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Kun Á, Hubai AG, Král A, Mokos J, Mikulecz BÁ, Radványi Á. Do pathogens always evolve to be less virulent? The virulence–transmission trade-off in light of the COVID-19 pandemic. Biol Futur 2023:10.1007/s42977-023-00159-2. [PMID: 37002448 PMCID: PMC10066022 DOI: 10.1007/s42977-023-00159-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/09/2023] [Indexed: 04/03/2023]
Abstract
AbstractThe direction the evolution of virulence takes in connection with any pathogen is a long-standing question. Formerly, it was theorized that pathogens should always evolve to be less virulent. As observations were not in line with this theoretical outcome, new theories emerged, chief among them the transmission–virulence trade-off hypotheses, which predicts an intermediate level of virulence as the endpoint of evolution. At the moment, we are very much interested in the future evolution of COVID-19’s virulence. Here, we show that the disease does not fulfill all the assumptions of the hypothesis. In the case of COVID-19, a higher viral load does not mean a higher risk of death; immunity is not long-lasting; other hosts can act as reservoirs for the virus; and death as a consequence of viral infection does not shorten the infectious period. Consequently, we cannot predict the short- or long-term evolution of the virulence of COVID-19.
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Goodreau SM, Stansfield SE, Mittler JE, Murphy JT, Abernethy NF, Gottlieb GS, Reid MC, Burke JC, Pollock ED, Herbeck JT. Why does age at HIV infection correlate with set point viral load? An evolutionary hypothesis. Epidemics 2022; 41:100629. [PMID: 36162386 PMCID: PMC9807138 DOI: 10.1016/j.epidem.2022.100629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/29/2022] [Accepted: 09/20/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Set-point viral load (SPVL) correlates with the age at which people acquire HIV. Although immunosenescence may seem like a parsimonious explanation for this, it does not easily explain the observation that the relationship between age and SPVL attenuates when accounting for source partner SPVL. Here we propose an alternative explanation that encompasses this latter finding: that decreasing risk of acquisition with older age generates a selection bottleneck that selects for more virulent strains with age. METHODS We adapted a previously published model of HIV transmission and evolution (EvoNetHIV), parameterized here for men who have sex with men (MSM). We conducted a series of simulation experiments that vary seven behavioral or clinical parameters that affect exposure risk as people age. We conducted regressions to determine the mean increase in SPVL per 10-year increase in seroconversion age, with and without source SPVL in the model. RESULTS All runs generated significant relationships between seroconversion age and SPVL when not including source SPVL. All saw attenuated relationships, most to near 0, with source SPVL included. Four of our behavioral measures (relational duration, age-related homophily, coital frequency, and mean age at relationship formation) had clear effects on this relationship, all in the hypothesized direction. Combining multiple forms of behavioral heterogeneity yielded an increase of 0.056 log10 copies/mL SPVL per 10-year increase in seroconversion age, nearly as large as that seen in two empirical studies of age-SPVL correlations in MSM. CONCLUSION The higher virulence of HIV among those infected later in life may be partly explained by a combination of selective bottlenecks and behavioral heterogeneity by age. Variation in the strength of this effect across populations may be in part due to different behavioral, epidemiological and clinical conditions, and not require assumptions about differences in patterns of immunosenescence among populations.
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Affiliation(s)
- Steven M Goodreau
- Departments of Anthropology & Epidemiology, University of Washington, Seattle, WA 98195, USA.
| | - Sarah E Stansfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - John E Mittler
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - James T Murphy
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Neil F Abernethy
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Geoffrey S Gottlieb
- Departments of Medicine & Global Health, Center for Emerging & Re-Emerging Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Molly C Reid
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Juandalyn C Burke
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Emily D Pollock
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
| | - Joshua T Herbeck
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
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Does HIV-1 virulence matter in the ART era? MED 2022; 3:217-219. [DOI: 10.1016/j.medj.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Rindler AE, Kusejko K, Kuster H, Neumann K, Leemann C, Zeeb M, Chaudron SE, Braun DL, Kouyos RD, Metzner KJ, Günthard HF. The interplay between replication capacity of HIV-1 and surrogate markers of disease. J Infect Dis 2022; 226:1057-1068. [PMID: 35299248 DOI: 10.1093/infdis/jiac100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/16/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND HIV-1 replication capacity (RC) of transmitted/founder viruses may influence the further course of HIV-1 infection. METHODS Replication capacities (RCs) of 355 whole genome primary HIV-1 isolates derived from samples acquired during acute and recent primary HIV-1 infection (PHI) were determined using a novel high throughput infection assay in primary cells. The RCs were used to elucidate potential factors that could be associated with RC during PHI. RESULTS Increased RC was found to be associated with increased set point viral load (VL), and significant differences in RCs among 13 different HIV-1 subtypes were discerned. Notably, we observed an increase in RCs for primary HIV-1 isolates of HIV-1 subtype B over a 17-year period. Associations were not observed between RC and CD4 count at sample date of RC measurement, CD4 recovery after initiation of antiretroviral treatment (ART), CD4 decline in untreated individuals, and acute retroviral syndrome severity scores. DISCUSSION These findings highlight that RCs of primary HIV-1 isolates acquired during the acute and recent phase of infection are more associated with viral factors, i.e., set point VL, than with host factors. Furthermore, we observed a temporal increase in RC for HIV-1 subtype B viruses over a period of 17 years.
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Affiliation(s)
- Audrey E Rindler
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Herbert Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Kathrin Neumann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Christine Leemann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marius Zeeb
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Sandra E Chaudron
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Abstract
[Figure: see text].
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Affiliation(s)
- Joel O Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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Wymant C, Bezemer D, Blanquart F, Ferretti L, Gall A, Hall M, Golubchik T, Bakker M, Ong SH, Zhao L, Bonsall D, de Cesare M, MacIntyre-Cockett G, Abeler-Dörner L, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Aubert V, Battegay M, Bernasconi E, Böni J, Braun DL, Bucher HC, Burton-Jeangros C, Calmy A, Cavassini M, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Gorgievski M, Günthard H, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Kahlert C, Kaiser L, Keiser O, Klimkait T, Kouyos R, Kovari H, Ledergerber B, Martinetti G, de Tejada BM, Marzolini C, Metzner K, Müller N, Nadal D, Nicca D, Pantaleo G, Rauch A, Regenass S, Rudin C, Schöni-Affolter F, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Vernazza P, Weber R, Yerly S, van der Valk M, Geerlings SE, Goorhuis A, Hovius JW, Lempkes B, Nellen FJB, van der Poll T, Prins JM, Reiss P, van Vugt M, Wiersinga WJ, Wit FWMN, van Duinen M, van Eden J, Hazenberg A, van Hes AMH, Rajamanoharan S, Robinson T, Taylor B, Brewer C, Mayr C, Schmidt W, Speidel A, Strohbach F, Arastéh K, Cordes C, Pijnappel FJJ, Stündel M, Claus J, Baumgarten A, Carganico A, Ingiliz P, Dupke S, Freiwald M, Rausch M, Moll A, Schleehauf D, Smalhout SY, Hintsche B, Klausen G, Jessen H, Jessen A, Köppe S, Kreckel P, Schranz D, Fischer K, Schulbin H, Speer M, Weijsenfeld AM, Glaunsinger T, Wicke T, Bieniek B, Hillenbrand H, Schlote F, Lauenroth-Mai E, Schuler C, Schürmann D, Wesselmann H, Brockmeyer N, Jurriaans S, Gehring P, Schmalöer D, Hower M, Spornraft-Ragaller P, Häussinger D, Reuter S, Esser S, Markus R, Kreft B, Berzow D, Back NKT, Christl A, Meyer A, Plettenberg A, Stoehr A, Graefe K, Lorenzen T, Adam A, Schewe K, Weitner L, Fenske S, Zaaijer HL, Hansen S, Stellbrink HJ, Wiemer D, Hertling S, Schmidt R, Arbter P, Claus B, Galle P, Jäger H, Jä Gel-Guedes E, Berkhout B, Postel N, Fröschl M, Spinner C, Bogner J, Salzberger B, Schölmerich J, Audebert F, Marquardt T, Schaffert A, Schnaitmann E, Cornelissen MTE, Trein A, Frietsch B, Müller M, Ulmer A, Detering-Hübner B, Kern P, Schubert F, Dehn G, Schreiber M, Güler C, Schinkel CJ, Gunsenheimer-Bartmeyer B, Schmidt D, Meixenberger K, Bannert N, Wolthers KC, Peters EJG, van Agtmael MA, Autar RS, Bomers M, Sigaloff KCE, Heitmuller M, Laan LM, Ang CW, van Houdt R, Jonges M, Kuijpers TW, Pajkrt D, Scherpbier HJ, de Boer C, van der Plas A, van den Berge M, Stegeman A, Baas S, Hage de Looff L, Buiting A, Reuwer A, Veenemans J, Wintermans B, Pronk MJH, Ammerlaan HSM, van den Bersselaar DNJ, de Munnik ES, Deiman B, Jansz AR, Scharnhorst V, Tjhie J, Wegdam MCA, van Eeden A, Nellen J, Brokking W, Elsenburg LJM, Nobel H, van Kasteren MEE, Berrevoets MAH, Brouwer AE, Adams A, van Erve R, de Kruijf-van de Wiel BAFM, Keelan-Phaf S, van de Ven B, van der Ven B, Buiting AGM, Murck JL, de Vries-Sluijs TEMS, Bax HI, van Gorp ECM, de Jong-Peltenburg NC, de Mendonç A Melo M, van Nood E, Nouwen JL, Rijnders BJA, Rokx C, Schurink CAM, Slobbe L, Verbon A, Bassant N, van Beek JEA, Vriesde M, van Zonneveld LM, de Groot J, Boucher CAB, Koopmans MPG, van Kampen JJA, Fraaij PLA, van Rossum AMC, Vermont CL, van der Knaap LC, Visser E, Branger J, Douma RA, Cents-Bosma AS, Duijf-van de Ven CJHM, Schippers EF, van Nieuwkoop C, van Ijperen JM, Geilings J, van der Hut G, van Burgel ND, Leyten EMS, Gelinck LBS, Mollema F, Davids-Veldhuis S, Tearno C, Wildenbeest GS, Heikens E, Groeneveld PHP, Bouwhuis JW, Lammers AJJ, Kraan S, van Hulzen AGW, Kruiper MSM, van der Bliek GL, Bor PCJ, Debast SB, Wagenvoort GHJ, Kroon FP, de Boer MGJ, Jolink H, Lambregts MMC, Roukens AHE, Scheper H, Dorama W, van Holten N, Claas ECJ, Wessels E, den Hollander JG, El Moussaoui R, Pogany K, Brouwer CJ, Smit JV, Struik-Kalkman D, van Niekerk T, Pontesilli O, Lowe SH, Oude Lashof AML, Posthouwer D, van Wolfswinkel ME, Ackens RP, Burgers K, Schippers J, Weijenberg-Maes B, van Loo IHM, Havenith TRA, van Vonderen MGA, Kampschreur LM, Faber S, Steeman-Bouma R, Al Moujahid A, Kootstra GJ, Delsing CE, van der Burg-van de Plas M, Scheiberlich L, Kortmann W, van Twillert G, Renckens R, Ruiter-Pronk D, van Truijen-Oud FA, Cohen Stuart JWT, Jansen ER, Hoogewerf M, Rozemeijer W, van der Reijden WA, Sinnige JC, Brinkman K, van den Berk GEL, Blok WL, Lettinga KD, de Regt M, Schouten WEM, Stalenhoef JE, Veenstra J, Vrouenraets SME, Blaauw H, Geerders GF, Kleene MJ, Kok M, Knapen M, van der Meché IB, Mulder-Seeleman E, Toonen AJM, Wijnands S, Wttewaal E, Kwa D, van Crevel R, van Aerde K, Dofferhoff ASM, Henriet SSV, Ter Hofstede HJM, Hoogerwerf J, Keuter M, Richel O, Albers M, Grintjes-Huisman KJT, de Haan M, Marneef M, Strik-Albers R, Rahamat-Langendoen J, Stelma FF, Burger D, Gisolf EH, Hassing RJ, Claassen M, Ter Beest G, van Bentum PHM, Langebeek N, Tiemessen R, Swanink CMA, van Lelyveld SFL, Soetekouw R, van der Prijt LMM, van der Swaluw J, Bermon N, van der Reijden WA, Jansen R, Herpers BL, Veenendaal D, Verhagen DWM, Lauw FN, van Broekhuizen MC, van Wijk M, Bierman WFW, Bakker M, Kleinnijenhuis J, Kloeze E, Middel A, Postma DF, Schölvinck EH, Stienstra Y, Verhage AR, Wouthuyzen-Bakker M, Boonstra A, de Groot-de Jonge H, van der Meulen PA, de Weerd DA, Niesters HGM, van Leer-Buter CC, Knoester M, Hoepelman AIM, Arends JE, Barth RE, Bruns AHW, Ellerbroek PM, Mudrikova T, Oosterheert JJ, Schadd EM, van Welzen BJ, Aarsman K, Griffioen-van Santen BMG, de Kroon I, van Berkel M, van Rooijen CSAM, Schuurman R, Verduyn-Lunel F, Wensing AMJ, Bont LJ, Geelen SPM, Loeffen YGT, Wolfs TFW, Nauta N, Rooijakkers EOW, Holtsema H, Voigt R, van de Wetering D, Alberto A, van der Meer I, Rosingh A, Halaby T, Zaheri S, Boyd AC, Bezemer DO, van Sighem AI, Smit C, Hillebregt M, de Jong A, Woudstra T, Bergsma D, Meijering