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201. Avian-Type Receptor-Binding Ability Can Increase Influenza Virus Pathogenicity in Macaques

Author

Watanabe, Tokiko, primary, Shinya, Kyoko, additional, Watanabe, Shinji, additional, Imai, Masaki, additional, Hatta, Masato, additional, Li, Chengjun, additional, Wolter, Ben F., additional, Neumann, Gabriele, additional, Hanson, Anthony, additional, Ozawa, Makoto, additional, Yamada, Shinya, additional, Imai, Hirotaka, additional, Sakabe, Saori, additional, Takano, Ryo, additional, Iwatsuki-Horimoto, Kiyoko, additional, Kiso, Maki, additional, Ito, Mutsumi, additional, Fukuyama, Satoshi, additional, Kawakami, Eiryo, additional, Gorai, Takeo, additional, Simmons, Heather A., additional, Schenkman, Daniel, additional, Brunner, Kevin, additional, Capuano, Saverio V., additional, Weinfurter, Jason T., additional, Nishio, Wataru, additional, Maniwa, Yoshimasa, additional, Igarashi, Tatsuhiko, additional, Makino, Akiko, additional, Travanty, Emily A., additional, Wang, Jieru, additional, Kilander, Anette, additional, Dudman, Susanne G., additional, Suresh, M., additional, Mason, Robert J., additional, Hungnes, Olav, additional, Friedrich, Thomas C., additional, and Kawaoka, Yoshihiro, additional

Published
2011
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204. The TRIM5α Genotype of Rhesus Macaques Affects Acquisition of Simian Immunodeficiency Virus SIVsmE660 Infection after Repeated Limiting-Dose Intrarectal Challenge

Author

Reynolds, Matthew R., primary, Sacha, Jonah B., additional, Weiler, Andrea M., additional, Borchardt, Gretta J., additional, Glidden, Chrystal E., additional, Sheppard, Neil C., additional, Norante, Francesca A., additional, Castrovinci, Philip A., additional, Harris, Jacqueline J., additional, Robertson, Henry T., additional, Friedrich, Thomas C., additional, McDermott, Adrian B., additional, Wilson, Nancy A., additional, Allison, David B., additional, Koff, Wayne C., additional, Johnson, Welkin E., additional, and Watkins, David I., additional

Published
2011
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206. Macaque Long-Term Nonprogressors Resist Superinfection with Multiple CD8 + T Cell Escape Variants of Simian Immunodeficiency Virus

Author

Weinfurter, Jason T., primary, May, Gemma E., additional, Soma, Taeko, additional, Hessell, Ann J., additional, León, Enrique J., additional, MacNair, Caitlin E., additional, Piaskowski, Shari M., additional, Weisgrau, Kim, additional, Furlott, Jessica, additional, Maness, Nicholas J., additional, Reed, Jason, additional, Wilson, Nancy A., additional, Rakasz, Eva G., additional, Burton, Dennis R., additional, and Friedrich, Thomas C., additional

Published
2011
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208. High Viremia Is Associated with High Levels of In Vivo Major Histocompatibility Complex Class I Downregulation in Rhesus Macaques Infected with Simian Immunodeficiency Virus SIVmac239

Author

Friedrich, Thomas C., primary, Piaskowski, Shari M., additional, León, Enrique J., additional, Furlott, Jessica R., additional, Maness, Nicholas J., additional, Weisgrau, Kimberly L., additional, Mac Nair, Caitlin E., additional, Weiler, Andrea M., additional, Loffredo, John T., additional, Reynolds, Matthew R., additional, Williams, K. Y., additional, Klimentidis, Yann C., additional, Wilson, Nancy A., additional, Allison, David B., additional, and Rakasz, Eva G., additional

Published
2010
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209. Extralymphoid CD8 + T Cells Resident in Tissue from Simian Immunodeficiency Virus SIVmac239Δnef-Vaccinated Macaques Suppress SIVmac239 Replication Ex Vivo

Author

Greene, Justin M., primary, Lhost, Jennifer J., additional, Burwitz, Benjamin J., additional, Budde, Melisa L., additional, Macnair, Caitlin E., additional, Weiker, Madelyn K., additional, Gostick, Emma, additional, Friedrich, Thomas C., additional, Broman, Karl W., additional, Price, David A., additional, O'Connor, Shelby L., additional, and O'Connor, David H., additional

Published
2010
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210. MHC Heterozygote Advantage in Simian Immunodeficiency Virus–Infected Mauritian Cynomolgus Macaques

Author

O’Connor, Shelby L., primary, Lhost, Jennifer J., additional, Becker, Ericka A., additional, Detmer, Ann M., additional, Johnson, Randall C., additional, MacNair, Caitlin E., additional, Wiseman, Roger W., additional, Karl, Julie A., additional, Greene, Justin M., additional, Burwitz, Benjamin J., additional, Bimber, Benjamin N., additional, Lank, Simon M., additional, Tuscher, Jennifer J., additional, Mee, Edward T., additional, Rose, Nicola J., additional, Desrosiers, Ronald C., additional, Hughes, Austin L., additional, Friedrich, Thomas C., additional, Carrington, Mary, additional, and O’Connor, David H., additional

