{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T01:31:54Z","timestamp":1792287114311,"version":"4.4.0"},"reference-count":43,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2016,7,11]],"date-time":"2016-07-11T00:00:00Z","timestamp":1468195200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R37 AI038518"],"award-info":[{"award-number":["R37 AI038518"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000026","name":"National Institute on Drug Abuse","doi-asserted-by":"publisher","award":["DP1 DA039543"],"award-info":[{"award-number":["DP1 DA039543"]}],"id":[{"id":"10.13039\/100000026","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001117","name":"amfAR, The Foundation for AIDS Research","doi-asserted-by":"publisher","award":["Mathilde Krim Fellowship in Basic Biomedical Research 109278-48-RKVA"],"award-info":[{"award-number":["Mathilde Krim Fellowship in Basic Biomedical Research 109278-48-RKVA"]}],"id":[{"id":"10.13039\/100001117","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["T32 AI083203"],"award-info":[{"award-number":["T32 AI083203"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"DOI":"10.1371\/journal.ppat.1005727","type":"journal-article","created":{"date-parts":[[2016,7,11]],"date-time":"2016-07-11T17:26:07Z","timestamp":1468257967000},"page":"e1005727","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":11,"title":["Adapting SHIVs In Vivo Selects for Envelope-Mediated Interferon-\u03b1 Resistance"],"prefix":"10.1371","volume":"12","author":[{"given":"David F.","family":"Boyd","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amit","family":"Sharma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daryl","family":"Humes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cecilia","family":"Cheng-Mayer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie","family":"Overbaugh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2016,7,11]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1038\/nature09907","article-title":"A diverse range of gene products are effectors of the type I interferon antiviral response","volume":"472","author":"JW Schoggins","year":"2011","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"4239","DOI":"10.1073\/pnas.1114981109","article-title":"Systematic identification of type I and type II interferon-induced antiviral factors","volume":"109","author":"S-Y Liu","year":"2012","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"3719","DOI":"10.1128\/JVI.01844-08","article-title":"Induction of a Striking Systemic Cytokine Cascade prior to Peak Viremia in Acute Human Immunodeficiency Virus Type 1 Infection, in Contrast to More Modest and Delayed Responses in Acute Hepatitis B and C Virus Infections","volume":"83","author":"AR Stacey","year":"2009","journal-title":"Journal of Virology"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"4598","DOI":"10.1182\/blood-2008-06-162651","article-title":"Primary infection with simian immunodeficiency virus: plasmacytoid dendritic cell homing to lymph nodes, type I interferon, and immune suppression","volume":"112","author":"B Malleret","year":"2008","journal-title":"Blood"},{"key":"ref5","article-title":"Nonpathogenic SIV infection of African green monkeys induces a strong but rapidly controlled type I IFN response","author":"B Jacquelin","year":"2009","journal-title":"J Clin Invest"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1038\/nature07831","article-title":"Glycerol monolaurate prevents mucosal SIV transmission","volume":"458","author":"Q Li","year":"2009","journal-title":"Nature"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"7886","DOI":"10.1128\/JVI.02612-09","article-title":"Downregulation of robust acute type I interferon responses distinguishes nonpathogenic simian immunodeficiency virus (SIV) infection of natural hosts from pathogenic SIV infection of rhesus macaques","volume":"84","author":"LD Harris","year":"2010","journal-title":"Journal of Virology"},{"key":"ref8","article-title":"HIV-1 and interferons: who's interfering with whom?","author":"T Doyle","year":"2015","journal-title":"Nature Publishing Group"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1038\/nature13554","article-title":"Type I interferon responses in rhesus macaques prevent SIV infection and slow disease progression","volume":"511","author":"NG Sandler","year":"2014","journal-title":"Nature"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"6626","DOI":"10.1073\/pnas.1304288110","article-title":"Phenotypic properties of transmitted founder HIV-1","volume":"110","author":"NF Parrish","year":"2013","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1186\/1742-4690-10-146","article-title":"Relative resistance of HIV-1 founder viruses to control by interferon-alpha","volume":"10","author":"AE Fenton-May","year":"2013","journal-title":"Retrovirology"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"a006940","DOI":"10.1101\/cshperspect.a006940","article-title":"HIV