Discussing publications with the lab.

Publications

Most of our research output is described in peer-reviewed manuscripts. Free, full-text versions of these papers are typically available in Pubmed Central (follow the links in the format PMC5736429).

I am also a strong proponent of submitting research to the Biorxiv pre-print server at the same time as papers are submitted for peer-review. These unpublished manuscripts will likely appear in the peer-reviewed literature within 6-12 months.

This is an accordion element with a series of buttons that open and close related content panels.

Biorxiv (not yet published in peer-reviewed journals)

  • Anna S. JaegerAndrea M. Weiler, Ryan V. Moriarty, Sierra Rybarczyk, Shelby L. O’Connor, David H. O’Connor, Davis M. Seelig, Michael K. Fritsch, Thomas C. Friedrich, Matthew T.
    Aliota 
    Spondweni virus causes fetal harm in a mouse model of vertical transmission and is transmitted by Aedes aegypti mosquitoes

  • Amelia K. HajMeghan E. BreitbachDavid A. BakerMariel S. MohnsGage K. MorenoNancy A. WilsonVictor LyamichevJigar PatelKim L. WeisgrauDawn M. DudleyDavid H. O’Connor Highthroughput identification of MHC class I binding peptides using an ultradense peptide array
  • Gage K. MorenoChristina M. NewmanMichelle R. KoenigMariel S. MohnsAndrea M. WeilerSierra RybarczykLogan J. VoslerNicholas PomplunNancy Schultz-DarkenEva RakaszDawn M. DudleyThomas C. FriedrichDavid H. O’Connor Long-term protection of rhesus macaques from Zika virus reinfection

2019

  • de Groot NG, Otting N, Maccari G, Robinson J, Hammond JA, Blancher A, Lafont BAP, Guethlein LA, Wroblewski EE, Marsh SGE, Shiina T, Walter L, Vigilant L, Parham P, O’Connor DH, Bontrop RE. Nomenclature report 2019: major histocompatibility complex genes and alleles of Great and Small Ape and Old and New World monkey species. Immunogenetics. 2019 Oct 17. doi: 10.1007/s00251-019-01132-x. [Epub ahead of print] Review. PMID:31624862
  • Robbiani DF, Olsen PC, Costa F, Wang Q, Oliveira TY, et al. Risk of Zika microcephaly correlates with features of maternal antibodies. J Exp Med. 2019 Oct 7;216(10):2302-2315. doi: 10.1084/jem.20191061. Epub 2019 Aug 14.PMID: 31413072

  • Breitbach ME, Newman CM, Dudley DM, Stewart LM, Aliota MT, Koenig MR, Shepherd PM, Yamamoto K, Crooks CM, Young G, Semler MR, Weiler AM, Barry GL, Heimsath H, Mohr EL, Eichkoff J, Newton W, Peterson E, Schultz-Darken N, Permar SR, Dean H, Capuano S 3rd, Osorio JE, Friedrich TC, O’Connor DH. Primary infection with dengue or Zika virus does not affect the severity of heterologous secondary infection in macaques. PLoS Pathog. 2019 Aug 1;15(8):e1007766. doi: 10.1371/journal.ppat.1007766. eCollection 2019 Aug. PMID: 31369649

  • Caskey JR, Wiseman RW, Karl JA, Baker DA, Lee T, Maddox RJ, Raveendran M, Harris RA, Hu J, Muzny DM, Rogers J, O’Connor DH. MHC genotyping from rhesus macaque exome sequences. Immunogenetics. 2019 Sep;71(8-9):531-544. doi: 10.1007/s00251-019-01125-w. Epub 2019 Jul 18. PMID: 31321455

  • Dudley DM, Aliota MT, Mohr EL, Newman CM, Golos TG, Friedrich TC, O’Connor DH. Using Macaques to Address Critical Questions in Zika Virus ResearchAnnu Rev Virol. 2019 Sep 29;6(1):481-500. doi: 10.1146/annurev-virology-092818-015732. Epub 2019 Jun 10. PMID: 31180813

  • Caì Y, Yú S, Jangra RK, Postnikova EN, Wada J, Tesh RB, Whelan SPJ, Lauck M, Wiley MR, Finch CL, Radoshitzky SR, O’Connor DH, Palacios G, Chandran K, Chiu CY, Kuhn JH. Human, Nonhuman Primate, and Bat Cells Are Broadly Susceptible to Tibrovirus Particle Cell Entry.Front Microbiol. 2019 Apr 26;10:856. doi: 10.3389/fmicb.2019.00856. eCollection 2019. PMID: 31105663

  • Cornish JP, Moore IN, Perry DL, Lara A, Minai M, Promeneur D, Hagen KR, Virtaneva K, Paneru M, Buechler CR, O’Connor DH, Bailey AL, Cooper K, Mazur S, Bernbaum JG, Pettitt J, Jahrling PB, Kuhn JH, Johnson RF. Clinical Characterization of Host Response to Simian Hemorrhagic Fever Virus Infection in Permissive and Refractory Hosts: A Model for Determining Mechanisms of VHF Pathogenesis. Viruses. 2019 Jan 15;11(1). pii: E67. doi: 10.3390/v11010067. PMID: 30650570
  • Haj AK, Arbanas JM, Yamniuk AP, Karl JA, Bussan HE, Drinkwater KY, Graham ME, Ericsen AJ, Prall TM, Moore K, Cheng L, Gao M, Graziano RF, Loffredo JT, Wiseman RW, O’Connor DH. Characterization of Mauritian Cynomolgus Macaque FcγR Alleles Using Long-Read Sequencing. J Immunol. 2019 Jan 1;202(1):151-159. doi: 10.4049/jimmunol.1800843. Epub 2018 Dec 10. PMID: 30530595

 

 

2018

  • Muniz CP, Cavalcante LTF, Dudley DM, Pissinatti A, O’Connor DH, Santos AF, Soares MA. First Complete Genome Sequence of a Simian Foamy Virus Infecting the Neotropical Primate Brachyteles arachnoides. Microbiol Resour Announc. 2018 Jul 19;7(2). pii: e00839-18. doi: 10.1128/MRA.00839-18. eCollection 2018 Jul. PMID: 30533805

  • Heffron AS, Mohr EL, Baker D, Haj AK, Buechler CR, Bailey A, Dudley DM, Newman CM, Mohns MS, Koenig M, Breitbach ME, Rasheed M, Stewart LM, Eickhoff J, Pinapati RS, Beckman E, Li H, Patel J, Tan JC, O’Connor DH. Antibody responses to Zika virus proteins in pregnant and non-pregnant macaques. PLoS Negl Trop Dis. 2018 Nov 27;12(11):e0006903. doi: 10.1371/journal.pntd.0006903. eCollection 2018 Nov. PMID: 30481182

  • Weger-Lucarelli J, Garcia SM, Rückert C, Byas A, O’Connor SL, Aliota MT, Friedrich TC, O’Connor DH, Ebel GD. Using barcoded Zika virus to assess virus population structure in vitro and in Aedes aegypti mosquitoes Virology. 2018 Aug;521:138-148. doi: 10.1016/j.virol.2018.06.004. Epub 2018 Jun 20. PMID: 29935423

  • Connor Buechler, Matthew Semler, David A. Baker, Christina Newman, Joseph P. Cornish, Deborah Chavez, Bernadette Guerra, Robert Lanford, Kathy Brasky, Jens H. Kuhn, Reed F. Johnson, David H.O’Connor, Adam Bailey Subclinical infection of macaques and baboons with a baboon simartevirus Viruses 2018 Dec 10;10(12). pii: E701. doi: 10.3390/v10120701. PMID: 30544677

  • Wu HL, Wiseman RW, Hughes CM et al. The Role of MHC-E in T Cell Immunity Is Conserved among Humans, Rhesus Macaques, and Cynomolgus Macaques.  J Immunol. 2018; 200(1) 49-60. doi:10.4049/jimmunol.1700841. PubMed PMID: 29150562. PMCID: PMC5736429.