Published
2010
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211. Infection with “Escaped” Virus Variants Impairs Control of Simian Immunodeficiency Virus SIVmac239 Replication in Mamu-B*08 -Positive Macaques

Author

Valentine, Laura E., primary, Loffredo, John T., additional, Bean, Alex T., additional, León, Enrique J., additional, MacNair, Caitlin E., additional, Beal, Dominic R., additional, Piaskowski, Shari M., additional, Klimentidis, Yann C., additional, Lank, Simon M., additional, Wiseman, Roger W., additional, Weinfurter, Jason T., additional, May, Gemma E., additional, Rakasz, Eva G., additional, Wilson, Nancy A., additional, Friedrich, Thomas C., additional, O'Connor, David H., additional, Allison, David B., additional, and Watkins, David I., additional

Published
2009
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212. Vaccine-Induced Cellular Responses Control Simian Immunodeficiency Virus Replication after Heterologous Challenge

Author

Wilson, Nancy A., primary, Keele, Brandon F., additional, Reed, Jason S., additional, Piaskowski, Shari M., additional, MacNair, Caitlin E., additional, Bett, Andrew J., additional, Liang, Xiaoping, additional, Wang, Fubao, additional, Thoryk, Elizabeth, additional, Heidecker, Gwendolyn J., additional, Citron, Michael P., additional, Huang, Lingyi, additional, Lin, Jing, additional, Vitelli, Salvatore, additional, Ahn, Chanook D., additional, Kaizu, Masahiko, additional, Maness, Nicholas J., additional, Reynolds, Matthew R., additional, Friedrich, Thomas C., additional, Loffredo, John T., additional, Rakasz, Eva G., additional, Erickson, Stephen, additional, Allison, David B., additional, Piatak, Michael, additional, Lifson, Jeffrey D., additional, Shiver, John W., additional, Casimiro, Danilo R., additional, Shaw, George M., additional, Hahn, Beatrice H., additional, and Watkins, David I., additional

Published
2009
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213. Gag- and Nef-specific CD4+T cells recognize and inhibit SIV replication in infected macrophages early after infection

Author

Sacha, Jonah B., primary, Giraldo-Vela, Juan P., additional, Buechler, Matthew B., additional, Martins, Mauricio A., additional, Maness, Nicholas J., additional, Chung, Chungwon, additional, Wallace, Lyle T., additional, León, Enrique J., additional, Friedrich, Thomas C., additional, Wilson, Nancy A., additional, Hiraoka, Atsunobu, additional, and Watkins, David I., additional

Published
2009
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214. Macaques vaccinated with live-attenuated SIV control replication of heterologous virus

Author

Reynolds, Matthew R., primary, Weiler, Andrea M., additional, Weisgrau, Kim L., additional, Piaskowski, Shari M., additional, Furlott, Jessica R., additional, Weinfurter, Jason T., additional, Kaizu, Masahiko, additional, Soma, Taeko, additional, León, Enrique J., additional, MacNair, Caitlin, additional, Leaman, Dan P., additional, Zwick, Michael B., additional, Gostick, Emma, additional, Musani, Solomon K., additional, Price, David A., additional, Friedrich, Thomas C., additional, Rakasz, Eva G., additional, Wilson, Nancy A., additional, McDermott, Adrian B., additional, Boyle, Rosanne, additional, Allison, David B., additional, Burton, Dennis R., additional, Koff, Wayne C., additional, and Watkins, David I., additional

Published
2008
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215. Differential Antigen Presentation Kinetics of CD8 + T-Cell Epitopes Derived from the Same Viral Protein

Author

Sacha, Jonah B., primary, Reynolds, Matthew R., additional, Buechler, Matthew B., additional, Chung, Chungwon, additional, Jonas, Anna K., additional, Wallace, Lyle T., additional, Weiler, Andrea M., additional, Lee, Wonhee, additional, Piaskowski, Shari M., additional, Soma, Taeko, additional, Friedrich, Thomas C., additional, Wilson, Nancy A., additional, and Watkins, David I., additional

Published
2008
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216. Comprehensive Immunological Evaluation Reveals Surprisingly Few Differences between Elite Controller and Progressor Mamu-B*17 -Positive Simian Immunodeficiency Virus-Infected Rhesus Macaques

Author

Maness, Nicholas J., primary, Yant, Levi J., additional, Chung, Chungwon, additional, Loffredo, John T., additional, Friedrich, Thomas C., additional, Piaskowski, Shari M., additional, Furlott, Jessica, additional, May, Gemma E., additional, Soma, Taeko, additional, León, Enrique J., additional, Wilson, Nancy A., additional, Piontkivska, Helen, additional, Hughes, Austin L., additional, Sidney, John, additional, Sette, Alessandro, additional, and Watkins, David I., additional

