UNAIDS (2022) IN DANGER: UNAIDS Global AIDS Update 2022

Taylor BS, Sobieszczyk ME, McCutchan FE, Hammer SM (2008) The challenge of HIV-1 subtype diversity. N Engl J Med 358(15):1590–1602

Article  PubMed  PubMed Central  CAS  Google Scholar 

Bbosa N, Kaleebu P, Ssemwanga D (2019) HIV subtype diversity worldwide. Curr Opin HIV AIDS 14(3):153–160

Article  PubMed  Google Scholar 

Hemelaar J, Elangovan R, Yun J, Dickson-Tetteh L, Fleminger I, Kirtley S, Williams B, Gouws-Williams E, Ghys PD, AlG A, Agwale S, Archibald C, Avidor B, Barbás MG, Barre-Sinoussi F, Barugahare B, Belabbes EH, Bertagnolio S, Birx D, Bobkov AF, Brandful J, Bredell H, Brennan CA, Brooks J, Bruckova M, Buonaguro L, Buonaguro F, Buttò S, Buve A, Campbell M, Carr J, Carrera A, Carrillo MG, Celum C, Chaplin B, Charles M, Chatzidimitriou D, Chen Z, Chijiwa K, Cooper D, Cunningham P, Dagnra A, de Gascun CF, Del Amo J, Delgado E, Dietrich U, Dwyer D, Ellenberger D, Ensoli B, Essex M, Gao F, Fleury H, Fonjungo PN, Foulongne V, Gadkari DA, García F, Garsia R, Gershy-Damet GM, Glynn JR, Goodall R, Grossman Z, Lindenmeyer-Guimarães M, Hahn B, Hamers RL, Hamouda O, Handema R, He X, Herbeck J, Ho DD, Holguin A, Hosseinipour M, Hunt G, Ito M, Bel Hadj Kacem MA, Kahle E, Kaleebu PK, Kalish M, Kamarulzaman A, Kang C, Kanki P, Karamov E, Karasi J-C, Kayitenkore K, Kelleher T, Kitayaporn D, Kostrikis LG, Kucherer C, Lara C, Leitner T, Liitsola K, Lingappa J, Linka M, Lorenzana de Rivera I, Lukashov V, Maayan S, Mayr L, McCutchan F, Meda N, Menu E, Mhalu F, Mloka D, Mokili JL, Montes B, Mor O, Morgado M, Mosha F, Moussi A, Mullins J, Najera R, Nasr M, Ndembi N, Neilson JR, Nerurkar VR, Neuhann F, Nolte C, Novitsky V, Nyambi P, Ofner M, Paladin FJ, Papa A, Pape J, Parkin N, Parry C, Peeters M, Pelletier A, Pérez-Álvarez L, Pillay D, Pinto A, Quang TD, Rademeyer C, Raikanikoda F, Rayfield MA, Reynes J-M, Rinke de Wit T, Robbins KE, Rolland M, Rousseau C, Salazar-Gonzales J, Salem H, Salminen M, Salomon H, Sandstrom P, Santiago ML, Sarr AD, Schroeder B, Segondy M, Selhorst P, Sempala S, Servais J, Shaik A, Shao Y, Slim A, Soares MA, Songok E, Stewart D, Stokes J, Subbarao S, Sutthent R, Takehisa J, Tanuri A, Tee KK, Thapa K, Thomson M, Tran T, Urassa W, Ushijima H, van de Perre P, van der Groen G, van Laethem K, van Oosterhout J, van Sighem A, van Wijngaerden E, Vandamme A-M, Vercauteren J, Vidal N, Wallace L, Williamson C, Wolday D, Xu J, Yang C, Zhang L, Zhang R (2019) Global and regional molecular epidemiology of HIV-1, 1990–2015: a systematic review, global survey, and trend analysis. Lancet Infect Dis 19(2):143–155

Article  PubMed  Google Scholar 

Salamango DJ, Harris RS (2020) Dual functionality of HIV-1 Vif in APOBEC3 counteraction and cell cycle arrest. Front Microbiol 11:622012

Article  PubMed  Google Scholar 

Jacobs GB, Nistal M, Laten A, van Rensburg EJ, Rethwilm A, Preiser W, Bodem J, Engelbrecht S (2008) Molecular analysis of HIV type 1 vif sequences from Cape Town, South Africa. AIDS Res Hum Retroviruses 24(7):991–994

Article  PubMed  CAS  Google Scholar 

Wang Y, Kinlock BL, Shao Q, Turner TM, Liu B (2014) HIV-1 Vif inhibits G to A hypermutations catalyzed by virus-encapsidated APOBEC3G to maintain HIV-1 infectivity. Retrovirology 11(1):89

Article  PubMed  PubMed Central  CAS  Google Scholar 

Stupfler B, Verriez C, Gallois-Montbrun S, Marquet R, Paillart JC (2021) Degradation-Independent Inhibition of APOBEC3G by the HIV-1 Vif Protein. Viruses 13(4):617

Khan MA, Aberham C, Kao S, Akari H, Gorelick R, Bour S, Strebel K (2001) Human immunodeficiency virus type 1 Vif protein is packaged into the nucleoprotein complex through an interaction with viral genomic RNA. J Virol 75(16):7252–7265

Article  PubMed  PubMed Central  CAS  Google Scholar 

Farrow MA, Somasundaran M, Zhang C, Gabuzda D, Sullivan JL, Greenough TC (2005) Nuclear localization of HIV type 1 Vif isolated from a long-term asymptomatic individual and potential role in virus attenuation. AIDS Res Hum Retroviruses 21(6):565–574

