Simian Immunodeficiency Virus 11723 Simian AIDS Simian Immunodeficiency Virus is a retrovirus that can infect at least 33 species of African primates. It has been present in primates for at least 32,000 years. Infections in the natural hosts appear to be generally non-pathogenic, except in the case of the Asian rhesus macaque, which will develop SAIDS (Wiki: Simian immunodeficiency virus). Baboon Papio cynocephalus 9556 Bank vole Clethrionomys glareolus 447135 Bear Ursus americanus 9643 Birds Passeroidea 175121 Brown Trout Salmo trutta 8032 Buffalo Bison bison 9901 Carnivores Vulpes 9625 Cat Felis catus 9685 Catfishes Siluriformes 7995 Cattle Bos taurus 9913 Chicken Gallus gallus 9031 Chimpanzee Pan troglodytes 9598 chinchillas Chinchillidae 10150 Copper Pheasant Syrmaticus soemmerringii 9067 Deer Cervus elaphus 9860 Deer mouse Peromyscus maniculatus 10042 Dog Canis familiaris 9615 Ducks Anas 8835 Ferret Mustela putorius furo 9669 Fish Hyperotreti 117565 Gerbil Gerbillina 10045 Goat Capra hircus 9925 Gray wolf Canis lupus 9612 Guinea pig Cavia porcellus 10141 Hamster Mesocricetus auratus 10036 Horse Equus caballus 9796 Human Homo sapiens 9606 Macaque Macaca fascicularis 9541 Mongolian Gerbil Meriones unguiculatus 10047 Monkey Platyrrhini 9479 Mouse Mus musculus 10090 None None Parrot Psittacidae 9224 Pig Sus scrofa 9823 Rabbit Oryctolagus cuniculus 9986 Rainbow trout Oncorhynchus mykiss 8022 Rat Rattus 10114 Raven Corvus corax 56781 sei whale Balaenoptera borealis 9768 Sheep Ovis aries 9940 Squirrel Spermophilus richardsonii 37591 Tree shrew Tupaiidae 9393 Trouts, salmons & chars Salmoninae 504568 Turkey Meleagris gallopavo 9103 Vole Microtus ochrogaster 79684 Water buffalo Bubalus bubalis 391902 rBCG-SIVgag VO_0004789 Recombinant vector vaccine Research Intradermal injection (i.d.) Intradermal injection (i.d.) M. bovis BCG-SIV Gag followed by boosting with rDIsSIVgag (Ami et al., 2005). Recombinant vector construction The SIV gag gene was used in generation of a recombinant vector vaccine (Ami et al., 2005). Macaca fascicularis The macaques were divided into 5 groups. Group 1 (control group) received rBCG-PSO246 followed by two inoculations of rDIsLacZ. Group 2 (rBCG group) received rBCG-SIVgag followed by two inoculations of rDIsLacZ. Group 3 (rBCG/rDIs group) received rBCG-SIVgag followed by two inoculations of rDIsSIVgag. Group 4 (rDIS group) received two inoculations of rDIsSIVgag followed by rBCG-pSO246. Group 5 (rDIs/rBCG group) received two inoculations of rDIsSIVgag followed by rBCG-SIVgag (Ami et al., 2005). VO_0003057 Only the macaques in group 3 (rBCG/rDIs) showed evidence of protective