Published
2008
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219. Patterns of CD8+Immunodominance May Influence the Ability ofMamu-B*08-Positive Macaques To Naturally Control Simian Immunodeficiency Virus SIVmac239 Replication

Author

Loffredo, John T., primary, Bean, Alex T., additional, Beal, Dominic R., additional, León, Enrique J., additional, May, Gemma E., additional, Piaskowski, Shari M., additional, Furlott, Jessica R., additional, Reed, Jason, additional, Musani, Solomon K., additional, Rakasz, Eva G., additional, Friedrich, Thomas C., additional, Wilson, Nancy A., additional, Allison, David B., additional, and Watkins, David I., additional

Published
2008
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220. CD8+ T Cells from SIV Elite Controller Macaques Recognize Mamu-B*08-Bound Epitopes and Select for Widespread Viral Variation

Author

Loffredo, John T., primary, Friedrich, Thomas C., additional, León, Enrique J., additional, Stephany, Jason J., additional, Rodrigues, Denise S., additional, Spencer, Sean P., additional, Bean, Alex T., additional, Beal, Dominic R., additional, Burwitz, Benjamin J., additional, Rudersdorf, Richard A., additional, Wallace, Lyle T., additional, Piaskowski, Shari M., additional, May, Gemma E., additional, Sidney, John, additional, Gostick, Emma, additional, Wilson, Nancy A., additional, Price, David A., additional, Kallas, Esper G., additional, Piontkivska, Helen, additional, Hughes, Austin L., additional, Sette, Alessandro, additional, and Watkins, David I., additional

Published
2007
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221. Pol-Specific CD8 + T Cells Recognize Simian Immunodeficiency Virus-Infected Cells Prior to Nef-Mediated Major Histocompatibility Complex Class I Downregulation

Author

Sacha, Jonah B., primary, Chung, Chungwon, additional, Reed, Jason, additional, Jonas, Anna K., additional, Bean, Alexander T., additional, Spencer, Sean P., additional, Lee, Wonhee, additional, Vojnov, Lara, additional, Rudersdorf, Richard, additional, Friedrich, Thomas C., additional, Wilson, Nancy A., additional, Lifson, Jeffrey D., additional, and Watkins, David I., additional

Published
2007
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222. AIDS virus–specific CD8+ T lymphocytes against an immunodominant cryptic epitope select for viral escape

Author

Maness, Nicholas J., primary, Valentine, Laura E., additional, May, Gemma E., additional, Reed, Jason, additional, Piaskowski, Shari M., additional, Soma, Taeko, additional, Furlott, Jessica, additional, Rakasz, Eva G., additional, Friedrich, Thomas C., additional, Price, David A., additional, Gostick, Emma, additional, Hughes, Austin L., additional, Sidney, John, additional, Sette, Alessandro, additional, Wilson, Nancy A., additional, and Watkins, David I., additional

Published
2007
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223. Subdominant CD8+T-Cell Responses Are Involved in Durable Control of AIDS Virus Replication

Author

Friedrich, Thomas C., primary, Valentine, Laura E., additional, Yant, Levi J., additional, Rakasz, Eva G., additional, Piaskowski, Shari M., additional, Furlott, Jessica R., additional, Weisgrau, Kimberly L., additional, Burwitz, Benjamin, additional, May, Gemma E., additional, León, Enrique J., additional, Soma, Taeko, additional, Napoe, Gnankang, additional, Capuano, Saverio V., additional, Wilson, Nancy A., additional, and Watkins, David I., additional

Published
2007
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224. The Antiviral Efficacy of Simian Immunodeficiency Virus-Specific CD8 + T Cells Is Unrelated to Epitope Specificity and Is Abrogated by Viral Escape

Author

Loffredo, John T., primary, Burwitz, Benjamin J., additional, Rakasz, Eva G., additional, Spencer, Sean P., additional, Stephany, Jason J., additional, Giraldo Vela, Juan Pablo, additional, Martin, Sarah R., additional, Reed, Jason, additional, Piaskowski, Shari M., additional, Furlott, Jessica, additional, Weisgrau, Kim L., additional, Rodrigues, Denise S., additional, Soma, Taeko, additional, Napoé, Gnankang, additional, Friedrich, Thomas C., additional, Wilson, Nancy A., additional, Kallas, Esper G., additional, and Watkins, David I., additional

Published
2007
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225. Gag-Specific CD8+ T Lymphocytes Recognize Infected Cells before AIDS-Virus Integration and Viral Protein Expression

Author

Sacha, Jonah B., primary, Chung, Chungwon, additional, Rakasz, Eva G., additional, Spencer, Sean P., additional, Jonas, Anna K., additional, Bean, Alexander T., additional, Lee, Wonhee, additional, Burwitz, Benjamin J., additional, Stephany, Jason J., additional, Loffredo, John T., additional, Allison, David B., additional, Adnan, Sama, additional, Hoji, Akihiko, additional, Wilson, Nancy A., additional, Friedrich, Thomas C., additional, Lifson, Jeffrey D., additional, Yang, Otto O., additional, and Watkins, David I., additional

