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

Hemelaar, Joris; Elangovan, Ramyiadarsini; Yun, Jason; Dickson-Tetteh, Leslie; Fleminger, Isabella; Kirtley, Shona; Williams, Brian; Gouws-Williams, Eleanor; Ghys, Peter D.; Abimiku, Alash’le; Agwale, Simon M; Archibald, Chris; Avidor, Boaz; Barbás, María Gabriela; Barré‐Sinoussi, Françoise; Barugahare, Banson; Belabbes, El Hadj; Bertagnolio, Silvia; Birx, Deborah L.; Bobkov, Aleksei; Brandful, James; Bredell, Helba; Brennan, Catherine A.; Brooks, James; Brûćková, M; Buonaguro, Luigi; Buonaguro, Franco M.; Buttò, Stefano; Buvé, Anne; Campbell, Mary S.; Carr, Jean K.; Carrera, Alex; Carrillo, Manuel; Celum, Connie; Chaplin, Beth; Charles, Macarthur; Chatzidimitriou, Dimitrios; Chen, Zhiwei; Chijiwa, Katsumi; Cooper, David R.; Cunningham, Philip; Dagnra, Anoumou; Gascun, Cillian F. De; Amo, Julia del; Delgado, Elena; Dietrich, Ursula; Dwyer, Dominic E.; Ellenberger, Dennis; Ensoli, Barbara; Essex, Max; Gao, Feng; Fleury, Hervé; Fonjungo, Peter N.; Foulongne, Vincent; Gadkari, Deepak A.; García, Féderico; Garsia, Roger; Gershy-Damet, G. M.; Glynn, Judith R.; Goodall, Ruth; Grossman, Zehava; Lindenmeyer-Guimarães, Monick; Hahn, Beatrice; Hamers, Raph L; Hamouda, Osamah; Handema, Ray; He, Xiang; Herbeck, Joshua T.; Ho, David D.; Holguín, África; Hosseinipour, Mina C.; Hunt, Gillian; Ito, Masahiko; Kacem, Mohamed Ali Bel Hadj; Kahle, Erin; Kaleebu, P.; Kalish, Marcia L.; Kamarulzaman, Adeeba; Kang, Chun; Kanki, Phyllis; Карамов, Э. В.; Karasi, Jean-Claude; Kayitenkore, Kayitesi; Kelleher, Anthony D.; Kitayaporn, Dwip; Kostrikis, Leondios G; Kücherer, Claudia; Lara, Claudia; Leitner, Thomas; Liitsola, Kirsi; Lingappa, Jai; Linka, Marek; Lorenzana, Ivette; Lukashov, Vladimir V.; Maayan, Shlomo; Mayr, Luzia; McCutchan, Francine; Méda, Nicolas; Menu, Elisabeth; Mhalu, Fred; Mloka, Doreen; Mokili, John L.; Montès, Brigitte; Mor, Orna; Morgado, Mariza G.; Mosha, Fausta; Moussi, Awatef El; Mullins, James I.; Nájera, Rafael; Nasr, Mejda; Ndembi, Nicaise; Neilson, Joel R.; Nerurkar, Vivek R.; Neuhann, Florian; Nolte, Claudine; Novitsky, Vlad; Nyambi, Philippe; Ofner, Marianna; Paladin, Fem Julia; Papa, Anna; Pape, Jean William; Parkin, Neil; Parry, Chris M.; Peeters, Martine; Pelletier, Alexandra; Pérez-Álvarez, Lucı́a; Pillay, Deenan; Pinto, Angie N; Quang, Trinh Duy; Rademeyer, Cecilia; Raikanikoda, Filimone; Rayfield, Mark; Reynes, Jean-Marc; Wit, Tobias Rinke de; Robbins, Kenneth E.; Rolland, Morgane; Rousseau, Christine; Salazar-Gonzales, Jesus; Salem, Hanan; Salminen, Mika; Salomón, Horacio; Sandstrom, Paul; Santiago, Mario L.; Sarr, Abdoulaye; Schroeder, Bryan; Segondy, Michel; Selhorst, Philippe; Sempala, S. D. K.; Servais, Jean; Shaik, Ansari; Shao, Yiming; Slim, Aminé; Soares, Marcelo A.; Songok, Elijah; Stewart, Debbie; Stokes, Julie; Subbarao, Shambavi; Sutthent, Ruengpung; Takehisa, Jun; Tanuri, Amílcar; Tee, Kok Keng; Thapa, Kiran; Thomson, Michael M.; Tran, Tyna; Urassa, Willy; Ushijima, Hiroshi; Perre, Philippe Van de; Groen, G van der; Laethem, Kristel Van; Oosterhout, Joep van; Sighem, Ard van; Wijngaerden, Eric Van; Vandamme, Anne‐Mieke; Vercauteren, Jürgen; Vidal, Nicole; Wallace, Lesley; Williamson, Carolyn; Wolday, Dawit; Xu, Jianqing; Yang, Chunfu; Zhang, Linqi; Zhang, Rong

doi:10.1016/s1473-3099(18)30647-9

Cited by 302 publications

(337 citation statements)

References 26 publications

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“…Based on the latest HIV molecular surveillance report, recombinant forms account for almost every fourth HIV infection globally (22.8%) . Circulating recombinant form (CRF) 02_AG (CRF02_AG) is the most predominant recombinant form and the fourth most predominant lineage in the world (7.7%).…”