immune responses, the macaques in this group remained clinically healthy for a one year observation period. During this same observation period, by day 170, 6 macaques in the other 4 groups had died with symptoms consistent with simian AIDS. The rBCG/rDIs group vaccinated with the priming-boosting regimen had a superior survival rate than the other groups receiving vaccine protocols and the control group (Ami et al., 2005). All groups were mucosally challenged with two thousand 50% tissue culture infectious doses of SHIV KS661c at 64 weeks after immunization, these were intrarectally administered (Ami et al., 2005). rMVA-SIV-CD40L VO_0004664 Recombinant vector vaccine Research Intramuscular injection (i.m.) Intramuscular injection (i.m.) SabRV-SIV VO_0004704 Recombinant vector vaccine Research Intramuscular injection (i.m.) New poliovirus vectors based on Sabin 1 and 2 vaccine strain viruses were constructed, and these vectors were used to generate a series of new viruses containing SIV gag, pol, env, nef, and tat in overlapping fragments (Crotty et al., 2001). Intramuscular injection (i.m.) Recombinant vector construction To construct pSabRV1, first the EcoRI and XhoI sites upstream of the T7 promoter of pS1 were eliminated to create plasmid pS1XT. Then the 747-bp BstEII fragment of pMoV2.11—containing the duplicated 2Apro cleavage site, the 5-glycine spacer, and the EcoRI, NotI, and XhoI cloning sites—was swapped into pS1XT to create pSabRV1 (Crotty et al., 2001). Recombinant vector construction To construct pSabRV1, first the EcoRI and XhoI sites upstream of the T7 promoter of pS1 were eliminated to create plasmid pS1XT. Then the 747-bp BstEII fragment of pMoV2.11—containing the duplicated 2Apro cleavage site, the 5-glycine spacer, and the EcoRI, NotI, and XhoI cloning sites—was swapped into pS1XT to create pSabRV1 (Crotty et al., 2001). Recombinant vector construction To construct pSabRV1, first the EcoRI and XhoI sites upstream of the T7 promoter of pS1 were eliminated to create plasmid pS1XT. Then the 747-bp BstEII fragment of pMoV2.11—containing the duplicated 2Apro cleavage site, the 5-glycine spacer, and the EcoRI, NotI, and XhoI cloning sites—was swapped into pS1XT to create pSabRV1 (Crotty et al., 2001). Seven animals were inoculated intranasally with 1 ml (5 × 10^7 PFU) of SabRV1-SIV on days 1, 3, 14, and 16, for a total of four immunizations. Nineteen weeks after the first series of inoculations, these same seven animals were given boosters of two intranasal inoculations of 1 ml (10^6 PFU/ml) of SabRV2-SIV, one at week 19 and a second at week 21 (Crotty et al., 2001). VO_0003057 