Published
2007
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228. The High-Frequency Major Histocompatibility Complex (MHC) Class I Allele Mamu-B*17 Is Associated with Control of Simian Immunodeficiency Virus SIVmac239 Replication

Author

Yant, Levi J., primary, Friedrich, Thomas C., additional, Johnson, Randall C., additional, May, Gemma E., additional, Maness, Nicholas J., additional, Enz, Alissa M., additional, Lifson, Jeffrey D., additional, O'Connor, David H., additional, Carrington, Mary, additional, and Watkins, David I., additional

Published
2006
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229. Vaccine-Induced Cellular Immune Responses Reduce Plasma Viral Concentrations after Repeated Low-Dose Challenge with Pathogenic Simian Immunodeficiency Virus SIVmac239

Author

Wilson, Nancy A., primary, Reed, Jason, additional, Napoe, Gnankang S., additional, Piaskowski, Shari, additional, Szymanski, Andy, additional, Furlott, Jessica, additional, Gonzalez, Edna J., additional, Yant, Levi J., additional, Maness, Nicholas J., additional, May, Gemma E., additional, Soma, Taeko, additional, Reynolds, Matthew R., additional, Rakasz, Eva, additional, Rudersdorf, Richard, additional, McDermott, Adrian B., additional, O'Connor, David H., additional, Friedrich, Thomas C., additional, Allison, David B., additional, Patki, Amit, additional, Picker, Louis J., additional, Burton, Dennis R., additional, Lin, Jing, additional, Huang, Lingyi, additional, Patel, Deepa, additional, Heindecker, Gwendolyn, additional, Fan, Jiang, additional, Citron, Michael, additional, Horton, Melanie, additional, Wang, Fubao, additional, Liang, Xiaoping, additional, Shiver, John W., additional, Casimiro, Danilo R., additional, and Watkins, David I., additional

Published
2006
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230. The High-Frequency Major Histocompatibility Complex Class I Allele Mamu-B*17 Is Associated with Control of Simian Immunodeficiency Virus SIVmac239 Replication

Author

Yant, Levi J., primary, Friedrich, Thomas C., additional, Johnson, Randall C., additional, May, Gemma E., additional, Maness, Nicholas J., additional, Enz, Alissa M., additional, Lifson, Jeffrey D., additional, O'Connor, David H., additional, Carrington, Mary, additional, and Watkins, David I., additional

Published
2006
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231. Consequences of Cytotoxic T-Lymphocyte Escape: Common Escape Mutations in Simian Immunodeficiency Virus Are Poorly Recognized in Naïve Hosts

Author

Friedrich, Thomas C., primary, McDermott, Adrian B., additional, Reynolds, Matthew R., additional, Piaskowski, Shari, additional, Fuenger, Sarah, additional, de Souza, Ivna P., additional, Rudersdorf, Richard, additional, Cullen, Candice, additional, Yant, Levi J., additional, Vojnov, Lara, additional, Stephany, Jason, additional, Martin, Sarah, additional, O'Connor, David H., additional, Wilson, Nancy, additional, and Watkins, David I., additional

Published
2004
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232. Extraepitopic Compensatory Substitutions Partially Restore Fitness to Simian Immunodeficiency Virus Variants That Escape from an Immunodominant Cytotoxic-T-Lymphocyte Response

Author

Friedrich, Thomas C., primary, Frye, Christopher A., additional, Yant, Levi J., additional, O'Connor, David H., additional, Kriewaldt, Nancy A., additional, Benson, Meghan, additional, Vojnov, Lara, additional, Dodds, Elizabeth J., additional, Cullen, Candice, additional, Rudersdorf, Richard, additional, Hughes, Austin L., additional, Wilson, Nancy, additional, and Watkins, David I., additional

Published
2004
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233. 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?

Author

Vogel, Thorsten U., primary, Friedrich, Thomas C., additional, O'Connor, David H., additional, Rehrauer, William, additional, Dodds, Elizabeth J., additional, Hickman, Heather, additional, Hildebrand, William, additional, Sidney, John, additional, Sette, Alessandro, additional, Hughes, Austin, additional, Horton, Helen, additional, Vielhuber, Kathy, additional, Rudersdorf, Richard, additional, de Souza, Ivna P., additional, Reynolds, Matthew R., additional, Allen, Todd M., additional, Wilson, Nancy, additional, and Watkins, David I., additional

Published
2002
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235. Influenza Vaccination Is Not Associated With Detection of Noninfluenza Respiratory Viruses in Seasonal Studies of Influenza Vaccine Effectiveness.

Author

Sundaram, Maria E., McClure, David L., VanWormer, Jeffrey J., Friedrich, Thomas C., Meece, Jennifer K., and Belongia, Edward A.