R, van de Sande L, Rutkens T, van der Vliet S, de Groot L, van den Akker M, Bakker Y, El Berkaoui A, Bezemer M, Brétin N, Djoechro E, Groters M, Kruijne E, Lelivelt KJ, Lodewijk C, Lucas E, Munjishvili L, Paling F, Peeck B, Ree C, Regtop R, Ruijs Y, Schoorl M, Schnörr P, Scheigrond A, Tuijn E, Veenenberg L, Visser KM, Witte EC, Ruijs Y, Van Frankenhuijsen M, Allegre T, Makhloufi D, Livrozet JM, Chiarello P, Godinot M, Brunel-Dalmas F, Gibert S, Trepo C, Peyramond D, Miailhes P, Koffi J, Thoirain V, Brochier C, Baudry T, Pailhes S, Lafeuillade A, Philip G, Hittinger G, Assi A, Lambry V, Rosenthal E, Naqvi A, Dunais B, Cua E, Pradier C, Durant J, Joulie A, Quinsat D, Tempesta S, Ravaux I, Martin IP, Faucher O, Cloarec N, Champagne H, Pichancourt G, Morlat P, Pistone T, Bonnet F, Mercie P, Faure I, Hessamfar M, Malvy D, Lacoste D, Pertusa MC, Vandenhende MA, Bernard N, Paccalin F, Martell C, Roger-Schmelz J, Receveur MC, Duffau P, Dondia D, Ribeiro E, Caltado S, Neau D, Dupont M, Dutronc H, Dauchy F, Cazanave C, Vareil MO, Wirth G, Le Puil S, Pellegrin JL, Raymond I, Viallard JF, Chaigne de Lalande S, Garipuy D, Delobel P, Obadia M, Cuzin L, Alvarez M, Biezunski N, Porte L, Massip P, Debard A, Balsarin F, Lagarrigue M, Prevoteau du Clary F, Aquilina C, Reynes J, Baillat V, Merle C, Lemoing V, Atoui N, Makinson A, Jacquet JM, Psomas C, Tramoni C, Aumaitre H, Saada M, Medus M, Malet M, Eden A, Neuville S, Ferreyra M, Sotto A, Barbuat C, Rouanet I, Leureillard D, Mauboussin JM, Lechiche C, Donsesco R, Cabie A, Abel S, Pierre-Francois S, Batala AS, Cerland C, Rangom C, Theresine N, Hoen B, Lamaury I, Fabre I, Schepers K, Curlier E, Ouissa R, Gaud C, Ricaud C, Rodet R, Wartel G, Sautron C, Beck-Wirth G, Michel C, Beck C, Halna JM, Kowalczyk J, Benomar M, Drobacheff-Thiebaut C, Chirouze C, Faucher JF, Parcelier F, Foltzer A, Haffner-Mauvais C, Hustache Mathieu M, Proust A, Piroth L, Chavanet P, Duong M, Buisson M, Waldner A, Mahy S, Gohier S, Croisier D, May T, Delestan M, Andre M, Zadeh MM, Martinot M, Rosolen B, Pachart A, Martha B, Jeunet N, Rey D, Cheneau C, Partisani M, Priester M, Bernard-Henry C, Batard ML, Fischer P, Berger JL, Kmiec I, Robineau O, Huleux T, Ajana F, Alcaraz I, Allienne C, Baclet V, Meybeck A, Valette M, Viget N, Aissi E, Biekre R, Cornavin P, Merrien D, Seghezzi JC, Machado M, Diab G, Raffi F, Bonnet B, Allavena C, Grossi O, Reliquet V, Billaud E, Brunet C, Bouchez S, Morineau-Le Houssine P, Sauser F, Boutoille D, Besnier M, Hue H, Hall N, Brosseau D, Souala F, Michelet C, Tattevin P, Arvieux C, Revest M, Leroy H, Chapplain JM, Dupont M, Fily F, Patra-Delo S, Lefeuvre C, Bernard L, Bastides F, Nau P, Verdon R, de la Blanchardiere A, Martin A, Feret P, Geffray L, Daniel C, Rohan J, Fialaire P, Chennebault JM, Rabier V, Abgueguen P, Rehaiem S, Luycx O, Niault M, Moreau P, Poinsignon Y, Goussef M, Mouton-Rioux V, Houlbert D, Alvarez-Huve S, Barbe F, Haret S, Perre P, Leantez-Nainville S, Esnault JL, Guimard T, Suaud I, Girard JJ, Simonet V, Debab Y, Schmit JL, Jacomet C, Weinberck P, Genet C, Pinet P, Ducroix S, Durox H, Denes É, Abraham B, Gourdon F, Antoniotti O, Molina JM, Ferret S, Lascoux-Combe C, Lafaurie M, Colin de Verdiere N, Ponscarme D, De Castro N, Aslan A, Rozenbaum W, Pintado C, Clavel F, Taulera O, Gatey C, Munier AL, Gazaigne S, Penot P, Conort G, Lerolle N, Leplatois A, Balausine S, Delgado J, Timsit J, Tabet M, Gerard L, Girard PM, Picard O, Tredup J, Bollens D, Valin N, Campa P, Bottero J, Lefebvre B, Tourneur M, Fonquernie L, Wemmert C, Lagneau JL, Yazdanpanah Y, Phung B, Pinto A, Vallois D, Cabras O, Louni F, Pialoux G, Lyavanc T, Berrebi V, Chas J, Lenagat S, Rami A, Diemer M, Parrinello M, Depond A, Salmon D, Guillevin L, Tahi T, Belarbi L, Loulergue P, Zak Dit Zbar O, Launay O, Silbermann B, Leport C, Alagna L, Pietri MP, Simon A, Bonmarchand M, Amirat N, Pichon F, Kirstetter M, Katlama C, Valantin MA, Tubiana R, Caby F, Schneider L, Ktorza N, Calin R, Merlet A, Ben Abdallah S, Weiss L, Buisson M, Batisse D, Karmochine M, Pavie J, Minozzi C, Jayle D, Castel P, Derouineau J, Kousignan P, Eliazevitch M, Pierre I, Collias L, Viard JP, Gilquin J, Sobel A, Slama L, Ghosn J, Hadacek B, Thu-Huyn N, Nait-Ighil L, Cros A, Maignan A, Duvivier C, Consigny PH, Lanternier F, Shoai-Tehrani M, Touam F, Jerbi S, Bodard L, Jung C, Goujard C, Quertainmont Y, Duracinsky M, Segeral O, Blanc A, Peretti D, Cheret A, Chantalat C, Dulucq MJ, Levy Y, Lelievre JD, Lascaux AS, Dumont C, Boue F, Chambrin V, Abgrall S, Kansau I, Raho-Moussa M, De Truchis P, Dinh A, Davido B, Marigot D, Berthe H, Devidas A, Chevojon P, Chabrol A, Agher N, Lemercier Y, Chaix F, Turpault I, Bouchaud O, Honore P, Rouveix E, Reimann E, Belan AG, Godin Collet C, Souak S, Mortier E, Bloch M, Simonpoli AM, Manceron V, Cahitte I, Hiraux E, Lafon E, Cordonnier F, Zeng AF, Zucman D, Majerholc C, Bornarel D, Uludag A, Gellen-Dautremer J, Lefort A, Bazin C, Daneluzzi V, Gerbe J, Jeantils V, Coupard M, Patey O, Bantsimba J, Delllion S, Paz PC, Cazenave B, Richier L, Garrait V, Delacroix I, Elharrar B, Vittecoq D, Bolliot C, Lepretre A, Genet P, Masse V, Perrone V, Boussard JL, Chardon P, Froguel E, Simon P, Tassi S, Avettand Fenoel V, Barin F, Bourgeois C, Cardon F, Chaix ML, Delfraissy JF, Essat A, Fischer H, Lecuroux C, Meyer L, Petrov-Sanchez V, Rouzioux C, Saez-Cirion A, Seng R, Kuldanek K, Mullaney S, Young C, Zucchetti A, Bevan MA, McKernan S, Wandolo E, Richardson C, Youssef E, Green P, Faulkner S, Faville R, Herman S, Care C, Blackman H, Bellenger K, Fairbrother K, Phillips A, Babiker A, Delpech V, Fidler S, Clarke M, Fox J, Gilson R, Goldberg D, Hawkins D, Johnson A, Johnson M, McLean K, Nastouli E, Post F, Kennedy N, Pritchard J, Andrady U, Rajda N, Donnelly C, McKernan S, Drake S, Gilleran G, White D, Ross J, Harding J, Faville R, Sweeney J, Flegg P, Toomer S, Wilding H, Woodward R, Dean G, Richardson C, Perry N, Gompels M, Jennings L, Bansaal D, Browing M, Connolly L, Stanley B, Estreich S, Magdy A, O'Mahony C, Fraser P, Jebakumar SPR, David L, Mette R, Summerfield H, Evans M, White C, Robertson R, Lean C, Morris S, Winter A, Faulkner S, Goorney B, Howard L, Fairley I, Stemp C, Short L, Gomez M, Young F, Roberts M, Green S, Sivakumar K, Minton J, Siminoni A, Calderwood J, Greenhough D, DeSouza C, Muthern L, Orkin C, Murphy S, Truvedi M, McLean K, Hawkins D, Higgs C, Moyes A, Antonucci S, McCormack S, Lynn W, Bevan M, Fox J, Teague A, Anderson J, Mguni S, Post F, Campbell L, Mazhude C, Russell H, Gilson R, Carrick G, Ainsworth J, Waters A, Byrne P, Johnson M, Fidler S, Kuldanek K, Mullaney S, Lawlor V, Melville R, Sukthankar A, Thorpe S, Murphy C, Wilkins E, Ahmad S, Green P, Tayal S, Ong E, Meaden J, Riddell L, Loay D, Peacock K, Blackman H, Harindra V, Saeed AM, Allen S, Natarajan U, Williams O, Lacey H, Care C, Bowman C, Herman S, Devendra SV, Wither J, Bridgwood A, Singh G, Bushby S, Kellock D, Young S, Rooney G, Snart B, Currie J, Fitzgerald M, Arumainayyagam J, Chandramani S. A highly virulent variant of HIV-1 circulating in the Netherlands. Science 2022; 375:540-545. [PMID: 35113714 DOI: 10.1126/science.abk1688] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log10 increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination, with increased transmissibility and an unfamiliar molecular mechanism of virulence.
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Affiliation(s)
- Chris Wymant
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France.,IAME, UMR 1137, INSERM, Université de Paris, Paris, France
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lele Zhao
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mariateresa de Cesare
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - George MacIntyre-Cockett
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Norbert Bannert
- Division for HIV and Other Retroviruses, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - M Kate Grabowski
- Department of Pathology, John Hopkins University, Baltimore, MD, USA
| | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Pia Kivelä
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Laurence Meyer
- INSERM CESP U1018, Université Paris Saclay, APHP, Service de Santé Publique, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Kholoud Porter
- Institute for Global Health, University College London, London, UK
| | - Matti Ristola
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | | | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Paul Kellam
- Kymab Ltd., Cambridge, UK.,Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Molecular Diagnostic Unit, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, Netherlands.,Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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7
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Nwagha TU, Ugwu AO, Nweke M. Does Sickle Cell Disease Protect against HIV Infection: A Systematic Review. Med Princ Pract 2022; 31:516-523. [PMID: 36096094 PMCID: PMC9841758 DOI: 10.1159/000526993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/22/2022] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVE The aim of this systematic review was to investigate whether sickle cell disease (SCD) protects against human immunodeficiency virus (HIV) infection by determining the association between SCD and the incidence and virulence of HIV infection. METHODS This is a systematic review that used MEDLINE, PubMed, CINAHL, and Academic Search Complete as data sources. Articles describing the relationship of SCD with HIV infection were included in this review. The effect measures were converted to correlation coefficients and synthesized accordingly to examine the putative protective role of SCD against HIV infection. Independent full-text screening and data extraction were conducted on all eligible studies. The risk of bias was assessed using the mixed methods appraisal tool. We employed a random-effects model of meta-analysis to estimate the pooled prevalence. We computed Cochrane's Q statistics, I2, and prediction interval to quantify effect size heterogeneity. RESULTS SCD reduces the risk of HIV infection by 75% (odds ratio [OR] = 0.25; r = -0.36, p < 0.001; I2 = 71.65). There was no publication bias (Egger's t value = 0.411; p = 0.721). Similarly, risk of HIV virulence was reduced by 77% (OR = 0.23; r = -0.38; p < 0.001; I2 = 63.07). The mechanisms implicated in the protective influence of SCD include autosplenectomy, reduced CCR5 expression, and increased expression of heme and iron-regulated genes. CONCLUSIONS SCD appears to protect against HIV infection and slows HIV progression.
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Affiliation(s)
- Theresa Ukamaka Nwagha
- Department of Haematology and Immunology, Faculty of Medicine, University of Nigeria Teaching Hospital Ituku-Ozalla, Enugu, Nigeria
| | - Angela Ogechukwu Ugwu
- Department of Haematology and Immunology, Faculty of Medicine, University of Nigeria Teaching Hospital Ituku-Ozalla, Enugu, Nigeria
- *Angela Ogechukwu Ugwu,
| | - Martins Nweke
- Fledgelight Evidence Consult, Enugu, Nigeria
- Physiotherapy Department, Evangel University Akaeze, Ebonyi State, Nigeria
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8
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Van Egeren D, Novokhodko A, Stoddard M, Tran U, Zetter B, Rogers MS, Joseph-McCarthy D, Chakravarty A. Controlling long-term SARS-CoV-2 infections can slow viral evolution and reduce the risk of treatment failure. Sci Rep 2021; 11:22630. [PMID: 34799659 PMCID: PMC8604936 DOI: 10.1038/s41598-021-02148-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/27/2021] [Indexed: 12/23/2022] Open
Abstract
The rapid emergence and expansion of novel SARS-CoV-2 variants threatens our ability to achieve herd immunity for COVID-19. These novel SARS-CoV-2 variants often harbor multiple point mutations, conferring one or more evolutionarily advantageous traits, such as increased transmissibility, immune evasion and longer infection duration. In a number of cases, variant emergence has been linked to long-term infections in individuals who were either immunocompromised or treated with convalescent plasma. In this paper, we used a stochastic evolutionary modeling framework to explore the emergence of fitter variants of SARS-CoV-2 during long-term infections. We found that increased viral load and infection duration favor emergence of such variants. While the overall probability of emergence and subsequent transmission from any given infection is low, on a population level these events occur fairly frequently. Targeting these low-probability stochastic events that lead to the establishment of novel advantageous viral variants might allow us to slow the rate at which they emerge in the patient population, and prevent them from spreading deterministically due to natural selection. Our work thus suggests practical ways to achieve control of long-term SARS-CoV-2 infections, which will be critical for slowing the rate of viral evolution.