  • Morgan RA, Karl JA, Bussan HE, Heimbruch KE, O’Connor DH, Dudley DM. Restricted MHC class I A locus diversity in olive and hybrid olive/yellow baboons from the Southwest National Primate Research Center. Immunogenetics. 2018; 70(7) 449-458. doi:10.1007/s00251-018-1057-3. PubMed PMID: 29594415.
  • Mavigner M, Raper J, Kovacs-Balint Z et al. Postnatal Zika virus infection is associated with persistent abnormalities in brain structure, function, and behavior in infant macaques. Sci Transl Med. 2018; 10(435) doi:10.1126/scitranslmed.aao6975. PubMed PMID: 29618564.
  • Mohr EL, Block LN, Newman CM et al. Ocular and uteroplacental pathology in a macaque pregnancy with congenital Zika virus infection. PLoS One. 2018; 13(1) e0190617. doi:10.1371/journal.pone.0190617. PubMed PMID: 29381706. PMCID: PMC5790226.
  • Semler MR, Wiseman RW, Karl JA, Graham ME, Gieger SM, O’Connor DH. Novel full-length major histocompatibility complex class I allele discovery and haplotype definition in pig-tailed macaques. Immunogenetics. 2018; 70(6) 381-399. doi:10.1007/s00251-017-1042-2. PubMed PMID: 29134258.
  • Aliota MT, Dudley DM, Newman CM et al. Molecularly barcoded Zika virus libraries to probe in vivo evolutionary dynamics. PLoS Pathog. 2018; 14(3) e1006964. doi:10.1371/journal.ppat.1006964. PubMed PMID: 29590202. PMCID: PMC5891079.
  • Dudley DM, Van Rompay KK, Coffey LL et al. Miscarriage and stillbirth following maternal Zika virus infection in nonhuman primates. Nat Med. 2018; 24(8) 1104-1107. doi:10.1038/s41591-018-0088-5. PubMed PMID: 29967348. PMCID: PMC6082723.
  • Imai H, Dinis JM, Zhong G et al. Diversity of Influenza A(H5N1) Viruses in Infected Humans, Northern Vietnam, 2004-2010. Emerg Infect Dis. 2018; 24(7) 1128-1238. doi:10.3201/eid2407.171441. PubMed PMID: 29912683. PMCID: PMC6038741.
  • Banerjee P, Ries M, Janaka SK et al. Diversification of Bw4 Specificity and Recognition of a Nonclassical MHC Class I Molecule Implicated in Maternal-Fetal Tolerance by Killer Cell Ig-like Receptors of the Rhesus Macaque. J Immunol. 2018; doi:10.4049/jimmunol.1800494. PubMed PMID: 30232137.

2017

  • Aliota MT, Bassit L, Bradrick SS et al. Zika in the Americas, year 2: What have we learned? What gaps remain? A report from the Global Virus Network. Antiviral Res. 2017; 144 223-246. doi:10.1016/j.antiviral.2017.06.001. PubMed PMID: 28595824. PMCID: PMC5920658.
  • Moncla LH, Weiler AM, Barry G et al. Within-Host Evolution of Simian Arteriviruses in Crab-Eating Macaques. J Virol. 2017; 91(4) doi:10.1128/JVI.02231-16. PubMed PMID: 27974564. PMCID: PMC5286893.
  • Otting N, Van Der Wiel MK, De Groot N et al. The orthologs of HLA-DQ and -DP genes display abundant levels of variability in macaque species. Immunogenetics. 2017; 69(2) 87-99. doi:10.1007/s00251-016-0954-6. PubMed PMID: 27771735.
  • Buechler CR, Bailey AL, Weiler AM et al. Seroprevalence of Zika Virus in Wild African Green Monkeys and Baboons. mSphere. 2017; 2 doi:10.1128/mSphere.00392-16. PubMed PMID: 28289727. PMCID: PMC5343173.
  • Bailey AL, Buechler CR, Matson DR et al. Pegivirus avoids immune recognition but does not attenuate acute-phase disease in a macaque model of HIV infection. PLoS Pathog. 2017; 13(10) e1006692. doi:10.1371/journal.ppat.1006692. PubMed PMID: 29073258. PMCID: PMC5675458.
  • Newman CM, Dudley DM, Aliota MT et al. Oropharyngeal mucosal transmission of Zika virus in rhesus macaques. Nat Commun. 2017; 8(1) 169. doi:10.1038/s41467-017-00246-8. PubMed PMID: 28765581. PMCID: PMC5539107.
  • Karl JA, Graham ME, Wiseman RW et al. Major histocompatibility complex haplotyping and long-amplicon allele discovery in cynomolgus macaques from Chinese breeding facilities. Immunogenetics. 2017; 69(4) 211-229. doi:10.1007/s00251-017-0969-7. PubMed PMID: 28078358. PMCID: PMC5352482.
  • Newman C, Friedrich TC, O’Connor DH. Macaque monkeys in Zika virus research: 1947-present. Curr Opin Virol. 2017; 25 34-40. doi:10.1016/j.coviro.2017.06.011. PubMed PMID: 28750247. PMCID: PMC5610623.
  • Ries M, Reynolds MR, Bashkueva K et al. KIR3DL01 upregulation on gut natural killer cells in response to SIV infection of KIR- and MHC class I-defined rhesus macaques. PLoS Pathog. 2017; 13(7) e1006506. doi:10.1371/journal.ppat.1006506. PubMed PMID: 28708886. PMCID: PMC5529027.
  • Dudley DM, Newman CM, Lalli J et al. Infection via mosquito bite alters Zika virus tissue tropism and replication kinetics in rhesus macaques. Nat Commun. 2017; 8(1) 2096. doi:10.1038/s41467-017-02222-8. PubMed PMID: 29235456. PMCID: PMC5727388.
  • Prall TM, Graham ME, Karl JA et al. Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques. Immunogenetics. 2017; 69(5) 325-339. doi:10.1007/s00251-017-0977-7. PubMed PMID: 28343239. PMCID: PMC5856007.
  • Nguyen SM, Antony KM, Dudley DM et al. Highly efficient maternal-fetal Zika virus transmission in pregnant rhesus macaques. PLoS Pathog. 2017; 13(5) e1006378. doi:10.1371/journal.ppat.1006378. PubMed PMID: 28542585. PMCID: PMC5444831.
  • Buechler CR, Bailey AL, Lauck M et al. Genome Sequence of a Novel Kunsagivirus (Picornaviridae: Kunsagivirus) from a Wild Baboon (Papio cynocephalus). Genome Announc. 2017; 5(18) doi:10.1128/genomeA.00261-17. PubMed PMID: 28473378. PMCID: PMC5477186.
  • Keasey SL, Pugh CL, Jensen SM et al. Antibody Responses to Zika Virus Infections in Environments of Flavivirus Endemicity. Clin Vaccine Immunol. 2017; 24(4) doi:10.1128/CVI.00036-17. PubMed PMID: 28228395. PMCID: PMC5382833.

