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

Author

Dawit Wolday, Neil Parkin, Bryan Schroeder, Mary S. Campbell, Barbara Ensoli, Jean-Claude Karasi, Connie Celum, Ard van Sighem, Marcia L. Kalish, Gillian Hunt, Jurgen Vercauteren, Dimitrios Chatzidimitriou, Beth Chaplin, Alex Carrera, Ruth L. Goodall, Guido van der Groen, Martine Peeters, Leondios G. Kostrikis, Edward Karamov, Francine E. McCutchan, Cecilia Rademeyer, Mina C. Hosseinipour, Michael M. Thomson, Fred Mhalu, Christopher M. Parry, Florian Neuhann, Jean-Marc Reynes, James I. Mullins, Vivek R. Nerurkar, Pontiano Kaleebu, Phyllis J. Kanki, Christine Rousseau, Deepak A Gadkari, Luzia Mayr, Kristel Van Laethem, Vincent Foulongne, Guy Michel Gershy-Damet, Lesley Wallace, Mika Salminen, Carolyn Williamson, John L. Mokili, África Holguín, Horacio Salomon, James Brandful, Alexandra Pelletier, Philippe Van de Perre, Xiang He, Tyna Tran, Marie Bruckova, Jianqing Xu, Monick Lindenmeyer-Guimarães, Stefano Buttò, Anoumou Y. Dagnra, Deenan Pillay, Doreen Mloka, Aleksei F Bobkov, Mejda Nasr, Ivette Lorenzana de Rivera, Kenneth E. Robbins, Elisabeth Menu, Ruengpung Sutthent, María Gabriela Barbás, Hervé Fleury, Joep J. van Oosterhout, Rong Zhang, Luigi Buonaguro, Linqi Zhang, David D. Ho, Kayitesi Kayitenkore, Chris P. Archibald, Mario L. Santiago, Dennis Ellenberger, Boaz Avidor, Peter N. Fonjungo, Claudine Nolte, Nicole Vidal, Silvia Bertagnolio, Mohamed Ali Bel Hadj Kacem, Philippe Nyambi, Marianna Ofner, Abdoulaye Dieng Sarr, Rafael Nájera, Chun Kang, Claudia Kücherer, Manuel Gómez Carrillo, El Hadj Belabbes, Simon Agwale, Zhiwei Chen, Zehava Grossman, Dominic M. Dwyer, Eric Van Wijngaerden, Jean W. Pape, Beatrice H. Hahn, Angie N Pinto, Tobias F. Rinke de Wit, Lucía Pérez-Álvarez, Peter D. Ghys, Franco M. Buonaguro, Sylvester Sempala, Vlad Novitsky, Banson Barugahare, Judith R. Glynn, Jason Yun, Macarthur Charles, Katsumi Chijiwa, Kok Keng Tee, Julia del Amo, Adeeba Kamarulzaman, Federico García, Awatef Moussi, Elena Delgado, Hiroshi Ushijima, Shambavi Subbarao, Ray Handema, Catherine A. Brennan, Paul Sandstrom, David A. Cooper, Joel R. Neilson, Ramyiadarsini Elangovan, Dwip Kitayaporn, Claudia Lara, Max Essex, Osamah Hamouda, Anna Papa, Hanan Salem, Elijah M. Songok, Fausta Mosha, Helba Bredell, Shlomo Maayan, Joshua T. Herbeck, Yiming Shao, Ansari Shaik, Kiran Thapa, Jean K. Carr, Raph L. Hamers, Chunfu Yang, Feng Gao, Orna Mor, Filimone Raikanikoda, Jesus Salazar-Gonzales, Nicolas Meda, Erin M. Kahle, Amilcar Tanuri, Tony Kelleher, Masahiko Ito, Fem J Paladin, J.R. Lingappa, Julie Stokes, Shona Kirtley, Vladimir Lukashov, Anne-Mieke Vandamme, Deborah L. Birx, Philip Cunningham, Amine Slim, Nicaise Ndembi, James Brooks, Alash'le Abimiku, Françoise Barré-Sinoussi, Trinh Duy Quang, Eleanor Gouws-Williams, Mariza G. Morgado, Jun Takehisa, Michel Segondy, Joris Hemelaar, Debbie Stewart, Cillian De Gascun, Marcelo A. Soares, Anne Buvé, Mark A. Rayfield, Marek Linka, Ursula Dietrich, Roger Garsia, Thomas Leitner, Philippe Selhorst, Jean Servais, Morgane Rolland, Kirsi Liitsola, Leslie Dickson-Tetteh, Brigitte Montes, Willy Urassa, Global Health, AII - Infectious diseases, Graduate School, Experimental Immunology, APH - Personalized Medicine, APH - Quality of Care, Nuffield Department of Population Health [Oxford], University of Oxford [Oxford], John Radcliffe Hospital [Oxford University Hospital], UNAIDS [Genève, Suisse] (ONUSIDA), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Pathogénèse et contrôle des infections chroniques (PCCI), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre Hospitalier Universitaire de Montpellier (CHU Montpellier )

