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Moström MJ, Yu S, Tran D, Saccoccio FM, Versoza CJ, Malouli D, Mirza A, Valencia S, Gilbert M, Blair RV, Hansen S, Barry P, Früh K, Jensen JD, Pfeifer SP, Kowalik TF, Permar SR, Kaur A. Protective effect of pre-existing natural immunity in a nonhuman primate reinfection model of congenital cytomegalovirus infection. PLoS Pathog 2023; 19:e1011646. [PMID: 37796819 PMCID: PMC10553354 DOI: 10.1371/journal.ppat.1011646] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/29/2023] [Indexed: 10/07/2023] Open
Abstract
Congenital cytomegalovirus (cCMV) is the leading infectious cause of neurologic defects in newborns with particularly severe sequelae in the setting of primary CMV infection in the first trimester of pregnancy. The majority of cCMV cases worldwide occur after non-primary infection in CMV-seropositive women; yet the extent to which pre-existing natural CMV-specific immunity protects against CMV reinfection or reactivation during pregnancy remains ill-defined. We previously reported on a novel nonhuman primate model of cCMV in rhesus macaques where 100% placental transmission and 83% fetal loss were seen in CD4+ T lymphocyte-depleted rhesus CMV (RhCMV)-seronegative dams after primary RhCMV infection. To investigate the protective effect of preconception maternal immunity, we performed reinfection studies in CD4+ T lymphocyte-depleted RhCMV-seropositive dams inoculated in late first / early second trimester gestation with RhCMV strains 180.92 (n = 2), or RhCMV UCD52 and FL-RhCMVΔRh13.1/SIVgag, a wild-type-like RhCMV clone with SIVgag inserted as an immunological marker, administered separately (n = 3). An early transient increase in circulating monocytes followed by boosting of the pre-existing RhCMV-specific CD8+ T lymphocyte and antibody response was observed in the reinfected dams but not in control CD4+ T lymphocyte-depleted dams. Emergence of SIV Gag-specific CD8+ T lymphocyte responses in macaques inoculated with the FL-RhCMVΔRh13.1/SIVgag virus confirmed reinfection. Placental transmission was detected in only one of five reinfected dams and there were no adverse fetal sequelae. Viral whole genome, short-read, deep sequencing analysis confirmed transmission of both reinfection RhCMV strains across the placenta with ~30% corresponding to FL-RhCMVΔRh13.1/SIVgag and ~70% to RhCMV UCD52, consistent with the mixed human CMV infections reported in infants with cCMV. Our data showing reduced placental transmission and absence of fetal loss after non-primary as opposed to primary infection in CD4+ T lymphocyte-depleted dams indicates that preconception maternal CMV-specific CD8+ T lymphocyte and/or humoral immunity can protect against cCMV infection.
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Affiliation(s)
- Matilda J. Moström
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, United States of America
| | - Shan Yu
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, United States of America
| | - Dollnovan Tran
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, United States of America
| | - Frances M. Saccoccio
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Cyril J. Versoza
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Daniel Malouli
- Oregon Health and Sciences University, Beaverton, Oregon, United States of America
| | - Anne Mirza
- University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Sarah Valencia
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Margaret Gilbert
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, United States of America
| | - Robert V. Blair
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, United States of America
| | - Scott Hansen
- Oregon Health and Sciences University, Beaverton, Oregon, United States of America
| | - Peter Barry
- University of California, Davis, California, United States of America
| | - Klaus Früh
- Oregon Health and Sciences University, Beaverton, Oregon, United States of America
| | - Jeffrey D. Jensen
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Susanne P. Pfeifer
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Timothy F. Kowalik
- University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Sallie R. Permar
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
- Weill Cornell Medicine, New York, New York State, United States of America
| | - Amitinder Kaur
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, United States of America
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2
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Moström M, Yu S, Tran D, Saccoccio F, Versoza CJ, Malouli D, Mirza A, Valencia S, Gilbert M, Blair R, Hansen S, Barry P, Früh K, Jensen JD, Pfeifer SP, Kowalik TF, Permar SR, Kaur A. Protective effect of pre-existing natural immunity in a nonhuman primate reinfection model of congenital cytomegalovirus infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536057. [PMID: 37090643 PMCID: PMC10120644 DOI: 10.1101/2023.04.10.536057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Congenital cytomegalovirus (cCMV) is the leading infectious cause of neurologic defects in newborns with particularly severe sequelae in the setting of primary CMV infection in the first trimester of pregnancy. The majority of cCMV cases worldwide occur after non-primary infection in CMV-seropositive women; yet the extent to which pre-existing natural CMV-specific immunity protects against CMV reinfection or reactivation during pregnancy remains ill-defined. We previously reported on a novel nonhuman primate model of cCMV in rhesus macaques where 100% placental transmission and 83% fetal loss were