2016 and earlier

  • Bailey AL, Lauck M, Sibley SD et al. Zoonotic Potential of Simian Arteriviruses. J Virol. 2016; 90(2) 630-635. doi:10.1128/JVI.01433-15. PubMed PMID: 26559828. PMCID: PMC4702702.
  • Arias JF, Colomer-Lluch M, Von Bredow B et al. Tetherin Antagonism by HIV-1 Group M Nef Proteins. J Virol. 2016; doi:10.1128/JVI.01465-16. PubMed PMID: 27654287. PMCID: PMC5110183.
  • Yu SQ, Cai Y, Lyons C et al. Specific Detection of Two Divergent Simian Arteriviruses Using RNAscope In Situ Hybridization. PLoS One. 2016; 11(3) e0151313. doi:10.1371/journal.pone.0151313. PubMed PMID: 26963736. PMCID: PMC4786270.
  • Kuhn JH, Lauck M, Bailey AL et al. Reorganization and expansion of the nidoviral family Arteriviridae. Arch Virol. 2016; 161(3) 755-768. doi:10.1007/s00705-015-2672-z. PubMed PMID: 26608064. PMCID: PMC5573231.
  • Kallas EG, O’Connor DH. Real-Time Sharing of Zika Virus Data in an Interconnected World. JAMA Pediatr. 2016; 170(7) 633-634. doi:10.1001/jamapediatrics.2016.0857. PubMed PMID: 27031608.
  • Pardee K, Green AA, Takahashi MK et al. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components. Cell. 2016; 165(5) 1255-1266. doi:10.1016/j.cell.2016.04.059. PubMed PMID: 27160350.
  • Simons ND, Ruiz-Lopez MJ, Chapman CA et al. Rapid Identification of Major Histocompatibility Complex Class I Haplotypes Using Deep Sequencing in an Endangered Old World Monkey. Conserv Genet Resour. 2016; 8(1) 23-26. doi:10.1007/s12686-016-0516-0. PubMed PMID: 27182286. PMCID: PMC4863455.
  • Bennett AJ, Sibley SD, Lauck M et al. Naturally Circulating Hepatitis A Virus in Olive Baboons, Uganda. Emerg Infect Dis. 2016; 22(7) 1308-1310. doi:10.3201/eid2207.151837. PubMed PMID: 27315373. PMCID: PMC4918173.
  • Ericsen AJ, Lauck M, Mohns MS et al. Microbial Translocation and Inflammation Occur in Hyperacute Immunodeficiency Virus Infection and Compromise Host Control of Virus Replication. PLoS Pathog. 2016; 12 e1006048. doi:10.1371/journal.ppat.1006048. PubMed PMID: 27926931. PMCID: PMC5142784.
  • Ericsen AJ, Lauck M, Mohns MS et al. Microbial Translocation and Inflammation Occur in Hyperacute Immunodeficiency Virus Infection and Compromise Host Control of Virus Replication. PLoS Pathog. 2016; 12 e1006048. doi:10.1371/journal.ppat.1006048. PubMed PMID: 27926931. PMCID: PMC5142784.
  • Aliota MT, Dudley DM, Newman CM et al. Heterologous Protection against Asian Zika Virus Challenge in Rhesus Macaques. PLoS Negl Trop Dis. 2016; 10(12) e0005168. doi:10.1371/journal.pntd.0005168. PubMed PMID: 27911897. PMCID: PMC5135040.
  • O’Connor DH, Osorio JE, Tanuri A, Kallas EG. Forging Collaborative Relationships in Brazil: From AIDS to ZIKV. Cell. 2016; 166(1) 2-4. doi:10.1016/j.cell.2016.06.023. PubMed PMID: 27368092.
  • Wahl-Jensen V, Johnson JC, Lauck M et al. Divergent Simian Arteriviruses Cause Simian Hemorrhagic Fever of Differing Severities in Macaques. MBio. 2016; 7(1) e02009-15. doi:10.1128/mBio.02009-15. PubMed PMID: 26908578. PMCID: PMC4791849.
  • Lee LM, Wallace RS, Clyde VL et al. Definitive Hosts of Versteria Tapeworms (Cestoda: Taeniidae) Causing Fatal Infection in North America. Emerg Infect Dis. 2016; 22(4) 707-710. doi:10.3201/eid2204.151446. PubMed PMID: 26983004. PMCID: PMC4806962.
  • Delvecchio R, Higa LM, Pezzuto P et al. Chloroquine, an Endocytosis Blocking Agent, Inhibits Zika Virus Infection in Different Cell Models. Viruses. 2016; 8(12) doi:10.3390/v8120322. PubMed PMID: 27916837. PMCID: PMC5192383.
  • Bailey AL, Lauck M, Ghai RR et al. Arteriviruses, Pegiviruses, and Lentiviruses Are Common among Wild African Monkeys. J Virol. 2016; 90(15) 6724-6737. doi:10.1128/JVI.00573-16. PubMed PMID: 27170760. PMCID: PMC4944300.
  • Dudley DM, Aliota MT, Mohr EL et al. A rhesus macaque model of Asian-lineage Zika virus infection. Nat Commun. 2016; 7 12204. doi:10.1038/ncomms12204. PubMed PMID: 27352279. PMCID: PMC4931337.
  • Ayala VI, Trivett MT, Coren LV et al. A novel SIV gag-specific CD4(+)T-cell clone suppresses SIVmac239 replication in CD4(+)T cells revealing the interplay between antiviral effector cells and their infected targets. Virology. 2016; 493 100-112. doi:10.1016/j.virol.2016.03.013. PubMed PMID: 27017056. PMCID: PMC4860118.
  • Ladner JT, Wiley MR, Beitzel B et al. A Multicomponent Animal Virus Isolated from Mosquitoes. Cell Host Microbe. 2016; 20(3) 357-367. doi:10.1016/j.chom.2016.07.011. PubMed PMID: 27569558. PMCID: PMC5025392.
  • Mothe BR, Lindestam Arlehamn CS, Dow C et al. The TB-specific CD4(+) T cell immune repertoire in both cynomolgus and rhesus macaques largely overlap with humans. Tuberculosis (Edinb). 2015; 95(6) 722-735. doi:10.1016/j.tube.2015.07.005. PubMed PMID: 26526557. PMCID: PMC4773292.
  • Warren WC, Jasinska AJ, Garcia-Perez R et al. The genome of the vervet (Chlorocebus aethiops sabaeus). Genome Res. 2015; 25(12) 1921-1933. doi:10.1101/gr.192922.115. PubMed PMID: 26377836. PMCID: PMC4665013.
  • Cai Y, Postnikova EN, Bernbaum JG et al. Simian hemorrhagic fever virus cell entry is dependent on CD163 and uses a clathrin-mediated endocytosis-like pathway. J Virol. 2015; 89(1) 844-856. doi:10.1128/JVI.02697-14. PubMed PMID: 25355889. PMCID: PMC4301170.
  • Heimbruch KE, Karl JA, Wiseman RW et al. Novel MHC class I full-length allele and haplotype characterization in sooty mangabeys. Immunogenetics. 2015; 67(8) 437-445. doi:10.1007/s00251-015-0847-0. PubMed PMID: 26009014. PMCID: PMC4498956.
  • Westbrook CJ, Karl JA, Wiseman RW et al. No assembly required: Full-length MHC class I allele discovery by PacBio circular consensus sequencing. Hum Immunol. 2015; 76(12) 891-896. doi:10.1016/j.humimm.2015.03.022. PubMed PMID: 26028281.
  • Bialas KM, Tanaka T, Tran D et al. Maternal CD4+ T cells protect against severe congenital cytomegalovirus disease in a novel nonhuman primate model of placental cytomegalovirus transmission. Proc Natl Acad Sci U S A. 2015; 112(44) 13645-13650. doi:10.1073/pnas.1511526112. PubMed PMID: 26483473. PMCID: PMC4640765.
  • Correll M, Bailey AL, Sarikaya A, O’Connor DH, Gleicher M. LayerCake: a tool for the visual comparison of viral deep sequencing data. Bioinformatics. 2015; 31(21) 3522-3528. doi:10.1093/bioinformatics/btv407. PubMed PMID: 26153515. PMCID: PMC4626748.
  • Lauck M, Alkhovsky SV, Bao Y et al. Historical Outbreaks of Simian Hemorrhagic Fever in Captive Macaques Were Caused by Distinct Arteriviruses. J Virol. 2015; 89(15) 8082-8087. doi:10.1128/JVI.01046-15. PubMed PMID: 25972539. PMCID: PMC4505640.
  • Lauck M, Yu SQ, Cai Y et al. Genome Sequence of Bivens Arm Virus, a Tibrovirus Belonging to the Species Tibrogargan virus (Mononegavirales: Rhabdoviridae). Genome Announc. 2015; 3(2) doi:10.1128/genomeA.00089-15. PubMed PMID: 25792044. PMCID: PMC4394750.
  • Lauck M, Bailey AL, Andersen KG, Goldberg TL, Sabeti PC, O’Connor DH. GB virus C coinfections in west African Ebola patients. J Virol. 2015; 89(4) 2425-2429. doi:10.1128/JVI.02752-14. PubMed PMID: 25473056. PMCID: PMC4338908.
  • Mohns MS, Greene JM, Cain BT et al. Expansion of Simian Immunodeficiency Virus (SIV)-Specific CD8 T Cell Lines from SIV-Naive Mauritian Cynomolgus Macaques for Adoptive Transfer. J Virol. 2015; 89(19) 9748-9757. doi:10.1128/JVI.00993-15. PubMed PMID: 26178985. PMCID: PMC4577914.