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Affiliation(s)
- Debra Van Egeren
- Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | | | | | - Uyen Tran
- Fractal Therapeutics, Cambridge, MA, USA
| | - Bruce Zetter
- Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Michael S Rogers
- Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
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9
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Hendrickx DM, Delva W, Hens N. Influence of sexual risk behaviour and STI co-infection dynamics on the evolution of HIV set point viral load in MSM. Epidemics 2021; 36:100474. [PMID: 34153622 DOI: 10.1016/j.epidem.2021.100474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/17/2021] [Accepted: 06/07/2021] [Indexed: 11/27/2022] Open
Abstract
HIV viral load (VL) is an important predictor of HIV progression and transmission. Anti-retroviral therapy (ART) has been reported to reduce HIV transmission by lowering VL. However, apart from this beneficial effect, increased levels of population mean set-point viral load (SPVL), an estimator for HIV virulence, have been observed in men who have sex with men (MSM) in the decade following the introduction of ART in The Netherlands. Several studies have been devoted to explain these counter-intuitive trends in SPVL. However, to our knowledge, none of these studies has investigated an explanation in which it arises as the result of a sexually transmitted infection (STI) co-factor in detail. In this study, we adapted an event-based, individual-based model to investigate how STI co-infection and sexual risk behaviour affect the evolution of HIV SPVL in MSM before and after the introduction of ART. The results suggest that sexual risk behaviour has an effect on SPVL and indicate that more data are needed to test the effect of STI co-factors on SPVL. Furthermore, the observed trends in SPVL cannot be explained by sexual risk behaviour and STI co-factors only. We recommend to develop mathematical models including also factors related to viral evolution as reported earlier in the literature. However, this requires more complex models, and the collection of more data for parameter estimation than what is currently available.
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Affiliation(s)
- Diana M Hendrickx
- I-BioStat, Data Science Institute, Hasselt University, Hasselt, Belgium.
| | - Wim Delva
- I-BioStat, Data Science Institute, Hasselt University, Hasselt, Belgium; The South African Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa; Department of Global Health, Faculty of Medicine and Health, Stellenbosch University, Stellenbosch, South Africa; International Centre for Reproductive Health, Ghent University, Ghent, Belgium; Rega Institute for Medical Research, KU Leuven, Leuven, Belgium; School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Niel Hens
- I-BioStat, Data Science Institute, Hasselt University, Hasselt, Belgium; Centre for Health Economics Research and Modelling Infectious Diseases, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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10
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Stansfield SE, Herbeck JT, Gottlieb GS, Abernethy NF, Murphy JT, Mittler JE, Goodreau SM. Test-and-treat coverage and HIV virulence evolution among men who have sex with men. Virus Evol 2021; 7:veab011. [PMID: 33633867 PMCID: PMC7893213 DOI: 10.1093/ve/veab011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV set point viral load (SPVL), the viral load established shortly after initial infection, is a proxy for HIV virulence: higher SPVLs lead to higher risk of transmission and faster disease progression. Three models of test-and-treat scenarios, mainly in heterosexual populations, found that increasing treatment coverage selected for more virulent viruses. We modeled virulence evolution in a population of men who have sex with men (MSM) with increasing test-and-treat coverage. We extended a stochastic, dynamic network model (EvoNetHIV). We varied relationship patterns (MSM vs. heterosexual), HIV transmission models (increasing vs. plateauing probability of transmission at very high viral loads), and treatment roll-out (with explicit testing or fixed intervals between infection and treatment). In scenarios most similar to previous models (longer relational durations and the plateauing transmission function), we replicated trends previously found: increasing treatment coverage led to increased virulence (0.12 log10 increase in mean population SPVL between 20% and 100% treatment coverage). In scenarios reflecting MSM behavioral data using the increasing transmission function, increasing treatment coverage selected for viruses with lower virulence (0.16 log10 decrease in mean population SPVL between 20% and 100% treatment coverage). These findings emphasize the impact of sexual network conditions and transmission function details on predicted epidemiological and evolutionary outcomes. Varying these features creates very different evolutionary environments, which in turn lead to opposite effects in mean population SPVL evolution. Our results suggest that, under some realistic conditions, effective test-and-treat strategies may not face the previously reported tradeoff in which increasing coverage leads to evolution of greater virulence. This suggests instead that a virtuous cycle of increasing treatment coverage and diminishing virulence is possible.
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Affiliation(s)
- Sarah E Stansfield
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Joshua T Herbeck
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Geoffrey S Gottlieb
- Departments of Medicine & Global Health, University of Washington, Seattle, WA 98195, USA
| | - Neil F Abernethy
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - James T Murphy
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - John E Mittler
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Steven M Goodreau
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
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11
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Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure. Curr Opin HIV AIDS 2020; 14:194-204. [PMID: 30925534 DOI: 10.1097/coh.0000000000000541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW The purpose of this review is to summarize recent advances in our understanding of HIV adaptation to human leukocyte antigen (HLA)-associated immune pressures and its relevance to HIV prevention and cure research. RECENT FINDINGS Recent research has confirmed that HLA is a major driver of individual and population-level HIV evolution, that HIV strains are adapting to the immunogenetic profiles of the different human ethnic groups in which they circulate, and that HIV adaptation has substantial clinical and immunologic consequences. As such, adaptation represents a major challenge to HIV prevention and cure. At the same time, there are opportunities: Studies of HIV adaptation are revealing why certain HLA alleles are protective in some populations and not others; they are identifying immunogenic viral epitopes that harbor high mutational barriers to escape, and they may help illuminate novel, vaccine-relevant HIV epitopes in regions where circulating adaptation is extensive. Elucidation of HLA-driven adapted and nonadapted viral forms in different human populations and HIV subtypes also renders 'personalized' immunogen selection, as a component of HIV cure strategies, conceptually feasible. SUMMARY Though adaptation represents a major challenge to HIV prevention and cure, achieving an in-depth understanding of this phenomenon can help move the design of such strategies forward.
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12
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Wertheim JO, Oster AM, Switzer WM, Zhang C, Panneer N, Campbell E, Saduvala N, Johnson JA, Heneine W. Natural selection favoring more transmissible HIV detected in United States molecular transmission network. Nat Commun 2019; 10:5788. [PMID: 31857582 PMCID: PMC6923435 DOI: 10.1038/s41467-019-13723-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/22/2019] [Indexed: 01/10/2023] Open
Abstract
HIV molecular epidemiology can identify clusters of individuals with elevated rates of HIV transmission. These variable transmission rates are primarily driven by host risk behavior; however, the effect of viral traits on variable transmission rates is poorly understood. Viral load, the concentration of HIV in blood, is a heritable viral trait that influences HIV infectiousness and disease progression. Here, we reconstruct HIV genetic transmission clusters using data from the United States National HIV Surveillance System and report that viruses in clusters, inferred to be frequently transmitted, have higher viral loads at diagnosis. Further, viral load is higher in people in larger clusters and with increased network connectivity, suggesting that HIV in the United States is experiencing natural selection to be more infectious and virulent. We also observe a concurrent increase in viral load at diagnosis over the last decade. This evolutionary trajectory may be slowed by prevention strategies prioritized toward rapidly growing transmission clusters.
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Affiliation(s)
- Joel O Wertheim
- Department of Medicine, University of California, San Diego, CA, USA.
| | - Alexandra M Oster
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - William M Switzer
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Chenhua Zhang
- ICF International, Atlanta, GA, USA
- SciMetrika LLC, Atlanta, GA, USA
| | - Nivedha Panneer
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ellsworth Campbell
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Jeffrey A Johnson
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Walid Heneine
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
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13
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Impact of HIV-1 Diversity on Its Sensitivity to Neutralization. Vaccines (Basel) 2019; 7:vaccines7030074. [PMID: 31349655 PMCID: PMC6789624 DOI: 10.3390/vaccines7030074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 12/15/2022] Open
Abstract
The HIV-1 pandemic remains a major burden on global public health and a vaccine to prevent HIV-1 infection is highly desirable but has not yet been developed. Among the many roadblocks to achieve this goal, the high antigenic diversity of the HIV-1 envelope protein (Env) is one of the most important and challenging to overcome. The recent development of broadly neutralizing antibodies has considerably improved our knowledge on Env structure and its interplay with neutralizing antibodies. This review aims at highlighting how the genetic diversity of HIV-1 thwarts current, and possibly future, vaccine developments. We will focus on the impact of HIV-1 Env diversification on the sensitivity to neutralizing antibodies and the repercussions of this continuous process at a population level.
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14
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Evolution of the Envelope Glycoprotein of HIV-1 Clade B toward Higher Infectious Properties over the Course of the Epidemic. J Virol 2019; 93:JVI.01171-18. [PMID: 30567994 DOI: 10.1128/jvi.01171-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/11/2018] [Indexed: 01/01/2023] Open
Abstract
We showed previously that during the HIV/AIDS epidemic, the envelope glycoprotein (Env) of HIV-1, and in particular, the gp120 subunit, evolved toward an increased resistance to neutralizing antibodies at a population level. Here, we considered whether the antigenic evolution of the HIV-1 Env is associated with modifications of its functional properties, focusing on cell entry efficacy and interactions with the receptor and coreceptors. We tested the infectivity of a panel of Env-pseudotyped viruses derived from patients infected by subtype B viruses at three periods of the epidemic (1987 to 1991, 1996 to 2000, and 2006 to 2010). Pseudotyped viruses harboring Env from patients infected during the most recent period were approximately 10-fold more infectious in cell culture than those from patients infected at the beginning of the epidemic. This was associated with faster viral entry kinetics: contemporary viruses entered target cells approximately twice as fast as historical viruses. Contemporary viruses were also twice as resistant as historical viruses to the fusion inhibitor enfuvirtide. Resistance to enfuvirtide correlated with a resistance to CCR5 antagonists, suggesting that contemporary viruses expanded their CCR5 usage efficiency. Viruses were equally captured by DC-SIGN, but after binding to DC-SIGN, contemporary viruses infected target cells more efficiently than historical viruses. Thus, we report evidence that the infectious properties of the envelope glycoprotein of HIV-1 increased during the course of the epidemic. It is plausible that these changes affected viral fitness during the transmission process and might have contributed to an increasing virulence of HIV-1.IMPORTANCE Following primary infection by HIV-1, neutralizing antibodies (NAbs) exert selective pressure on the HIV-1 envelope glycoprotein (Env), driving the evolution of the viral population. Previous studies suggested that, as a consequence, Env has evolved at the HIV species level since the start of the epidemic so as to display greater resistance to NAbs. Here, we investigated whether the antigenic evolution of the HIV-1 Env is associated with modifications of its functional properties, focusing on cell entry efficacy and interactions with the receptor and coreceptors. Our data provide evidence that the infectious properties of the HIV-1 Env increased during the course of the epidemic. These changes may have contributed to increasing virulence of HIV-1 and an optimization of transmission between individuals.
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Abstract
How virulence evolves after a virus jumps to a new host species is central to disease emergence. Our current understanding of virulence evolution is based on insights drawn from two perspectives that have developed largely independently: long-standing evolutionary theory based on limited real data examples that often lack a genomic basis, and experimental studies of virulence-determining mutations using cell culture or animal models. A more comprehensive understanding of virulence mutations and their evolution can be achieved by bridging the gap between these two research pathways through the phylogenomic analysis of virus genome sequence data as a guide to experimental study.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.