Four of the seven vaccinated animals exhibited substantial protection against the vaginal SIV challenge (Crotty et al., 2001). The animals were challenged with 10^5 TCID50 of SIVmac251 intravaginally, using the SIVmac251 (5/98) stock (Crotty et al., 2001). Simian Immunodeficiency Virus nef mutant vaccine VO_0002994 Live, attenuated vaccine Research Intravenous injection (i.v.) Intravenous injection (i.v.) Gene mutation This nef mutant is from Simian Immunodeficiency Virus (Daniel et al., 1992). A nef mutant is attenuated in rhesus monkeys (Daniel et al., 1992). A nef mutant induces protection in rhesus monkeys from challenge with wild type SIV (Daniel et al., 1992). SIV DNA vaccine pSIVgag and pmacIL-15 encoding SIV core protein VO_0004346 DNA vaccine Research pCSIVgag plasmid [Ref2220:Boyer et al., 2007] Intramuscular injection (i.m.) IL-15 (Boyer et al., 2007) Intramuscular injection (i.m.) DNA vaccine construction This DNA vaccine expressed a 37-kDa fragment of the SIV core protein (Boyer et al., 2007). VO_0000286 The vaccine groups were protected from ongoing infection, and the IL-15 covaccinated group showed a more rapidly controlled infection than the group treated with DNA vaccine alone (Boyer et al., 2007). SIV DNA vaccine pVacc4 encoding env from mac239 VO_0004343 DNA vaccine Research pVacc4, modified vaccinia virus Ankara (MVA) [Ref2201:Bertley et al., 2004] oculo-nasal route IL-2/Ig (Bertley et al., 2004) oculo-nasal route DNA vaccine construction VO_0000286 After rectal challenge of vaccinated and naive animals with SHIV89.6P, all animals became infected. However a subset were protected from CD4+ T cell loss and AIDS development. Thus, nasal vaccination with SHIV-DNA plus IL-2/Ig DNA and rMVA can provide significant protection from disease progression (Bertley et al., 2004). SIV recombinant vector vaccine rAd5/rLCMV VO_0004564 Recombinant vector vaccine Research Recombinant adenovirus type 5 (rAd5) priming, replication-defective lymphocytic choriomeningitis virus boosting [Ref2690:Flatz et al., 2012] Intramuscular injection (i.m.) Intramuscular injection (i.m.) a mismatched SIV envelope (Env) gene derived from simian immunodeficiency virus SIVmac239 (Flatz et al., 2012) Recombinant adenovirus type 5 (rAd5) prime followed by replication-defective lymphocytic choriomeningitis virus (rLCMV) boost elicited robust CD4 and CD8 T-cell and humoral immune responses. In addition, there was a presence of neutralizing antibodies to the challenge viruses tested in peripheral blood mononuclear cells (Flatz et al., 2012). VO_0003057 To evaluate the infectibility of immunized and control animals, 