Subjects
VACCINATION complications, INFLUENZA vaccines, RESPIRATORY diseases, REVERSE transcriptase polymerase chain reaction, VIRUS diseases
Abstract

Influenza vaccination was not associated with detection of noninfluenza respiratory viruses in young children or older adults with acute respiratory illness. Use of influenza-negative controls did not generate a biased estimate of vaccine effectiveness due to an effect of vaccination on other respiratory virus infections.Background. The test-negative control study design is the basis for observational studies of influenza vaccine effectiveness (VE). Recent studies have suggested that influenza vaccination increases the risk of noninfluenza respiratory virus infection. Such an effect could create bias in VE studies using influenza-negative controls. We investigated the association between influenza infection, vaccination, and detection of other respiratory viruses among children <5 years old and adults ≥50 years old with acute respiratory illness who participated in seasonal studies of influenza vaccine effectiveness.Methods. Nasal/nasopharyngeal samples collected from 2004–2005 through 2009–2010 were tested for 19 respiratory virus targets using a multiplex reverse-transcription polymerase chain reaction (RT-PCR) platform. Vaccination status was determined using a validated registry. Adjusted odds ratios for influenza and vaccination status were calculated using three different control groups: influenza-negative, other respiratory virus positive, and pan-negative.Results. Influenza was detected in 12% of 2010 children and 20% of 1738 adults. Noninfluenza respiratory viruses were detected in 70% of children and 38% of adults without influenza. The proportion vaccinated did not vary between virus-positive controls and pan-negative controls in children (P = .62) or adults (P = .33). Influenza infection was associated with reduced odds of vaccination, but adjusted odds ratios differed by no more than 0.02 when the analysis used influenza-negative or virus-positive controls.Conclusions. Influenza vaccination was not associated with detection of noninfluenza respiratory viruses. Use of influenza-negative controls did not generate a biased estimate of vaccine effectiveness due to an effect of vaccination on other respiratory virus infections. [ABSTRACT FROM PUBLISHER]

Published
2013
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236. An outbreak of the 2009 influenza a (H1N1) virus in a children's hospital.

Author

Bearden, Allison, Friedrich, Thomas C., Goldberg, Tony L., Byrne, Barbara, Spiegel, Carol, Schult, Peter, and Safdar, Nasia

Subjects
*H1N1 influenza, *DISEASE outbreaks, *CHILDREN'S hospitals, *INFLUENZA transmission, *HEMATOLOGY, *POLYMERASE chain reaction
Abstract

Please cite this paper as: Bearden et al. (2012) An outbreak of the 2009 influenza a (H1N1) virus in a children's hospital. Influenza and Other Respiratory Viruses 6(5), 374-379. Context Preventing nosocomial transmission of influenza is essential to reduce the morbidity and mortality associated with this infection. In October 2009, an outbreak of the 2009 influenza A (H1N1) virus occurred in a hematology ward of a children's hospital over a 21-day period and involved two patients and four healthcare workers. Objective To investigate nosocomial transmission of the 2009 influenza A (H1N1) virus in patients and healthcare workers. Design, setting, and participants An outbreak investigation was initiated in response to suspected nosocomial transmission of the 2009 influenza A (H1N1) virus during the peak of the 2009 pandemic. Cases were confirmed using a polymerase chain reaction (PCR) test specific for the 2009 H1N1 influenza A virus. Viruses isolated from nasopharyngeal swabs were genetically characterized using Sanger sequencing of uncloned 'bulk' PCR products. Main outcome measures Virus sequencing to investigate nosocomial transmission. Results Two immunocompromised patients and four healthcare workers were found to be part of a nosocomial outbreak of the 2009 influenza A (H1N1) virus. One immunocompromised patient had a second episode of clinical influenza infection after isolation precautions had been discontinued, resulting in additional exposures. Strain-specific PCR showed that all cases were caused by infection of the 2009 H1N1 virus. Sequencing of viral genes encoding hemagglutinin and polymerase basic subunit 2 (PB2) revealed that all viruses isolated were genetically identical at these loci, including the two episodes occurring in the same immunocompromised patient. Conclusions Prompt institution of isolation precautions is essential in preventing nosocomial outbreaks of the 2009 novel influenza A (H1N1) virus. Our data suggest that isolation precautions may need to be continued for a prolonged period of time in immunocompromised patients with influenza infection. [ABSTRACT FROM AUTHOR]

Published
2012
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237. Experimental Analysis of Sources of Error in Evolutionary Studies Based on Roche/454 Pyrosequencing of Viral Genomes.

Author

Becker, Ericka A., Burns, Charles M., León, Enrique J., Rajabojan, Saravanan, Friedman, Robert, Friedrich, Thomas C., O'Connor, Shelby L., and Hughes, Austin L.