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Torti C, Raffetti E, Donato F, Castelli F, Maggiolo F, Angarano G, Mazzotta F, Gori A, Sighinolfi L, Pan A, Cauda R, Scalzini A, Quiros-Roldan E, Nasta P, Gregis G, Benatti S, Digiambenedetto S, Ladisa N, Giralda M, Saracino A, Castelnuovo F, Di Pietro M, Lo Caputo S, Lapadula G, Costarelli S, Lorenzotti S, Mazzini N, Paraninfo G, Casari S, Focà E, Pezzoli C, Fabbiani M, Monno L, Pierotti P, Ble C, Leone S, Postorino MC, Fornabaio C, Zacchi F, Zoncada A, Carosi G. Cohort Profile: Standardized Management of Antiretroviral Therapy Cohort (MASTER Cohort). Int J Epidemiol 2018; 46:e12. [PMID: 26445966 DOI: 10.1093/ije/dyv192] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2015] [Indexed: 12/14/2022] Open
Affiliation(s)
- Carlo Torti
- Unità di Malattie Infettive e Tropicali, Dipartimento di Scienze Mediche e Chirurgiche, Università Magna Grecia di Catanzaro, Catanzaro, Italia
| | - Elena Raffetti
- Unità di Igiene, Epidemiologia e Sanità Pubblica, Università degli Studi di Brescia, Brescia, Italia
| | - Francesco Donato
- Unità di Igiene, Epidemiologia e Sanità Pubblica, Università degli Studi di Brescia, Brescia, Italia
| | - Francesco Castelli
- Divisione Universitaria di Malattie Infettive Spedali Civili di Brescia-Università degli Studi di Brescia, Brescia, Italia
| | - Franco Maggiolo
- Malattie Infettive Ospedale Papa Giovanni XXIII, Bergamo, Italia
| | | | | | - Andrea Gori
- Malattie Infettive Ospedale San Gerardo di Monza, Monza, Italia
| | - Laura Sighinolfi
- Malattie Infettive Nuovo Polo Ospedaliero di Cona, Ferrara, Italia
| | - Angelo Pan
- Malattie Infettive Istituti Ospitalieri di Cremona, Cremona, Italia
| | - Roberto Cauda
- Clinica di Malattie Infettive Policlinico A. Gemelli-Università Cattolica di Roma, Roma, Italia
| | - Alfredo Scalzini
- Divisione Ospedaliera di Malattie Infettive Spedali Civili, Brescia, Italia and
| | - Eugenia Quiros-Roldan
- Divisione Universitaria di Malattie Infettive Spedali Civili di Brescia-Università degli Studi di Brescia, Brescia, Italia
| | - Paola Nasta
- Divisione Universitaria di Malattie Infettive Spedali Civili di Brescia-Università degli Studi di Brescia, Brescia, Italia
| | | | - Simone Benatti
- Malattie Infettive Ospedale Papa Giovanni XXIII, Bergamo, Italia
| | - Simona Digiambenedetto
- Clinica di Malattie Infettive Policlinico A. Gemelli-Università Cattolica di Roma, Roma, Italia
| | | | - Mariarosaria Giralda
- Divisione Universitaria di Malattie Infettive Spedali Civili di Brescia-Università degli Studi di Brescia, Brescia, Italia
| | | | - Filippo Castelnuovo
- Divisione Ospedaliera di Malattie Infettive Spedali Civili, Brescia, Italia and
| | | | | | | | | | | | - Nicola Mazzini
- Fondazione Malattie Infettive e Salute Internazionale, Brescia, Italia
| | - Giuseppe Paraninfo
- Divisione Universitaria di Malattie Infettive Spedali Civili di Brescia-Università degli Studi di Brescia, Brescia, Italia
| | - Salvatore Casari
- Divisione Universitaria di Malattie Infettive Spedali Civili di Brescia-Università degli Studi di Brescia, Brescia, Italia
| | - Emanuele Focà
- Divisione Universitaria di Malattie Infettive Spedali Civili di Brescia-Università degli Studi di Brescia, Brescia, Italia
| | - Chiara Pezzoli
- Divisione Universitaria di Malattie Infettive Spedali Civili di Brescia-Università degli Studi di Brescia, Brescia, Italia
| | - Massimiliano Fabbiani
- Clinica di Malattie Infettive Policlinico A. Gemelli-Università Cattolica di Roma, Roma, Italia
| | - Laura Monno
- Clinica di Malattie Infettive Policlinico di Bari, Bari, Italia
| | | | - Claudio Ble
- Malattie Infettive S.M. Annunziata, Firenze, Italia
| | | | - Maria Concetta Postorino
- Unità di Malattie Infettive e Tropicali, Dipartimento di Scienze Mediche e Chirurgiche, Università Magna Grecia di Catanzaro, Catanzaro, Italia
| | - Chiara Fornabaio
- Malattie Infettive Istituti Ospitalieri di Cremona, Cremona, Italia
| | - Fabio Zacchi
- Malattie Infettive Istituti Ospitalieri di Cremona, Cremona, Italia
| | - Alessia Zoncada
- Malattie Infettive Istituti Ospitalieri di Cremona, Cremona, Italia
| | - Giampiero Carosi
- Fondazione Malattie Infettive e Salute Internazionale, Brescia, Italia
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17
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Goodreau SM, Stansfield SE, Murphy JT, Peebles KC, Gottlieb GS, Abernethy NF, Herbeck JT, Mittler JE. Relational concurrency, stages of infection, and the evolution of HIV set point viral load. Virus Evol 2018; 4:vey032. [PMID: 30483403 PMCID: PMC6249390 DOI: 10.1093/ve/vey032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
HIV viral load (VL) predicts both transmission potential and rate of disease progression. For reasons that are still not fully understood, the set point viral load (SPVL) established after acute infection varies across individuals and populations. Previous studies have suggested that population mean SPVL (MSPVL) has evolved near an optimum that reflects a trade-off between transmissibility and host survival. Sexual network structures affect rates of potential exposure during different within-host phases of infection marked by different transmission probabilities, and thus affect the number and timing of transmission events. These structures include relational concurrency, which has been argued to explain key differences in HIV burden across populations. We hypothesize that concurrency will alter the fitness landscape for SPVL in ways that differ from other network features whose impacts accrue at other times during infection. To quantitatively test this hypothesis, we developed a dynamic, stochastic, data-driven network model of HIV transmission, and evolution to assess the impact of key sexual network phenomena on MSPVL evolution. Experiments were repeated in sensitivity runs that made different assumptions about transmissibility during acute infection, SPVL heritability, and the functional form of the relationship between VL and transmissibility. For our main transmission model, scenarios yielded MSPVLs ranging from 4.4 to 4.75 log10 copies/ml, covering much of the observed empirical range. MSPVL evolved to be higher in populations with high concurrency and shorter relational durations, with values varying over a clinically significant range. In linear regression analyses on these and other predictors, main effects were significant (P < 0.05), as were interaction terms, indicating that effects are interdependent. We also noted a strong correlation between two key emergent properties measured at the end of the simulations-MSPVL and HIV prevalence-most clearly for phenomena that affect transmission networks early in infection. Controlling for prevalence, high concurrency yielded higher MSPVL than other network phenomena. Interestingly, we observed lower prevalence in runs in which SPVL heritability was zero, indicating the potential for viral evolution to exacerbate disease burden over time. Future efforts to understand empirical variation in MSPVL should consider local HIV burden and basic sexual behavioral and network structure.
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Affiliation(s)
- Steven M Goodreau
- Department of Anthropology, Campus Box 353100, Seattle, WA 98195, USA
| | | | - James T Murphy
- Department of Microbiology, Campus Box 357735, Seattle, WA 98195, USA
| | - Kathryn C Peebles
- Department of Epidemiology, Campus Box 357236, Seattle, WA 98195, USA
| | - Geoffrey S Gottlieb
- Departments of Medicine and Global Health, Campus Box 356420, Seattle, WA 98195, USA
| | - Neil F Abernethy
- Department of Biomedical Informatics and Medical Education, Campus Box 358047, Seattle, WA 98195, USA
| | - Joshua T Herbeck
- Department of Global Health, University of Washington, Campus Box 353100, Seattle, WA 98195, USA
| | - John E Mittler
- Department of Microbiology, Campus Box 357735, Seattle, WA 98195, USA
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18
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Sofonea MT, Aldakak L, Boullosa LFVV, Alizon S. Can Ebola virus evolve to be less virulent in humans? J Evol Biol 2018; 31:382-392. [PMID: 29288541 DOI: 10.1111/jeb.13229] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/06/2017] [Accepted: 12/08/2017] [Indexed: 11/29/2022]
Abstract
Understanding Ebola virus (EBOV) virulence evolution not only is timely but also raises specific questions because it causes one of the most virulent human infections and it is capable of transmission after the death of its host. Using a compartmental epidemiological model that captures three transmission routes (by regular contact, via dead bodies and by sexual contact), we infer the evolutionary dynamics of case fatality ratio on the scale of an outbreak and in the long term. Our major finding is that the virus's specific life cycle imposes selection for high levels of virulence and that this pattern is robust to parameter variations in biological ranges. In addition to shedding a new light on the ultimate causes of EBOV's high virulence, these results generate testable predictions and contribute to informing public health policies. In particular, burial management stands out as the most appropriate intervention since it decreases the R0 of the epidemics, while imposing selection for less virulent strains.
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Affiliation(s)
- M T Sofonea
- Laboratoire MIVEGEC (UMR CNRS 5290, IRD 224, UM), Montpellier Cedex 5, France
| | - L Aldakak
- Laboratoire MIVEGEC (UMR CNRS 5290, IRD 224, UM), Montpellier Cedex 5, France.,Erasmus Mundus Master Programme in Evolutionary Biology (MEME), Montpellier, France
| | - L F V V Boullosa
- Laboratoire MIVEGEC (UMR CNRS 5290, IRD 224, UM), Montpellier Cedex 5, France.,Erasmus Mundus Master Programme in Evolutionary Biology (MEME), Montpellier, France
| | - S Alizon
- Laboratoire MIVEGEC (UMR CNRS 5290, IRD 224, UM), Montpellier Cedex 5, France
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19
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Fanshawe TR, Shaw LF, Spence GT. A large-scale assessment of temporal trends in meta-analyses using systematic review reports from the Cochrane Library. Res Synth Methods 2017; 8:404-415. [PMID: 28493383 DOI: 10.1002/jrsm.1238] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 01/09/2017] [Accepted: 02/17/2017] [Indexed: 11/07/2022]
Abstract
INTRODUCTION Previous studies suggest that many systematic reviews contain meta-analyses that display temporal trends, such as the first study's result being more extreme than later studies' or a drift in the pooled estimate. We assessed the extent and characteristics of temporal trends using all Cochrane intervention reports published 2008-2012. METHODS We selected the largest meta-analysis within each report and analysed trends using methods including a Z-test (first versus subsequent estimates); generalised least squares; and cumulative sum charts. Predictors considered include meta-analysis size and review group. RESULTS Of 1288 meta-analyses containing at least 4 studies, the point estimate from the first study was more extreme and in the same direction as the pooled estimate in 738 (57%), with a statistically significant difference (first versus subsequent) in 165 (13%). Generalised least squares indicated trends in 717 (56%); 18% of fixed effects analyses had at least one violation of cumulative sum limits. For some methods, meta-analysis size was associated with temporal patterns and use of a random effects model, but there was no consistent association with review group. CONCLUSIONS All results suggest that more meta-analyses demonstrate temporal patterns than would be expected by chance. Hence, assuming the standard meta-analysis model without temporal trend is sometimes inappropriate. Factors associated with trends are likely to be context specific.
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Affiliation(s)
- Thomas R Fanshawe
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Luke F Shaw
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Graeme T Spence
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
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20
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Johnson LF, May MT, Dorrington RE, Cornell M, Boulle A, Egger M, Davies MA. Estimating the impact of antiretroviral treatment on adult mortality trends in South Africa: A mathematical modelling study. PLoS Med 2017; 14:e1002468. [PMID: 29232366 PMCID: PMC5726614 DOI: 10.1371/journal.pmed.1002468] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 11/07/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Substantial reductions in adult mortality have been observed in South Africa since the mid-2000s, but there has been no formal evaluation of how much of this decline is attributable to the scale-up of antiretroviral treatment (ART), as previous models have not been calibrated to vital registration data. We developed a deterministic mathematical model to simulate the mortality trends that would have been expected in the absence of ART, and with earlier introduction of ART. METHODS AND FINDINGS Model estimates of mortality rates in ART patients were obtained from the International Epidemiology Databases to Evaluate AIDS-Southern Africa (IeDEA-SA) collaboration. The model was calibrated to HIV prevalence data (1997-2013) and mortality data from the South African vital registration system (1997-2014), using a Bayesian approach. In the 1985-2014 period, 2.70 million adult HIV-related deaths occurred in South Africa. Adult HIV deaths peaked at 231,000 per annum in 2006 and declined to 95,000 in 2014, a reduction of 74.7% (95% CI: 73.3%-76.1%) compared to the scenario without ART. However, HIV mortality in 2014 was estimated to be 69% (95% CI: 46%-97%) higher in 2014 (161,000) if the model was calibrated only to HIV prevalence data. In the 2000-2014 period, the South African ART programme is estimated to have reduced the cumulative number of HIV deaths in adults by 1.72 million (95% CI: 1.58 million-1.84 million) and to have saved 6.15 million life years in adults (95% CI: 5.52 million-6.69 million). This compares with a potential saving of 8.80 million (95% CI: 7.90 million-9.59 million) life years that might have been achieved if South Africa had moved swiftly to implement WHO guidelines (2004-2013) and had achieved high levels of ART uptake in HIV-diagnosed individuals from 2004 onwards. The model is limited by its reliance on all-cause mortality data, given the lack of reliable cause-of-death reporting, and also does not allow for changes over time in tuberculosis control programmes and ART effectiveness. CONCLUSIONS ART has had a dramatic impact on adult mortality in South Africa, but delays in the rollout of ART, especially in the early stages of the ART programme, have contributed to substantial loss of life. This is the first study to our knowledge to calibrate a model of ART impact to population-level recorded death data in Africa; models that are not calibrated to population-level death data may overestimate HIV-related mortality.
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Affiliation(s)
- Leigh F. Johnson
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa
- * E-mail:
| | - Margaret T. May
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Rob E. Dorrington
- Centre for Actuarial Research, University of Cape Town, Cape Town, South Africa
| | - Morna Cornell
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa
| | - Andrew Boulle
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa
| | - Matthias Egger
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Mary-Ann Davies
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa
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Naranbhai V, Carrington M. Host genetic variation and HIV disease: from mapping to mechanism. Immunogenetics 2017; 69:489-498. [PMID: 28695282 PMCID: PMC5537324 DOI: 10.1007/s00251-017-1000-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 12/12/2022]
Abstract
This review aims to provide a summary of current knowledge of host genetic effects on human immunodeficiency virus (HIV) disease. Mapping of simple single nucleotide polymorphisms (SNP) has been largely successful in HIV, but more complex genetic associations involving haplotypic or epigenetic variation, for example, remain elusive. Mechanistic insights explaining SNP associations are incomplete, but continue to be forthcoming. The number of robust immunogenetic correlates of HIV is modest and their discovery mostly predates the genome-wide era. Nevertheless, genome-wide evaluations have nicely validated the impact of HLA and CCR5 variants on HIV disease, and importantly, made clear the many false positive associations that were previously suggested by studies using the candidate gene approach. We describe how multiple HIV outcome measures such as acquisition, viral control, and immune decline have been studied in adults and in children, but that collectively these identify only the two replicable loci responsible for modifying HIV disease, CCR5, and HLA. Recent heritability estimates in this disease corroborate the modest impact of genetic determinants and their oligogenic nature. While the mechanism of protection afforded by genetic variants that diminish CCR5 expression is clear, new aspects of HLA class I-mediated protection continue to be uncovered. We describe how these genetic findings have enhanced insights into immunobiology, been clinically translated into CCR5 antagonists, allowed prioritization of antigens for vaccination efforts, and identified targets for genome-editing interventions. Finally, we describe how studies of genetically complex parts of the genome using new tools may begin revealing additional correlates.
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Affiliation(s)
- Vivek Naranbhai
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA.
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
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22
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Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser C. Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe. PLoS Biol 2017; 15:e2001855. [PMID: 28604782 PMCID: PMC5467800 DOI: 10.1371/journal.pbio.2001855] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/09/2017] [Indexed: 12/20/2022] Open
Abstract
HIV-1 set-point viral load-the approximately stable value of viraemia in the first years of chronic infection-is a strong predictor of clinical outcome and is highly variable across infected individuals. To better understand HIV-1 pathogenesis and the evolution of the viral population, we must quantify the heritability of set-point viral load, which is the fraction of variation in this phenotype attributable to viral genetic variation. However, current estimates of heritability vary widely, from 6% to 59%. Here we used a dataset of 2,028 seroconverters infected between 1985 and 2013 from 5 European countries (Belgium, Switzerland, France, the Netherlands and the United Kingdom) and estimated the heritability of set-point viral load at 31% (CI 15%-43%). Specifically, heritability was measured using models of character evolution describing how viral load evolves on the phylogeny of whole-genome viral sequences. In contrast to previous studies, (i) we measured viral loads using standardized assays on a sample collected in a strict time window of 6 to 24 months after infection, from which the viral genome was also sequenced; (ii) we compared 2 models of character evolution, the classical "Brownian motion" model and another model ("Ornstein-Uhlenbeck") that includes stabilising selection on viral load; (iii) we controlled for covariates, including age and sex, which may inflate estimates of heritability; and (iv) we developed a goodness of fit test based on the correlation of viral loads in cherries of the phylogenetic tree, showing that both models of character evolution fit the data well. An overall heritability of 31% (CI 15%-43%) is consistent with other studies based on regression of viral load in donor-recipient pairs. Thus, about a third of variation in HIV-1 virulence is attributable to viral genetic variation.