Restriction Factors and Mechanisms of Evasion","volume":"2","author":"MH Malim","year":"2012","journal-title":"Cold Spring Harb Perspect Med"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1038\/nri3295","article-title":"Evolutionary conflicts between viruses and restriction factors shape immunity","volume":"12","author":"NK Duggal","year":"2012","journal-title":"Nat Rev Immunol"},{"key":"ref14","first-page":"852","article-title":"Animal models for HIV\/AIDS research","volume":"10","author":"T Hatziioannou","year":"2012","journal-title":"Nature Publishing Group"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1111\/j.1600-0684.1999.tb00265.x","article-title":"In vivo adaptation of SHIV(SF162): chimeric virus expressing a NSI, CCR5-specific envelope protein","volume":"28","author":"RC Tan","year":"1999","journal-title":"Journal of Medical Primatology"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"8729","DOI":"10.1128\/JVI.00558-06","article-title":"Molecularly Cloned SHIV-1157ipd3N4: a Highly Replication- Competent, Mucosally Transmissible R5 Simian-Human Immunodeficiency Virus Encoding HIV Clade C env","volume":"80","author":"RJ Song","year":"2006","journal-title":"Journal of Virology"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"6137","DOI":"10.1128\/JVI.00178-13","article-title":"Generation of Lineage-Related, Mucosally Transmissible Subtype C R5 Simian-Human Immunodeficiency Viruses Capable of AIDS Development, Induction of Neurological Disease, and Coreceptor Switching in Rhesus Macaques","volume":"87","author":"W Ren","year":"2013","journal-title":"Journal of Virology"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"5255","DOI":"10.1128\/JVI.73.7.5255-5264.1999","article-title":"Variants from the diverse virus population identified at seroconversion of a clade A human immunodeficiency virus type 1-infected woman have distinct biological properties","volume":"73","author":"M Poss","year":"1999","journal-title":"Journal of Virology"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1097\/QAD.0b013e32805e8727","article-title":"HIV-1 subtype A envelope variants from early in infection have variable sensitivity to neutralization and to inhibitors of viral entry","volume":"21","author":"CA Blish","year":"2007","journal-title":"AIDS"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1128\/JVI.80.2.835-844.2006","article-title":"Neutralization escape variants of human immunodeficiency virus type 1 are transmitted from mother to infant","volume":"80","author":"X Wu","year":"2006","journal-title":"Journal of Virology"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"19769","DOI":"10.1073\/pnas.1217443109","article-title":"Most rhesus macaques infected with the CCR5-tropic SHIV(AD8) generate cross-reactive antibodies that neutralize multiple HIV-1 strains","volume":"109","author":"M Shingai","year":"2012","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"7490","DOI":"10.1073\/pnas.92.16.7490","article-title":"Persistent infection of rhesus macaques with T-cell-line-tropic and macrophage-tropic clones of simian\/human immunodeficiency viruses (SHIV)","volume":"92","author":"PA Luciw","year":"1995","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1990","DOI":"10.1128\/JVI.75.4.1990-1995.2001","article-title":"Mucosal Transmission and Induction of Simian AIDS by CCR5-Specific Simian\/Human Immunodeficiency Virus SHIVSF162P3","volume":"75","author":"JM Harouse","year":"2001","journal-title":"Journal of Virology"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"12472","DOI":"10.1128\/JVI.02176-12","article-title":"A Species-Specific Amino Acid Difference in the Macaque CD4 Receptor Restricts Replication by Global Circulating HIV-1 Variants Representing Viruses from Recent Infection","volume":"86","author":"D Humes","year":"2012","journal-title":"Journal of Virology"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1111\/j.1600-0684.2009.00383.x","article-title":"Ex vivoexpansion and lentiviral transduction of Macaca nemestrinaCD4 +T cells","volume":"38","author":"NM Mu\u00f1oz","year":"2009","journal-title":"Journal of Medical Primatology"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"11214","DOI":"10.1128\/JVI.79.17.11214-11224.2005","article-title":"Human immunodeficiency virus type 1 subtype B ancestral envelope protein is functional and elicits neutralizing antibodies in rabbits similar to those elicited by a circulating subtype B envelope","volume":"79","author":"NA Doria-Rose","year":"2005","journal-title":"Journal of Virology"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"2019","DOI":"10.1126\/science.1093137","article-title":"Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission","volume":"303","author":"CA Derdeyn","year":"2004","journal-title":"Science"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"8575","DOI":"10.1073\/pnas.86.21.8575","article-title":"Isolates