  • Breed MW, Elser SE, Torben W et al. Elite Control, Gut CD4 T Cell Sparing, and Enhanced Mucosal T Cell Responses in Macaca nemestrina Infected by a Simian Immunodeficiency Virus Lacking a gp41 Trafficking Motif. J Virol. 2015; 89(20) 10156-10175. doi:10.1128/JVI.01134-15. PubMed PMID: 26223646. PMCID: PMC4580161.
  • Breed MW, Elser SE, Torben W et al. Elite Control, Gut CD4 T Cell Sparing, and Enhanced Mucosal T Cell Responses in Macaca nemestrina Infected by a Simian Immunodeficiency Virus Lacking a gp41 Trafficking Motif. J Virol. 2015; 89(20) 10156-10175. doi:10.1128/JVI.01134-15. PubMed PMID: 26223646. PMCID: PMC4580161.
  • Bailey AL, Lauck M, Mohns M et al. Durable sequence stability and bone marrow tropism in a macaque model of human pegivirus infection. Sci Transl Med. 2015; 7(305) 305ra144. doi:10.1126/scitranslmed.aab3467. PubMed PMID: 26378244. PMCID: PMC4605385.
  • Wang Z, Metcalf B, Kasheta M et al. Characterization of MHC class I alleles in sooty mangabeys as a tool for evaluating cellular immunity in natural hosts of SIV infection. Immunogenetics. 2015; 67(8) 447-461. doi:10.1007/s00251-015-0853-2. PubMed PMID: 26129855. PMCID: PMC4536953.
  • Ericsen AJ, Starrett GJ, Greene JM et al. Whole genome sequencing of SIV-infected macaques identifies candidate loci that may contribute to host control of virus replication. Genome Biol. 2014; 15(11) 478. doi:10.1186/s13059-014-0478-z. PubMed PMID: 25418588. PMCID: PMC4223156.
  • Bailey AL, Lauck M, Sibley SD et al. Two novel simian arteriviruses in captive and wild baboons (Papio spp.). J Virol. 2014; 88(22) 13231-13239. doi:10.1128/JVI.02203-14. PubMed PMID: 25187550. PMCID: PMC4249091.
  • Burwitz BJ, Wu HL, Reed JS et al. Tertiary mutations stabilize CD8+ T lymphocyte escape-associated compensatory mutations following transmission of simian immunodeficiency virus. J Virol. 2014; 88(6) 3598-3604. doi:10.1128/JVI.03304-13. PubMed PMID: 24371068. PMCID: PMC3957937.
  • Karl JA, Heimbruch KE, Vriezen CE et al. Survey of major histocompatibility complex class II diversity in pig-tailed macaques. Immunogenetics. 2014; 66(11) 613-623. doi:10.1007/s00251-014-0797-y. PubMed PMID: 25129472. PMCID: PMC4198495.
  • Greene JM, Weiler AM, Reynolds MR et al. Rapid, repeated, low-dose challenges with SIVmac239 infect animals in a condensed challenge window. Retrovirology. 2014; 11 66. doi:10.1186/s12977-014-0066-z. PubMed PMID: 25125288. PMCID: PMC4149191.
  • Gooneratne SL, Alinejad-Rokny H, Ebrahimi D et al. Linking pig-tailed macaque major histocompatibility complex class I haplotypes and cytotoxic T lymphocyte escape mutations in simian immunodeficiency virus infection. J Virol. 2014; 88(24) 14310-14325. doi:10.1128/JVI.02428-14. PubMed PMID: 25275134. PMCID: PMC4249162.
  • Schafer JL, Colantonio AD, Neidermyer WJ et al. KIR3DL01 recognition of Bw4 ligands in the rhesus macaque: maintenance of Bw4 specificity since the divergence of apes and Old World monkeys. J Immunol. 2014; 192(4) 1907-1917. doi:10.4049/jimmunol.1302883. PubMed PMID: 24453246. PMCID: PMC4162532.
  • Bailey AL, Lauck M, Weiler A et al. High genetic diversity and adaptive potential of two simian hemorrhagic fever viruses in a wild primate population. PLoS One. 2014; 9(3) e90714. doi:10.1371/journal.pone.0090714. PubMed PMID: 24651479. PMCID: PMC3961216.
  • Lauck M, Palacios G, Wiley MR et al. Genome Sequences of Simian Hemorrhagic Fever Virus Variant NIH LVR42-0/M6941 Isolates (Arteriviridae: Arterivirus). Genome Announc. 2014; 2(5) doi:10.1128/genomeA.00978-14. PubMed PMID: 25301647. PMCID: PMC4192379.
  • Dudley DM, Karl JA, Creager HM, Bohn PS, Wiseman RW, O’Connor DH. Full-length novel MHC class I allele discovery by next-generation sequencing: two platforms are better than one. Immunogenetics. 2014; 66(1) 15-24. doi:10.1007/s00251-013-0744-3. PubMed PMID: 24241691. PMCID: PMC3910708.
  • Goldberg TL, Gendron-Fitzpatrick A, Deering KM et al. Fatal metacestode infection in Bornean orangutan caused by unknown Versteria species. Emerg Infect Dis. 2014; 20(1) 109-113. doi:10.3201/eid2001.131191. PubMed PMID: 24377497. PMCID: PMC3884733.
  • Lauck M, Switzer WM, Sibley SD et al. Discovery and full genome characterization of a new SIV lineage infecting red-tailed guenons (Cercopithecus ascanius schmidti) in Kibale National Park, Uganda. Retrovirology. 2014; 11 55. doi:10.1186/1742-4690-11-55. PubMed PMID: 24996566. PMCID: PMC4226943.
  • Sibley SD, Lauck M, Bailey AL et al. Discovery and characterization of distinct simian pegiviruses in three wild African Old World monkey species. PLoS One. 2014; 9(2) e98569. doi:10.1371/journal.pone.0098569. PubMed PMID: 24918769. PMCID: PMC4053331.
  • Dudley DM, Bailey AL, Mehta SH et al. Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq. Retrovirology. 2014; 11 122. doi:10.1186/s12977-014-0122-8. PubMed PMID: 25533166. PMCID: PMC4302432.
  • Silveira EL, Fogg MH, Leskowitz RM et al. Therapeutic vaccination against the rhesus lymphocryptovirus EBNA-1 homologue, rhEBNA-1, elicits T cell responses to novel epitopes in rhesus macaques. J Virol. 2013; 87(24) 13904-13910. doi:10.1128/JVI.01947-13. PubMed PMID: 24089556. PMCID: PMC3838282.
  • Cain BT, Pham NH, Budde ML et al. T cell response specificity and magnitude against SIVmac239 are not concordant in major histocompatibility complex-matched animals. Retrovirology. 2013; 10 116. doi:10.1186/1742-4690-10-116. PubMed PMID: 24156675. PMCID: PMC3874790.
  • Cain BT, Pham NH, Budde ML et al. T cell response specificity and magnitude against SIVmac239 are not concordant in major histocompatibility complex-matched animals. Retrovirology. 2013; 10 116. doi:10.1186/1742-4690-10-116. PubMed PMID: 24156675. PMCID: PMC3874790.
  • Wilker PR, Dinis JM, Starrett G et al. Selection on haemagglutinin imposes a bottleneck during mammalian transmission of reassortant H5N1 influenza viruses. Nat Commun. 2013; 4 2636. doi:10.1038/ncomms3636. PubMed PMID: 24149915. PMCID: PMC3845350.
  • Karl JA, Bohn PS, Wiseman RW et al. Major histocompatibility complex class I haplotype diversity in Chinese rhesus macaques. G3 (Bethesda). 2013; 3(7) 1195-1201. doi:10.1534/g3.113.006254. PubMed PMID: 23696100. PMCID: PMC3704247.
  • Wiseman RW, Karl JA, Bohn PS, Nimityongskul FA, Starrett GJ, O’Connor DH. Haplessly hoping: macaque major histocompatibility complex made easy. ILAR J. 2013; 54(2) 196-210. doi:10.1093/ilar/ilt036. PubMed PMID: 24174442. PMCID: PMC3814398.
  • Lauck M, Sibley SD, Hyeroba D et al. Exceptional simian hemorrhagic fever virus diversity in a wild African primate community. J Virol. 2013; 87(1) 688-691. doi:10.1128/JVI.02433-12. PubMed PMID: 23077302. PMCID: PMC3536393.
  • Lauck M, Switzer WM, Sibley SD et al. Discovery and full genome characterization of two highly divergent simian immunodeficiency viruses infecting black-and-white colobus monkeys (Colobus guereza) in Kibale National Park, Uganda. Retrovirology. 2013; 10 107. doi:10.1186/1742-4690-10-107. PubMed PMID: 24139306. PMCID: PMC4016034.