seen in CD4 + T lymphocyte-depleted rhesus CMV (RhCMV)-seronegative dams after primary RhCMV infection. To investigate the protective effect of preconception maternal immunity, we performed reinfection studies in CD4+ T lymphocyte-depleted RhCMV-seropositive dams inoculated in late first / early second trimester gestation with RhCMV strains 180.92 ( n =2), or RhCMV UCD52 and FL-RhCMVΔRh13.1/SIV gag , a wild-type-like RhCMV clone with SIV gag inserted as an immunological marker ( n =3). An early transient increase in circulating monocytes followed by boosting of the pre-existing RhCMV-specific CD8+ T lymphocyte and antibody response was observed in the reinfected dams but not in control CD4+ T lymphocyte-depleted dams. Emergence of SIV Gag-specific CD8+ T lymphocyte responses in macaques inoculated with the FL-RhCMVΔRh13.1/SIV gag virus confirmed reinfection. Placental transmission was detected in only one of five reinfected dams and there were no adverse fetal sequelae. Viral whole genome, short-read, deep sequencing analysis confirmed transmission of both reinfection RhCMV strains across the placenta with ∼30% corresponding to FL-RhCMVΔRh13.1/SIV gag and ∼70% to RhCMV UCD52, consistent with the mixed human CMV infections reported in infants with cCMV. Our data showing reduced placental transmission and absence of fetal loss after non-primary as opposed to primary infection in CD4+ T lymphocyte-depleted dams indicates that preconception maternal CMV-specific CD8+ T lymphocyte and/or humoral immunity can protect against cCMV infection. Author Summary Globally, pregnancies in CMV-seropositive women account for the majority of cases of congenital CMV infection but the immune responses needed for protection against placental transmission in mothers with non-primary infection remains unknown. Recently, we developed a nonhuman primate model of primary rhesus CMV (RhCMV) infection in which placental transmission and fetal loss occurred in RhCMV-seronegative CD4+ T lymphocyte-depleted macaques. By conducting similar studies in RhCMV-seropositive dams, we demonstrated the protective effect of pre-existing natural CMV-specific CD8+ T lymphocytes and humoral immunity against congenital CMV after reinfection. A 5-fold reduction in congenital transmission and complete protection against fetal loss was observed in dams with pre-existing immunity compared to primary CMV in this model. Our study is the first formal demonstration in a relevant model of human congenital CMV that natural pre-existing CMV-specific maternal immunity can limit congenital CMV transmission and its sequelae. The nonhuman primate model of non-primary congenital CMV will be especially relevant to studying immune requirements of a maternal vaccine for women in high CMV seroprevalence areas at risk of repeated CMV reinfections during pregnancy.
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Affiliation(s)
- Matilda Moström
- Tulane National Primate Research Center, Tulane University, Covington LA
| | - Shan Yu
- Tulane National Primate Research Center, Tulane University, Covington LA
| | - Dollnovan Tran
- Tulane National Primate Research Center, Tulane University, Covington LA
| | | | - Cyril J. Versoza
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ
| | | | - Anne Mirza
- University of Massachusetts Chan Medical School, Worcester, MA
| | - Sarah Valencia
- Duke Human Vaccine Institute, Duke University, Durham, NC
| | - Margaret Gilbert
- Tulane National Primate Research Center, Tulane University, Covington LA
| | - Robert Blair
- Tulane National Primate Research Center, Tulane University, Covington LA
| | - Scott Hansen
- Oregon Health and Sciences University, Beaverton, OR
| | | | - Klaus Früh
- Oregon Health and Sciences University, Beaverton, OR
| | - Jeffrey D. Jensen
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ
| | - Susanne P. Pfeifer
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ
| | | | - Sallie R. Permar
- Duke Human Vaccine Institute, Duke University, Durham, NC
- Weill Cornell Medicine, New York, NY
| | - Amitinder Kaur
- Tulane National Primate Research Center, Tulane University, Covington LA
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3
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Terbot JW, Johri P, Liphardt SW, Soni V, Pfeifer SP, Cooper BS, Good JM, Jensen JD. Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples. PLoS Pathog 2023; 19:e1011265. [PMID: 37018331 PMCID: PMC10075409 DOI: 10.1371/journal.ppat.1011265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
Over the past 3 years, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread through human populations in several waves, resulting in a global health crisis. In response, genomic surveillance efforts have proliferated in the hopes of tracking and anticipating the evolution of this virus, resulting in millions of patient isolates now being available in public databases. Yet, while there is a tremendous focus on identifying newly emerging adaptive viral variants, this quantification is far from trivial. Specifically, multiple co-occurring and interacting evolutionary processes are constantly in operation and must be jointly considered and modeled in order to perform accurate inference. We here outline critical individual components of such an evolutionary baseline model-mutation rates, recombination rates, the distribution of fitness effects, infection dynamics, and compartmentalization-and describe the current state of knowledge pertaining to the related parameters of each in SARS-CoV-2. We close with a series of recommendations for future clinical sampling, model construction, and statistical analysis.
