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1. Global associations of key populations with HIV-1 recombinants: a systematic review, global survey, and individual participant data meta-analysis

Author

Nkazi Nchinda, Ramyiadarsini Elangovan, 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, Barbás María Gabriela, 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, Herve 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, and Rong Zhang

Subjects
HIV, key populations, recombinant, CRF, URF, molecular epidemiology, Public aspects of medicine, RA1-1270
Abstract

IntroductionGlobal HIV infections due to HIV-1 recombinants are increasing and impede prevention and treatment efforts. Key populations suffer most new HIV infections, but their role in the spread of HIV-1 recombinants is unknown. We conducted a global analysis of the associations between key populations and HIV-1 recombinants.MethodsWe searched PubMed, EMBASE, CINAHL, and Global Health for HIV-1 subtyping studies published from 1/1/1990 to 31/12/2015. Unpublished data was collected through a global survey. We included studies with HIV-1 subtyping data of key populations collected during 1990-2015. Key populations assessed were heterosexual people (HET), men who have sex with men (MSM), people who inject drugs (PWID), vertical transmissions (VERT), commercial sex workers (CSW), and transfusion-associated infections (BLOOD). Logistic regression was used to determine associations of key populations with HIV-1 recombinants. Subgroup analyses were performed for circulating recombinant forms (CRFs), unique recombinant forms (URFs), regions, and time periods.ResultsEight hundred and eighty five datasets including 77,284 participants from 83 countries were included. Globally, PWID were associated with the greatest odds of recombinants and CRFs (OR 2.6 [95% CI 2.46–2.74] and 2.99 [2.83–3.16]), compared to HET. CSW were associated with increased odds of recombinants and URFs (1.59 [1.44–1.75] and 3.61 [3.15–4.13]). VERT and BLOOD were associated with decreased odds of recombinants (0.58 [0.54–0.63] and 0.43 [0.33–0.56]). MSM were associated with increased odds of recombinants in 2010–2015 (1.43 [1.35–1.51]). Subgroup analyses supported our main findings.DiscussionAs PWID, CSW, and MSM are associated with HIV-1 recombinants, increased preventative measures and HIV-1 molecular surveillance are crucial within these key populations.Systematic review registrationPROSPERO [CRD42017067164].

Published
2023
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2. Role of rotavirus vaccination on G9P[8] rotavirus strain during a seasonal outbreak in Japan

Author

Kimiko Kawata, Sheikh Ariful Hoque, Shuichi Nishimura, Fumihiro Yagyu, Mohammad Tajul Islam, Laila Shamima Sharmin, Ngan Thi Kim Pham, Yuko Onda-Shimizu, Trinh Duy Quang, Sayaka Takanashi, Shoko Okitsu, Pattara Khamrin, Niwat Maneekarn, Satoshi Hayakawa, and Hiroshi Ushijima

Subjects
rotavirus, vaccine, effectiveness, g9p[8]i2, japan, Immunologic diseases. Allergy, RC581-607, Therapeutics. Pharmacology, RM1-950
Abstract

Although two live oral rotavirus (RV) vaccines, Rotarix and RotaTeq, play a critical role toward reducing disease severity, hospitalization, and death rate in RV infections, regular monitoring of vaccine effectiveness (VE) is yet necessary because the segmented genome structure and reassortment capability of RVs pose considerable threats toward waning VE. In this study, we examined the VE by a test-negative study design against G9P[8]I2 strain during a seasonal outbreak in February–May, 2018, in an outpatient clinic in Kyoto Prefecture, Japan. It remains important because G9P[8]I2 strain remains partially heterotypic to these vaccines and predominating in post-vaccination era. During year-long surveillance, RV infections were detected only from February to May. During this outbreak, 33 (42.3%) children out of 78 with acute gastroenteritis (AGE) remained RV-positive, of which 29 (87.8%) children were infected with G9P[8]I2. Two immunochromatographic (IC) assay kits exhibited 100% sensitivity and specificity to detect G9P[8]I2 strain. Only 23.2% children were found to be vaccinated. Yet, significant VE 69.7% (95% CI: 2.5%-90.6%) was recognized against all RV strains that increased with disease severity. Similar significant VE 71.8% (95% CI: 1%-92%) was determined against G9P[8]I2 strain. The severity score remained substantially low in vaccinated children. Our data reveal that vaccine-preventable G9P[8]I2 strain yet may cause outbreak where vaccination coverage remains low. Thus, this study emphasizes the necessity of global introduction of RV-vaccines in national immunization programs of every country.