  • Ghai RR, Sibley SD, Lauck M et al. Deep sequencing identifies two genotypes and high viral genetic diversity of human pegivirus (GB virus C) in rural Ugandan patients. J Gen Virol. 2013; 94(Pt 12) 2670-2678. doi:10.1099/vir.0.055509-0. PubMed PMID: 24077364. PMCID: PMC3836497.
  • Del Prete GQ, Scarlotta M, Newman L et al. Comparative characterization of transfection- and infection-derived simian immunodeficiency virus challenge stocks for in vivo nonhuman primate studies. J Virol. 2013; 87(8) 4584-4595. doi:10.1128/JVI.03507-12. PubMed PMID: 23408608. PMCID: PMC3624367.
  • Thurber MI, Ghai RR, Hyeroba D et al. Co-infection and cross-species transmission of divergent Hepatocystis lineages in a wild African primate community. Int J Parasitol. 2013; 43(8) 613-619. doi:10.1016/j.ijpara.2013.03.002. PubMed PMID: 23603520. PMCID: PMC3676718.
  • Greene JM, Lhost JJ, Hines PJ et al. Adoptive transfer of lymphocytes isolated from simian immunodeficiency virus SIVmac239Deltanef-vaccinated macaques does not affect acute-phase viral loads but may reduce chronic-phase viral loads in major histocompatibility complex-matched recipients. J Virol. 2013; 87(13) 7382-7392. doi:10.1128/JVI.00348-13. PubMed PMID: 23616658. PMCID: PMC3700297.
  • Walsh AD, Bimber BN, Das A et al. Acute phase CD8+ T lymphocytes against alternate reading frame epitopes select for rapid viral escape during SIV infection. PLoS One. 2013; 8(5) e61383. doi:10.1371/journal.pone.0061383. PubMed PMID: 23671565. PMCID: PMC3645990.
  • Lauck M, Sibley SD, Lara J et al. A novel hepacivirus with an unusually long and intrinsically disordered NS5A protein in a wild Old World primate. J Virol. 2013; 87(16) 8971-8981. doi:10.1128/JVI.00888-13. PubMed PMID: 23740998. PMCID: PMC3754081.
  • Lank SM, Golbach BA, Creager HM et al. Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing. BMC Genomics. 2012; 13 378. doi:10.1186/1471-2164-13-378. PubMed PMID: 22866951. PMCID: PMC3575390.
  • Budde ML, Greene JM, Chin EN et al. Specific CD8+ T cell responses correlate with control of simian immunodeficiency virus replication in Mauritian cynomolgus macaques. J Virol. 2012; 86(14) 7596-7604. doi:10.1128/JVI.00716-12. PubMed PMID: 22573864. PMCID: PMC3416303.
  • Hughes AL, Becker EA, Lauck M et al. SIV genome-wide pyrosequencing provides a comprehensive and unbiased view of variation within and outside CD8 T lymphocyte epitopes. PLoS One. 2012; 7(10) e47818. doi:10.1371/journal.pone.0047818. PubMed PMID: 23112852. PMCID: PMC3480401.
  • De Groot NG, Otting N, Robinson J et al. Nomenclature report on the major histocompatibility complex genes and alleles of Great Ape, Old and New World monkey species. Immunogenetics. 2012; 64(8) 615-631. doi:10.1007/s00251-012-0617-1. PubMed PMID: 22526602. PMCID: PMC3396756.
  • Dudley DM, Chin EN, Bimber BN et al. Low-cost ultra-wide genotyping using Roche/454 pyrosequencing for surveillance of HIV drug resistance. PLoS One. 2012; 7(5) e36494. doi:10.1371/journal.pone.0036494. PubMed PMID: 22574170. PMCID: PMC3344889.
  • Rout N, Greene J, Yue S et al. Loss of effector and anti-inflammatory natural killer T lymphocyte function in pathogenic simian immunodeficiency virus infection. PLoS Pathog. 2012; 8(9) e1002928. doi:10.1371/journal.ppat.1002928. PubMed PMID: 23028326. PMCID: PMC3447755.
  • Johnson ZP, Eady RD, Ahmad SF et al. Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets. Immunogenetics. 2012; 64(4) 329-336. doi:10.1007/s00251-011-0587-8. PubMed PMID: 22080300. PMCID: PMC3514553.
  • Rasmussen RA, Siddappa NB, Lakhashe SK et al. High-level, lasting antiviral immunity induced by a bimodal AIDS vaccine and boosted by live-virus exposure: prevention of viremia. AIDS. 2012; 26(2) 149-155. doi:10.1097/QAD.0b013e32834d3c4f. PubMed PMID: 21941166. PMCID: PMC3767758.
  • Lang Kuhs KA, Ginsberg AA, Yan J et al. Hepatitis C virus NS3/NS4A DNA vaccine induces multiepitope T cell responses in rhesus macaques mimicking human immune responses [corrected]. Mol Ther. 2012; 20(3) 669-678. doi:10.1038/mt.2011.188. PubMed PMID: 21952169. PMCID: PMC3293616.
  • Mclaren PJ, Ripke S, Pelak K et al. Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans. Hum Mol Genet. 2012; 21(19) 4334-4347. doi:10.1093/hmg/dds226. PubMed PMID: 22718199. PMCID: PMC3441117.
  • Greene JM, Chin EN, Budde ML et al. Ex vivo SIV-specific CD8 T cell responses in heterozygous animals are primarily directed against peptides presented by a single MHC haplotype. PLoS One. 2012; 7(8) e43690. doi:10.1371/journal.pone.0043690. PubMed PMID: 22928016. PMCID: PMC3425510.
  • Mudd PA, Ericsen AJ, Burwitz BJ et al. Escape from CD8(+) T cell responses in Mamu-B*00801(+) macaques differentiates progressors from elite controllers. J Immunol. 2012; 188(7) 3364-3370. doi:10.4049/jimmunol.1102470. PubMed PMID: 22387557. PMCID: PMC3883130.
  • O’Connor SL, Becker EA, Weinfurter JT et al. Conditional CD8+ T cell escape during acute simian immunodeficiency virus infection. J Virol. 2012; 86(1) 605-609. doi:10.1128/JVI.05511-11. PubMed PMID: 22013056. PMCID: PMC3255930.
  • O’Connor SL, Becker EA, Weinfurter JT et al. Conditional CD8+ T cell escape during acute simian immunodeficiency virus infection. J Virol. 2012; 86(1) 605-609. doi:10.1128/JVI.05511-11. PubMed PMID: 22013056. PMCID: PMC3255930.
  • Lauck M, Alvarado-Mora MV, Becker EA et al. Analysis of hepatitis C virus intrahost diversity across the coding region by ultradeep pyrosequencing. J Virol. 2012; 86(7) 3952-3960. doi:10.1128/JVI.06627-11. PubMed PMID: 22278255. PMCID: PMC3302523.
  • Dietrich EA, Brennan G, Ferguson B, Wiseman RW, O’Connor D, Hu SL. Variable prevalence and functional diversity of the antiretroviral restriction factor TRIMCyp in Macaca fascicularis. J Virol. 2011; 85(19) 9956-9963. doi:10.1128/JVI.00097-11. PubMed PMID: 21795330. PMCID: PMC3196437.
  • Budde ML, Lhost JJ, Burwitz BJ et al. Transcriptionally abundant major histocompatibility complex class I alleles are fundamental to nonhuman primate simian immunodeficiency virus-specific CD8+ T cell responses. J Virol. 2011; 85(7) 3250-3261. doi:10.1128/JVI.02355-10. PubMed PMID: 21270169. PMCID: PMC3067831.
  • Reed JS, Sidney J, Piaskowski SM et al. The role of MHC class I allele Mamu-A*07 during SIV(mac)239 infection. Immunogenetics. 2011; 63(12) 789-807. doi:10.1007/s00251-011-0541-9. PubMed PMID: 21732180. PMCID: PMC3706270.
  • Burwitz BJ, Ende Z, Sudolcan B et al. Simian immunodeficiency virus SIVmac239Deltanef vaccination elicits different Tat28-35SL8-specific CD8+ T-cell clonotypes compared to a DNA prime/adenovirus type 5 boost regimen in rhesus macaques. J Virol. 2011; 85(7) 3683-3689. doi:10.1128/JVI.02112-10. PubMed PMID: 21270159. PMCID: PMC3067854.
  • Fernandez CS, Reece JC, Saepuloh U et al. Screening and confirmatory testing of MHC class I alleles in pig-tailed macaques. Immunogenetics. 2011; 63(8) 511-521. doi:10.1007/s00251-011-0529-5. PubMed PMID: 21556859.
  • Burwitz BJ, Sacha JB, Reed JS et al. Pyrosequencing reveals restricted patterns of CD8+ T cell escape-associated compensatory mutations in simian immunodeficiency virus. J Virol. 2011; 85(24) 13088-13096. doi:10.1128/JVI.05650-11. PubMed PMID: 21994463. PMCID: PMC3233179.