10 vaccinated Macaca mulatta animals and 10 controls were challenged intrarectally with SIVsmE660 six weeks after the rLCMV boost. In the vaccinated group, three of the 10 monkeys became infected after 99 challenges (3% infection rate per challenge), while in the control null group, eight of the 10 monkeys were infected after 47 challenges (17% infection rate per challenge), indicating a protective efficacy of 82% per challenge (Flatz et al., 2012). Core protein Simian immunodeficiency virus 54312018 CDD:109591 CDD:201337 CDD:199156 11723 ? core protein 510 gag gene protein p17 (matrix protein); pfam00540 >gi|54312018|dbj|BAD66663.1| core protein [Simian immunodeficiency virus] MGVRNSVLSGKKADELEKIRLRPNGKKKYMLKHVVWAANELDRFGLAESLLENKEGCQKILSVLAPLVPT GSENLKSLYNTVCVIWCIHAEEKVKHTEEAKQIVQRHLVVETGTTETMPKTSRPTAPSSGRGGNYPVQQI GGNYVHLPLSPRTLNAWVKLIEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIRDIINEE AADWDLQHPQPAPQQGQLREPSGSDIAGTTSSVDEQIQWMYRQQNPIPVGNIYRRWIQLGLQKCVRMYNP TNILDVKQGPKEPFQSYVDRFYKSLRAEQTDAAVKNWMTQTLLIQNANPDCKLVLKGLGVNPTLEEMLTA CQGVGGPGQKARLMAEALKEALAPVPIPFAAAQQRGPRKPIKCWNCGKEGHSARQCRAPRRQGCWKCGKM DHVMAKCPDRQAGFLGLGPWGKKPRNFPMAQVHQGLMPTAPPEDPAVDLLKNYMQLGKQQREKQRESREK PYKEVTEDLLHLNSLFGGDQ Other env Simian immunodeficiency virus 532231 CDD:109567 CDD:197369 11723 ? envelope glycoprotein 881 Envelope glycoprotein GP120; pfam00516 >gi|532231|gb|AAB00470.1| envelope glycoprotein [Simian immunodeficiency virus] MGCLGNQLLIAILLLSVYGIYCTQYVTVFYGVPAWRNATIPLFCATKNRDTWGTTQCLPDNGDYSELALN VTESFDAWNNTVTEQAIEDVWQLFETSIRPCVKLSPLCITMRCNKSETDKWGLTKSSTTTASTTTTTPTT ASKIDMVNETSSCITHDNCTGLEQEQMISCKFNMTGLKRDKKKEYNETWYSTDLVCEQGNSTDNESRCYM NHCNTSVIQESCDKHYWDTIRFRYCAPPGYALLRCNDTNYSGFMPKCSKVVVSSCTRMMETQTSTWFGFN GTRAENRTYIYWHGRDNRTIISLSKYYNLTMKCRRPGNKTVLPVTIMSGLVFHSQPINDRPKQAWCWFGG EWKDAIKEVKQTIVKHPRYTGTNNTDKINLTAPGGGDPEVTFMWTNCRGEFLYCKMNWFLNWVEDRNTTN QKPNEQHKRNYVPCHIRQIINTWHKVGKNVYLPPREGDLTCNSTVTSLIANIDWTDGNQTNITMSAEVAE LYRLELGDYKLVEITPIGLAPTNVKRYTTGGTSRNKRGVFVLGFLGFLATAGSAMGAASLTLTAQSRTLL AGIVQQQQQLLDVVKRQQELLRLTVWGTKNLQTRVTAIEKYLKDQAQLNAWGCAFRQVCHTTVPWPNASL TPDWNNDTWQEWERKVDFLEENITALLEEAQIQQEKNMYELQKLNSWDVFGNWFDLASWIKYIQYGIYMV VGVILLRIVIYIVQMLAKLRQGYRPVFSSPPSYFQQTHIQQDPALPTREGKEGDGGEGGGNSSWPWQIEY IHFLIRQLIRLLTWLFSNCRTLLSRAYQILQPIFQRLSATLQRIREVLRTELTYLQYGWSYFQEAVQVGW RSATETLAGAWGDLWETLRRGGRWILAIPRRIRQGLELTLL Other env receptor binding subunit Simian immunodeficiency virus 603752 CDD:109567 11723 ? envelope glycoprotein gp120 receptor binding subunit 527 Envelope glycoprotein GP120; pfam00516 >gi|603752|gb|AAA57442.1| envelope glycoprotein gp120 receptor binding subunit, partial [Simian immunodeficiency