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Affiliation(s)
- John W Terbot
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Parul Johri
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Schuyler W Liphardt
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Vivak Soni
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Susanne P Pfeifer
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Brandon S Cooper
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Jeffrey M Good
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Jeffrey D Jensen
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
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Le-Trilling VTK, Jagnjić A, Brizić I, Eilbrecht M, Wohlgemuth K, Rožmanić C, Herdman A, Hoffmann K, Westendorf AM, Hengel H, Jonjić S, Trilling M. Maternal antibodies induced by a live attenuated vaccine protect neonatal mice from cytomegalovirus. NPJ Vaccines 2023; 8:8. [PMID: 36737485 PMCID: PMC9898546 DOI: 10.1038/s41541-023-00602-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Human cytomegalovirus (HCMV) frequently causes congenital infections, resulting in birth defects and developmental disorders. A vaccine is needed, but unavailable. We analyzed the potential of CMV mutants, lacking their STAT2 antagonists to serve as live attenuated vaccine viruses in mice. Infections with attenuated viruses elicited strong ELISA-reactive binding IgG responses and induced neutralizing antibodies as well as antibodies stimulating cellular Fcγ receptors, including the antibody-dependent cellular cytotoxicity (ADCC)-eliciting receptors FcγRIII/CD16 and FcγRIV. Accordingly, vaccinated mice were fully protected against challenge infections. Female mice vaccinated prior to gestation transmitted CMV-specific IgG to their offspring, which protected the progeny from perinatal infections in a mouse model for congenital CMV disease. To define the role of maternal antibodies, female mice either capable or incapable of producing antibodies were vaccinated and subsequently bred to males of the opposite genotype. Challenge infections of the genotypically identical F1 generation revealed the indispensability of maternal antibodies for vaccine-induced protection against cytomegaloviruses.
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Affiliation(s)
- Vu Thuy Khanh Le-Trilling
- grid.5718.b0000 0001 2187 5445Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Andreja Jagnjić
- grid.5718.b0000 0001 2187 5445Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ilija Brizić
- grid.22939.330000 0001 2236 1630Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Mareike Eilbrecht
- grid.5718.b0000 0001 2187 5445Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kerstin Wohlgemuth
- grid.5718.b0000 0001 2187 5445Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Carmen Rožmanić
- grid.22939.330000 0001 2236 1630Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Alan Herdman
- grid.5718.b0000 0001 2187 5445Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Katja Hoffmann
- grid.5963.9Institute of Virology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Astrid M. Westendorf
- grid.5718.b0000 0001 2187 5445Institute for Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Hartmut Hengel
- grid.5963.9Institute of Virology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stipan Jonjić
- grid.22939.330000 0001 2236 1630Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Mirko Trilling
- grid.5718.b0000 0001 2187 5445Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Morales-Arce AY, Johri P, Jensen JD. Inferring the distribution of fitness effects in patient-sampled and experimental virus populations: two case studies. Heredity (Edinb) 2022; 128:79-87. [PMID: 34987185 PMCID: PMC8728706 DOI: 10.1038/s41437-021-00493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 11/19/2022] Open
Abstract
We here propose an analysis pipeline for inferring the distribution of fitness effects (DFE) from either patient-sampled or experimentally-evolved viral populations, that explicitly accounts for non-Wright-Fisher and non-equilibrium population dynamics inherent to pathogens. We examine the performance of this approach via extensive power and performance analyses, and highlight two illustrative applications - one from an experimentally-passaged RNA virus, and the other from a clinically-sampled DNA virus. Finally, we discuss how such DFE inference may shed light on major research questions in virus evolution, ranging from a quantification of the population genetic processes governing genome size, to the role of Hill-Robertson interference in dictating adaptive outcomes, to the potential design of novel therapeutic approaches to eradicate within-patient viral populations via induced mutational meltdown.