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Affiliation(s)
- François Blanquart
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Chris Wymant
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands
| | - Astrid Gall
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands
| | | | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Swee Hoe Ong
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Norbert Bannert
- Division for HIV and other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Katrien Fransen
- HIV/STI reference laboratory, WHO collaborating centre, Institute of Tropical Medicine, Department of Clinical Science, Antwerpen, Belgium
| | - Annabelle J. Gourlay
- Department of Infection and Population Health, University College London, London, United Kingdom
| | - M. Kate Grabowski
- Department of Epidemiology, John Hopkins University, Baltimore, Maryland, United States of America
| | | | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Pia Kivelä
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Oliver Laeyendecker
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Kirsi Liitsola
- Department of Health Security, National Institute for Health and Welfare, Helsinki, Finland
| | - Laurence Meyer
- INSERM CESP U1018, Université Paris Sud, Université Paris Saclay, APHP, Service de Santé Publique, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Kholoud Porter
- Department of Infection and Population Health, University College London, London, United Kingdom
| | - Matti Ristola
- Department of Health Security, National Institute for Health and Welfare, Helsinki, Finland
| | | | - Guido Vanham
- Virology Unit, Immunovirology Research Pole, Biomedical Sciences Department, Institute of Tropical Medicine, Antwerpen, Belgium
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands
| | - Paul Kellam
- Kymab Ltd, Cambridge, United Kingdom
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
| | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, the Netherlands
- Department of Global Health, Academic Medical Center, Amsterdam, the Netherlands
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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A national study of the molecular epidemiology of HIV-1 in Australia 2005-2012. PLoS One 2017; 12:e0170601. [PMID: 28489920 PMCID: PMC5425008 DOI: 10.1371/journal.pone.0170601] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/06/2017] [Indexed: 12/12/2022] Open
Abstract
Introduction Rates of new HIV-1 diagnoses are increasing in Australia, with evidence of an increasing proportion of non-B HIV-1 subtypes reflecting a growing impact of migration and travel. The present study aims to define HIV-1 subtype diversity patterns and investigate possible HIV-1 transmission networks within Australia. Methods The Australian Molecular Epidemiology Network (AMEN) HIV collaborating sites in Western Australia, South Australia, Victoria, Queensland and western Sydney (New South Wales), provided baseline HIV-1 partial pol sequence, age and gender information for 4,873 patients who had genotypes performed during 2005–2012. HIV-1 phylogenetic analyses utilised MEGA V6, with a stringent classification of transmission pairs or clusters (bootstrap ≥98%, genetic distance ≤1.5% from at least one other sequence in the cluster). Results HIV-1 subtype B represented 74.5% of the 4,873 sequences (WA 59%, SA 68.4%, w-Syd 73.8%, Vic 75.6%, Qld 82.1%), with similar proportion of transmission pairs and clusters found in the B and non-B cohorts (23% vs 24.5% of sequences, p = 0.3). Significantly more subtype B clusters were comprised of ≥3 sequences compared with non-B clusters (45.0% vs 24.0%, p = 0.021) and significantly more subtype B pairs and clusters were male-only (88% compared to 53% CRF01_AE and 17% subtype C clusters). Factors associated with being in a cluster of any size included; being sequenced in a more recent time period (p<0.001), being younger (p<0.001), being male (p = 0.023) and having a B subtype (p = 0.02). Being in a larger cluster (>3) was associated with being sequenced in a more recent time period (p = 0.05) and being male (p = 0.008). Conclusion This nationwide HIV-1 study of 4,873 patient sequences highlights the increased diversity of HIV-1 subtypes within the Australian epidemic, as well as differences in transmission networks associated with these HIV-1 subtypes. These findings provide epidemiological insights not readily available using standard surveillance methods and can inform the development of effective public health strategies in the current paradigm of HIV prevention in Australia.
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Abstract
The human immunodeficiency virus (HIV) evolves rapidly owing to the combined activity of error-prone reverse transcriptase, recombination, and short generation times, leading to extensive viral diversity both within and between hosts. This diversity is a major contributing factor in the failure of the immune system to eradicate the virus and has important implications for the development of suitable drugs and vaccines to combat infection. This review will discuss the recent technological advances that have shed light on HIV evolution and will summarise emerging concepts in this field.
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Affiliation(s)
- Sophie M Andrews
- Nuffield Department of Clinical Medicine, University of Oxford, NDMRB, Oxford, UK
| | - Sarah Rowland-Jones
- Nuffield Department of Clinical Medicine, University of Oxford, NDMRB, Oxford, UK
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25
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Park SW, Bolker BM. Effects of contact structure on the transient evolution of HIV virulence. PLoS Comput Biol 2017; 13:e1005453. [PMID: 28362805 PMCID: PMC5391972 DOI: 10.1371/journal.pcbi.1005453] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 04/14/2017] [Accepted: 03/10/2017] [Indexed: 02/07/2023] Open
Abstract
Early in an epidemic, high densities of susceptible hosts select for relatively high parasite virulence; later in the epidemic, lower susceptible densities select for lower virulence. Thus over the course of a typical epidemic the average virulence of parasite strains increases initially, peaks partway through the epidemic, then declines again. However, precise quantitative outcomes, such as the peak virulence reached and its timing, may depend sensitively on epidemiological details. Fraser et al. proposed a model for the eco-evolutionary dynamics of HIV that incorporates the tradeoffs between transmission and virulence (mediated by set-point viral load, SPVL) and their heritability between hosts. Their model used implicit equations to capture the effects of partnership dynamics that are at the core of epidemics of sexually transmitted diseases. Our models combine HIV virulence tradeoffs with a range of contact models, explicitly modeling partnership formation and dissolution and allowing for individuals to transmit disease outside of partnerships. We assess summary statistics such as the peak virulence (corresponding to the maximum value of population mean log10 SPVL achieved throughout the epidemic) across models for a range of parameters applicable to the HIV epidemic in sub-Saharan Africa. Although virulence trajectories are broadly similar across models, the timing and magnitude of the virulence peak vary considerably. Previously developed implicit models predicted lower virulence and slower progression at the peak (a maximum of 3.5 log10 SPVL) compared both to more realistic models and to simple random-mixing models with no partnership structure at all (both with a maximum of ≈ 4.7 log10 SPVL). In this range of models, the simplest random-mixing structure best approximates the most realistic model; this surprising outcome occurs because the dominance of extra-pair contact in the realistic model swamps the effects of partnership structure. Pathogens such as HIV can evolve rapidly when the environment changes. One important aspect of a pathogen’s environment is the probability that an infectious contact (a sneeze for a respiratory disease, or an unprotected sex act for a sexually transmitted disease) encounters an uninfected person and thus has a chance to transmit the pathogen. As an epidemic grows the number of uninfected people shrinks, changing evolutionary pressures on the pathogen. While researchers have used models to explore pathogen evolution during epidemics, their models usually neglect important processes such as people entering and leaving sexual partnerships. We compared several evolutionary models for HIV that include partnership dynamics as well as sexual contact outside of stable partnerships. Models of intermediate complexity predicted lower virulence midway through the epidemic (a minimum of 15 years to progress to AIDS) than either more realistic models or simple models with no partnership structure (both with a minimum of 7.25 years to progress to AIDS), because random sexual contacts tended to wash out the effects of stable partnerships. Researchers trying to predict the evolution of pathogens must try to understand the implications of their modeling choices; models of intermediate complexity may not produce intermediate conclusions.
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Affiliation(s)
- Sang Woo Park
- Department of Mathematics & Statistics, McMaster University, Hamilton, Ontario, Canada
| | - Benjamin M. Bolker
- Department of Mathematics & Statistics, McMaster University, Hamilton, Ontario, Canada
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
- Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
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26
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Smith DRM, Mideo N. Modelling the evolution of HIV-1 virulence in response to imperfect therapy and prophylaxis. Evol Appl 2017; 10:297-309. [PMID: 28250813 PMCID: PMC5322411 DOI: 10.1111/eva.12458] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/15/2016] [Indexed: 12/11/2022] Open
Abstract
Average HIV-1 virulence appears to have evolved in different directions in different host populations since antiretroviral therapy first became available, and models predict that HIV drugs can select for either higher or lower virulence, depending on how treatment is administered. However, HIV virulence evolution in response to "leaky" therapy (treatment that imperfectly suppresses viral replication) and the use of preventive drugs (pre-exposure prophylaxis) has not been explored. Using adaptive dynamics, we show that higher virulence can evolve when antiretroviral therapy is imperfectly effective and that this evolution erodes some of the long-term clinical and epidemiological benefits of HIV treatment. The introduction of pre-exposure prophylaxis greatly reduces infection prevalence, but can further amplify virulence evolution when it, too, is leaky. Increasing the uptake rate of these imperfect interventions increases selection for higher virulence and can lead to counterintuitive increases in infection prevalence in some scenarios. Although populations almost always fare better with access to interventions than without, untreated individuals could experience particularly poor clinical outcomes when virulence evolves. These findings predict that antiretroviral drugs may have underappreciated evolutionary consequences, but that maximizing drug efficacy can prevent this evolutionary response. We suggest that HIV virulence evolution should be closely monitored as access to interventions continues to improve.
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Affiliation(s)
- David R. M. Smith
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Nicole Mideo
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
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27
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Golden MR, Hughes JP, Dombrowski JC. Optimizing the Timing of HIV Screening as Part of Routine Medical Care. AIDS Patient Care STDS 2017; 31:27-32. [PMID: 28051896 DOI: 10.1089/apc.2016.0185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
US federal guidelines recommend that medical providers test all adolescents and adults for HIV infection at least once before the age of 64. The wide age range included in these guidelines may limit their utility and impact. We created an arithmetic model to estimate how HIV screening at different ages would impact the total number of years of undiagnosed HIV infection in the population and the number of persons developing clinical manifestations of HIV/AIDS. Our base case model assumed that age of infection in the screened population was the same as the estimated age of infection among all persons diagnosed with HIV in the United States in 2010. We parameterized a second model assuming age of infection was similar to the younger age distribution observed in African Americans. In the base case model, the number of years of undiagnosed HIV infection and number of persons with clinical manifestations of HIV/AIDS were both minimized by screening at age 34. If age of infection was similar to that estimated to occur among African Americans, testing at age 24 and 27 would minimize the number of years of undiagnosed infection and clinical cases, respectively. For both parameterization scenarios, testing between the ages of 21 and 38 resulted in outcomes within 10% of the model's estimated optimal age for screening. Focusing HIV screening on a narrower age range than is currently recommended may improve the impact of routine HIV screening efforts.
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Affiliation(s)
- Matthew R. Golden
- Division of Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington
- Public Health—Seattle & King County, HIV/STD Program, Seattle, Washington
| | - James P. Hughes
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Julia C. Dombrowski
- Division of Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington
- Public Health—Seattle & King County, HIV/STD Program, Seattle, Washington
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28
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Blanquart F, Grabowski MK, Herbeck J, Nalugoda F, Serwadda D, Eller MA, Robb ML, Gray R, Kigozi G, Laeyendecker O, Lythgoe KA, Nakigozi G, Quinn TC, Reynolds SJ, Wawer MJ, Fraser C. A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda. eLife 2016; 5:e20492. [PMID: 27815945 PMCID: PMC5115872 DOI: 10.7554/elife.20492] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/01/2016] [Indexed: 01/25/2023] Open
Abstract
Evolutionary theory hypothesizes that intermediate virulence maximizes pathogen fitness as a result of a trade-off between virulence and transmission, but empirical evidence remains scarce. We bridge this gap using data from a large and long-standing HIV-1 prospective cohort, in Uganda. We use an epidemiological-evolutionary model parameterised with this data to derive evolutionary predictions based on analysis and detailed individual-based simulations. We robustly predict stabilising selection towards a low level of virulence, and rapid attenuation of the virus. Accordingly, set-point viral load, the most common measure of virulence, has declined in the last 20 years. Our model also predicts that subtype A is slowly outcompeting subtype D, with both subtypes becoming less virulent, as observed in the data. Reduction of set-point viral loads should have resulted in a 20% reduction in incidence, and a three years extension of untreated asymptomatic infection, increasing opportunities for timely treatment of infected individuals.
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Affiliation(s)
- François Blanquart
- MRC Centre for Outbreak Analysis and Modelling, Imperial College London, London, United Kingdom
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- School of Public Health, Imperial College London, London, United Kingdom
| | - Mary Kate Grabowski
- Department of Epidemiology, Johns Hopkins University, Baltimore, United States
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, United States
| | - Joshua Herbeck
- International Clinical Research Center, University of Washington, Seattle, United States
- Department of Global Health, University of Washington, Seattle, United States
| | | | - David Serwadda
- Rakai Health Sciences Program, Entebbe, Uganda
- School of Public Health, Makerere University, Kampala, Uganda
| | - Michael A Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, United States
| | - Ronald Gray
- Department of Epidemiology, Johns Hopkins University, Baltimore, United States
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, United States
- Rakai Health Sciences Program, Entebbe, Uganda
| | | | - Oliver Laeyendecker
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Katrina A Lythgoe
- MRC Centre for Outbreak Analysis and Modelling, Imperial College London, London, United Kingdom
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- School of Public Health, Imperial College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Thomas C Quinn
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Steven J Reynolds
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Maria J Wawer
- Department of Epidemiology, Johns Hopkins University, Baltimore, United States
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, United States
| | - Christophe Fraser
- MRC Centre for Outbreak Analysis and Modelling, Imperial College London, London, United Kingdom
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- School of Public Health, Imperial College London, London, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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29
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Arcia D, Acevedo-Sáenz L, Rugeles MT, Velilla PA. Role of CD8 + T Cells in the Selection of HIV-1 Immune Escape Mutations. Viral Immunol 2016; 30:3-12. [PMID: 27805477 DOI: 10.1089/vim.2016.0095] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus type-1 (HIV-1) infection represents one of the biggest public health problems worldwide. The immune response, mainly the effector mechanisms mediated by CD8+ T cells, induces the selection of mutations that allows the virus to escape the immune control. These mutations are generally selected within CD8+ T cell epitopes restricted to human leukocyte antigen class I (HLA-I), leading to a decrease in the presentation and recognition of the epitope, decreasing the activation of CD8+ T cells. However, these mutations may also affect cellular processing of the peptide or recognition by the T cell receptor. Escape mutations often carry a negative impact in viral fitness that is partially or totally compensated by the selection of compensatory mutations. The selection of either escape mutations or compensatory mutations may negatively affect the course of the infection. In addition, these mutations are a major barrier for the development of new therapeutic strategies focused on the induction of specific CD8+ T cell responses.