virus] MGCLGNQLLIAILLLSVYGIYCTLYVTVFYGVPAWRNATIPLFCATKNRDTWGTTQCLPDNGDYSEMALN VTESFDAWNNTVTEQAIEDVWQLFETSIKPCVRLSPLCITMRCNKSETDRWGLTKSITTTAPTASTTASA EVDMVNETSSCIAQDNCTGLEQEQMISCKFNMTGLKRNKKKEYNETWYSADLVCEQGNNTGNESRCYMNH CNTSVIQESCDKHYWDAIRFRYCAPPGYALLRCNDTNYSGFMPKCSKVVVSSCTRMMETQTSTWFGFNGT RAENRTYIYWHGRNNRTIISLNKYYNLTMKCRRPGNKTVLPVTIMSGLVFHSQPINGRPKQAWCWFEGKW KDAIKEVKQTIVKHPRYTGTNNTDKINLTAPRGGNPEVTFMWTNCRGEFLYCKMNWFLNWVEDRNTANQK PNEQHKRNYVPCHIRQIINTWHKVGKNVYLPPREGDLTCNSTVTSLIANIDWIDGNQTNISMSAEVAELY RLELGDYKLVEITPIGLAPTSVKRYTTGGTSRNKRGV Other gag Simian immunodeficiency virus SIV-mnd 2 956108 27311167 Siv2gp1 AF367411 NP_758886 159122 736 2289 + gag protein 8.78 55072.29 517 >gi|27311166:736-2289 Simian immunodeficiency virus SIV-mnd 2, complete genome AATGGGCGCGAGCGCGTCAGGTCTTAGGGGAGAAAAATTGGACGAGCTGGAAAAGATTAGGTTACGGCCC TCCGGAAAAAAGAAATACCAGCTGAAACACATAATATGGGTAAGCAAGGAACTAGACAGATTTGGCCTTC ATGAAAAGCTGTTAGAAAGTAAGGAAGGATGCGAGAAAATTCTTAGCGTACTCTTTCCACTAGTTCCTAC AGGGTCAGAAAATTTAATCTCGCTGTACAACACCTGCTGCTGCGTATGGTGCGTACATGCGAAAGAGAAA GTAACAGATACAGAGGAAGCGAAAGAGAAAGTAAAACAAAAGCTCCATCTAGTGGCCGAAAAGGAAAATG CAGCATCAGAAAAAGAACAAAGAGCAATAGTGACACCTAGTGGCCGCTCAAAAAATTACCCAATACAGAT AATAAATCAGACCCCAGTCCATCAGGGAATTTCACCGCGCACGCTGAATGCGTGGGTAAAATGCATAGAA GAGAAGAAGTTTAGCCCAGAAATAGTGCCCATGTTCATAGCCTTGTCTGAAGGGTGCCTCCCCTATGATC TCAATGGCATGCTCAATGCTATTGGAGACCATCAGGGAGCGCTTCAAATAGTGAAGGATGTCATCAATGA GGAAGCTGCAGACTGGAACTTGAGACACCCACAAGTGGGTCCTATGCCCCAAGGTGTCTTGAGAAACCCA ACGGGCAGTGATATTGCTGGAACAACAAGCTCCATAGAAGAGCAGATAGAATGGACTACAAGGGAGCAAG ATGCAGTAAATGTGGGAGGAATATATAAACAATGGATAGTTTTAGGGCTTCAGAAGTGTGTAAGCATGTA TAATCCAGTAAACATCCTGGACATAAAGCAAGGACCAAAGGAGCCGTTCAAGGACTATGTGGACAGGTTT TACAAAGCTCTGCGGGCGGAGCGGACTGATCCACAAGTCAAAACCTGGATGACACAAACTTTGCTCATCC AGAATGCTAACCCAGATTGTAAATCCATCCTTAAAGGGCTAGGCATGAATCCCTCTTTAGAAGAGATGCC GCTAGCCTGCCAAGGGGTAGGAGGCCCTAAATATAAAGCACAAATGATGGCAGAGGCTATGAAGGAAGCC CAGTCAGCTGTAATGATGCAGAATTCGGGAGGGCCACCGCGGGGCCCCCCGAGACAACCTCCTAGAAACA TCAGATGCCCTAACTGTGGAAAATTTGGTCATGGGCTGAGGGACTGTATAAGCCCTCGAAAAAAGGGATG CTTCAAGTGTGGAGATCTAGGACACATAATGAGAAATTGCCCAAAGATGGTGAATTTTTTAGGGAATACC CCCTGGGGCAGTGGCAAACCCAGGAACTTCCCGGCGATGCCATTGACCCCAACGGCCCCTCCAATGCCAG GGATGGAAGACCCAGCAGAGAGAATGCTGTTAGATTACATGAAGAAAGGGCAACAGCAGAAAGCGGAAAG CAAACAGGAAAAGAAAGAGAGGGGTCCATACGAGGCAGCTTACAACTCCCTCAGTTCTCTCTTTGGAACA GACCAACTACAGTA >gi|27311167|ref|NP_758886.1| gag protein [Simian immunodeficiency virus SIV-mnd 2] MGASASGLRGEKLDELEKIRLRPSGKKKYQLKHIIWVSKELDRFGLHEKLLESKEGCEKILSVLFPLVPT GSENLISLYNTCCCVWCVHAKEKVTDTEEAKEKVKQKLHLVAEKENAASEKEQRAIVTPSGRSKNYPIQI INQTPVHQGISPRTLNAWVKCIEEKKFSPEIVPMFIALSEGCLPYDLNGMLNAIGDHQGALQIVKDVINE