  • Lauck M, Hyeroba D, Tumukunde A et al. Novel, divergent simian hemorrhagic fever viruses in a wild Ugandan red colobus monkey discovered using direct pyrosequencing. PLoS One. 2011; 6(4) e19056. doi:10.1371/journal.pone.0019056. PubMed PMID: 21544192. PMCID: PMC3081318.
  • Belisle SE, Yin J, Shedlock DJ et al. Long-term programming of antigen-specific immunity from gene expression signatures in the PBMC of rhesus macaques immunized with an SIV DNA vaccine. PLoS One. 2011; 6 e19681. doi:10.1371/journal.pone.0019681. PubMed PMID: 21701683. PMCID: PMC3119060.
  • Colantonio AD, Bimber BN, Neidermyer WJJ et al. KIR polymorphisms modulate peptide-dependent binding to an MHC class I ligand with a Bw6 motif. PLoS Pathog. 2011; 7(3) e1001316. doi:10.1371/journal.ppat.1001316. PubMed PMID: 21423672. PMCID: PMC3053351.
  • Vojnov L, Martins MA, Almeida JR et al. GagCM9-specific CD8+ T cells expressing limited public TCR clonotypes do not suppress SIV replication in vivo. PLoS One. 2011; 6(8) e23515. doi:10.1371/journal.pone.0023515. PubMed PMID: 21887264. PMCID: PMC3162554.
  • Keskin DB, Reinhold B, Lee SY et al. Direct identification of an HPV-16 tumor antigen from cervical cancer biopsy specimens. Front Immunol. 2011; 2 75. doi:10.3389/fimmu.2011.00075. PubMed PMID: 22566864. PMCID: PMC3342284.
  • Greene JM, Wiseman RW, Lank SM et al. Differential MHC class I expression in distinct leukocyte subsets. BMC Immunol. 2011; 12 39. doi:10.1186/1471-2172-12-39. PubMed PMID: 21762519. PMCID: PMC3155488.
  • Nadazdin O, Boskovic S, Wee SL et al. Contributions of direct and indirect alloresponses to chronic rejection of kidney allografts in nonhuman primates. J Immunol. 2011; 187(9) 4589-4597. doi:10.4049/jimmunol.1003253. PubMed PMID: 21957140. PMCID: PMC3197941.
  • Moreland AJ, Guethlein LA, Reeves RK et al. Characterization of killer immunoglobulin-like receptor genetics and comprehensive genotyping by pyrosequencing in rhesus macaques. BMC Genomics. 2011; 12 295. doi:10.1186/1471-2164-12-295. PubMed PMID: 21645414. PMCID: PMC3125267.
  • Creager HM, Becker EA, Sandman KK et al. Characterization of full-length MHC class II sequences in Indonesian and Vietnamese cynomolgus macaques. Immunogenetics. 2011; 63(9) 611-618. doi:10.1007/s00251-011-0537-5. PubMed PMID: 21614582. PMCID: PMC3156323.
  • Bimber BN, Dudley DM, Lauck M et al. Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing. J Virol. 2010; 84(22) 12087-12092. doi:10.1128/JVI.01378-10. PubMed PMID: 20844037. PMCID: PMC2977871.
  • Bolton DL, Minang JT, Trivett MT et al. Trafficking, persistence, and activation state of adoptively transferred allogeneic and autologous Simian Immunodeficiency Virus-specific CD8(+) T cell clones during acute and chronic infection of rhesus macaques. J Immunol. 2010; 184(1) 303-314. doi:10.4049/jimmunol.0902413. PubMed PMID: 19949089. PMCID: PMC2797565.
  • Pereyra F, Jia X, Mclaren PJ et al. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science. 2010; 330(6010) 1551-1557. doi:10.1126/science.1195271. PubMed PMID: 21051598. PMCID: PMC3235490.
  • Nadazdin O, Boskovic S, Murakami T et al. Phenotype, distribution and alloreactive properties of memory T cells from cynomolgus monkeys. Am J Transplant. 2010; 10(6) 1375-1384. doi:10.1111/j.1600-6143.2010.03119.x. PubMed PMID: 20486921. PMCID: PMC2893326.
  • Nadazdin O, Boskovic S, Murakami T et al. Phenotype, distribution and alloreactive properties of memory T cells from cynomolgus monkeys. Am J Transplant. 2010; 10(6) 1375-1384. doi:10.1111/j.1600-6143.2010.03119.x. PubMed PMID: 20486921. PMCID: PMC2893326.
  • O’Connor SL, Lhost JJ, Becker EA et al. MHC heterozygote advantage in simian immunodeficiency virus-infected Mauritian cynomolgus macaques. Sci Transl Med. 2010; 2(22) 22ra18. doi:10.1126/scitranslmed.3000524. PubMed PMID: 20375000. PMCID: PMC2865159.
  • Berman DM, Willman MA, Han D et al. Mesenchymal stem cells enhance allogeneic islet engraftment in nonhuman primates. Diabetes. 2010; 59(10) 2558-2568. doi:10.2337/db10-0136. PubMed PMID: 20622174. PMCID: PMC3279532.
  • Budde ML, Lhost JJ, Dudley DM, Rakasz EG, O’Connor DH. Integrin alpha4beta7 is downregulated on the surfaces of simian immunodeficiency virus SIVmac239-infected cells. J Virol. 2010; 84(13) 6344-6351. doi:10.1128/JVI.00430-10. PubMed PMID: 20410278. PMCID: PMC2903238.
  • Cafaro A, Bellino S, Titti F et al. Impact of viral dose and major histocompatibility complex class IB haplotype on viral outcome in mauritian cynomolgus monkeys vaccinated with Tat upon challenge with simian/human immunodeficiency virus SHIV89.6P. J Virol. 2010; 84(17) 8953-8958. doi:10.1128/JVI.00377-10. PubMed PMID: 20554774. PMCID: PMC2919029.
  • Greene JM, Lhost JJ, Burwitz BJ et al. Extralymphoid CD8+ T cells resident in tissue from simian immunodeficiency virus SIVmac239{Delta}nef-vaccinated macaques suppress SIVmac239 replication ex vivo. J Virol. 2010; 84(7) 3362-3372. doi:10.1128/JVI.02028-09. PubMed PMID: 20089651. PMCID: PMC2838091.
  • Casimiro DR, Cox K, Tang A et al. Efficacy of multivalent adenovirus-based vaccine against simian immunodeficiency virus challenge. J Virol. 2010; 84(6) 2996-3003. doi:10.1128/JVI.00969-09. PubMed PMID: 20042509. PMCID: PMC2826028.
  • Hughes AL, O’Connor S, Dudley DM, Burwitz BJ, Bimber BN, O’Connor D. Dynamics of haplotype frequency change in a CD8+TL epitope of simian immunodeficiency virus. Infect Genet Evol. 2010; 10(4) 555-560. doi:10.1016/j.meegid.2010.02.001. PubMed PMID: 20149896. PMCID: PMC2863052.
  • Budde ML, Wiseman RW, Karl JA, Hanczaruk B, Simen BB, O’Connor DH. Characterization of Mauritian cynomolgus macaque major histocompatibility complex class I haplotypes by high-resolution pyrosequencing. Immunogenetics. 2010; 62(11-12) 773-780. doi:10.1007/s00251-010-0481-9. PubMed PMID: 20882385. PMCID: PMC3077881.
  • Yamada S, Hatta M, Staker BL et al. Biological and structural characterization of a host-adapting amino acid in influenza virus. PLoS Pathog. 2010; 6(8) e1001034. doi:10.1371/journal.ppat.1001034. PubMed PMID: 20700447. PMCID: PMC2916879.
  • Lank SM, Wiseman RW, Dudley DM, O’Connor DH. A novel single cDNA amplicon pyrosequencing method for high-throughput, cost-effective sequence-based HLA class I genotyping. Hum Immunol. 2010; 71(10) 1011-1017. doi:10.1016/j.humimm.2010.07.012. PubMed PMID: 20650293. PMCID: PMC3191540.
  • Bimber BN, Burwitz BJ, O’Connor S et al. Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques. J Virol. 2009; 83(16) 8247-8253. doi:10.1128/JVI.00897-09. PubMed PMID: 19515775. PMCID: PMC2715741.
  • Kanthaswamy S, Capitanio JP, Dubay CJ et al. Resources for genetic management and genomics research on non-human primates at the National Primate Research Centers (NPRCs). J Med Primatol. 2009; 38 Suppl 1 17-23. doi:10.1111/j.1600-0684.2009.00371.x. PubMed PMID: 19863674.
  • Burwitz BJ, Greene JM, O’Connor DH. Pirate primates in uncharted waters: lymphocyte transfers in unrelated, MHC-matched macaques. Curr HIV Res. 2009; 7(1) 51-56. PubMed PMID: 19149554. PMCID: PMC4509675.
  • Bimber BN, Chugh P, Giorgi EE et al. Nef gene evolution from a single transmitted strain in acute SIV infection. Retrovirology. 2009; 6 57. doi:10.1186/1742-4690-6-57. PubMed PMID: 19505314. PMCID: PMC2701916.