Published
2021
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3. 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, and Rong Zhang

Subjects
HIV, subtype, recombinant, CRF, URF, vaccine, Microbiology, QR1-502
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
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4. Role of rotavirus vaccination on G9P[8] rotavirus strain during a seasonal outbreak in Japan

Author

Sayaka Takanashi, Shoko Okitsu, Niwat Maneekarn, Sheikh Ariful Hoque, Satoshi Hayakawa, Ngan Thi Kim Pham, Kimiko Kawata, Fumihiro Yagyu, Laila Shamima Sharmin, Shuichi Nishimura, Trinh Duy Quang, Mohammad Tajul Islam, Yuko Onda-Shimizu, Pattara Khamrin, and Hiroshi Ushijima

Subjects
Rotavirus, Genotype, 030231 tropical medicine, Immunology, Reassortment, medicine.disease_cause, Rotavirus vaccination, Rotavirus Infections, Disease Outbreaks, 03 medical and health sciences, 0302 clinical medicine, Japan, Humans, Immunology and Allergy, Medicine, Outpatient clinic, 030212 general & internal medicine, Child, Pharmacology, Strain (chemistry), business.industry, Mortality rate, Vaccination, Rotavirus Vaccines, Infant, Outbreak, Virology, Immunization, Seasons, business, Research Paper
Abstract

Although two live oral rotavirus (RV) vaccines, Rotarix and RotaTeq, play a critical role toward reducing disease severity, hospitalization, and death rate in RV infections, regular monitoring of vaccine effectiveness (VE) is yet necessary because the segmented genome structure and reassortment capability of RVs pose considerable threats toward waning VE. In this study, we examined the VE by a test-negative study design against G9P[8]I2 strain during a seasonal outbreak in February-May, 2018, in an outpatient clinic in Kyoto Prefecture, Japan. It remains important because G9P[8]I2 strain remains partially heterotypic to these vaccines and predominating in post-vaccination era. During year-long surveillance, RV infections were detected only from February to May. During this outbreak, 33 (42.3%) children out of 78 with acute gastroenteritis (AGE) remained RV-positive, of which 29 (87.8%) children were infected with G9P[8]I2. Two immunochromatographic (IC) assay kits exhibited 100% sensitivity and specificity to detect G9P[8]I2 strain. Only 23.2% children were found to be vaccinated. Yet, significant VE 69.7% (95% CI: 2.5%-90.6%) was recognized against all RV strains that increased with disease severity. Similar significant VE 71.8% (95% CI: 1%-92%) was determined against G9P[8]I2 strain. The severity score remained substantially low in vaccinated children. Our data reveal that vaccine-preventable G9P[8]I2 strain yet may cause outbreak where vaccination coverage remains low. Thus, this study emphasizes the necessity of global introduction of RV-vaccines in national immunization programs of every country.