EAADWNLRHPQVGPMPQGVLRNPTGSDIAGTTSSIEEQIEWTTREQDAVNVGGIYKQWIVLGLQKCVSMY NPVNILDIKQGPKEPFKDYVDRFYKALRAERTDPQVKTWMTQTLLIQNANPDCKSILKGLGMNPSLEEMP LACQGVGGPKYKAQMMAEAMKEAQSAVMMQNSGGPPRGPPRQPPRNIRCPNCGKFGHGLRDCISPRKKGC FKCGDLGHIMRNCPKMVNFLGNTPWGSGKPRNFPAMPLTPTAPPMPGMEDPAERMLLDYMKKGQQQKAES KQEKKERGPYEAAYNSLSSLFGTDQLQ Other gag-pol Simian immunodeficiency virus 1490009 22535297 SIVgp1 M66437 NP_687035 11723 896 5313 + Gag-Pol 8.66 157171.22 1472 >gi|9627204:896-5313 Simian immunodeficiency virus, complete genome AATGGGCGGGGGTCACTCAGCACTGTCAGGGAGAAGCCTCGACACGTTCGAGAAGATTAGGCTACGTCCG AACGGGAAAAAGAAGTACCAAATTAAACATTTAATATGGGCAGGAAAAGAAATGGAACGATTTGGGTTAC ATGAGAAACTTTTAGAAACAAAAGAAGGCTGTCAAAAAATCATAGAAGTTTTAACCCCGTTGGAACCGAC AGGCTCCGAGGGGCTAAAAGCTCTGTTTAATTTGTGCTGCGTCATTTGGTGCATTCACGCAGAACAGAAA GTGAAAGACACAGAGGAAGCTGTAGTAACAGTTAAGCAACACTACCATCTAGTGGACAAAAATGAGAAAG CAGCTAAAAAGAAAAATGAGACAACAGCGCCACCTGGTGGCGAATCAAGAAATTACCCAGTAGTAAATCA GAATAATGCCTGGGTACACCAGCCTTTGTCTCCGCGCACGTTAAATGCGTGGGTCAAATGCGTGGAGGAA AAAAGGTGGGGAGCAGAAGTAGTCCCCATGTTCCAAGCACTCTCAGAGGGATGTCTCTCCTATGATGTAA ATCAGATGCTCAATGTAATAGGAGACCATCAGGGGGCATTACAAATTCTTAAGGAAGTCATTAATGAAGA AGCAGCAGAGTGGGACAGGACACACAGACCACCAGCTGGCCCGTTACCAGCAGGGCAGCTAAGAGACCCG ACAGGGTCAGATATAGCAGGAACTACCAGCTCAATTCAGGAACAAATAGAGTGGACCTTCAATGCCAATC CAAGAATAGACGTAGGGGCACAATACAGAAAATGGGTTATTTTGGGCTTACAAAAGGTAGTGCAGATGTA CAATCCCCAAAAGGTCCTAGACATTCGACAGGGACCTAAAGAACCCTTCCAGGACTATGTAGACAGATTC TATAAAGCCCTGAGAGCAGAACAAGCACCACAGGATGTTAAAAATTGGATGACACAAACTTTGCTTATCC AGAATGCCAATCCGGATTGTAAATTGATTCTGAAAGGATTGGGAATGAATCCAACCTTGGAGGAAATGCT AATAGCTTGCCAGGGAGTAGGAGGGCCACAACATAAGGCTAAGCTAATGGTAGAAATGATGAGTAATGGA CAGAATATGGTCCAAGTGGGACCTCAGAAAAAGGGCCCCCGAGGGCCGCTAAAATGCTTTAATTGTGGCA AATTTGGACATATGCAAAGGGAATGCAAGGCACCAAGACAGATCAAATGCTTTAAGTGCGGCAAAATTGG CCATATGGCAAAAGACTGCAAGAATGGACAGGCAAATTTTTTAGGGTATGGCCATTGGGGAGGAGCGAAA CCAAGAAATTTTGTGCAATACAGAGGAGACACAGTTGGTCTGGAACCAACAGCCCCCCCAATGGAAACAG CTTACGATCCAGCAAAGAAGCTCCTCCAGCAGTATGCAGAGAAGGGACAGCGCCTGAGAGAGGAGAGAGA ACAGACAAGGAAACAGAAGGAGAAAGAAGTGGAGGATGTTTCCTTGAGCTCCCTCTTTGGAGGAGACCAA TGAAACGAGTCATCATAGAAGGAACGCCAGTGCAAGCCTTGTTAGATACAGGAGCAGATGACACTATAAT TCAAGAAAAGGACTTGCACTTTCCCCCACATAAACCATGGCGTTCCAAGGTAGTAGGAGGTATAGGAGGA GGGATTCATGTCAAAGAATATCAGGGGGTACAAGTACAATTGGAGGATAAAATCATCACCGGCTCAATTC TAATAGGAAGTACACCAATCAATATTATAGGAAGAAATATTTTAGCTCAGGCAGGCATGAAATTAGTTAT GGGAGTTCTATCTAGTCAGATTGAGGAAACAAAAGTACAACTAAAAGAAGGGAAAGATGGACCTAAATTG AAACAATGGCCCTTATCAAGAGAAAAAATTGAAGCTTTAACAGAAATATGCAAACAAATGGAAGAGGAGG GAAAATTATCTAGGATAGGAGGAGAAAATCCTTATAATACACCAGTGTTTGCCATAAAGAAAAAGGATAA AACACAATGGAGAATGCTTGTAGATTTCAGGGAACTAAACAAAGCTACTCAAGACTTTTTTGAGGTTCAG