Article  PubMed  CAS  Google Scholar 

Peng J, Ao Z, Matthews C, Wang X, Ramdahin S, Chen X, Li J, Chen L, He J, Ball B, Fowke K, Plummer F, Embree J, Yao X (2013) A naturally occurring Vif mutant (I107T) attenuates anti-APOBEC3G activity and HIV-1 replication. J Mol Biol 425(16):2840–2852

Article  PubMed  CAS  Google Scholar 

Yang X, Goncalves J, Gabuzda D (1996) Phosphorylation of Vif and its role in HIV-1 replication. J Biol Chem 271(17):10121–10129

Article  PubMed  CAS  Google Scholar 

Scriba TJ, Treurnicht FK, Zeier M, Engelbrecht S, van Rensburg EJ (2001) Characterization and phylogenetic analysis of South African HIV-1 subtype C accessory genes. AIDS Res Hum Retroviruses 17(8):775–781

Article  PubMed  CAS  Google Scholar 

Bell CM, Connell BJ, Capovilla A, Venter WD, Stevens WS, Papathanasopoulos MA (2007) Molecular characterization of the HIV type 1 subtype C accessory genes vif, vpr, and vpu. AIDS Res Hum Retroviruses 23(2):322–330

Article  PubMed  CAS  Google Scholar 

Struck D, Lawyer G, Ternes AM, Schmit JC, Bercoff DP (2014) COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification. Nucleic Acids Res 42(18):e144

Article  PubMed  PubMed Central  Google Scholar 

McGuffin LJ, Bryson K, Jones DT (2000) The PSIPRED protein structure prediction server. Bioinformatics 16(4):404–405

Article  PubMed  CAS  Google Scholar 

Ma Y, Liu Y, Cheng J (2018) Protein secondary structure prediction based on data partition and semi-random subspace method. Sci Rep 8(1):9856

Article  PubMed  PubMed Central  Google Scholar 

Jones DT, Cozzetto D (2015) DISOPRED3: precise disordered region predictions with annotated protein-binding activity. Bioinformatics 31(6):857–863

Article  PubMed  CAS  Google Scholar 

Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5(4):725–738

Article  PubMed  PubMed Central  CAS  Google Scholar 

Zhang Y (2014) Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10. Proteins: Struct Funct Bioinf 82:175–187

Article  CAS  Google Scholar 

Zhang Y, Arakaki AK, Skolnick J (2005) TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins: Struct Funct Bioinf 61(S7):91–98

Article  CAS  Google Scholar 

Zhang J, Yang J, Jang R, Zhang Y (2015) GPCR-I-TASSER: a hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome. Structure 23(8):1538–1549

Article  PubMed  PubMed Central  CAS  Google Scholar 

Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26(2):283–291

Article  CAS  Google Scholar 

Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2(9):1511–1519

Article  PubMed  PubMed Central  CAS  Google Scholar 

Messaoudi A, Belguith H, Ben Hamida J (2013) Homology modeling and virtual screening approaches to identify potent inhibitors of VEB-1 β-lactamase. Theor Biol Med Model 10(1):22

Article  PubMed  PubMed Central  CAS  Google Scholar 

Isaacs D, Mikasi SG, Obasa AE, Ikomey GM, Shityakov S, Cloete R, Jacobs GB (2020) Structural comparison of diverse HIV-1 subtypes using molecular modelling and docking analyses of integrase inhibitors. Viruses 12(9):936

Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5(4):823–826

Article  PubMed  PubMed Central  CAS  Google Scholar 

Gupta P, Karthik K, Sreevathsa R, Rai R, Dash PK (2022) Cloning and characterization of phloroglucinol biosynthetic gene phl C from an Indian strain of Pseudomonas fluorescens. Indian J Exp Biol (IJEB) 60(08):607–614

CAS  Google Scholar 

Xu D, Zhang Y (2011) Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys J 101(10):2525–2534

Article  PubMed  PubMed Central  CAS  Google Scholar 

Kouno T, Luengas EM, Shigematsu M, Shandilya SM, Zhang J, Chen L, Hara M, Schiffer CA, Harris RS, Matsuo H (2015) Structure of the Vif-binding domain of the antiviral enzyme APOBEC3G. Nat Struct Mol Biol 22(6):485–491

Article  PubMed  PubMed Central  CAS  Google Scholar 

Russell RA, Pathak VK (2007) Identification of two distinct human immunodeficiency virus type 1 Vif determinants critical for interactions with human APOBEC3G and APOBEC3F. J Virol 81(15):8201–8210

Article  PubMed  PubMed Central  CAS  Google Scholar 

Pery E, Rajendran KS, Brazier AJ, Gabuzda D (2009) Regulation of APOBEC3 proteins by a novel YXXL motif in human immunodeficiency virus type 1 Vif and simian immunodeficiency virus SIVagm Vif. J Virol 83(5):2374–2381

Article  PubMed  CAS  Google Scholar 

Chen G, He Z, Wang T, Xu R, Yu XF (2009) A patch of positively charged amino acids surrounding the human immunodeficiency virus type 1 Vif SLVx4Yx9Y motif influences its interaction with APOBEC3G. J Virol 83(17):8674–8682

Article  PubMed  PubMed Central  CAS  Google Scholar 

Dang Y, Wang X, Zhou T, York IA, Zheng YH (2009) Identification of a novel WxSLVK motif in the N terminus of human immunodeficiency virus and simian immunodeficiency virus Vif that is critical for APOBEC3G and APOBEC3F neutralization. J Virol 83(17):8544–8552

Article  PubMed  PubMed Central  CAS  Google Scholar 

Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A (2016) PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. Bioinformatics 32(23):3676–3678