Subjects
PYROSEQUENCING, VIRAL genomes, SIMIAN immunodeficiency virus, NUCLEOTIDE sequence, NUCLEOTIDE separation
Abstract

Factors affecting the reliability of Roche/454 pyrosequencing for analyzing sequence polymorphism in within-host viral populations were assessed by two experiments: 1) sequencing four clonal simian immunodeficiency virus (SIV) stocks and 2) sequencing mixtures in different proportions of two SIV strains with known fixed nucleotide differences. Observed nucleotide diversity and frequency of undetermined nucleotides were increased at sites in homopolymer runs of four or more identical nucleotides, particularly at AT sites. However, in the mixed-strain experiments, the effects on estimated nucleotide diversity of such errors were small in comparison to known strain differences. The results suggest that biologically meaningful variants present at a frequency of around 10% and possibly much lower are easily distinguished from artifacts of the sequencing process. Analysis of the clonal stocks revealed numerous rare variants that showed the signature of purifying selection and that elimination of variants at frequencies of less than 1% reduced estimates of nucleotide diversity by about an order of magnitude. Thus, using a 1% frequency cutoff for accepting a variant as real represents a conservative standard, which may be useful in studies that are focused on the discovery of specific mutations (such as those conferring immune escape or drug resistance). On the other hand, if the goal is to estimate nucleotide diversity, an optimal strategy might be to include all observed variants (even those at less than 1% frequency), while masking out homopolymer runs of four or more nucleotides. [ABSTRACT FROM AUTHOR]

Published
2012
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238. #20: Modeling Zika virus tissue tropism in rhesus macaques to define the risk of donor derived transmission

Author

Treadway, Taylor A, Shepherd, Phoenix M, Newman, Christina M, Mohr, Emma L, Dudley, Dawn M, Breitbach, Meghan E, Yamamoto, Keisuke, Stewart, Laurel M, Koenig, Michelle R, Bliss, Mason, Rybarczyk, Sierra L, Weiler, Andrea M, Semler, Matthew R, Mitzey, Ann, Razo, Elaina, Schotzko, Michele, Peterson, Eric, Simmons, Heather A, Mejia, Andres, Golos, Thaddeus G, Friedrich, Thomas C, and O’Connor, David H

Published
2021
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239. MHC Heterozygote Advantage in Simian Immunodeficiency Virus-Infected Mauritian Cynomolgus Macaques.

Author

O'Connor, Shelby L., Lhost, Jennifer J., Becker, Ericka A., Detmer, Ann M., Johnson, Randall C., MacNair, Caitlin E., Wiseman, Roger W., Karl, Julie A., Greene, Justin M., Burwitz, Benjamin J., Bimber, Benjamin N., Lank, Simon M., Tuscher, Jennifer J., Mee, Edward T., Rose, Nicola J., Desrosiers, Ronald C., Hughes, Austin L., Friedrich, Thomas C., Carrington, Mary, and O'Connor, David H.

Published
2010
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240. Naturally Circulating Hepatitis A Virus in Olive Baboons, Uganda.

Author

Bennett, Andrew J., Sibley, Samuel D., Lauck, Michael, Weny, Geoffrey, Hyeroba, David, Tumukunde, Alex, Friedrich, Thomas C., O'Connor, David H., Johnson, Caley A., Rothman, Jessica M., and Goldberg, Tony L.

Subjects
HEPATITIS A virus, OLIVE baboon, HEPATITIS viruses, NUCLEOTIDE sequencing, VIRAL shedding, KIBALE National Park (Uganda), DISEASES
Abstract

The article discusses a study which examined hepatitis A virus (HAV) on olive baboons from Kibale National Park in Uganda. The study identified the virus by next-generations sequencing HAV in the animal's blood. It also examined a paired fecal sample of olive babbons to determine evidence of viral shedding.

Published
2016
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241. Gag- and Nef-specific CD4+ T cells recognize and inhibit SIV replication in infected macrophages early after infection.

Author

Sacha, Jonah B., GiraIdo-Vela, Juan P., Buechler, Matthew B., Martins, Mauricio A., Maness, Nicholas J., Chungwon Chung, Wallace, Lyle T., León, Enrique J., Friedrich, Thomas C., Wilson, Nancy A., Hiraoka, Atsunobu, and Watkins, David I.

Subjects
T cells, MACROPHAGES, RETROVIRUS diseases, IMMUNE response, EXPERIMENTAL design, EPITOPES
Abstract

The precise immunological role played by CD4+ T cells in retroviral infections is poorly defined. Here, we describe a new function of these cells, the elimination of retrovirus-infected macrophages. After experimental CD8+ cell depletion, elite controlling macaques with set-point viral loads ≤500 viral RNA copies/mL mounted robust Gag-and Nef-specific CD4+ T cell responses during reestablishment of control with ≥54% of all virus-specific CD4+ T cells targeting these 2 proteins. Ex vivo, these simian immunodeficiency virus (SIV)-specific CD4+ T cells neither recognized nor suppressed viral replication in SIV-infected CD4+ T cells. In contrast, they recognized SIV-infected macrophages as early as 2 h postinfection because of presentation of epitopes derived from virion-associated Gag and Nef proteins. Furthermore, virus-specific CD4+ T cells displayed direct effector function and eliminated SIV-infected macrophages. These results suggest that retrovirus-specific CD4+ T cells may contribute directly to elite control by inhibiting viral replication in macrophages. [ABSTRACT FROM AUTHOR]

Published
2009
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242. Repeated Intravaginal Inoculation with Cell-Associated Simian Immunodeficiency Virus Results in Persistent Infection of Nonhuman Primates.