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Affiliation(s)
- Ana Y. Morales-Arce
- grid.215654.10000 0001 2151 2636Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ USA
| | - Parul Johri
- grid.215654.10000 0001 2151 2636Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ USA
| | - Jeffrey D. Jensen
- grid.215654.10000 0001 2151 2636Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ USA
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Pathogenesis of wild-type-like rhesus cytomegalovirus strains following oral exposure of immune-competent rhesus macaques. J Virol 2021; 96:e0165321. [PMID: 34788083 DOI: 10.1128/jvi.01653-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhesus cytomegalovirus (RhCMV) infection of rhesus macaques (Macaca mulatta) is a valuable nonhuman primate model of human CMV (HCMV) persistence and pathogenesis. In vivo studies predominantly use tissue culture-adapted variants of RhCMV that contain multiple genetic mutations compared to wild-type (WT) RhCMV. In many studies, animals have been inoculated by non-natural routes (e.g., subcutaneous, intravenous) that do not recapitulate disease progression via the normative route of mucosal exposure. Accordingly, the natural history of RhCMV would be more accurately reproduced by infecting macaques with strains of RhCMV that reflect the WT genome using natural routes of mucosal transmission. Herein, we tested two WT-like RhCMV strains, UCD52 and UCD59, and demonstrated that systemic infection and frequent, high-titer viral shedding in bodily fluids occurred following oral inoculation. RhCMV disseminated to a broad range of tissues, including the central nervous system and reproductive organs. Commonly infected tissues included the thymus, spleen, lymph nodes, kidneys, bladder, and salivary glands. Histological examination revealed prominent nodular hyperplasia in spleens and variable levels of lymphoid lymphofollicular hyperplasia in lymph nodes. One of six inoculated animals had limited viral dissemination and shedding, with commensurately weak antibody responses to RhCMV antigens. These data suggest that long-term RhCMV infection parameters might be restricted by local innate factors and/or de novo host immune responses in a minority of primary infections. Together, we have established an oral RhCMV infection model that mimics natural HCMV infection. The virological and immunological parameters characterized in this study will greatly inform HCMV vaccine designs for human immunization. IMPORTANCE Human cytomegalovirus (HCMV) is globally ubiquitous with high seroprevalence rates in all communities. HCMV infections can occur vertically following mother-to-fetus transmission across the placenta and horizontally following shedding of virus in bodily fluids in HCMV infected hosts and subsequent exposure of susceptible individuals to virus-laden fluids. Intrauterine HCMV has long been recognized as an infectious threat to fetal growth and development. Since vertical HCMV infections occur following horizontal HCMV transmission to the pregnant mother, the nonhuman primate model of HCMV pathogenesis was used to characterize the virological and immunological parameters of infection following primary mucosal exposures to rhesus cytomegalovirus.
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7
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Wang HY, Valencia SM, Pfeifer SP, Jensen JD, Kowalik TF, Permar SR. Common Polymorphisms in the Glycoproteins of Human Cytomegalovirus and Associated Strain-Specific Immunity. Viruses 2021; 13:v13061106. [PMID: 34207868 PMCID: PMC8227702 DOI: 10.3390/v13061106] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/18/2022] Open
Abstract
Human cytomegalovirus (HCMV), one of the most prevalent viruses across the globe, is a common cause of morbidity and mortality for immunocompromised individuals. Recent clinical observations have demonstrated that mixed strain infections are common and may lead to more severe disease progression. This clinical observation illustrates the complexity of the HCMV genome and emphasizes the importance of taking a population-level view of genotypic evolution. Here we review frequently sampled polymorphisms in the glycoproteins of HCMV, comparing the variable regions, and summarizing their corresponding geographic distributions observed to date. The related strain-specific immunity, including neutralization activity and antigen-specific cellular immunity, is also discussed. Given that these glycoproteins are common targets for vaccine design and anti-viral therapies, this observed genetic variation represents an important resource for future efforts to combat HCMV infections.
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Affiliation(s)
- Hsuan-Yuan Wang
- Department of Pediatrics, Weill Cornell Medicine, New York, NY 10065, USA;
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA;
| | - Sarah M. Valencia
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA;
| | - Susanne P. Pfeifer
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (S.P.P.); (J.D.J.)
| | - Jeffrey D. Jensen
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (S.P.P.); (J.D.J.)
| | - Timothy F. Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA;
| | - Sallie R. Permar
- Department of Pediatrics, Weill Cornell Medicine, New York, NY 10065, USA;
- Correspondence: ; Tel.: +1-212-746-4111
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8
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Mussi-Pinhata MM, Yamamoto AY. Natural History of Congenital Cytomegalovirus Infection in Highly Seropositive Populations. J Infect Dis 2021; 221:S15-S22. [PMID: 32134482 DOI: 10.1093/infdis/jiz443] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Maternal preconceptional cytomegalovirus (CMV) immunity does not protect the fetus from acquiring congenital CMV infection (cCMV). Nonprimary infections due to recurrence of latent infections or reinfection with new virus strains during pregnancy can result in fetal infection. Because the prevalence of cCMV increases with increasing maternal CMV seroprevalence, the vast majority of the cases of cCMV throughout the world follow nonprimary maternal infections and is more common in individuals of lower socioeconomic background. Horizontal exposures to persons shedding virus in bodily secretions (young children, sexual activity, household crowding, low income) probably increase the risk of acquisition of an exogenous nonprimary CMV infection and fetal transmission. In addition, more frequent acquisition of new antibody reactivities in transmitter mothers suggest that maternal reinfection by new viral strains could be a major source of congenital infection in such populations. However, the exact frequency of CMV nonprimary infection in seroimmune women during pregnancy and the rate of intrauterine transmission in these women are yet to be defined. Usually, the birth prevalence of cCMV is high (≥7:1000) in highly seropositive populations. There is increasing evidence that the frequency and severity of the clinical and laboratory abnormalities in infants with congenital CMV infection born to mothers with nonprimary CMV infection are similar to infants born after a primary maternal infection. This is particularly true for sensorineural hearing loss, which contributes to one third of all early-onset hearing loss in seropositive populations. This brief overview will discuss the need for more research to better clarify the natural history of cCMV in highly seropositive populations, which, in almost all populations, remains incompletely defined.