CTGGGAATTCCTCACCCAGCGGGCCTTCAGAAAAAGAAGCAAATCACAGTAATAGACATAGGGGATGCCT ATTATTCAATACCATTATGCAAGGAATTCAGAAAATATACAGCATTTACCATCCCCTCAGTAAATAATAC AGGGCCAGGGATAAGGTATCAGTTCAATTGTCTGCCTCAGGGATGGAAAGGATCTCCTACAATTTTCCAG AATACGGCAGCAAACATTTTAGAGGAGATCAAAAGGCACACTCCTGGGTTAGAAATTGTCCAATACATGG ACGATTTGTGGTTGGCGTCAGACCATGATGAGACTAGACATAATCAACAGGTAGACATAGTAAGAAAGAT GCTGCTAGAAAAAGGTCTAGAAACCCCAGACAAGAAAGTCCAAAGAGAACCGCCATGGGAATGGATGGGG TATAAATTGCATCCGAATAAATGGACCATTAACAAAATAGAATTACCCCCCTTAGAAGGAGAATGGACAG TAAACAAAATACAGAAGGTAGTAGGAGTTCTAAATTGGGCAAGTCAAATTTATCCAGGAATTAAAACCAA ACATACCTGTGCCATGTTGAGAGGGAAAAAGAACCTCCTAGAAGAAATAGTATGGACAGAAGAGGCAGAG GCAGAATATAAGAACAATCAAGGGATAGTGCAGGAAACACAAGAAGGAACATACTATGACCCTCTCAAAG AATTAATAGCAACAGTTCAAAAGCAAGGAGAAGGGCAATGGACATACCAATTCACCCAAGAAGGGGCAGT ATTAAAGGTGGGAAGATATGCCAAGCAAAGAGAAACTCATACTAATGATCTAAGGACTCTAGCACACCTT GTCCAAAAAATCTGTAAGGAAGCACTTACCATTTGGGGAAGACTTCCACGAGTACAACTCCCAGTAGACA AGAAAACATGGGATATGTGGTGGCAGGACTATTGGCAAGTATCCTGGATACCAGAATGGGAGTTTGTTAG CACACCACTCCTAGTAAAACTGTGGTATTCCTTAGTAAAAGAACCAATCAAAGGAGAAGATGTTTATTAT GTGGATGGGGCAGCATCCAAAGTGACCAAATTAGGTAAGGCAGGATATCTGTCAGAGAGAGGAAAAAGTA GAATTAGGGAATTAGAAAACACCACTAACCAACAAGCAGAATTAACAGCAGTTAAGATGGCATTGGAGGA CAGTGGAGAAAATGTAAATATAGTCACAGATTCTCAATATGTAATGAACATCTTGACAGCATGTCCACAG GAAAGTAACTCACCCTTAGTGGAACAGATAATACAAGCCCTAATGAAAAAGAGGCAGGTCTACTTACAAT GGGTACCAGCTCATAAGGGGATAGGAGGCAATACAGAAATAGATAAATTAGTAAGCAAAGGAATAAGACA GATCCTCTTCTTAGATAGAATAGAAGAAGCACAAGATGACCATGCAAAGTACCATAACAATTGGAGAAGT ATGGTACAGGAATTTGGATTACCTAATATAGTAGCAAAAGAGATAGTAGCGGCATGTCCCAAATGCCAAA TAAGAGGAGAACCTAAGCATGGACAGGTAGACGCCTCCATTGAAACTTGGCAGATGGACTGCACCCATTT AGAAGGAAAAGTTATAATAGTAGCAGTACATGTAGCCAGTGGATTCATAGAAGCAGAGGTGATCCCAAGA GAAACTGGGAAGGAGACAGCACACTTTCTGCTGAAACTGTTAGCAAGATGGCCAGTGAAACATCTACACA CTGATAATGGCCCAAACTTTACCTCTCAGAATGTGGCAGCGGTGTGCTGGTGGGGTAATATAGAGCACAC CACTGGAATACCTTATAACCCACAGTCACAGGGTAGTGTAGAAAGCATGAACAGACAGCTCAAGGAAATC ATCTCTCAAATAAGAGATGATTGTGAGAGATTGGAGACAGCAGTGCAAATGGCTACGCATATCCACAATT TTAAAAGAAAGGGAGGAATAGGGGGTATCTCTAGTGCAGAAAGATTGGTTAATATGCTAACAACACAACT AGAACTAAATACTCTACAAAACCAAATCCAAAAAATTTTGAATTTTAAGGTCTACTACAGAGAAGGTAGA GATCCAGTGTGGAAAGGACCAGCGCGACTCATCTGGAAAGGAGAAGGCGCGGTGGTAATTAAAGAGGGGG AAGACATCAAGGTAGTCCCCAGGAGAAAGGCTAAGATTATCAAAGATTATGGAGAGAGAAAAACAATGGA TAGTGAGGGTAGTATGGAGGGTGTCAGAGAGGCAAATAAGCAGATGGAGGGGGATAGTGACTTACAAGAT CAGGAATA >gi|22535297|ref|NP_687035.1| Gag-Pol [Simian immunodeficiency virus] MGGGHSALSGRSLDTFEKIRLRPNGKKKYQIKHLIWAGKEMERFGLHEKLLETKEGCQKIIEVLTPLEPT GSEGLKALFNLCCVIWCIHAEQKVKDTEEAVVTVKQHYHLVDKNEKAAKKKNETTAPPGGESRNYPVVNQ NNAWVHQPLSPRTLNAWVKCVEEKRWGAEVVPMFQALSEGCLSYDVNQMLNVIGDHQGALQILKEVINEE