Published
2021
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5. 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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6. Emergence of intragenotype recombinant sapovirus in Japan

Author

Sayaka Takanashi, Pattara Khamrin, Shuvra Kanti Dey, Trinh Duy Quang, Niwat Maneekarn, Tung Gia Phan, Hiroshi Ushijima, and Shoko Okitsu

Subjects
Microbiology (medical), Genotype, Molecular Sequence Data, Sequence Homology, Nucleotide level, Microbiology, Sapovirus, law.invention, Japan, law, Genetics, Humans, Base sequence, Child, Molecular Biology, Phylogeny, Ecology, Evolution, Behavior and Systematics, Feces, Recombination, Genetic, Base Sequence, biology, Outbreak, Acute gastroenteritis, biology.organism_classification, Virology, Infectious Diseases, Recombinant DNA, Capsid Proteins
Abstract

Sapovirus is an important causative agent of sporadic cases as well as of outbreaks of acute gastroenteritis in humans worldwide. A total of 603 fecal specimens collected from July 2005 to June 2006 from children with acute gastroenteritis in five localities in Japan (Maizuru, Tokyo, Sapporo, Saga, and Osaka) were screened for sapovirus by RT-PCR. It was found that 17 specimens were positive for sapovirus and it represented 2.8%. Interestingly, intragenotype recombinant sapovirus GI/1 emerged with 76.4% (13 of 17) and rapidly became the leading cause of acute gastroenteritis in Japan for the first time. The lower frequency of sapovirus GI/2 and GI/4 (each of 11.8%), which were the second prevailing genotypes, was also detected. A novel nomenclature of sapovirus was proposed, in which worldwide sapovirus strains were classified into seven genogroups. Of these, novel sapovirus genogroups VI and VII demonstrated the very low homologies, only 32.8-41.6% at the amino acid level and 43.6-49.9% at the nucleotide level, to those of sapovirus genogroups I-V. Of note, two distinct clusters of sapovirus were co-circulating in porcine. Interestingly, the worldwide sapovirus strains shared the 25 nucleotide-conserved region, covering the polymerase-capsid junction which differed according to each species due to multiple nucleotide substitutions. The finding suggests that the sapovirus recombination between human and animal hardly takes place in nature. This is also the first, to our best knowledge, demonstrating the emergence of the intragenotype recombinant sapovirus with its causing diarrheal illness in Japan.

Published
2007
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7. Detection and genetic characterization of group A rotavirus strains circulating among children with acute gastroenteritis in Japan

Author

Trinh Duy Quang, Hiroshi Ushijima, Sayaka Takanashi, Tung Gia Phan, Shoko Okitsu, Shuvra Kanti Dey, Niwat Maneekarn, and Pattara Khamrin

Subjects
Rotavirus, Genotype, viruses, Immunology, Amino Acid Motifs, Molecular Sequence Data, Reoviridae, medicine.disease_cause, Microbiology, Group A, Virus, Rotavirus Infections, Feces, fluids and secretions, Japan, Phylogenetics, Virology, medicine, Prevalence, Cluster Analysis, Humans, Amino Acid Sequence, Child, Phylogeny, biology, Phylogenetic tree, Base Sequence, Reverse Transcriptase Polymerase Chain Reaction, virus diseases, Sequence Analysis, DNA, biology.organism_classification, Gastroenteritis, Genetic Diversity and Evolution, Insect Science, Sequence Alignment
Abstract

A total of 603 fecal specimens collected from July 2005 to June 2006 from children with acute gastroenteritis, encompassing five different localities in Japan, were screened for group A rotavirus by reverse transcription-PCR. It was found that 117 fecal specimens (19.4%) were positive for group A rotavirus. Rotavirus infection was detected continuously from November to June, with the highest prevalence in April. The G (VP7 genotypes) and P (VP4 genotypes) types were further investigated. The predominant genotype was G1P[8] (70.1%), followed by G3P[8] (17.9%), G9P[8] (6.8%), and G2P[4] (2.6%). A number of unusual G1P[4] combinations were also detected during this study period. A novel nomenclature for G1 is proposed, in which worldwide rotavirus G1 strains are classified into 11 lineages with 17 sublineages. A wide range of amino acid substitutions (up to 34) in VP7 that are specific for G1 lineages and sublineages were identified. Interestingly, only short amino acid motifs located at positions 29 to 75 and 211 to 213 of VP7 defined correctly the phylogenetic G1 lineages and sublineages. Examination of the deduced sequences of antigenic regions of VP7 also revealed multiple particular amino acid substitutions that correlated with the phylogenetic G1 lineages and sublineages. Of note, at least three distinct clusters of rotavirus G1 isolates were cocirculating in the Japanese pediatric population studied.

