HIV Life Cycle & enetics! etroviruses (and transposable elements) appear to be part of every cell's genome! From bacteria to yeast, flies, fish, and humans! ome endogenous retroviruses (most notably in mice and chickens) can be activated to replicate and induce tumors! The great majority of sequences in eukaryotic genomes that are related to retroviruses seem innocuous! Composition of the human genome:! % LT elements! % etrotransposons! 7% Human endogenous human retroviruses (HV)! HV-K! ~0 full-length proviruses (at least are intact)! 0-50 partial! ~000 solo LTs!.5% Unique coding sequences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
WHB&.$($0-#&"-&4")?("+0-!"#$%&'()*+,-.$/0*(& Overview of the HIV lifecycle The Impact of HIV enetics on the Fight gainst I is Broad Mo le c u la r pidemiology Therapy and rug esistance 5 Vaccine evelopment isease evelopment
N genome of a simple retrovirus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enome organization of the major retrovirus groups: N replication intermediates 5 7 9kb Open eading Frames (OF) employed to encode each protein *-&;*"$-7&Y("4*&;Y:&4"&0&WHBCZL vpr rev env pol gag v i f tat vpu tat nef 000 000 000 4000 5000 5 6000 6 7000 7 000 9000 9kb KLM>N>KO!<PHP rev :)!'$+6-)!5)./4+$&()(!-$)!*%6'5)7!-.!).*%)!-.!-(!=)!+.*%6'5))5=!&.)$(%%!-$$-=! %;!)7'$)((+%.!$)#&5-%$(!).*%)!?=!-&7+5+-$=!#).)(!;%&.!+.!)!*).$-5!"?)B)).!!"#! -.!$%&0!-.!T!"B++.!$%&!-.!?)B)).!$%&!-.!L0!$)#+%.(!%;!)!4+$-5!#).%6) :)()!#).)(!-$)!)7'$)(()!;$%6!-!()$+)(!%;!+U)$)./-55=!('5+*)!6HK( '('!-.!)$&!-$)!)!%.5=!)(()./-5!-&7+5+-$=!#).)( etrovirus genes are written in: lower case italics, etrovirus proteins are written in: first letter Upper case %&-6)74$&.-9&$%&'()*+,-.!#/'7")/-&%#$'/%++#/-$$)%#'*&#)0#&,%# /&'"-+7)/#/'$%##&,%#()$-""#%0/'%# $%(%$+%#&$-0+/$)&-+%#9:;<#-0#:=-+%># %0?7%+@# ;,%#+)0"%#+&$-0%#'+)4(%#+&$-0#()$-"# :=!#)+#/')%#&'#-#'*"%#+&$-0%#B=!# )0&%$7%)-&%@ ;,%#$%+*"40#")0%-$#+B=!#/'0&-)0+# &%$7)0-"#$%%-&+#'5#+%C*%0/%+#*0)C*%#&'# &,%##-0#F#%0+#'5#&,%#()$-"#:=!#9# -0#F#$%)'0+<#-0#$%%-&%#-&#'&,# %0+#'5#&,%#:=!#9:<@#;,%#$%+*"40# %"%7%0&+#-$%#/-""%#"'0#&%$7)0-"#$%%-&+# 9H;:<@ N N N N N N N Cellular tn N N N N N N,&7"
H-)*7("+0- H)0%-$#'*"%#+&$-0%#")0%-$# ()$-"#B=!#&$-(%"+#5$'7#&,%# /&'"-+7#&'#&,%#0*/"%*+I#.,%$%#)-#%#/)$/*"-$)?%# 9-#%-#%0<#'$#)0&%$-&%# )0&'#/%""*"-$#B=!#&,$'*,#&,%# -/4'0#'5#&,%#()$-""#%0/'%# ":#$'&%)0@#;,%#&%$7)0-"## -+%#-)$+#9<#'5#()$-"#B=!# -$%#$%7'(%#-0#&,%#/%""*"-$# ).&5+,-.$4)&#-$%# *")/-&%#)0#&,)+#$'/%++@#;,%# $%+*"40#)0&%$-&%#+&$*/&*$%# )+#/-""%#-#'-6)74@# HIV replicates at an enormous rate: ~0 0 virions/day / life of virions in the blood ~h / life of most infected cells ~d ome infected cells harbor latent virus, with activation occurring slowly, potentially over many years HIV evolves ~ million times faster than the human genome: Transmission and the formation of an HIV quasispecies Transmission Purifying election Immediate descendents of one sequence predominates (usually) ~ll daughter viruses are genetically distinct ~ error is incorporated into every HIV genome Our most extensive sampling has been trivial: ~00 sequences/sample: ~/00 billionth of yearly output!"#$%$&'(%'$! efers to the entire collection, pool, or cloud of virus variants in the given setting referred to. The setting could be a tissue, a fluid compartment, a person, a collection of people or the entire earth s population of infected individuals. Citation for its use in HIV research (Meyerhans et al, Cell (9) 5:90), term s originator (M. igen, ci. mer., /9, 69:4-49)
Viral Population iversity (within sample variation) ivergence T= 5 T= 4 Founder strain T= T= Point mutations T= ecombination Founder $") %P&"!'#( #"* %P&"!!'( N -", %p/"!*( N 4!")) %P&"!!'( P +") %P&"!+( +"* %P&"!!'( *"# %P&"!!'( #"# %P&"!!'( $"* %P&"!!*(,"* %P&"!!+( N N P #", %P&"!!'( -". %P&"!!'( P P #") %P&"!!'( -"+ %N( Plasma Viral Load!"#$yr %P&"!!'( 7 6 5 4 0 volution of HIV env genes in the blood of a person over time % 0000 000 6000 4000 0 000 4 5 6 7 Years of ge C! Cells HIV explores New volutionary pace in ach Infection Herbeck (06) VI, 0:67 Pt. Pt.7 HIVU95460 Pt.6 Pt.9 HIVU596 Pt. Pt. HIVU64 Pt. Patient #6 from Wolinsky et al. HIVU607 HIVU605 HIVU590 0% HIV ecovers ncestral Features uring arly Infection Pt.5