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Pang J, Slyker JA, Roy S, Bryant J, Atkinson C, Cudini J, Farquhar C, Griffiths P, Kiarie J, Morfopoulou S, Roxby AC, Tutil H, Williams R, Gantt S, Goldstein RA, Breuer J. Mixed cytomegalovirus genotypes in HIV-positive mothers show compartmentalization and distinct patterns of transmission to infants. eLife 2020; 9:e63199. [PMID: 33382036 PMCID: PMC7806273 DOI: 10.7554/elife.63199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/31/2020] [Indexed: 12/15/2022] Open
Abstract
Cytomegalovirus (CMV) is the commonest cause of congenital infection and particularly so among infants born to HIV-infected women. Studies of congenital CMV infection (cCMVi) pathogenesis are complicated by the presence of multiple infecting maternal CMV strains, especially in HIV-positive women, and the large, recombinant CMV genome. Using newly developed tools to reconstruct CMV haplotypes, we demonstrate anatomic CMV compartmentalization in five HIV-infected mothers and identify the possibility of congenitally transmitted genotypes in three of their infants. A single CMV strain was transmitted in each congenitally infected case, and all were closely related to those that predominate in the cognate maternal cervix. Compared to non-transmitted strains, these congenitally transmitted CMV strains showed statistically significant similarities in 19 genes associated with tissue tropism and immunomodulation. In all infants, incident superinfections with distinct strains from breast milk were captured during follow-up. The results represent potentially important new insights into the virologic determinants of early CMV infection.
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Affiliation(s)
- Juanita Pang
- Division of Infection and Immunity, University College London, Cruciform BuildingLondonUnited Kingdom
| | - Jennifer A Slyker
- Departments of Global Health and Epidemiology, University of WashingtonSeattleUnited States
| | - Sunando Roy
- Division of Infection and Immunity, University College London, Cruciform BuildingLondonUnited Kingdom
| | - Josephine Bryant
- Division of Infection and Immunity, University College London, Cruciform BuildingLondonUnited Kingdom
| | - Claire Atkinson
- Institute of Immunology and Transplantation, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Juliana Cudini
- Division of Infection and Immunity, University College London, Cruciform BuildingLondonUnited Kingdom
| | - Carey Farquhar
- Departments of Global Health, Epidemiology, Medicine (Div. Allergy and Infectious Diseases), University of WashingtonSeattleUnited States
| | - Paul Griffiths
- Institute of Immunology and Transplantation, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - James Kiarie
- University of Nairobi, Department of Obstetrics and Gynaecology, World Health OrganizationNairobiKenya
| | - Sofia Morfopoulou
- Division of Infection and Immunity, University College London, Cruciform BuildingLondonUnited Kingdom
| | - Alison C Roxby
- Departments of Global Health, Epidemiology, Medicine (Div. Allergy and Infectious Diseases), University of WashingtonSeattleUnited States
| | - Helena Tutil
- Division of Infection and Immunity, University College London, Cruciform BuildingLondonUnited Kingdom
| | - Rachel Williams
- Division of Infection and Immunity, University College London, Cruciform BuildingLondonUnited Kingdom
| | - Soren Gantt
- Research Centre of the Sainte-Justine University Hospital, Department of Microbiology, Infectious Diseases and Immunology, University of Montréal QCMontréalCanada
| | - Richard A Goldstein
- Division of Infection and Immunity, University College London, Cruciform BuildingLondonUnited Kingdom
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College LondonLondonUnited Kingdom
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10
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Marshall EE, Malouli D, Hansen SG, Gilbride RM, Hughes CM, Ventura AB, Ainslie E, Selseth AN, Ford JC, Burke D, Kreklywich CN, Womack J, Legasse AW, Axthelm MK, Kahl C, Streblow D, Edlefsen PT, Picker LJ, Früh K. Enhancing safety of cytomegalovirus-based vaccine vectors by engaging host intrinsic immunity. Sci Transl Med 2020; 11:11/501/eaaw2603. [PMID: 31316006 DOI: 10.1126/scitranslmed.aaw2603] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/14/2019] [Accepted: 06/13/2019] [Indexed: 12/29/2022]
Abstract
Rhesus cytomegalovirus (RhCMV)-based vaccines maintain effector memory T cell responses (TEM) that protect ~50% of rhesus monkeys (RMs) challenged with simian immunodeficiency virus (SIV). Because human CMV (HCMV) causes disease in immunodeficient subjects, clinical translation will depend upon attenuation strategies that reduce pathogenic potential without sacrificing CMV's unique immunological properties. We demonstrate that "intrinsic" immunity can be used to attenuate strain 68-1 RhCMV vectors without impairment of immunogenicity. The tegument proteins pp71 and UL35 encoded by UL82 and UL35 of HCMV counteract cell-intrinsic restriction via degradation of host transcriptional repressors. When the corresponding RhCMV genes, Rh110 and Rh59, were deleted from 68-1 RhCMV (ΔRh110 and ΔRh59), we observed only a modest growth defect in vitro, but in vivo, these modified vectors manifested little to no amplification at the injection site and dissemination to distant sites, in contrast to parental 68-1 RhCMV. ΔRh110 was not shed at any time after infection and was not transmitted to naïve hosts either by close contact (mother to infant) or by leukocyte transfusion. In contrast, ΔRh59 was both shed and transmitted by leukocyte transfusion, indicating less effective attenuation than pp71 deletion. The T cell immunogenicity of ΔRh110 was essentially identical to 68-1 RhCMV with respect to magnitude, TEM phenotype, epitope targeting, and durability. Thus, pp71 deletion preserves CMV vector immunogenicity while stringently limiting vector spread, making pp71 deletion an attractive attenuation strategy for HCMV vectors.
