated with assembled nuclear 20S proteasomes and stimulated the chymotryptic and tryptic activities of the 20S proteasome, independent of the induction of the LMP2 and LMP7 proteasome subunits. Confocal microscopy revealed a partial colocalisation of Tax with nuclear proteasomes. A panel of Tax mutants was generated and their subcellular localisation and association with the 20S proteasome analysed. This analysis revealed that both the N- and C-terminus of Tax play a role in proteasome binding of Tax and further showed that proteasome binding was not sufficient for nuclear localisation of Tax. Therefore, Tax probably translocates into the nucleus prior to and independent of proteasome association. Tax specific CTL clones were generated and characterised using tetrameric MHC class I/peptide complexes. These CTL clones were used to investigate the requirements for processing and presentation of Tax for recognition by CTL. It was found that Tax was a metabolically very stable protein and that the presentation of the immunodominant Tax 11-19 epitope was dependent on the transporter associated with antigen presentation (TAP), independent of the expression of LMP2 and LMP7 proteasome subunits and resistant to treatment with the proteasome inhibitor lactacystin. It is proposed that the interaction between Tax and the 20S proteasome plays a role in Tax mediated transcriptional activation, leading to cellular activation and proliferation, and may not determine the immunodominance of Tax in the CTL response against HTLV-1.

Published
2016

49. Role of HIV-specific CD8+ T cells in pediatric HIV cure strategies after widespread early viral escape

Author

Leitman, Ellen M., primary, Thobakgale, Christina F., additional, Adland, Emily, additional, Ansari, M. Azim, additional, Raghwani, Jayna, additional, Prendergast, Andrew J., additional, Tudor-Williams, Gareth, additional, Kiepiela, Photini, additional, Hemelaar, Joris, additional, Brener, Jacqui, additional, Tsai, Ming-Han, additional, Mori, Masahiko, additional, Riddell, Lynn, additional, Luzzi, Graz, additional, Jooste, Pieter, additional, Ndung’u, Thumbi, additional, Walker, Bruce D., additional, Pybus, Oliver G., additional, Kellam, Paul, additional, Naranbhai, Vivek, additional, Matthews, Philippa C., additional, Gall, Astrid, additional, and Goulder, Philip J.R., additional

Published
2017
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