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Affiliation(s)
- David Arcia
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
| | - Liliana Acevedo-Sáenz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
| | - María Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
| | - Paula A Velilla
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
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30
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Roberts HE, Goulder PJR, McLean AR. The impact of antiretroviral therapy on population-level virulence evolution of HIV-1. J R Soc Interface 2016; 12:20150888. [PMID: 26609066 PMCID: PMC4707861 DOI: 10.1098/rsif.2015.0888] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In HIV-infected patients, an individual's set point viral load (SPVL) strongly predicts disease progression. Some think that SPVL is evolving, indicating that the virulence of the virus may be changing, but the data are not consistent. In addition, the widespread use of antiretroviral therapy (ART) has the potential to drive virulence evolution. We develop a simple deterministic model designed to answer the following questions: what are the expected patterns of virulence change in the initial decades of an epidemic? Could administration of ART drive changes in virulence evolution and, what is the potential size and direction of this effect? We find that even without ART we would not expect monotonic changes in average virulence. Transient decreases in virulence following the peak of an epidemic are not necessarily indicative of eventual evolution to avirulence. In the short term, we would expect widespread ART to cause limited downward pressure on virulence. In the long term, the direction of the effect is determined by a threshold condition, which we define. We conclude that, given the surpassing benefits of ART to the individual and in reducing onward transmission, virulence evolution considerations need have little bearing on how we treat.
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Affiliation(s)
- Hannah E Roberts
- Nuffield Department of Clinical Medicine, The Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Philip J R Goulder
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, UK HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Angela R McLean
- The Institute for Emerging Infections, The Oxford Martin School, Oxford OX1 3BD, UK Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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31
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Herbeck JT, Mittler JE, Gottlieb GS, Goodreau SM, Murphy JT, Cori A, Pickles M, Fraser C. Evolution of HIV virulence in response to widespread scale up of antiretroviral therapy: a modeling study. Virus Evol 2016; 2:vew028. [PMID: 29492277 PMCID: PMC5822883 DOI: 10.1093/ve/vew028] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
There are global increases in the use of HIV antiretroviral therapy (ART), guided by clinical benefits of early ART initiation and the efficacy of treatment as prevention of transmission. Separately, it has been shown theoretically and empirically that HIV virulence can evolve over time; observed virulence levels may reflect an adaptive balance between infected lifespan and per-contact transmission rate. However, the potential effects of widespread ART usage on HIV virulence are unknown. To predict these effects, we used an agent-based stochastic model to simulate evolutionary trends in HIV virulence, using set point viral load as a proxy for virulence. We calibrated our model to prevalence and incidence trends of South Africa. We explored two distinct ART scenarios: (1) ART initiation based on HIV-infected individuals reaching a CD4 count threshold; and (2) ART initiation based on individual time elapsed since HIV infection (a scenario that mimics "universal testing and treatment" (UTT) aspirations). In each case, we considered a range in population uptake of ART. We found that HIV virulence is generally unchanged in scenarios of CD4-based initiation. However, with ART initiation based on time since infection, virulence can increase moderately within several years of ART rollout, under high coverage levels and early treatment initiation (albeit within the context of epidemics that are rapidly decreasing in size). Sensitivity analyses suggested the impact of ART on virulence is relatively insensitive to model calibration. Our modeling study suggests that increasing HIV virulence driven by UTT is likely not a major public health concern, but should be monitored in sentinel surveillance, in a manner similar to transmitted resistance to antiretroviral drugs.
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Affiliation(s)
- Joshua T Herbeck
- International Clinical Research Center, Department of Global Health, University of Washington, Seattle, WA 98104, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- Departments of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
- Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - John E Mittler
- International Clinical Research Center, Department of Global Health, University of Washington, Seattle, WA 98104, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- Departments of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
- Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - Geoffrey S Gottlieb
- International Clinical Research Center, Department of Global Health, University of Washington, Seattle, WA 98104, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- Departments of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
- Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - Steven M Goodreau
- International Clinical Research Center, Department of Global Health, University of Washington, Seattle, WA 98104, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- Departments of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
- Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - James T Murphy
- International Clinical Research Center, Department of Global Health, University of Washington, Seattle, WA 98104, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- Departments of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
- Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - Anne Cori
- International Clinical Research Center, Department of Global Health, University of Washington, Seattle, WA 98104, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- Departments of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
- Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - Michael Pickles
- International Clinical Research Center, Department of Global Health, University of Washington, Seattle, WA 98104, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- Departments of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
- Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - Christophe Fraser
- International Clinical Research Center, Department of Global Health, University of Washington, Seattle, WA 98104, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- Departments of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
- Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
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32
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Johnson LF, Chiu C, Myer L, Davies MA, Dorrington RE, Bekker LG, Boulle A, Meyer-Rath G. Prospects for HIV control in South Africa: a model-based analysis. Glob Health Action 2016; 9:30314. [PMID: 27282146 PMCID: PMC4901512 DOI: 10.3402/gha.v9.30314] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 05/07/2016] [Accepted: 05/18/2016] [Indexed: 01/17/2023] Open
Abstract
Background The goal of virtual elimination of horizontal and mother-to-child HIV transmission in South Africa (SA) has been proposed, but there have been few systematic investigations of which interventions are likely to be most critical to reducing HIV incidence. Objective This study aims to evaluate SA's potential to achieve virtual elimination targets and to identify which interventions will be most critical to achieving HIV incidence reductions. Design A mathematical model was developed to simulate the population-level impact of different HIV interventions in SA. Probability distributions were specified to represent uncertainty around 32 epidemiological parameters that could be influenced by interventions, and correlation coefficients (r) were calculated to assess the sensitivity of the adult HIV incidence rates and mother-to-child transmission rates (2015–2035) to each epidemiological parameter. Results HIV incidence in SA adults (ages 15–49) is expected to decline from 1.4% in 2011–2012 to 0.29% by 2035 (95% CI: 0.10–0.62%). The parameters most strongly correlated with future adult HIV incidence are the rate of viral suppression after initiating antiretroviral treatment (ART) (r=−0.56), the level of condom use in non-marital relationships (r=−0.40), the phase-in of intensified risk-reduction counselling for HIV-positive adults (r=0.29), the uptake of medical male circumcision (r=−0.24) and the phase-in of universal ART eligibility (r=0.22). The paediatric HIV parameters most strongly associated with mother-to-child transmission rates are the relative risk of transmission through breastfeeding when the mother is receiving ART (r=0.70) and the rate of ART initiation during pregnancy (r=−0.16). Conclusions The virtual elimination target of a 0.1% incidence rate in adults will be difficult to achieve. Interventions that address the infectiousness of patients after ART initiation will be particularly critical to achieving long-term HIV incidence declines in South Africa.
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Affiliation(s)
- Leigh F Johnson
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa;
| | - Calvin Chiu
- Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Landon Myer
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.,Division of Epidemiology and Biostatistics, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Mary-Ann Davies
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Rob E Dorrington
- Centre for Actuarial Research, University of Cape Town, Cape Town, South Africa
| | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Andrew Boulle
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Gesine Meyer-Rath
- Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Center for Global Health and Development, Boston University, Boston, MA, USA
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33
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Saxena D, Spino M, Tricta F, Connelly J, Cracchiolo BM, Hanauske AR, D’Alliessi Gandolfi D, Mathews MB, Karn J, Holland B, Park MH, Pe’ery T, Palumbo PE, Hanauske-Abel HM. Drug-Based Lead Discovery: The Novel Ablative Antiretroviral Profile of Deferiprone in HIV-1-Infected Cells and in HIV-Infected Treatment-Naive Subjects of a Double-Blind, Placebo-Controlled, Randomized Exploratory Trial. PLoS One 2016; 11:e0154842. [PMID: 27191165 PMCID: PMC4871512 DOI: 10.1371/journal.pone.0154842] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 04/18/2016] [Indexed: 01/19/2023] Open
Abstract
UNLABELLED Antiretrovirals suppress HIV-1 production yet spare the sites of HIV-1 production, the HIV-1 DNA-harboring cells that evade immune detection and enable viral resistance on-drug and viral rebound off-drug. Therapeutic ablation of pathogenic cells markedly improves the outcome of many diseases. We extend this strategy to HIV-1 infection. Using drug-based lead discovery, we report the concentration threshold-dependent antiretroviral action of the medicinal chelator deferiprone and validate preclinical findings by a proof-of-concept double-blind trial. In isolate-infected primary cultures, supra-threshold concentrations during deferiprone monotherapy caused decline of HIV-1 RNA and HIV-1 DNA; did not allow viral breakthrough for up to 35 days on-drug, indicating resiliency against viral resistance; and prevented, for at least 87 days off-drug, viral rebound. Displaying a steep dose-effect curve, deferiprone produced infection-independent deficiency of hydroxylated hypusyl-eIF5A. However, unhydroxylated deoxyhypusyl-eIF5A accumulated particularly in HIV-infected cells; they preferentially underwent apoptotic DNA fragmentation. Since the threshold, ascertained at about 150 μM, is achievable in deferiprone-treated patients, we proceeded from cell culture directly to an exploratory trial. HIV-1 RNA was measured after 7 days on-drug and after 28 and 56 days off-drug. Subjects who attained supra-threshold concentrations in serum and completed the protocol of 17 oral doses, experienced a zidovudine-like decline of HIV-1 RNA on-drug that was maintained off-drug without statistically significant rebound for 8 weeks, over 670 times the drug's half-life and thus clearance from circulation. The uniform deferiprone threshold is in agreement with mapping of, and crystallographic 3D-data on, the active site of deoxyhypusyl hydroxylase (DOHH), the eIF5A-hydroxylating enzyme. We propose that deficiency of hypusine-containing eIF5A impedes the translation of mRNAs encoding proline cluster ('polyproline')-containing proteins, exemplified by Gag/p24, and facilitated by the excess of deoxyhypusine-containing eIF5A, releases the innate apoptotic defense of HIV-infected cells from viral blockade, thus depleting the cellular reservoir of HIV-1 DNA that drives breakthrough and rebound. TRIAL REGISTRATION ClinicalTrial.gov NCT02191657.
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Affiliation(s)
- Deepti Saxena
- Department of Pediatrics, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Michael Spino
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
- ApoPharma Inc., Toronto, Ontario, Canada
| | | | | | - Bernadette M. Cracchiolo
- Department of Obstetrics, Gynecology and Women’s Health, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Axel-Rainer Hanauske
- Oncology Center and Medical Clinic III, Asklepios Klinik St. Georg, Hamburg, Germany
| | | | - Michael B. Mathews
- Department of Medicine, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Bart Holland
- Department of Medicine, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Myung Hee Park
- Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, National Institute of Health, Bethesda, Maryland, United States of America
| | - Tsafi Pe’ery
- Department of Medicine, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Paul E. Palumbo
- Department of Pediatrics, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
- * E-mail: (PEP); (HMHA)
| | - Hartmut M. Hanauske-Abel
- Department of Pediatrics, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
- Department of Obstetrics, Gynecology and Women’s Health, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
- * E-mail: (PEP); (HMHA)
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Castley AS, Gaudieri S, James I, Gizzarelli LS, Guelfi G, John M, Nolan D. Longitudinal Trends in Western Australian HIV-1 Sequence Diversity and Viral Transmission Networks and Their Influence on Clinical Parameters: 2000-2014. AIDS Res Hum Retroviruses 2016; 32:211-9. [PMID: 26530340 DOI: 10.1089/aid.2015.0206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We examined baseline HIV-1 protease and reverse transcriptase sequences and HIV clinical parameters from 1,021 consecutive patients (814 male, 207 female) through the Royal Perth Hospital HIV service to investigate HIV-1 subtype diversity and local phylogenetic networks from 2000 to 2014. HIV-1 subtype B virus sequences were demonstrated in 619 (61%) of cases, with increasing non-B HIV-1 subtypes from 23.2% (2000-2003) to 48% (2008-2011) and 43% (2012-2014) (p < 0.001), including the CRF01_AE subtype [6.6% (2000-2003) to 21.5% (2008-2011)] and HIV-1 C subtype [9.5% (2000-2003) to 20.2% (2008-2011)]. More HIV-1 B subtypes were assigned to phylogenetic clusters compared to non-B subtypes (34% vs. 18%; p < 0.001), with larger clusters identified (cluster size >2: 135/211; 64% vs. 13/69; 19%; p = 0.001), including one cluster of 53 HIV-1 B subtype sequences that evolved from 2008 to 2014. Non-B subtype HIV-1 was associated with lower baseline CD4 T cell count (p = 0.005) but not plasma HIV-1 RNA levels (p = 0.31), suggesting relatively delayed diagnosis. Baseline viral load was strongly associated with calendar time [mean 18,620 copies/ml in 2000-2003; 75,858 copies/ml in 2012-2014 (p < 0.001)], and was also associated with larger phylogenetic clusters (size >2) in adjusted analyses (p = 0.03). This study identifies a number of temporal trends over the past 15 years, including an increasing prevalence of non-B subtype HIV-1 that highlights the growing influence of migration and travel on the Australian HIV-1 epidemic and the associated increased role of heterosexual HIV-1 transmission in this context. At the same time, these data indicate that local transmission within predominantly male networks remains a challenging issue for HIV-1 prevention.