AAEWDRTHRPPAGPLPAGQLRDPTGSDIAGTTSSIQEQIEWTFNANPRIDVGAQYRKWVILGLQKVVQMY NPQKVLDIRQGPKEPFQDYVDRFYKALRAEQAPQDVKNWMTQTLLIQNANPDCKLILKGLGMNPTLEEML IACQGVGGPQHKAKLMVEMMSNGQNMVQVGPQKKGPRGPLKCFNCGKFGHMQRECKAPRQIKCFKCGKIG HMAKDCKNGQANFFRVWPLGRSETKKFCAIQRRHSWSGTNSPPNGNSLRSSKEAPPAVCREGTAPERGER TDKETEGERSGGCFLELPLWRRPMKRVIIEGTPVQALLDTGADDTIIQEKDLHFPPHKPWRSKVVGGIGG GIHVKEYQGVQVQLEDKIITGSILIGSTPINIIGRNILAQAGMKLVMGVLSSQIEETKVQLKEGKDGPKL KQWPLSREKIEALTEICKQMEEEGKLSRIGGENPYNTPVFAIKKKDKTQWRMLVDFRELNKATQDFFEVQ LGIPHPAGLQKKKQITVIDIGDAYYSIPLCKEFRKYTAFTIPSVNNTGPGIRYQFNCLPQGWKGSPTIFQ NTAANILEEIKRHTPGLEIVQYMDDLWLASDHDETRHNQQVDIVRKMLLEKGLETPDKKVQREPPWEWMG YKLHPNKWTINKIELPPLEGEWTVNKIQKVVGVLNWASQIYPGIKTKHTCAMLRGKKNLLEEIVWTEEAE AEYKNNQGIVQETQEGTYYDPLKELIATVQKQGEGQWTYQFTQEGAVLKVGRYAKQRETHTNDLRTLAHL VQKICKEALTIWGRLPRVQLPVDKKTWDMWWQDYWQVSWIPEWEFVSTPLLVKLWYSLVKEPIKGEDVYY VDGAASKVTKLGKAGYLSERGKSRIRELENTTNQQAELTAVKMALEDSGENVNIVTDSQYVMNILTACPQ ESNSPLVEQIIQALMKKRQVYLQWVPAHKGIGGNTEIDKLVSKGIRQILFLDRIEEAQDDHAKYHNNWRS MVQEFGLPNIVAKEIVAACPKCQIRGEPKHGQVDASIETWQMDCTHLEGKVIIVAVHVASGFIEAEVIPR ETGKETAHFLLKLLARWPVKHLHTDNGPNFTSQNVAAVCWWGNIEHTTGIPYNPQSQGSVESMNRQLKEI ISQIRDDCERLETAVQMATHIHNFKRKGGIGGISSAERLVNMLTTQLELNTLQNQIQKILNFKVYYREGR DPVWKGPARLIWKGEGAVVIKEGEDIKVVPRRKAKIIKDYGERKTMDSEGSMEGVREANKQMEGDSDLQD QE Other nef Simian immunodeficiency virus 1490008 9627209 SIVgp7 M66437 NP_054373 3IOZ 11723 8599 9270 ? nef protein 6.4 24504.09 223 >gi|9627204:8599-9270 Simian immunodeficiency virus, complete genome TATGGGCTCCAGCAACTCCAAGAGGCAGCAACAGGGCTTGCTCAAGCTCTGGCGAGGGCTGCGAGGGAAG CCTGGGGCAGACTGGGTGCTATTGTCCGATCCGCTTATCGGGCAGTCATCAACAGTCCAAGAAGAGTGCG GCAAGGCCTTGAAAAAGTCCTGGGGTAAAGGTAAAATGACTCCAGACGGCCGCCGCCTGCAAGAAGGAGA CACCTTTGATGAGTGGGATGATGATGAAGAAGAAGTAGGCTTCCCTGTGCAACCTCGAGTCCCCTTAAGA CAGATGACCTATAAATTAGCAGTGGACTTTTCCCACTTTTTAAAATCAAAGGGGGGACTGGATGGGATAT ATTACTCTGAAAGAAGAGAAAAGATCCTGAATTTGTATGCCTTGAACGAGTGGGGAATAATAGATGATTG GCAAGCTTACTCACCAGGCCCGGGGATAAGGTACCCGAGAGTCTTTGGCTTCTGCTTTAAGCTAGTCCCA GTGGACCTGCATGAGGAGGCACGCAACTGTGAGAGACACTGTCTGATGCATCCAGCACAGATGGGGGAAG ATCCTGATGGAATAGATCATGGAGAAGTCTTGGTCTGGAAGTTTGACCCGAAGTTGGCGGTGGAGTACCG CCCGGACATGTTTAAGGACATGCACGAACATGCAAAGCGCTA >gi|9627209|ref|NP_054373.1| nef protein [Simian immunodeficiency virus] MGSSNSKRQQQGLLKLWRGLRGKPGADWVLLSDPLIGQSSTVQEECGKALKKSWGKGKMTPDGRRLQEGD TFDEWDDDEEEVGFPVQPRVPLRQMTYKLAVDFSHFLKSKGGLDGIYYSERREKILNLYALNEWGIIDDW QAYSPGPGIRYPRVFGFCFKLVPVDLHEEARNCERHCLMHPAQMGEDPDGIDHGEVLVWKFDPKLAVEYR PDMFKDMHEHAKR Virmugen A SIV nef mutant is attenuated in rhesus monkeys and induces protection from challenge with wild type SIV [Ref2001:Daniel et al., 1992]. 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