of human immunodeficiency virus type 1 from the brain may constitute a special group of the AIDS virus","volume":"86","author":"C Cheng-Mayer","year":"1989","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1089\/aid.1996.12.191","article-title":"Construction and characterization of a stable full-length macrophage-tropic HIV type 1 molecular clone that directs the production of high titers of progeny virions","volume":"12","author":"TS Theodore","year":"1996","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1016\/j.chom.2014.08.003","article-title":"Selection of Unadapted, Pathogenic SHIVsEncoding Newly Transmitted HIV-1 Envelope Proteins","volume":"16","author":"GQ Del Prete","year":"2014","journal-title":"Cell Host and Microbe. Elsevier Inc"},{"key":"ref31","first-page":"37","article-title":"Infection of monkeys by simian-human immunodeficiency viruses with transmitted\/founder clade C HIV-1 envelopes","volume":"475C","author":"M Asmal","year":"2014","journal-title":"Virology"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1965","DOI":"10.1128\/JVI.03279-14","article-title":"Generation and evaluation of clade C simian-human immunodeficiency virus challenge stocks","volume":"89","author":"H-W Chang","year":"2015","journal-title":"Journal of Virology"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"6678","DOI":"10.1128\/JVI.00338-13","article-title":"A Variant Macaque-Tropic Human Immunodeficiency Virus Type 1 Is Resistant to Alpha Interferon-Induced Restriction in Pig-Tailed Macaque CD4+ T Cells","volume":"87","author":"R Thippeshappa","year":"2013","journal-title":"Journal of Virology"},{"key":"ref34","first-page":"1","article-title":"Quantifying the Antiviral Effectof IFN on HIV-1 Replication in CellCulture","author":"H Ikeda","year":"2015","journal-title":"Nature Publishing Group"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"11920","DOI":"10.1073\/pnas.172384599","article-title":"Restriction of lentivirus in monkeys","volume":"99","author":"C Besnier","year":"2002","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"11914","DOI":"10.1073\/pnas.162299499","article-title":"Cellular inhibitors with Fv1-like activity restrict human and simian immunodeficiency virus tropism","volume":"99","author":"S Cowan","year":"2002","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"1298","DOI":"10.1073\/pnas.0337541100","article-title":"Abrogation of postentry restriction of HIV-1-based lentiviral vector transduction in simian cells","volume":"100","author":"NA Kootstra","year":"2003","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1016\/j.virol.2006.03.013","article-title":"Saturation of TRIM5 alpha-mediated restriction of HIV-1 infection depends on the stability of the incoming viral capsid","volume":"350","author":"J Shi","year":"2006","journal-title":"Virology"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"e1005154","DOI":"10.1371\/journal.ppat.1005154","article-title":"Heterosexual Transmission of Subtype C HIV-1 Selects Consensus-Like Variants without Increased Replicative Capacity or Interferon-\u03b1 Resistance","volume":"11","author":"MJ Deymier","year":"2015","journal-title":"PLoS Pathog"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"e1000908","DOI":"10.1371\/journal.ppat.1000908","article-title":"Few and far between: how HIV may be evading antibody avidity","volume":"6","author":"JS Klein","year":"2010","journal-title":"PLoS Pathog"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/j.tim.2015.02.003","article-title":"HIV cell-to-cell transmission: effects on pathogenesis and antiretroviral therapy","volume":"23","author":"LM Agosto","year":"2015","journal-title":"Trends in Microbiology"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/j.virol.2011.09.032","article-title":"The role of amino acid changes in the human immunodeficiency virus type 1 transmembrane domain in antibody binding and neutralization","volume":"421","author":"E Lovelace","year":"2011","journal-title":"Virology"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1038\/nprot.2008.73","article-title":"Analyzing real-time PCR data by the comparative CT method","volume":"3","author":"TD Schmittgen","year":"2008","journal-title":"Nat Protoc"}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.ppat.1005727","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,23]],"date-time":"2020-09-23T19:49:49Z","timestamp":1600890589000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1005727"}},"subtitle":[],"editor":[{"given":"Guido","family":"Silvestri","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,7,11]]},"references-count":43,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2016,7,11]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1005727","relation":{},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,7,11]]}}}