Subjects
0301 basic medicine, medicine.medical_specialty, Genotype, Epidemiology, Immunology, HIV Infections, MESH: Global Health, Global Health, MESH: Genotype, MESH: HIV-1, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Global health, medicine, Humans, MESH: Molecular Epidemiology, 030212 general & internal medicine, MESH: Genetic Variation, HIV vaccine, CRFS, Molecular Epidemiology, MESH: Humans, Molecular epidemiology, business.industry, Genetic Variation, virus diseases, MESH: HIV Infections, 030112 virology, Subtyping, 3. Good health, Infectious Diseases, Systematic review, MESH: Reassortant Viruses, HIV-1, [SDV.IMM]Life Sciences [q-bio]/Immunology, business, Viral load, Reassortant Viruses, Demography
Abstract

International audience; Background: Global HIV-1 genetic diversity and evolution form a major challenge to treatment and prevention efforts. An increasing number of distinct HIV-1 recombinants have been identified worldwide, but their contribution to the global epidemic is unknown. We aimed to estimate the global and regional distribution of HIV-1 recombinant forms during 1990-2015.Methods: We assembled a global HIV-1 molecular epidemiology database through a systematic literature review and a global survey. We searched the PubMed, Embase (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) databases for HIV-1 subtyping studies published from Jan 1, 1990, to Dec 31, 2015. Unpublished original HIV-1 subtyping data were collected through a survey among experts in the field who were members of the WHO-UNAIDS Network for HIV Isolation and Characterisation. We included prevalence studies with HIV-1 subtyping data collected during 1990-2015. Countries were grouped into 14 regions and analyses were done for four time periods (1990-99, 2000-04, 2005-09, and 2010-15). The distribution of 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 in each country to generate regional and global estimates of numbers and proportions of HIV-1 recombinants in each time period. The systematic review is registered with PROSPERO, CRD42017067164.Findings: Our global data collection yielded an HIV-1 molecular epidemiology database of 383 519 samples from 116 countries in 1990-2015. We found that the proportion of recombinants increased over time, both globally and in most regions, reaching 22·8% (7 978 517 of 34 921 639) of global HIV-1 infections in 2010-15. Both the proportion and the number of distinct CRFs detected increased over time to 16·7% and 57 CRFs in 2010-15. The global and regional distribution of HIV-1 recombinants was diverse and evolved over time, and we found large regional variation in the numbers (0-44 CRFs), types (58 distinct CRFs), and proportions (0-80·5%) of HIV-1 recombinants. Globally, CRF02_AG was the most prevalent recombinant, accounting for 33·9% (2 701 364 of 7 978 517) of all recombinant infections in 2010-15. URFs accounted for 26·7% (2 131 450 of 7 978 517), CRF01_AE for 23·0% (1 838 433), and other CRFs for 16·4% (1 307 270) of all recombinant infections in 2010-15. Although other CRFs accounted for small proportions of infections globally (

Published
2020
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2. Global and Regional Estimates for Subtype-Specific Therapeutic and Prophylactic HIV-1 Vaccines: A Modeling Study

Author

Ramyiadarsini Elangovan, Michael Jenks, Jason Yun, Leslie Dickson-Tetteh, Shona Kirtley, Joris Hemelaar, WHO-UNAIDS Network for HIV Isolation and 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 Buvé, 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, Hervé Fleury, Peter N Fonjungo, Vincent Foulongne, Deepak A Gadkari, Feng Gao, 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, 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, Philippe van de Perre, Guido van 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, Rong Zhang, and Characterisation, WHO-UNAIDS Network for HIV Isolation and

Subjects
Microbiology (medical), Recombinant, URF, Human immunodeficiency virus (HIV), Subtype, virus diseases, HIV, CRF, Biology, medicine.disease_cause, Genome, Virology, Microbiology, QR1-502, subtype, vaccine, medicine, HIV vaccine, recombinant, Vaccine, Genetic composition, Original Research
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.