Author

Kaizu, Masahiko, Weiler, Andrea M., Weisgrau, Kim L., Vielhuber, Kathleen A., May, Gemma, Piaskowski, Shari M., Furlott, Jessica, Maness, Nicholas J., Friedrich, Thomas C., Loffredo, John T., Usborne, Amy, and Rakasz, Eva G.

Subjects
HIV infections, INFECTIOUS disease transmission, CHEMOPREVENTION, VIRAL vaccines, KRA, PRIMATES
Abstract

The goal of the present study was to develop a nonhuman primate model of intravaginal human immunodeficiency virus (HIV) transmission with cell-associated virus. Reproductively mature, cycling cynomolgus macaques with or without chemically induced, transient ulcers of the lower female reproductive tract repeatedly received challenge with a variable amount of in vitro simian immunodeficiency virus mac239-infected peripheral blood mononuclear cells. Persistent viremia was established with surprisingly few infectious lymphocytes containing physiologically relevant quantities of cell-associated virus. This model will be indispensable for the testing of vaccines and topical agents that are aimed toward the prevention of heterosexual transmission of HIV. [ABSTRACT FROM AUTHOR]

Published
2006
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243. Reversion of CTL escape-variant immunodeficiency viruses in vivo.

Author

Friedrich, Thomas C., Dodds, Elizabeth J., Yant, Levi J., Vojnov, Lara, Rudersdorf, Richard, Cullen, Candice, Evans, David T., Desrosiers, Ronald C., Mothé, Bianca R., Sidney, John, Sette, Alessandro, Kunstman, Kevin, Wolinsky, Steven, Piatak, Michael, Lifson, Jeffrey, Hughes, Austin L., Wilson, Nancy, O'Connor, David H., and Watkins, David I.

Subjects
*T cells, *ANTINEOPLASTIC agents, *LYMPHOCYTES, *CELL-mediated lympholysis, *HIV, *IMMUNODEFICIENCY
Abstract

Engendering cytotoxic T-lymphocyte (CTL) responses is likely to be an important goal of HIV vaccines. However, CTLs select for viral variants that escape immune detection. Maintenance of such escape variants in human populations could pose an obstacle to HIV vaccine development. We first observed that escape mutations in a heterogeneous simian immunodeficiency virus (SIV) isolate were lost upon passage to new animals. We therefore infected macaques with a cloned SIV bearing escape mutations in three immunodominant CTL epitopes, and followed viral evolution after infection. Here we show that each mutant epitope sequence continued to evolve in vivo, often re-establishing the original, CTL-susceptible sequence. We conclude that escape from CTL responses may exact a cost to viral fitness. In the absence of selective pressure upon transmission to new hosts, these original escape mutations can be lost. This suggests that some HIV CTL epitopes will be maintained in human populations. [ABSTRACT FROM AUTHOR]

Published
2004
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244. Characterization of the SARS-CoV-2 B.1.621 (Mu) variant

Author

Halfmann, Peter J., Kuroda, Makoto, Armbrust, Tammy, Theiler, James, Balaram, Ariane, Moreno, Gage K., Accola, Molly A., Iwatsuki-Horimoto, Kiyoko, Valdez, Riccardo, Stoneman, Emily, Braun, Katarina, Yamayoshi, Seiya, Somsen, Elizabeth, Baczenas, John J., Mitamura, Keiko, Hagihara, Masao, Adachi, Eisuke, Koga, Michiko, McLaughlin, Matthew, Rehrauer, William, Imai, Masaki, Yamamoto, Shinya, Tsutsumi, Takeya, Saito, Makoto, Friedrich, Thomas C., O’Connor, Shelby L., O’Connor, David H., Gordon, Aubree, Korber, Bette, and Kawaoka, Yoshihiro

Abstract

The SARS-CoV-2 B.1.621 (Mu) variant emerged in January 2021 and was categorized as a variant of interest by the World Health Organization in August 2021. This designation prompted us to study the sensitivity of this variant to antibody neutralization. In a live virus neutralization assay with serum samples from individuals vaccinated with the Pfizer/BioNTech or Moderna mRNA vaccines, we measured neutralization antibody titers against B.1.621, an early isolate (spike 614D), and a variant of concern (B.1.351, beta variant). We observed reduced neutralizing antibody titers against the B.1.621 variant (3.4 to 7-fold reduction, depending on the serum sample and time after the second vaccination) compared to the early isolate and a similar reduction when compared to B.1.351. Likewise, convalescent serum from hamsters previously infected with an early isolate neutralized B.1.621 to a lower degree. Despite this antibody titer reduction, hamsters could not be efficiently re-challenged with the B.1.621 variant, suggesting the immune response to the first infection is adequate to provide protection against a subsequent infection with the B.1.621 variant.