HIV- env N roup Molecular M roup IVcpz / O roup B U Kaliningrad outbreak: F B/ I! Cross species transmission and the origins of human infections! escription and spread of the pandemic (65 million pidemiology Central China outbreak: B/C 0% infections, tens of thousands of partial genome sequences, a few thousand whole viral genomes) C H! pread of emerging epidemics! Transmission linkages IVcpz Clades "HIV ubtypes# within the HIV$% phylogenetic tree are becoming more obscure& Virus recombinants are becoming more evident and are signi'cant in emerging epidemics& lobal distribution of HIV subtypes HIV Types, roups and ubtypes There are two types of HIV: HIV- and HIV- Both types are transmitted by sexual contact, through blood, and from mother to child, and they appear to cause clinically indistinguishable I. HIV- is less easily transmitted, and the period between initial infection and illness is longer Worldwide, the predominant virus is HIV-, with HIV- type concentrated in West frica and rarely elsewhere Based on genetic similarities, the numerous virus strains may be classified into types, groups and subtypes. The strains of HIV- can be classified into three groups: the "major" group M, the "outlier" group O and the "new" group N. These three groups represent three separate introductions of simian immunodeficiency virus (from chimps..?) into humans. roup O appears to be restricted to west-central frica and group N - discovered in 99 in Cameroon - is extremely rare. Within group M there are known to be at least nine genetically distinct subtypes (or clades) of HIV-. These are subtypes, B, C,, (), F,, H, and K.
Intra ubtype iversity - % 6% 4% N Botswana Burundi India outh frica Tanzania Zimbabwe Botswana 7.%.7% 5.% 7.%.% 9.9% Burundi 5.% 5.9% 9.0% 7.7%.6% India 4 0.% 5.5% 6.% 7.% outh frica 55 7.% 9.% 9.6% Tanzania 9.0%.6% Zimbabwe 0.7% volution from genomic chimerization (recombination) % 0% % 6% vs India vs Other vs Botswana vs Burundi vs outh frica vs Tanzania vs Zimbabwe One person is infected from two sources 4% % 0% 0.0 0.0 0.05 0.07 0.09 0. 0. 0.5 0.7 0.9 0. 0. 0.5 0.7 0.9 More Two virions from different sources infect the same cell Nucleotide istance Chimera formation Fate of infecting strains Interpretation ach virion goes through reverse transcription, integration and produces viral N One of each N is packaged in a single virion The hybrid virion infects a new cell, reverse transcription occurs and T switches between templates, creating a chimeric proviral genome Lin Lin B Time Lineage extinction and replacement in nonoverlapping target cell populations. Coexistent independent lineages in non-overlapping target cell populations Formation of complex recombinant lineages in shared target cell populations
WHB&$#&"%+.")*&)'(0?7'&)'*& #"4*&40/*%?/"(&(*7?/")0(& #$7-"/#&)'")&"%+.")*&)'*&I>[& %*//&)0&(*#0-&)0&"-&$-*%+0- T (transactivator response region) N'*(*0(*@&0-%*&)'*& $44?-*&##)*4&$#&"%+.")*& )0&(0)*%)&)'*&*(#0-@&)'*&.$(?#&$#&"%+.")*&"-&P$//#& )'*&$44?-*&%*//# Transactivation by Tat 0 ev function Vif function Blocks synthesis and packaging into virions
Vpu effects Nef down-modulates several receptors from the surface of infected C4 + T cells to:.educe cytotoxic T lymphocyte (CTL) lysis,.suppress cell migration,.facilitate virus release and 4.modulate signal transduction by the immunological synapse Nef induces downstream signalling events to: 5.activate nuclear factor of activated T cells (NF-T), 6.nuclear factor-b (NF-B) and 7.activator protein (P), Nef induces efficient transcription of:.the viral long terminal repeat (LT) promoter, 9.inflammatory cytokines, 0.activation markers and.death receptors Nef effects Vpu targets C4 for degradation in the proteasome and counteracts tetherin (also known as BT), an interferon- (IFN)-induced host restriction factor, by an as-yetunknown mechanism. Consequently, Vpu facilitates virus release and the incorporation of functional gp0 into progeny virions =\"%'4*-)&"-&*-)(&0&WHB& 6)?$*#&0-&WHB&0.*(&)'*&"#)&]&*"(#&'".*&*/?%$")*&$)#&*-)(&(0%*##&)0&)'*& *7(**&)'")&$)&$#&)'*&5*#)&?-*(#)00&0&"-&'?4"-&.$(?#M&N'*&)0&.$("/& *-.*/0*&7/%0(0)*$-#@&7Z^_&"-&7[Z@&"(*&(*#0-#$5/*&0(&"\"%'4*-)&"-& 4*45("-*&?#$0-@&(*#*%+.*/M&N'*&%*//&#?("%*&7/%0(0)*$-&I>[&$#&?#*&"#& )'*&($4"(&(*%*)0(@&"-&0-*&0&"&*&0)'*(&(0)*$-#&"(*&?#*&"#&%0C (*%*)0(#&)$%"//&II;]&"-&I`I;[:M