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Affiliation(s)
- Alison S.L. Castley
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia
- School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia
| | - Silvana Gaudieri
- Institute of Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
- School of Anatomy, Physiology and Human Biology, University of Western Australia, Nedlands, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Ian James
- Institute of Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Laila S. Gizzarelli
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia
| | - George Guelfi
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia
| | - Mina John
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia
- Institute of Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - David Nolan
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia
- Institute of Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
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Girerd-Genessay I, Baratin D, Ferry T, Chidiac C, Ronin V, Vanhems P. Higher HIV RNA Viral Load in Recent Patients with Symptomatic Acute HIV Infection in Lyon University Hospitals. PLoS One 2016; 11:e0146978. [PMID: 26799390 PMCID: PMC4723228 DOI: 10.1371/journal.pone.0146978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 12/23/2015] [Indexed: 11/23/2022] Open
Abstract
Introduction Increased human immunodeficiency virus (HIV) virulence at infection has been suggested by a meta-analysis based on viral load and CD4 T lymphocytes (CD4) count during acute infection. This result was obtained after secondary analyses of large databases, facilitating the detection of differences. Similar finding in cohorts of more modest sample size would indicate that the effect could be more substantial. Methods Change from initial CD4 count and HIV viral load after acute HIV infection by calendar year was explored in patients treated at Lyon University hospitals. All patients admitted to our hospitals with acute HIV infection between 1996 and 2013 were included in our study. Initial CD4 count and viral load before the start of anti-retroviral treatment were analyzed. Trends over time were assessed in linear models. Results Initial CD4 count remained similar over time. However, in 2006–2013, initial viral load rose significantly (+1.12 log10/ml/year, p = 0.01). Conclusion Our data, obtained from a single hospital cohort, confirmed findings from a large meta-analysis, showed increased initial viremia at acute HIV infection since 2006 and suggesting potentially higher HIV virulence in recent years.
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Affiliation(s)
- Isabelle Girerd-Genessay
- Infection Control and Epidemiology Unit, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
| | - Dominique Baratin
- Infection Control and Epidemiology Unit, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
| | - Tristan Ferry
- Department of Infectious Diseases, Hospices Civils de Lyon, Lyon, France
| | - Christian Chidiac
- Department of Infectious Diseases, Hospices Civils de Lyon, Lyon, France
| | - Vincent Ronin
- Infection Control and Epidemiology Unit, Hôpital Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Philippe Vanhems
- Infection Control and Epidemiology Unit, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
- Emerging Pathogens Laboratory, Fondation Mérieux, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, ENS de Lyon, UCBL1, 21, Avenue Tony Garnier, Lyon, 69007, France
- * E-mail:
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Kløverpris HN, Leslie A, Goulder P. Role of HLA Adaptation in HIV Evolution. Front Immunol 2016; 6:665. [PMID: 26834742 PMCID: PMC4716577 DOI: 10.3389/fimmu.2015.00665] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/27/2015] [Indexed: 01/22/2023] Open
Abstract
Killing of HIV-infected cells by CD8+ T-cells imposes strong selection pressure on the virus toward escape. The HLA class I molecules that are successful in mediating some degree of control over the virus are those that tend to present epitopes in conserved regions of the proteome, such as in p24 Gag, in which escape also comes at a significant cost to viral replicative capacity (VRC). In some instances, compensatory mutations can fully correct for the fitness cost of such an escape variant; in others, correction is only partial. The consequences of these events within the HIV-infected host, and at the population level following transmission of escape variants, are discussed. The accumulation of escape mutants in populations over the course of the epidemic already shows instances of protective HLA molecules losing their impact, and in certain cases, a modest decline in HIV virulence in association with population-level increase in mutants that reduce VRC.
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Affiliation(s)
- Henrik N Kløverpris
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Alasdair Leslie
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R Mandela School of Medicine, University of KwaZulu-Natal , Durban , South Africa
| | - Philip Goulder
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa; Department of Paediatrics, University of Oxford, Oxford, UK
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CD4+ cell dynamics in untreated HIV-1 infection: overall rates, and effects of age, viral load, sex and calendar time. AIDS 2015; 29:2435-46. [PMID: 26558543 PMCID: PMC4645962 DOI: 10.1097/qad.0000000000000854] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Background: CD4+ cell count is a key measure of HIV disease progression, and the basis of successive international guidelines for treatment initiation. CD4+ cell dynamics are used in mathematical and econometric models for evaluating public health need and interventions. Here, we estimate rates of CD4+ decline, stratified by relevant covariates, in a form that is clinically transparent and can be directly used in such models. Methods: We analyse the AIDS Therapy Evaluation in the Netherlands cohort, including individuals with date of seroconversion estimated to be within 1 year and with intensive clinical follow-up prior to treatment initiation. Owing to the fact that CD4+ cell counts are intrinsically noisy, we separate the analysis into long-term trends of smoothed CD4+ cell counts and an observation model relating actual CD4+ measurements to the underlying smoothed counts. We use a monotonic spline smoothing model to describe the decline of smoothed CD4+ cell counts through categories CD4+ above 500, 350–500, 200–350 and 200 cells/μl or less. We estimate the proportion of individuals starting in each category after seroconversion and the average time spent in each category. We examine individual-level cofactors which influence these parameters. Results: Among untreated individuals, the time spent in each compartment was 3.32, 2.70, 5.50 and 5.06 years. Only 76% started in the CD4+ cell count above 500 cells/μl compartment after seroconversion. Set-point viral load (SPVL) was an important factor: individuals with at least 5 log10 copies/ml took 5.37 years to reach CD4+ cell count less than 200 cells/μl compared with 15.76 years for SPVL less than 4 log10 copies/ml. Conclusion: Many individuals already have CD4+ cell count below 500 cells/μl after seroconversion. SPVL strongly influences the rate of CD4+ decline. Treatment guidelines should consider measuring SPVL, whereas mathematical models should incorporate SPVL stratification.
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Abstract
Rigorous testing of new HIV-prevention strategies is a time-consuming and expensive undertaking. Thus, making well informed decisions on which candidate-prevention approaches are most likely to provide the most benefit is critical to appropriately prioritizing clinical testing. In the case of biological interventions, the decision to test a given prevention approach in human trials rests largely on evidence of protection in preclinical studies. The ability of preclinical studies to predict efficacy in humans may depend on how well the model recapitulates key biological features of HIV transmission relevant to the question at hand. Here, we review our current understanding of the biology of HIV transmission based on data from animal models, cell culture, and viral sequence analysis from human infection. We summarize studies of the bottleneck in viral transmission; the characteristics of transmitted viruses; the establishment of infection; and the contribution of cell-free and cell-associated virus. We seek to highlight the implications of HIV-transmission biology for development of prevention interventions, and to discuss the limitations of existing preclinical models.
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Herbeck J, Celum C. The changing virulence of HIV. Lancet HIV 2015; 1:e99-e100. [PMID: 26424124 DOI: 10.1016/s2352-3018(14)00004-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022]
Affiliation(s)
- Joshua Herbeck
- International Clinical Research Center, Department of Global Health, University of Washington, Seattle, WA 98104 USA.
| | - Connie Celum
- International Clinical Research Center, Department of Global Health, University of Washington, Seattle, WA 98104 USA
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Ndawinz JDA, Anglaret X, Delaporte E, Koulla-Shiro S, Gabillard D, Minga A, Costagliola D, Supervie V. New indicators for delay in initiation of antiretroviral treatment: estimates for Cameroon. Bull World Health Organ 2015; 93:521-8. [PMID: 26478609 PMCID: PMC4581657 DOI: 10.2471/blt.14.147892] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 11/27/2022] Open
Abstract
Objective To propose two new indicators for monitoring access to antiretroviral treatment (ART) for human immunodeficiency virus (HIV); (i) the time from HIV seroconversion to ART initiation, and (ii) the time from ART eligibility to initiation, referred to as delay in ART initiation. To estimate values of these indicators in Cameroon. Methods We used linear regression to model the natural decline in CD4+ T-lymphocyte (CD4+ cell) numbers in HIV-infected individuals over time. The model was fitted using data from a cohort of 351 people in Côte d’Ivoire. We used the model to estimate the time from seroconversion to ART initiation and the delay in ART initiation in a representative sample of 4154 HIV-infected people who started ART in Cameroon between 2007 and 2010. Findings In Cameroon, the median CD4+ cell counts at ART initiation increased from 140 cells/μl (interquartile range, IQR: 66 to 210) in 2007–2009 to 163 cells/μl (IQR: 73 to 260) in 2010. The estimated average time from seroconversion to ART initiation decreased from 10.4 years (95% confidence interval, CI: 10.3 to 10.5) to 9.8 years (95% CI: 9.6 to 10.0). Delay in ART initiation increased from 3.4 years (95% CI: 3.1 to 3.7) to 5.8 years (95% CI: 5.6 to 6.2). Conclusion The estimated time to initiate ART and the delay in ART initiation indicate that progress in Cameroon is insufficient. These indicators should help monitor whether public health interventions to accelerate ART initiation are successful.
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Affiliation(s)
- Jacques D A Ndawinz
- INSERM, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013, Paris, France
| | | | | | - Sinata Koulla-Shiro
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon
| | | | | | - Dominique Costagliola
- INSERM, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013, Paris, France
| | - Virginie Supervie
- INSERM, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013, Paris, France
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McLaren PJ, Carrington M. The impact of host genetic variation on infection with HIV-1. Nat Immunol 2015; 16:577-83. [PMID: 25988890 PMCID: PMC6296468 DOI: 10.1038/ni.3147] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 03/12/2015] [Indexed: 12/16/2022]
Abstract
The outcome after infection with the human immunodeficiency virus type 1 (HIV-1) is a complex phenotype determined by interactions among the pathogen, the human host and the surrounding environment. An impact of host genetic variation on HIV-1 susceptibility was identified early in the pandemic, with a major role attributed to the genes encoding class I human leukocyte antigens (HLA) and the chemokine receptor CCR5. Studies using genome-wide data sets have underscored the strength of these associations relative to variants located throughout the rest of the genome. However, the extent to which additional polymorphisms influence HIV-1 disease progression, and how much of the variability in outcome can be attributed to host genetics, remain largely unclear. Here we discuss findings concerning the functional impact of associated variants, outline methods for quantifying the host genetic component and examine how available genome-wide data sets may be leveraged to discover gene variants that affect the outcome of HIV-1 infection.
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Affiliation(s)
- Paul J McLaren
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mary Carrington
- 1] Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA. [2] The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
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Watanabe D, Suzuki S, Ashida M, Shimoji Y, Hirota K, Ogawa Y, Yajima K, Kasai D, Nishida Y, Uehira T, Shirasaka T. Disease progression of HIV-1 infection in symptomatic and asymptomatic seroconverters in Osaka, Japan: a retrospective observational study. AIDS Res Ther 2015; 12:19. [PMID: 26000028 PMCID: PMC4440509 DOI: 10.1186/s12981-015-0059-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 04/27/2015] [Indexed: 01/19/2023] Open
Abstract
Background Estimates of the interval from HIV-1 infection to disease progression may be affected by selection bias, and data concerning asymptomatic early seroconverters are limited. We examined the interval until disease progression in HIV-1 seroconverters in whom the timing of infection could be estimated within 1 year before diagnosis. Methods Subjects included newly diagnosed patients at Osaka National Hospital between 2003 and 2010 who had either (1) symptomatic acute HIV-1 infection with a negative or intermediate reaction on Western blotting and a positive reaction on an HIV RNA test (symptomatic acute group) or (2) a positive reaction on Western blotting at diagnosis and a <1-year interval from the last negative HIV test until the first positive test. The latter was divided into symptomatic recent or asymptomatic recent groups based on the presence or absence, respectively, of any transient fever between the last negative and first positive tests. Disease progression was defined as a fall in the CD4 count to <350 cells/microL on 2 consecutive tests, the start of anti-HIV therapy, or the onset of AIDS-indicator diseases. Information was retrospectively collected from medical records. Results Subjects included 210 patients: 91 in the symptomatic acute group, 72 in the symptomatic recent group, and 47 in the asymptomatic recent group. In the symptomatic acute (0.8 years) and symptomatic recent (2.2 years) groups, the Kaplan-Meier estimate of median interval until disease progression was significantly shorter than that in the asymptomatic recent group (2.9 years). Multivariate analysis by Cox’s proportional hazards test showed that the symptomatic acute group (vs. asymptomatic recent group: hazard ratio: 1.93; 95% confidence interval: 1.14–3.36; p = 0.0140) and a baseline CD4 count of <400 cells/microL (hazard ratio: 3.88; 95% confidence interval: 2.57–5.96; p < 0.0001) were independent prognostic factors associated with early disease progression. Conclusions Symptomatic seroconversion was associated with early disease progression. Furthermore, the estimated median interval until the CD4 count was <350 cells/microL was only 2.9 years even in patients with asymptomatic seroconversion. These results suggest the importance of early diagnosis in early seroconverters.
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Bonhoeffer S, Fraser C, Leventhal GE. High heritability is compatible with the broad distribution of set point viral load in HIV carriers. PLoS Pathog 2015; 11:e1004634. [PMID: 25658741 PMCID: PMC4450065 DOI: 10.1371/journal.ppat.1004634] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/16/2014] [Indexed: 11/23/2022] Open
Abstract
Set point viral load in HIV patients ranges over several orders of magnitude and is a key determinant of disease progression in HIV. A number of recent studies have reported high heritability of set point viral load implying that viral genetic factors contribute substantially to the overall variation in viral load. The high heritability is surprising given the diversity of host factors associated with controlling viral infection. Here we develop an analytical model that describes the temporal changes of the distribution of set point viral load as a function of heritability. This model shows that high heritability is the most parsimonious explanation for the observed variance of set point viral load. Our results thus not only reinforce the credibility of previous estimates of heritability but also shed new light onto mechanisms of viral pathogenesis. Following an initial peak in viremia, the viral load in HIV infected patients settles down to a set point which remains more or less stable during chronic HIV infection. This set point viral load is one of the key factors determining the rate of disease progression. The extent to which it is determined by the virus versus host genetics is thus central to developing a better understanding of disease progression. Here we develop an analytical model that describes the changes of the distribution of set point viral load in the HIV carrier population over a full cycle of transmission. Applying this model to patient data we find that the most parsimonious explanation for the observed large variation of set point viral load across HIV patients is that set point viral load is highly heritable from donors to recipients. This implies that set point viral load is to a considerable extent under the genetic control of the virus.