  • Mee ET, Badhan A, Karl JA et al. MHC haplotype frequencies in a UK breeding colony of Mauritian cynomolgus macaques mirror those found in a distinct population from the same geographic origin. J Med Primatol. 2009; 38(1) 1-14. doi:10.1111/j.1600-0684.2008.00299.x. PubMed PMID: 19018947. PMCID: PMC4509677.
  • Burwitz BJ, Pendley CJ, Greene JM et al. Mauritian cynomolgus macaques share two exceptionally common major histocompatibility complex class I alleles that restrict simian immunodeficiency virus-specific CD8+ T cells. J Virol. 2009; 83(12) 6011-6019. doi:10.1128/JVI.00199-09. PubMed PMID: 19339351. PMCID: PMC2687399.
  • Wiseman RW, Karl JA, Bimber BN et al. Major histocompatibility complex genotyping with massively parallel pyrosequencing. Nat Med. 2009; 15(11) 1322-1326. doi:10.1038/nm.2038. PubMed PMID: 19820716. PMCID: PMC2824247.
  • Valentine LE, Loffredo JT, Bean AT et al. Infection with “escaped” virus variants impairs control of simian immunodeficiency virus SIVmac239 replication in Mamu-B*08-positive macaques. J Virol. 2009; 83(22) 11514-11527. doi:10.1128/JVI.01298-09. PubMed PMID: 19726517. PMCID: PMC2772717.
  • O’leary CE, Wiseman RW, Karl JA et al. Identification of novel MHC class I sequences in pig-tailed macaques by amplicon pyrosequencing and full-length cDNA cloning and sequencing. Immunogenetics. 2009; 61(10) 689-701. doi:10.1007/s00251-009-0397-4. PubMed PMID: 19777225. PMCID: PMC2813950.
  • Karl JA, Wiseman RW, O’Connor DH. Cost-effective sequence-based nonhuman primate MHC class I genotyping from RNA. Methods. 2009; 49(1) 11-17. doi:10.1016/j.ymeth.2009.05.002. PubMed PMID: 19442739. PMCID: PMC2732760.
  • Campbell KJ, Detmer AM, Karl JA et al. Characterization of 47 MHC class I sequences in Filipino cynomolgus macaques. Immunogenetics. 2009; 61(3) 177-187. doi:10.1007/s00251-008-0351-x. PubMed PMID: 19107381. PMCID: PMC2666003.
  • Blasky AJ, Karl JA, Wiseman RW, Read DS, O’Connor DH. Rapid high-resolution MHC class I genotyping of Chinese rhesus macaques by capillary reference strand-mediated conformational analysis. Immunogenetics. 2008; 60(10) 575-584. doi:10.1007/s00251-008-0315-1. PubMed PMID: 18629489. PMCID: PMC2561256.
  • Pendley CJ, Becker EA, Karl JA et al. MHC class I characterization of Indonesian cynomolgus macaques. Immunogenetics. 2008; 60(7) 339-351. doi:10.1007/s00251-008-0292-4. PubMed PMID: 18504574. PMCID: PMC2612123.
  • Bimber B, O’Connor DH. KIRigami: the case for studying NK cell receptors in SIV+ macaques. Immunol Res. 2008; 40(3) 235-243. doi:10.1007/s12026-007-8010-0. PubMed PMID: 17989940.
  • Karl JA, Wiseman RW, Campbell KJ et al. Identification of MHC class I sequences in Chinese-origin rhesus macaques. Immunogenetics. 2008; 60(1) 37-46. doi:10.1007/s00251-007-0267-x. PubMed PMID: 18097659. PMCID: PMC2830873.
  • Bimber BN, Moreland AJ, Wiseman RW, Hughes AL, O’Connor DH. Complete characterization of killer Ig-like receptor (KIR) haplotypes in Mauritian cynomolgus macaques: novel insights into nonhuman primate KIR gene content and organization. J Immunol. 2008; 181(9) 6301-6308. PubMed PMID: 18941221. PMCID: PMC2832209.
  • Florese RH, Wiseman RW, Venzon D et al. Comparative study of Tat vaccine regimens in Mauritian cynomolgus and Indian rhesus macaques: influence of Mauritian MHC haplotypes on susceptibility/resistance to SHIV(89.6P) infection. Vaccine. 2008; 26 3312-3321. doi:10.1016/j.vaccine.2008.03.100. PubMed PMID: 18486283. PMCID: PMC2577850.
  • Greene JM, Burwitz BJ, Blasky AJ et al. Allogeneic lymphocytes persist and traffic in feral MHC-matched mauritian cynomolgus macaques. PLoS One. 2008; 3(6) e2384. doi:10.1371/journal.pone.0002384. PubMed PMID: 18545705. PMCID: PMC2408966.
  • Wiseman RW, Wojcechowskyj JA, Greene JM et al. Simian immunodeficiency virus SIVmac239 infection of major histocompatibility complex-identical cynomolgus macaques from Mauritius. J Virol. 2007; 81(1) 349-361. doi:10.1128/JVI.01841-06. PubMed PMID: 17035320. PMCID: PMC1797269.
  • Wojcechowskyj JA, Yant LJ, Wiseman RW, O’Connor SL, O’Connor DH. Control of simian immunodeficiency virus SIVmac239 is not predicted by inheritance of Mamu-B*17-containing haplotypes. J Virol. 2007; 81(1) 406-410. doi:10.1128/JVI.01636-06. PubMed PMID: 17079280. PMCID: PMC1797263.
  • O’Connor SL, Blasky AJ, Pendley CJ et al. Comprehensive characterization of MHC class II haplotypes in Mauritian cynomolgus macaques. Immunogenetics. 2007; 59(6) 449-462. doi:10.1007/s00251-007-0209-7. PubMed PMID: 17384942. PMCID: PMC2836927.
  • O’Connor SL, Blasky AJ, Pendley CJ et al. Comprehensive characterization of MHC class II haplotypes in Mauritian cynomolgus macaques. Immunogenetics. 2007; 59(6) 449-462. doi:10.1007/s00251-007-0209-7. PubMed PMID: 17384942. PMCID: PMC2836927.
  • Wilson NA, Reed J, Napoe GS et al. Vaccine-induced cellular immune responses reduce plasma viral concentrations after repeated low-dose challenge with pathogenic simian immunodeficiency virus SIVmac239. J Virol. 2006; 80(12) 5875-5885. doi:10.1128/JVI.00171-06. PubMed PMID: 16731926. PMCID: PMC1472612.
  • Yant LJ, Friedrich TC, Johnson RC et al. The high-frequency major histocompatibility complex class I allele Mamu-B*17 is associated with control of simian immunodeficiency virus SIVmac239 replication. J Virol. 2006; 80(10) 5074-5077. doi:10.1128/JVI.80.10.5074-5077.2006. PubMed PMID: 16641299. PMCID: PMC1472056.
  • Pratt BF, O’Connor DH, Lafont BA et al. MHC class I allele frequencies in pigtail macaques of diverse origin. Immunogenetics. 2006; 58(12) 995-1001. doi:10.1007/s00251-006-0164-8. PubMed PMID: 17096100.
  • O’Connor DH, Burton DR. Immune responses and HIV: a little order from the chaos. J Exp Med. 2006; 203(3) 501-503. doi:10.1084/jem.20060216. PubMed PMID: 16533889. PMCID: PMC2118239.
  • Hughes AL, Piontkivska H, Krebs KC, O’Connor DH, Watkins DI. Within-host evolution of CD8+-TL epitopes encoded by overlapping and non-overlapping reading frames of simian immunodeficiency virus. Bioinformatics. 2005; 21 Suppl 3 iii39-44. doi:10.1093/bioinformatics/bti1203. PubMed PMID: 16306391.
  • Krebs KC, Jin Z, Rudersdorf R, Hughes AL, O’Connor DH. Unusually high frequency MHC class I alleles in Mauritian origin cynomolgus macaques. J Immunol. 2005; 175(8) 5230-5239. PubMed PMID: 16210628.
  • Smith MZ, Fernandez CS, Chung A et al. The pigtail macaque MHC class I allele Mane-A*10 presents an immundominant SIV Gag epitope: identification, tetramer development and implications of immune escape and reversion. J Med Primatol. 2005; 34(5-6) 282-293. doi:10.1111/j.1600-0684.2005.00126.x. PubMed PMID: 16128923.
  • Loffredo JT, Sidney J, Piaskowski S et al. The high frequency Indian rhesus macaque MHC class I molecule, Mamu-B*01, does not appear to be involved in CD8+ T lymphocyte responses to SIVmac239. J Immunol. 2005; 175(9) 5986-5997. PubMed PMID: 16237093.
  • Fernandez CS, Stratov I, De Rose R et al. Rapid viral escape at an immunodominant simian-human immunodeficiency virus cytotoxic T-lymphocyte epitope exacts a dramatic fitness cost. J Virol. 2005; 79(9) 5721-5731. doi:10.1128/JVI.79.9.5721-5731.2005. PubMed PMID: 15827187. PMCID: PMC1082732.