Published
2022
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245. Persistent SARS-CoV-2 infection: significance and implications.

Author

Machkovech, Heather M, Hahn, Anne M, Garonzik Wang, Jacqueline, Grubaugh, Nathan D, Halfmann, Peter J, Johnson, Marc C, Lemieux, Jacob E, O'Connor, David H, Piantadosi, Anne, Wei, Wanting, and Friedrich, Thomas C

Subjects
*SARS-CoV-2, *VIRAL replication, *IMMUNOCOMPROMISED patients, *HERD immunity, *INFECTION
Abstract

SARS-CoV-2 causes persistent infections in a subset of individuals, which is a major clinical and public health problem that should be prioritised for further investigation for several reasons. First, persistent SARS-CoV-2 infection often goes unrecognised, and therefore might affect a substantial number of people, particularly immunocompromised individuals. Second, the formation of tissue reservoirs (including in non-respiratory tissues) might underlie the pathophysiology of the persistent SARS-CoV-2 infection and require new strategies for diagnosis and treatment. Finally, persistent SARS-CoV-2 replication, particularly in the setting of suboptimal immune responses, is a possible source of new, divergent virus variants that escape pre-existing immunity on the individual and population levels. Defining optimal diagnostic and treatment strategies for patients with persistent virus replication and monitoring viral evolution are therefore urgent medical and public health priorities. [ABSTRACT FROM AUTHOR]

Published
2024
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246. Development and Characterization of a cDNA-Launch Recombinant Simian Hemorrhagic Fever Virus Expressing Enhanced Green Fluorescent Protein: ORF 2b' Is Not Required for In Vitro Virus Replication.

Author

Cai, Yingyun, Yu, Shuiqing, Fang, Ying, Bollinger, Laura, Li, Yanhua, Lauck, Michael, Postnikova, Elena N., Mazur, Steven, Johnson, Reed F., Finch, Courtney L., Radoshitzky, Sheli R., Palacios, Gustavo, Friedrich, Thomas C., Goldberg, Tony L., O'Connor, David H., Jahrling, Peter B., Kuhn, Jens H., Garcia-Blanco, Mariano Agustin, Sessions, October, and Ooi, Eng Eong

Subjects
GREEN fluorescent protein, HEMORRHAGIC fever, VIRAL replication, STOP codons, CELL lines, ANTISENSE DNA, CERCOPITHECUS aethiops
Abstract

Simian hemorrhagic fever virus (SHFV) causes acute, lethal disease in macaques. We developed a single-plasmid cDNA-launch infectious clone of SHFV (rSHFV) and modified the clone to rescue an enhanced green fluorescent protein-expressing rSHFV-eGFP that can be used for rapid and quantitative detection of infection. SHFV has a narrow cell tropism in vitro, with only the grivet MA-104 cell line and a few other grivet cell lines being susceptible to virion entry and permissive to infection. Using rSHFV-eGFP, we demonstrate that one cricetid rodent cell line and three ape cell lines also fully support SHFV replication, whereas 55 human cell lines, 11 bat cell lines, and three rodent cells do not. Interestingly, some human and other mammalian cell lines apparently resistant to SHFV infection are permissive after transfection with the rSHFV-eGFP cDNA-launch plasmid. To further demonstrate the investigative potential of the infectious clone system, we introduced stop codons into eight viral open reading frames (ORFs). This approach suggested that at least one ORF, ORF 2b', is dispensable for SHFV in vitro replication. Our proof-of-principle experiments indicated that rSHFV-eGFP is a useful tool for illuminating the understudied molecular biology of SHFV. [ABSTRACT FROM AUTHOR]

Published
2021
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248. Effector function does not contribute to protection from virus challenge by a highly potent HIV broadly neutralizing antibody in nonhuman primates

Author

Hangartner, Lars, Beauparlant, David, Rakasz, Eva, Nedellec, Rebecca, Hozé, Nathanaël, McKenney, Katherine, Martins, Mauricio A., Seabright, Gemma E., Allen, Joel D., Weiler, Andrea M., Friedrich, Thomas C., Regoes, Roland R., Crispin, Max, and Burton, Dennis R.

Abstract

Effector function is not required for a potent HIV envelope–specific broadly neutralizing antibody to protect nonhuman primates from SHIV infection.

Published
2021
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249. #79: Modeling Zika Virus Tissue Tropism in Rhesus Macaques to Define the Risk of Donor-derived Transmission

Author

Treadway, Taylor A, Shepherd, Phoenix M, Newman, Christina M, Mohr, Emma L, Dudley, Dawn M, Breitbach, Meghan E, Yamamoto, Keisuke, Stewart, Laurel M, Koenig, Michelle R, Bliss, Mason, Rybarczyk, Sierra L, Weiler, Andrea M, Semler, Matthew R, Mitzey, Ann, Razo, Elaina, Schotzko, Michele, Peterson, Eric, Simmons, Heather A, Mejia, Andres, Golos, Thaddeus G, Friedrich, Thomas C, and O’Connor, David H

Published
2021
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