Published
2021

3. The World Health Organization African Region Laboratory Accreditation Process

Author

Fatim Cham, Guy-Michel Gershy-Damet, Clement Zeh, Daniel E. Sesse, Glen Fine, John N. Nkengasong, Souleymane Mboup, David Cross, Patrick Njukeng, Jean-Bosco Ndihokubwayo, Tsehaynesh Messele, El Hadj Belabbes, Philip Rotz, and Deborah L. Birx

Subjects
Engineering management, business.industry, Interim, Medical laboratory, Developing country, Medicine, General Medicine, business, Grading (education), Stepwise approach, Certification and Accreditation, World health, Accreditation
Abstract

Few developing countries have established laboratory quality standards that are affordable and easy to implement and monitor. To address this challenge, the World Health Organization Regional Office for Africa (WHO AFRO) established a stepwise approach, using a 0- to 5-star scale, to the recognition of evolving fulfillment of the ISO 15189 standard rather than pass-fail grading. Laboratories that fail to achieve an assessment score of at least 55% will not be awarded a star ranking. Laboratories that achieve 95% or more will receive a 5-star rating. This stepwise approach acknowledges to laboratories where they stand, supports them with a series of evaluations to use to demonstrate improvement, and recognizes and rewards their progress. WHO AFRO’s accreditation process is not intended to replace established ISO 15189 accreditation schemes, but rather to provide an interim pathway to the realization of international laboratory standards. Laboratories that demonstrate outstanding performance in the WHO-AFRO process will be strongly encouraged to enroll in an established ISO 15189 accreditation scheme. We believe that the WHO-AFRO approach for laboratory accreditation is affordable, sustainable, effective, and scalable.

Published
2010
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4. First Observation of HIV Type 1 Drug Resistance Mutations in Algeria

Author

Hervé Fleury, Salima Bouzeghoub, Marie Hélène Schrive, Bernard Masquelier, Valérie Jauvin, Achour Amrane, El Hadj Belabbes, Patricia Pinson, and Anne Cecile Jeannot

Subjects
Anti-HIV Agents, Immunology, Mutation, Missense, Human immunodeficiency virus (HIV), Sequence Homology, HIV Infections, Drug resistance, medicine.disease_cause, Treatment failure, Virus, Health services, HIV Protease, immune system diseases, Virology, Drug Resistance, Viral, Humans, Medicine, Treatment Failure, Phylogeny, Mutation, biology, business.industry, virus diseases, Sequence Analysis, DNA, biology.organism_classification, HIV Reverse Transcriptase, Infectious Diseases, Sequence homology, Algeria, Lentivirus, HIV-1, RNA, Viral, business
Abstract

This study demonstrates for the first time HIV-1 resistance mutations to all classes of antiretroviral drugs available in Algeria (NRTIs, NNRTIs, PIs) in treated patients at failure. Moreover, it is shown that mutations to NRTIs and PIs can be observed in untreated patients in this country where there is high HIV-1 diversity.

Published
2008
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5. High Diversity of HIV Type 1 in Algeria

Author

Isabelle Garrigue, Patricia Recordon-Pinson, Achour Amrane, Salima Bouzeghoub, El-Hadj Belabbes, Hervé Fleury, and Valérie Jauvin

Subjects
Adult, Male, Adolescent, Genes, Viral, Research methodology, media_common.quotation_subject, Immunology, Human immunodeficiency virus (HIV), HIV Infections, Drug resistance, medicine.disease_cause, Virus, Health services, HIV Protease, Species Specificity, Virology, Prevalence, medicine, Humans, Child, Phylogeny, media_common, Molecular Epidemiology, biology, Phylogenetic tree, Sequence Analysis, RNA, business.industry, Genetic Variation, Middle Aged, Viral Load, biology.organism_classification, HIV Reverse Transcriptase, Infectious Diseases, Algeria, Child, Preschool, Lentivirus, HIV-1, RNA, Viral, Female, business, Diversity (politics)
Abstract