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Affiliation(s)
- Emily E Marshall
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Daniel Malouli
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Roxanne M Gilbride
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Colette M Hughes
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Abigail B Ventura
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Emily Ainslie
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Andrea N Selseth
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Julia C Ford
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - David Burke
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Craig N Kreklywich
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Jennie Womack
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Alfred W Legasse
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Michael K Axthelm
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Christoph Kahl
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Daniel Streblow
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Paul T Edlefsen
- Statistical Center for HIV/AIDS Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Louis J Picker
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA.
| | - Klaus Früh
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA.
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11
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Abstract
The evolutionary dynamics of a virus can differ within hosts and across populations. Studies of within-host evolution provide an important link between experimental studies of virus evolution and large-scale phylodynamic analyses. They can determine the extent to which global processes are recapitulated on local scales and how accurately experimental infections model natural ones. They may also inform epidemiologic models of disease spread and reveal how host-level dynamics contribute to a virus's evolution at a larger scale. Over the last decade, advances in viral sequencing have enabled detailed studies of viral genetic diversity within hosts. I review how within-host diversity is sampled, measured, and expressed, and how comparative studies of viral diversity can be leveraged to elucidate a virus's evolutionary dynamics. These concepts are illustrated with detailed reviews of recent research on the within-host evolution of influenza virus, dengue virus, and cytomegalovirus.
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Affiliation(s)
- Adam S Lauring
- Division of Infectious Diseases, Department of Internal Medicine, and Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA;
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12
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Britt WJ. Human Cytomegalovirus Infection in Women With Preexisting Immunity: Sources of Infection and Mechanisms of Infection in the Presence of Antiviral Immunity. J Infect Dis 2020; 221:S1-S8. [PMID: 32134479 PMCID: PMC7057782 DOI: 10.1093/infdis/jiz464] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Human cytomegalovirus (HCMV) infection remains an important cause of neurodevelopmental sequelae in infants infected in utero. Unique to the natural history of perinatal HCMV infections is the occurrence of congenital HCMV infections (cCMV) in women with existing immunity to HCMV, infections that have been designated as nonprimary maternal infection. In maternal populations with a high HCMV seroprevalence, cCMV that follows nonprimary maternal infections accounts for 75%-90% of all cases of cCMV infections as well as a large proportion of infected infants with neurodevelopmental sequelae. Although considerable effort has been directed toward understanding immune correlates that can modify maternal infections and intrauterine transmission, the source of virus leading to nonprimary maternal infections and intrauterine transmission is not well defined. Previous paradigms that included reactivation of latent virus as the source of infection in immune women have been challenged by studies demonstrating acquisition and transmission of antigenically distinct viruses, a finding suggesting that reinfection through exposure to an exogenous virus is responsible for some cases of nonprimary maternal infection. Additional understanding of the source(s) of virus that leads to nonprimary maternal infection will be of considerable value in the development and testing of interventions such as vaccines designed to limit the incidence of cCMV in populations with high HCMV seroprevalence.