Published
2007

8. Novel intragenotype recombination in sapovirus

Author

Tung Gia, Phan, Hainian, Yan, Pattara, Khamrin, Trinh Duy, Quang, Shuvra Kanti, Dey, Fumihiro, Yagyu, Shoko, Okitsu, Werner E G, Müller, and Hiroshi, Ushijima

Subjects
Recombination, Genetic, Base Sequence, Species Specificity, Molecular Sequence Data, Sequence Analysis, DNA, Sequence Alignment, Phylogeny, Sapovirus, Gastroenteritis
Abstract

Based on the genetic analysis, a novel, naturally occurring recombination between two distinct sapovirus subtypes (subtype a and subtype b) within genogroup I genotype 1 was identified. Breakpoint analysis of recombinant sapovirus showed that the recombination site was at the polymerase-capsid junction. This is the first report of the existence of acute gastroenteritis caused by intragenotype recombinant sapovirus. The results also provided evidence that the natural recombination occurs not only in sapovirus genogroup II but also in sapovirus genogroup I.

Published
2006

9. Genetic characterization of group A rotavirus strains circulating among children with acute gastroenteritis in Japan in 2004-2005

Author

Osamu Nishio, Hiroshi Ushijima, Trinh Duy Quang, Shuvra Kanti Dey, Fumihiro Yagyu, Tung Gia Phan, Shoko Okitsu, and Pattara Khamrin

Subjects
Microbiology (medical), Diarrhea, Rotavirus, Molecular Sequence Data, Biology, medicine.disease_cause, Microbiology, Group A, Rotavirus Infections, Multiple point, Feces, Japan, Genotype, Genetics, medicine, Prevalence, Humans, Amino Acid Sequence, Child, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Phylogeny, Amino Acid Motifs, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, RNA, Acute gastroenteritis, Virology, Gastroenteritis, Infectious Diseases, Acute Disease, Pediatric population
Abstract

A total of 752 fecal specimens collected from July 2004 to June 2005 from children with acute gastroenteritis in four localities in Japan (Maizuru, Tokyo, Sapporo, and Osaka) were screened for group A rotavirus by RT-PCR. It was found that 82 (10.9%) specimens were positive for group A rotavirus. The G-(VP7 genotypes) and P-(VP4 genotypes) types were further investigated. The P-types of 18 rotavirus strains, which could not be typed by RT-PCR, were determined by sequencing analysis. Of these, 94% (17/18) were P[8] with multiple point mutations at the VP4 primer-binding site. Another sample turned out to be a rare genotype P[9], which was closely related to feline rotavirus. The predominant genotype was G1P[8] (46.4%), followed by G3P[8] (32.9%) and G2P[4] (12.2%). A number of unusual combinations including, G1P[4] (1.2%), G2P[8] (1.2%), G3P[9] (1.2%), G1G3P[8] (1.2%), and G2G3P[8] (3.7%), were also detected. A new nomenclature of P[8] was proposed, in which worldwide rotavirus P[8] strains were classified into four sub-lineages, namely IA, IB, IIA, and IIB. A wide range of amino acid substitutions (up to 22) specific for P[8] lineages and sub-lineages were also identified. Interestingly, only short amino acid motifs located at positions 32–35, 121–135, and 195–236 of VP4 correctly defined the phylogenetic P[8] lineages and sub-lineages. Of note, at least two distinct clusters of rotavirus P[8] were co-circulating in the Japanese pediatric population studied.

Published
2006

10. Detection and Genetic Characterization of Group A Rotavirus Strains Circulating among Children with Acute Gastroenteritis in Japan.