We have sequenced different genes of HIV-1 strains from infected individuals recruited in various geographic parts of Algeria; phylogenetic trees were constructed yielding molecular characterization of these strains. Subtype B accounts for 56% of the samples studied and is therefore the predominant subtype, particularly in the north part of the country; but there is a high diversity of the virus including CRF02_AG, CRF06_cpx, CRF02/CRF06 interrecombinants, and different other intersubtype and/or inter-CRF recombinants. The prevalence of these non-B viruses increases in the south part of Algeria that borders sub-Saharan African countries. The high diversity of HIV-1 in Algeria has implications for virological follow-up, resistance surveys, and vaccine design.

Published
2006
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6. The World Health Organization African region laboratory accreditation process: improving the quality of laboratory systems in the African region

Author

Guy-Michel, Gershy-Damet, Philip, Rotz, David, Cross, El Hadj, Belabbes, Fatim, Cham, Jean-Bosco, Ndihokubwayo, Glen, Fine, Clement, Zeh, Patrick A, Njukeng, Souleymane, Mboup, Daniel E, Sesse, Tsehaynesh, Messele, Deborah L, Birx, and John N, Nkengasong

Subjects
Quality Control, Clinical Laboratory Techniques, Africa, Medical Laboratory Personnel, Laboratories, World Health Organization, Developing Countries, Accreditation
Abstract

Few developing countries have established laboratory quality standards that are affordable and easy to implement and monitor. To address this challenge, the World Health Organization Regional Office for Africa (WHO AFRO) established a stepwise approach, using a 0- to 5-star scale, to the recognition of evolving fulfillment of the ISO 15189 standard rather than pass-fail grading. Laboratories that fail to achieve an assessment score of at least 55% will not be awarded a star ranking. Laboratories that achieve 95% or more will receive a 5-star rating. This stepwise approach acknowledges to laboratories where they stand, supports them with a series of evaluations to use to demonstrate improvement, and recognizes and rewards their progress. WHO AFRO's accreditation process is not intended to replace established ISO 15189 accreditation schemes, but rather to provide an interim pathway to the realization of international laboratory standards. Laboratories that demonstrate outstanding performance in the WHO-AFRO process will be strongly encouraged to enroll in an established ISO 15189 accreditation scheme. We believe that the WHO-AFRO approach for laboratory accreditation is affordable, sustainable, effective, and scalable.

Published
2010

7. Epidemic non-A, non-B viral hepatitis in Algeria: strong evidence for its spreading by water

Author

Ahmed Benatallah, Gana Illoul, El‐Hadj Belabbes, and Abdelmadjid Bouguermouh

Subjects
Adult, Male, Adolescent, Hepatitis, Viral, Human, Sewage, Disease Outbreaks, Pregnancy, Virology, Medicine, Humans, Hepatitis Antibodies, Pregnancy Complications, Infectious, Water pollution, Child, Hepatitis, business.industry, Incidence (epidemiology), Hepatobiliary disease, Water Pollution, Age Factors, Hepatitis A, Hepatitis C, Middle Aged, medicine.disease, Infectious Diseases, Algeria, Female, Viral disease, business, Water Microbiology
Abstract

A waterborne epidemic of non-A, non-B hepatitis occurred in Medea, an Algerian town of 68,000 inhabitants during the autumn and winter of 1980-1981. About 6 weeks before the epidemic, there had been a chlorination failure and an accidental sewage contamination of the river water that supplied large parts of the town. From October, 1980, to January, 1981, 788 cases were notified. This epidemic affected mostly young adults, who usually recovered; however, a high rate of mortality was noted among pregnant women (nine patients, nine deaths). Serological examinations performed on 57 hospitalized patients excluded both hepatitis A and B. The waterborne nature of the epidemic was suggested by a study of the case distribution according to water supplies. The epidemic was severe in the areas supplied by the untreated river water. Few cases were reported in the areas receiving spring water, where chlorination never failed. A mild incidence of infection was noted in the areas supplied by a mixture of untreated river water and chlorinated spring water.

Published
1985

8. 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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