Section: Introductionmentioning

confidence: 99%

“…Circulating recombinant form (CRF) 02_AG (CRF02_AG) is the most predominant recombinant form and the fourth most predominant lineage in the world (7.7%). Also, there has been a consistent and ongoing rise in the percentage of unique recombinant forms (URFs) globally, which currently constitute the fifth most prevalent group of HIV viruses (6.1%) . Comparing the periods 1990 to 1999 and 2010 to 2015, URFs almost doubled (1.7x) globally and increased more than four‐fold (4.6x) in West Africa .…”

Section: Introductionmentioning

confidence: 99%

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Near full genome characterization of HIV‐1 unique recombinant forms in Cameroon reveals dominant CRF02_AG and F2 recombination patterns

et al. 2019

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Introduction In Cameroon, a manifold diversity of HIV strains exists with CRF02_AG and unique recombinant forms (URFs) being the predominant strains. In recent years, a steady increase in URFs and clade F2 viruses has been monitored through partial genome sequencing. There is an information gap in the characterization of emerging URFs along the full genome, which is needed to address the challenges URFs pose towards diagnosis, treatment and HIV‐1 vaccine design. Method Eighteen Cameroonian URFs from samples collected between the years 2000 and 2015 were studied using a newly developed near full genome sequencing (NFGS) protocol based on variable nested RT‐PCRs with a versatile primer set. Near full genomes were characterized for recombination patterns and sequence signatures with possible impact on antiretroviral treatment or Env‐directed immune responses. Third‐generation sequencing (3GS) of near full or half genomes (HGs) gave insight into intra‐patient URF diversity. Results The characterized URFs were composed of a broad variety of subtypes and recombinants including A, F, G, CRF01_AE, CRF02_AG and CRF22_01A1. Phylogenetic analysis unveiled dominant CRF02_AG and F2 recombination patterns. 3GS indicated a high intra‐patient URF diversity with up to four distinct viral sub‐populations present in plasma at the same time. URF pol genomic analysis revealed a number of accessory drug resistance mutations (DRMs) in the ART‐naïve participants. Genotypic env analysis suggests CCR5 usage in 14/18 samples and identified deviations at residues, critical for gp120/gp41 interphase and CD4 binding site broadly neutralizing antibodies in more than half of the studied URFs. V1V2 sites of immune pressure in the human RV144 vaccine study varied in more than a third of URFs. Conclusions This study identified novel mosaic patterns in URFs in Cameroon. In line with the regional predominance of CRF_02AG and the increased prevalence of clade F2, prominent CRF_02AG and F2 background patterns were observed underlying the URFs. In the context of the novel mosaic genomes, the impact of the identified accessory DRMs and Env epitope variations on treatment and immune control remains elusive. The evolving diversity of HIV‐1 URFs in Cameroon requires continuous monitoring to respond to the increasing challenges for diagnosis, antiretroviral treatment and prevention.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Near full genome characterization of HIV‐1 unique recombinant forms in Cameroon reveals dominant CRF02_AG and F2 recombination patterns

et al. 2019

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“…A Phage-DMS library encoding peptides from two immunodominant regions of HIV Env -the V3 region of gp120 and the gp41 ectodomain -was generated in the background of envelope sequences from two common HIV-1 circulating clades 14 : clade A (two variants: BG505, BF520) and clade C (ZA1197) (Supplemental Table 1). A total of 12,160 sequences were included.…”

Section: Generation and Characterization Of Gp41/v3 Hiv Envelope Phagmentioning

confidence: 99%

Phage-DMS: a comprehensive method for fine mapping of antibody epitopes

Garrett

Itell

Crawford

et al. 2020

Preprint

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Understanding the antibody response is critical to developing vaccine and antibody-based therapies and has inspired the recent development of new methods to isolate antibodies. However, methods to define the antibody-antigen interactions that determine specificity or allow escape have not kept pace. We developed Phage-DMS, a method which combines two powerful approachesimmunoprecipitation of phage peptide libraries and deep mutational scanning (DMS) -to enable highthroughput fine mapping of antibody epitopes. As an example, we designed sequences encoding all possible amino acid variants of HIV Envelope to create phage display libraries. Using Phage-DMS, we identified sites of escape predicted using other approaches for four well characterized HIV monoclonal antibodies with known linear epitopes. In some cases, the results of Phage-DMS refined the epitope beyond what was determined in previous studies. This method has the potential to rapidly and comprehensively screen many antibodies in a single experiment to define sites essential for binding to antigen.

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“…CD8 þ T cell responses may act soon after infection and promote the selection of escape mutants (Bull et al, 2015). The difficulties for the control of virus disease derived from the adaptive potential of viruses (Domingo, 1989;Domingo and Holland, 1992;Bailey et al, 2004;Hamelaar et al, 2019) require the judicious application of existing tools and innovative approaches that are still in their infancy.…”

Section: Antiviral Vaccines and The Adaptive Potential Of Virusesmentioning

confidence: 99%

Quasispecies dynamics in disease prevention and control

Domingo

2020

Virus as Populations

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

Cited by 302 publications

References 26 publications

Near full genome characterization of HIV‐1 unique recombinant forms in Cameroon reveals dominant CRF02_AG and F2 recombination patterns

Near full genome characterization of HIV‐1 unique recombinant forms in Cameroon reveals dominant CRF02_AG and F2 recombination patterns

Phage-DMS: a comprehensive method for fine mapping of antibody epitopes

Quasispecies dynamics in disease prevention and control

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