  • Mcdermott AB, O’Connor DH, Fuenger S et al. Cytotoxic T-lymphocyte escape does not always explain the transient control of simian immunodeficiency virus SIVmac239 viremia in adenovirus-boosted and DNA-primed Mamu-A*01-positive rhesus macaques. J Virol. 2005; 79(24) 15556-15566. doi:10.1128/JVI.79.24.15556-15566.2005. PubMed PMID: 16306626. PMCID: PMC1315992.
  • Casimiro DR, Wang F, Schleif WA et al. Attenuation of simian immunodeficiency virus SIVmac239 infection by prophylactic immunization with dna and recombinant adenoviral vaccine vectors expressing Gag. J Virol. 2005; 79(24) 15547-15555. doi:10.1128/JVI.79.24.15547-15555.2005. PubMed PMID: 16306625. PMCID: PMC1315991.
  • Smith MZ, Dale CJ, De Rose R et al. Analysis of pigtail macaque major histocompatibility complex class I molecules presenting immunodominant simian immunodeficiency virus epitopes. J Virol. 2005; 79(2) 684-695. doi:10.1128/JVI.79.2.684-695.2005. PubMed PMID: 15613296. PMCID: PMC538543.
  • Friedrich TC, Dodds EJ, Yant LJ et al. Reversion of CTL escape-variant immunodeficiency viruses in vivo. Nat Med. 2004; 10(3) 275-281. doi:10.1038/nm998. PubMed PMID: 14966520.
  • Loffredo JT, Sidney J, Wojewoda C et al. Identification of seventeen new simian immunodeficiency virus-derived CD8+ T cell epitopes restricted by the high frequency molecule, Mamu-A*02, and potential escape from CTL recognition. J Immunol. 2004; 173(8) 5064-5076. PubMed PMID: 15470050.
  • Friedrich TC, Frye CA, Yant LJ et al. Extraepitopic compensatory substitutions partially restore fitness to simian immunodeficiency virus variants that escape from an immunodominant cytotoxic-T-lymphocyte response. J Virol. 2004; 78(5) 2581-2585. PubMed PMID: 14963161. PMCID: PMC369222.
  • Matano T, Kobayashi M, Igarashi H et al. Cytotoxic T lymphocyte-based control of simian immunodeficiency virus replication in a preclinical AIDS vaccine trial. J Exp Med. 2004; 199(12) 1709-1718. doi:10.1084/jem.20040432. PubMed PMID: 15210746. PMCID: PMC2212812.
  • Friedrich TC, Mcdermott AB, Reynolds MR et al. Consequences of cytotoxic T-lymphocyte escape: common escape mutations in simian immunodeficiency virus are poorly recognized in naive hosts. J Virol. 2004; 78(18) 10064-10073. doi:10.1128/JVI.78.18.10064-10073.2004. PubMed PMID: 15331739. PMCID: PMC515024.
  • O’Connor DH, Mcdermott AB, Krebs KC et al. A dominant role for CD8+-T-lymphocyte selection in simian immunodeficiency virus sequence variation. J Virol. 2004; 78(24) 14012-14022. doi:10.1128/JVI.78.24.14012-14022.2004. PubMed PMID: 15564508. PMCID: PMC533930.
  • O’Connor DH, Mothe BR, Weinfurter JT et al. Major histocompatibility complex class I alleles associated with slow simian immunodeficiency virus disease progression bind epitopes recognized by dominant acute-phase cytotoxic-T-lymphocyte responses. J Virol. 2003; 77(16) 9029-9040. PubMed PMID: 12885919. PMCID: PMC167227.
  • Allen TM, Mortara L, Mothe BR et al. Tat-vaccinated macaques do not control simian immunodeficiency virus SIVmac239 replication. J Virol. 2002; 76(8) 4108-4112. PubMed PMID: 11907251. PMCID: PMC136098.
  • Altfeld M, Allen TM, Yu XG et al. HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus. Nature. 2002; 420(6914) 434-439. doi:10.1038/nature01200. PubMed PMID: 12459786.
  • Vogel TU, Friedrich TC, O’Connor DH et al. Escape in one of two cytotoxic T-lymphocyte epitopes bound by a high-frequency major histocompatibility complex class I molecule, Mamu-A*02: a paradigm for virus evolution and persistence. J Virol. 2002; 76(22) 11623-11636. PubMed PMID: 12388723. PMCID: PMC136802.
  • Allen TM, Jing P, Calore B et al. Effects of cytotoxic T lymphocytes (CTL) directed against a single simian immunodeficiency virus (SIV) Gag CTL epitope on the course of SIVmac239 infection. J Virol. 2002; 76(20) 10507-10511. PubMed PMID: 12239328. PMCID: PMC136573.
  • Vogel TU, Horton H, Fuller DH et al. Differences between T cell epitopes recognized after immunization and after infection. J Immunol. 2002; 169(8) 4511-4521. PubMed PMID: 12370388.
  • Vogel TU, Horton H, Fuller DH et al. Differences between T cell epitopes recognized after immunization and after infection. J Immunol. 2002; 169(8) 4511-4521. PubMed PMID: 12370388.
  • O’Connor DH, Allen TM, Watkins DI. Cytotoxic T-lymphocyte escape monitoring in simian immunodeficiency virus vaccine challenge studies. DNA Cell Biol. 2002; 21(9) 659-664. doi:10.1089/104454902760330192. PubMed PMID: 12396608.
  • Horton H, Vogel T, O’Connor D, Picker L, Watkins DI. Analysis of the immune response and viral evolution during the acute phase of SIV infection. Vaccine. 2002; 20(15) 1927-1932. PubMed PMID: 11983247.
  • O’Connor DH, Allen TM, Vogel TU et al. Acute phase cytotoxic T lymphocyte escape is a hallmark of simian immunodeficiency virus infection. Nat Med. 2002; 8(5) 493-499. doi:10.1038/nm0502-493. PubMed PMID: 11984594.
  • O’Connor D, Allen T, Watkins DI. Vaccination with CTL epitopes that escape: an alternative approach to HIV vaccine development. Immunol Lett. 2001; 79(1-2) 77-84. PubMed PMID: 11595292.
  • O’Connor D, Friedrich T, Hughes A, Allen TM, Watkins D. Understanding cytotoxic T-lymphocyte escape during simian immunodeficiency virus infection. Immunol Rev. 2001; 183 115-126. PubMed PMID: 11782252.
  • Hughes AL, Westover K, Da Silva J, O’Connor DH, Watkins DI. Simultaneous positive and purifying selection on overlapping reading frames of the tat and vpr genes of simian immunodeficiency virus. J Virol. 2001; 75(17) 7966-7972. PubMed PMID: 11483741. PMCID: PMC115040.
  • Allen TM, Mothe BR, Sidney J et al. CD8(+) lymphocytes from simian immunodeficiency virus-infected rhesus macaques recognize 14 different epitopes bound by the major histocompatibility complex class I molecule mamu-A*01: implications for vaccine design and testing. J Virol. 2001; 75(2) 738-749. doi:10.1128/JVI.75.2.738-749.2001. PubMed PMID: 11134287. PMCID: PMC113970.
  • Allen TM, O’Connor DH, Jing P et al. Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia. Nature. 2000; 407(6802) 386-390. doi:10.1038/35030124. PubMed PMID: 11014195.
  • Evans DT, Jing P, Allen TM et al. Definition of five new simian immunodeficiency virus cytotoxic T-lymphocyte epitopes and their restricting major histocompatibility complex class I molecules: evidence for an influence on disease progression. J Virol. 2000; 74(16) 7400-7410. PubMed PMID: 10906193. PMCID: PMC112260.
  • Evans DT, O’Connor DH, Jing P et al. Virus-specific cytotoxic T-lymphocyte responses select for amino-acid variation in simian immunodeficiency virus Env and Nef. Nat Med. 1999; 5(11) 1270-1276. doi:10.1038/15224. PubMed PMID: 10545993.
  • Vogel TU, Evans DT, Urvater JA, O’Connor DH, Hughes AL, Watkins DI. Major histocompatibility complex class I genes in primates: co-evolution with pathogens. Immunol Rev. 1999; 167 327-337. PubMed PMID: 10319271.
  • O’Connor DH, Watkins DI. Houdini’s box: towards an understanding of AIDS virus escape from the cytotoxic T-lymphocyte response. Immunogenetics. 1999; 50(3-4) 237-241. PubMed PMID: 10602884.