Author

Tung Gia Phan, Pattara Khamrin, Trinh Duy Quang, Shuvra Kanti Dey, Takanashi, Sayaka, Okitsu, Shoko, Maneekarn, Niwat, and Ushijima, Hiroshi

Subjects
*GASTROINTESTINAL diseases, *JUVENILE diseases, *ROTAVIRUSES, *AMINO acids, *PEDIATRICS
Abstract

A total of 603 fecal specimens collected from July 2005 to June 2006 from children with acute gastroenteritis, encompassing five different localities in Japan, were screened for group A rotavirus by reverse transcription-PCR. It was found that 117 fecal specimens (19.4%) were positive for group A rotavirus. Rotavirus infection was detected continuously from November to June, with the highest prevalence in April. The G (VP7 genotypes) and P (VP4 genotypes) types were further investigated. The predominant genotype was G1P[8] (70.1%), followed by G3P[8] (17.9%), G9P[8] (6.8%), and G2P[4] (2.6%). A number of unusual G1P[4] combinations were also detected during this study period. A novel nomenclature for G1 is proposed, in which worldwide rotavirus G1 strains are classified into 11 lineages with 17 sublineages. A wide range of amino acid substitutions (up to 34) in VP7 that are specific for G1 lineages and sublineages were identified. Interestingly, only short amino acid motifs located at positions 29 to 75 and 211 to 213 of VP7 defined correctly the phylogenetic G1 lineages and sublineages. Examination of the deduced sequences of antigenic regions of VP7 also revealed multiple particular amino acid substitutions that correlated with the phylogenetic G1 lineages and sublineages. Of note, at least three distinct clusters of rotavirus G1 isolates were cocirculating in the Japanese pediatric population studied. [ABSTRACT FROM AUTHOR]

Published
2007
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11. 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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12. Genetic characterization of group A rotavirus strains circulating among children with acute gastroenteritis in Japan in 2004-2005.

Author

Phan TG, Khamrin P, Trinh DQ, Dey SK, Yagyu F, Okitsu S, Nishio O, and Ushijima H

Subjects
Acute Disease, Amino Acid Sequence, Child, Diarrhea virology, Feces virology, Gastroenteritis epidemiology, Humans, Japan, Molecular Sequence Data, Phylogeny, Prevalence, Reverse Transcriptase Polymerase Chain Reaction, Rotavirus classification, Rotavirus isolation & purification, Rotavirus Infections epidemiology, Sequence Analysis, RNA, Gastroenteritis virology, Rotavirus genetics, Rotavirus Infections virology
Abstract

A total of 752 fecal specimens collected from July 2004 to June 2005 from children with acute gastroenteritis in four localities in Japan (Maizuru, Tokyo, Sapporo, and Osaka) were screened for group A rotavirus by RT-PCR. It was found that 82 (10.9%) specimens were positive for group A rotavirus. The G-(VP7 genotypes) and P-(VP4 genotypes) types were further investigated. The P-types of 18 rotavirus strains, which could not be typed by RT-PCR, were determined by sequencing analysis. Of these, 94% (17/18) were P[8] with multiple point mutations at the VP4 primer-binding site. Another sample turned out to be a rare genotype P[9], which was closely related to feline rotavirus. The predominant genotype was G1P[8] (46.4%), followed by G3P[8] (32.9%) and G2P[4] (12.2%). A number of unusual combinations including, G1P[4] (1.2%), G2P[8] (1.2%), G3P[9] (1.2%), G1G3P[8] (1.2%), and G2G3P[8] (3.7%), were also detected. A new nomenclature of P[8] was proposed, in which worldwide rotavirus P[8] strains were classified into four sub-lineages, namely IA, IB, IIA, and IIB. A wide range of amino acid substitutions (up to 22) specific for P[8] lineages and sub-lineages were also identified. Interestingly, only short amino acid motifs located at positions 32-35, 121-135, and 195-236 of VP4 correctly defined the phylogenetic P[8] lineages and sub-lineages. Of note, at least two distinct clusters of rotavirus P[8] were co-circulating in the Japanese pediatric population studied.

Published
2007
Full Text
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