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Affiliation(s)
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
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Carlson JM, Le AQ, Shahid A, Brumme ZL. HIV-1 adaptation to HLA: a window into virus-host immune interactions. Trends Microbiol 2015; 23:212-24. [PMID: 25613992 DOI: 10.1016/j.tim.2014.12.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/04/2014] [Accepted: 12/16/2014] [Indexed: 11/26/2022]
Abstract
HIV-1 develops specific mutations within its genome that allow it to escape detection by human leukocyte antigen (HLA) class I-restricted immune responses, notably those of CD8(+) cytotoxic T lymphocytes (CTL). HLA thus represents a major force driving the evolution and diversification of HIV-1 within individuals and at the population level. Importantly, the study of HIV-1 adaptation to HLA also represents an opportunity to identify what qualities constitute an effective immune response, how the virus in turn adapts to these pressures, and how we may harness this information to design HIV-1 vaccines that stimulate effective cellular immunity.
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Affiliation(s)
| | - Anh Q Le
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
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van Dorp CH, van Boven M, de Boer RJ. Immuno-epidemiological modeling of HIV-1 predicts high heritability of the set-point virus load, while selection for CTL escape dominates virulence evolution. PLoS Comput Biol 2014; 10:e1003899. [PMID: 25522184 PMCID: PMC4270429 DOI: 10.1371/journal.pcbi.1003899] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 09/07/2014] [Indexed: 02/07/2023] Open
Abstract
It has been suggested that HIV-1 has evolved its set-point virus load to be optimized for transmission. Previous epidemiological models and studies into the heritability of set-point virus load confirm that this mode of adaptation within the human population is feasible. However, during the many cycles of replication between infection of a host and transmission to the next host, HIV-1 is under selection for escape from immune responses, and not transmission. Here we investigate with computational and mathematical models how these two levels of selection, within-host and between-host, are intertwined. We find that when the rate of immune escape is comparable to what has been observed in patients, immune selection within hosts is dominant over selection for transmission. Surprisingly, we do find high values for set-point virus load heritability, and argue that high heritability estimates can be caused by the 'footprints' left by differing hosts' immune systems on the virus.
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Affiliation(s)
- Christiaan H. van Dorp
- Theoretical Biology and Bioinformatics, Universiteit Utrecht, Utrecht, The Netherlands
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- * E-mail:
| | - Michiel van Boven
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Rob J. de Boer
- Theoretical Biology and Bioinformatics, Universiteit Utrecht, Utrecht, The Netherlands
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Payne R, Muenchhoff M, Mann J, Roberts HE, Matthews P, Adland E, Hempenstall A, Huang KH, Brockman M, Brumme Z, Sinclair M, Miura T, Frater J, Essex M, Shapiro R, Walker BD, Ndung'u T, McLean AR, Carlson JM, Goulder PJR. Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence. Proc Natl Acad Sci U S A 2014; 111:E5393-400. [PMID: 25453107 PMCID: PMC4273423 DOI: 10.1073/pnas.1413339111] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
It is widely believed that epidemics in new hosts diminish in virulence over time, with natural selection favoring pathogens that cause minimal disease. However, a tradeoff frequently exists between high virulence shortening host survival on the one hand but allowing faster transmission on the other. This is the case in HIV infection, where high viral loads increase transmission risk per coital act but reduce host longevity. We here investigate the impact on HIV virulence of HIV adaptation to HLA molecules that protect against disease progression, such as HLA-B*57 and HLA-B*58:01. We analyzed cohorts in Botswana and South Africa, two countries severely affected by the HIV epidemic. In Botswana, where the epidemic started earlier and adult seroprevalence has been higher, HIV adaptation to HLA including HLA-B*57/58:01 is greater compared with South Africa (P = 7 × 10(-82)), the protective effect of HLA-B*57/58:01 is absent (P = 0.0002), and population viral replicative capacity is lower (P = 0.03). These data suggest that viral evolution is occurring relatively rapidly, and that adaptation of HIV to the most protective HLA alleles may contribute to a lowering of viral replication capacity at the population level, and a consequent reduction in HIV virulence over time. The potential role in this process played by increasing antiretroviral therapy (ART) access is also explored. Models developed here suggest distinct benefits of ART, in addition to reducing HIV disease and transmission, in driving declines in HIV virulence over the course of the epidemic, thereby accelerating the effects of HLA-mediated viral adaptation.
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Affiliation(s)
- Rebecca Payne
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
| | | | - Jaclyn Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4013, South Africa
| | - Hannah E Roberts
- The Institute for Emerging Infections, The Oxford Martin School, University of Oxford, Oxford OX1 3BD, United Kingdom; Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Philippa Matthews
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Emily Adland
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Allison Hempenstall
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Kuan-Hsiang Huang
- The Institute for Emerging Infections, The Oxford Martin School, University of Oxford, Oxford OX1 3BD, United Kingdom; Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Mark Brockman
- Faculty of Health Sciences, Simon Fraser University, Vancouver, BC V5A 1S6, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Zabrina Brumme
- Faculty of Health Sciences, Simon Fraser University, Vancouver, BC V5A 1S6, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Marc Sinclair
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
| | | | - John Frater
- The Institute for Emerging Infections, The Oxford Martin School, University of Oxford, Oxford OX1 3BD, United Kingdom; Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, United Kingdom; Oxford National Institute of Health Research, Biomedical Research Centre, Oxford OX1 3SY, United Kingdom
| | - Myron Essex
- Botswana Harvard AIDS Institute Partnership, Gaborone BO 320, Botswana; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02215
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone BO 320, Botswana; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02215
| | - Bruce D Walker
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4013, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA 02139
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4013, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA 02139
| | - Angela R McLean
- The Institute for Emerging Infections, The Oxford Martin School, University of Oxford, Oxford OX1 3BD, United Kingdom; Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom; and
| | | | - Philip J R Goulder
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom; HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4013, South Africa;
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Pantazis N, Porter K, Costagliola D, De Luca A, Ghosn J, Guiguet M, Johnson AM, Kelleher AD, Morrison C, Thiebaut R, Wittkop L, Touloumi G. Temporal trends in prognostic markers of HIV-1 virulence and transmissibility: an observational cohort study. Lancet HIV 2014; 1:e119-26. [PMID: 26424120 DOI: 10.1016/s2352-3018(14)00002-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/28/2014] [Indexed: 12/16/2022]
Abstract
BACKGROUND Measures of CD4 T-cell count and HIV-1 plasma viral load before antiretroviral therapy are proxies for virulence. Whether these proxies are changing over time has implications for prevention and treatment. The aim of this study was to investigate those trends. METHODS Data were derived from the Concerted Action on SeroConversion to AIDS and Death in Europe (CASCADE) collaboration of mainly European seroconverter cohorts. Longitudinal CD4 cell counts and plasma viral load measurements before the initiation of antiretroviral therapy or AIDS onset were analysed by use of linear or fractional polynomials mixed models adjusting for all available potential confounders. Calendar time effects were modelled through natural cubic splines. FINDINGS 15 875 individuals seroconverting from 1979 to 2008 fulfilled the inclusion criteria; 3215 (20·3%) were women; median follow-up was 31 months (IQR 14-62); dropout before starting antiretroviral therapy or AIDS onset was 8·1%. Estimated CD4 counts at seroconversion for a typical individual declined from about 770 cells per μL (95% CI 750-800) in the early 1980s to a plateau of about 570 cells per μL (555-585) after 2002. CD4 cell rate of loss increased up to 2002. Estimated set-point plasma viral loads increased from 4·05 log10 copies per mL (95% CI 3·98-4·12) in 1980 to 4·50 log10 copies per mL (4·45-4·54) in 2002 with a tendency of returning to lower loads thereafter. Results were similar when we restricted analyses to various subsets, including adjusting for plasma viral load assay, censored follow-up at 3 years, or used variations of the main statistical approach. INTERPRETATION Our results provide strong indications of increased HIV-1 virulence and transmissibility during the course of the epidemic and a potential plateau effect after about 2002. FUNDING European Union Seventh Framework Programme.
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Affiliation(s)
| | | | - Dominique Costagliola
- INSERM, U1136, Paris, France; UPMC Université Paris 06, UMR S1136, Paris, France; AP-HP, Groupe hospitalier Pitié-Salpétrière, Service des maladies infectieuses et tropicales, Paris, France
| | - Andrea De Luca
- Clinic of Infectious Diseases, Catholic University of Sacred Heart, Rome, Italy; Unit of Infectious Diseases, Siena University Hospital, Siena, Italy
| | - Jade Ghosn
- AP-HP, Hôpital Bicêtre, Service de médecine interne, Le Kremlin-Bicêtre, Paris, France; Faculté de Médecine site Necker, Université Paris Descartes, EA 3620, Paris, France
| | - Marguerite Guiguet
- INSERM, U1136, Paris, France; UPMC Université Paris 06, UMR S1136, Paris, France
| | - Anne M Johnson
- Research Department of Infection and Population Health, University College London, London, UK
| | | | | | - Rodolphe Thiebaut
- INSERM U897 Centre of Epidemiology and Biostatistics, ISPED Bordeaux School of Public Health, University Bordeaux Segalen, Bordeaux, France
| | - Linda Wittkop
- INSERM U897 Centre of Epidemiology and Biostatistics, ISPED Bordeaux School of Public Health, University Bordeaux Segalen, Bordeaux, France
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Potential future impact of a partially effective HIV vaccine in a southern African setting. PLoS One 2014; 9:e107214. [PMID: 25207973 PMCID: PMC4160197 DOI: 10.1371/journal.pone.0107214] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 07/02/2014] [Indexed: 11/19/2022] Open
Abstract
Background It is important for public health and within the HIV vaccine development field to understand the potential population level impact of an HIV vaccine of partial efficacy—both in preventing infection and in reducing viral load in vaccinated individuals who become infected—in the context of a realistic future implementation scenario in resource limited settings. Methods An individual level model of HIV transmission, progression and the effect of antiretroviral therapy was used to predict the outcome to 2060 of introduction in 2025 of a partially effective vaccine with various combinations of efficacy characteristics, in the context of continued ART roll-out in southern Africa. Results In the context of our base case epidemic (in 2015 HIV prevalence 28% and incidence 1.7 per 100 person years), a vaccine with only 30% preventative efficacy could make a substantial difference in the rate with which HIV incidence declines; the impact on incidence in relative terms is projected to increase over time, with a projected 67% lower HIV incidence in 2060 compared with no vaccine introduction. The projected mean decline in the general adult population death rate 2040–2060 is 11%. A vaccine with no prevention efficacy but which reduces viral load by 1 log is predicted to result in a modest (14%) reduction in HIV incidence and an 8% reduction in death rate in the general adult population (mean 2040–2060). These effects were broadly similar in multivariable uncertainty analysis. Interpretation Introduction of a partially effective preventive HIV vaccine would make a substantial long-term impact on HIV epidemics in southern Africa, in addition to the effects of ART. Development of an HIV vaccine, even of relatively low apparent efficacy at the individual level, remains a critical global public health goal.
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Highly pathogenic adapted HIV-1 strains limit host immunity and dictate rapid disease progression. AIDS 2014; 28:1261-72. [PMID: 24732774 DOI: 10.1097/qad.0000000000000293] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The study of HIV-1 rapid progressors has been limited to specific case reports. Nevertheless, identification and characterization of the viral and host factors involved in rapid progression are crucial when attempting to uncover the correlates of rapid disease outcome. DESIGN We carried out comparative functional analyses in rapid progressors (n = 46) and standard progressors (n = 46) early after HIV-1 seroconversion (≤1 year). The viral traits tested were viral replicative capacity, co-receptor usage, and genomic variation. Host CD8(+) T-cell responses, humoral activity, and HLA immunogenetic markers were also determined. RESULTS Our data demonstrate an unusual convergence of highly pathogenic HIV-1 strains in rapid progressors. Compared with standard progressors, rapid progressor viral strains show higher in-vitro replicative capacity (81.5 vs. 67.9%; P = 0.025) and greater X4/DM co-receptor usage (26.3 vs. 2.8%; P = 0.006) in early infection. Limited or absent functional HIV-1 CD8(+) T-cell responses and neutralizing activity were measured in rapid progressors. Moreover, the increase in common HLA allele-restricted CD8(+) T-cell escape mutations in rapid progressors acts as a signature of uncontrolled HIV-1 replication and early impairment of adaptive cellular responses. CONCLUSION Our data support a dominant role for viral factors in rapid progressors. Robust HIV-1 replication and intrinsic viral properties limit host adaptive immune responses, thus driving rapid disease progression.
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50
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Herbeck JT, Mittler JE, Gottlieb GS, Mullins JI. An HIV epidemic model based on viral load dynamics: value in assessing empirical trends in HIV virulence and community viral load. PLoS Comput Biol 2014; 10:e1003673. [PMID: 24945322 PMCID: PMC4063664 DOI: 10.1371/journal.pcbi.1003673] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 04/15/2014] [Indexed: 11/18/2022] Open
Abstract
Trends in HIV virulence have been monitored since the start of the AIDS pandemic, as studying HIV virulence informs our understanding of HIV epidemiology and pathogenesis. Here, we model changes in HIV virulence as a strictly evolutionary process, using set point viral load (SPVL) as a proxy, to make inferences about empirical SPVL trends from longitudinal HIV cohorts. We develop an agent-based epidemic model based on HIV viral load dynamics. The model contains functions for viral load and transmission, SPVL and disease progression, viral load trajectories in multiple stages of infection, and the heritability of SPVL across transmissions. We find that HIV virulence evolves to an intermediate level that balances infectiousness with longer infected lifespans, resulting in an optimal SPVL∼4.75 log10 viral RNA copies/mL. Adaptive viral evolution may explain observed HIV virulence trends: our model produces SPVL trends with magnitudes that are broadly similar to empirical trends. With regard to variation among studies in empirical SPVL trends, results from our model suggest that variation may be explained by the specific epidemic context, e.g. the mean SPVL of the founding lineage or the age of the epidemic; or improvements in HIV screening and diagnosis that results in sampling biases. We also use our model to examine trends in community viral load, a population-level measure of HIV viral load that is thought to reflect a population's overall transmission potential. We find that community viral load evolves in association with SPVL, in the absence of prevention programs such as antiretroviral therapy, and that the mean community viral load is not necessarily a strong predictor of HIV incidence.
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Affiliation(s)
- Joshua T. Herbeck
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - John E. Mittler
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Geoffrey S. Gottlieb
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
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