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Affiliation(s)
- William J Britt
- Departments of Pediatrics, Microbiology, Neurobiology, University of Alabama School of Medicine, Birmingham, Alabama
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13
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Vera Cruz D, Nelson CS, Tran D, Barry PA, Kaur A, Koelle K, Permar SR. Intrahost cytomegalovirus population genetics following antibody pretreatment in a monkey model of congenital transmission. PLoS Pathog 2020; 16:e1007968. [PMID: 32059027 PMCID: PMC7046290 DOI: 10.1371/journal.ppat.1007968] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 02/27/2020] [Accepted: 12/02/2019] [Indexed: 12/12/2022] Open
Abstract
Human cytomegalovirus (HCMV) infection is the leading non-genetic cause of congenital birth defects worldwide. While several studies have addressed the genetic composition of viral populations in newborns diagnosed with HCMV, little is known regarding mother-to-child viral transmission dynamics and how therapeutic interventions may impact within-host viral populations. Here, we investigate how preexisting CMV-specific antibodies shape the maternal viral population and intrauterine virus transmission. Specifically, we characterize the genetic composition of CMV populations in a monkey model of congenital CMV infection to examine the effects of passively-infused hyperimmune globulin (HIG) on viral population genetics in both maternal and fetal compartments. In this study, 11 seronegative, pregnant monkeys were challenged with rhesus CMV (RhCMV), including a group pretreated with a standard potency HIG preparation (n = 3), a group pretreated with a high-neutralizing potency HIG preparation (n = 3), and an untreated control group (n = 5). Targeted amplicon deep sequencing of RhCMV glycoprotein B and L genes revealed that one of the three strains present in the viral inoculum (UCD52) dominated maternal and fetal viral populations. We identified minor haplotypes of this strain and characterized their dynamics. Many of the identified haplotypes were consistently detected at multiple timepoints within sampled maternal tissues, as well as across tissue compartments, indicating haplotype persistence over time and transmission between maternal compartments. However, haplotype numbers and diversity levels were not appreciably different between control, standard-potency, and high-potency pretreatment groups. We found that while the presence of maternal antibodies reduced viral load and congenital infection, it had no apparent impact on intrahost viral genetic diversity at the investigated loci. Interestingly, some minor haplotypes present in fetal and maternal-fetal interface tissues were also identified as minor haplotypes in corresponding maternal tissues, providing evidence for a loose RhCMV mother-to-fetus transmission bottleneck even in the presence of preexisting antibodies.
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Affiliation(s)
- Diana Vera Cruz
- Computational Biology and Bioinformatics program / Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Cody S. Nelson
- Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Dollnovan Tran
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, United States of America
| | - Peter A. Barry
- Center for Comparative Medicine, Department of Pathology and Laboratory Medicine, University of California, Davis, California, United States of America
| | - Amitinder Kaur
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, United States of America
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - Sallie R. Permar
- Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
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14
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Purswani MU, Russell JS, Dietrich M, Malee K, Spector SA, Williams PL, Frederick T, Burchett S, Redmond S, Hoffman HJ, Torre P, Lee S, Rice ML, Yao TJ. Birth Prevalence of Congenital Cytomegalovirus Infection in HIV-Exposed Uninfected Children in the Era of Combination Antiretroviral Therapy. J Pediatr 2020; 216:82-87.e2. [PMID: 31668479 PMCID: PMC6930703 DOI: 10.1016/j.jpeds.2019.09.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/21/2019] [Accepted: 09/11/2019] [Indexed: 12/22/2022]
Abstract
OBJECTIVES To estimate birth prevalence of congenital cytomegalovirus (cCMV) in HIV-exposed uninfected children born in the current era of combination antiretroviral therapy and describe cCMV-related neurodevelopmental and hearing outcomes. STUDY DESIGN The Surveillance Monitoring for ART Toxicities cohort study follows HIV-exposed uninfected children at 22 sites in the US and Puerto Rico. Birth cCMV prevalence was estimated in a subset of participants who had blood pellets collected within three weeks of birth and underwent ≥1 of 6 assessments evaluating cognitive and language development including an audiologic examination between 1 and 5 years of age. Detection of CMV DNA by polymerase chain reaction testing of peripheral blood mononuclear cells was used to diagnose cCMV. Proportions of suboptimal assessment scores were compared by cCMV status using Fisher exact test. RESULTS Mothers of 895 eligible HIV-exposed uninfected children delivered between 2007 and 2015. Most (90%) were on combination antiretroviral therapy, 88% had an HIV viral load of ≤400 copies/mL, and 93% had CD4 cell counts of ≥200 cells/μL. Eight infants were diagnosed with cCMV, yielding an estimated prevalence of 0.89% (95% CI, 0.39%-1.75%). After adjusting for a sensitivity of 70%-75% for the testing method, projected prevalence was 1.2%-1.3%. No differences were observed in cognitive, language and hearing assessments by cCMV status. CONCLUSIONS Although birth cCMV prevalence in HIV-exposed uninfected children born to women with well-controlled HIV is trending down compared with earlier combination antiretroviral therapy-era estimates, it is above the 0.4% reported for the general US population. HIV-exposed uninfected children remain at increased risk for cCMV.
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Affiliation(s)
- Murli U. Purswani
- Division of Pediatric Infectious Disease, Department of Pediatrics, BronxCare Health System, Bronx, NY,Icahn School of Medicine at Mount Sinai, NY
| | - Jonathan S. Russell
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Monika Dietrich
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA
| | - Kathleen Malee
- Psychiatry and Behavioral Science, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Stephen A. Spector
- Department of Pediatrics, University of California San Diego, La Jolla, and Rady Children’s, Hospital, San Diego, CA
| | - Paige L. Williams
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, MA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Toni Frederick
- Maternal, Child and Adolescent Program for Infectious Diseases and Virology, Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, CA
| | - Sandra Burchett
- Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA
| | - Sean Redmond
- Department of Communication Sciences and Disorders, University of Utah, Salt Lake City, UT
| | - Howard J. Hoffman
- Epidemiology and Statistics Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD
| | - Peter Torre
- School of Speech, Language and Hearing Sciences, San Diego State University, San Diego, CA
| | - Sonia Lee
- Maternal and Pediatric Infectious Disease Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Mabel L. Rice
- Child Language Doctoral Program, University of Kansas, Lawrence, KS
| | - Tzy-Jyun Yao
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, MA
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15
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A consideration of within-host human cytomegalovirus genetic variation. Proc Natl Acad Sci U S A 2019; 117:816-817. [PMID: 31874930 DOI: 10.1073/pnas.1915295117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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16
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Caposio P, van den Worm S, Crawford L, Perez W, Kreklywich C, Gilbride RM, Hughes CM, Ventura AB, Ratts R, Marshall EE, Malouli D, Axthelm MK, Streblow D, Nelson JA, Picker LJ, Hansen SG, Früh K. Characterization of a live-attenuated HCMV-based vaccine platform. Sci Rep 2019; 9:19236. [PMID: 31848362 PMCID: PMC6917771 DOI: 10.1038/s41598-019-55508-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023] Open
Abstract
Vaccines based on cytomegalovirus (CMV) demonstrate protection in animal models of infectious disease and cancer. Vaccine efficacy is associated with the ability of CMV to elicit and indefinitely maintain high frequencies of circulating effector memory T cells (TEM) providing continuous, life-long anti-pathogen immune activity. To allow for the clinical testing of human CMV (HCMV)-based vaccines we constructed and characterized as a vector backbone the recombinant molecular clone TR3 representing a wildtype genome. We demonstrate that TR3 can be stably propagated in vitro and that, despite species incompatibility, recombinant TR3 vectors elicit high frequencies of TEM to inserted antigens in rhesus macaques (RM). Live-attenuated versions of TR3 were generated by deleting viral genes required to counteract intrinsic and innate immune responses. In addition, we eliminated subunits of a viral pentameric glycoprotein complex thus limiting cell tropism. We show in a humanized mouse model that such modified vectors were able to establish persistent infection but lost their ability to reactivate from latency. Nevertheless, attenuated TR3 vectors preserved the ability to elicit and maintain TEM to inserted antigens in RM. We further demonstrate that attenuated TR3 can be grown in approved cell lines upon elimination of an anti-viral host factor using small interfering RNA, thus obviating the need for a complementing cell line. In sum, we have established a versatile platform for the clinical development of live attenuated HCMV-vectored vaccines and immunotherapies.
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Affiliation(s)
- Patrizia Caposio
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Sjoerd van den Worm
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
- Batavia Biosciences B.V., Zernikedreef 16, 2333 CL, Leiden, Netherlands
| | - Lindsey Crawford
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Wilma Perez
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Craig Kreklywich
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Roxanne M Gilbride
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Colette M Hughes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Abigail B Ventura
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Robert Ratts
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
- Vir Biotechnology, 4640, SW Macadam Avenue, Portland, OR, 97239, USA
| | - Emily E Marshall
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
- Vir Biotechnology, 4640, SW Macadam Avenue, Portland, OR, 97239, USA
| | - Daniel Malouli
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Michael K Axthelm
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Daniel Streblow
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Jay A Nelson
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Louis J Picker
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA.
| | - Klaus Früh
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA.
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17
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Dobbins GC, Patki A, Chen D, Tiwari HK, Hendrickson C, Britt WJ, Fowler K, Chen JY, Boppana SB, Ross SA. Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection. BMC Infect Dis 2019; 19:1046. [PMID: 31822287 PMCID: PMC6905059 DOI: 10.1186/s12879-019-4681-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/29/2019] [Indexed: 12/23/2022] Open
Abstract
Background Congenital cytomegalovirus (cCMV) infection is the most common congenital infection and a leading cause of long-term neurological and sensory sequelae, the most common being sensorineural hearing loss (SNHL). Despite extensive research, clinical or laboratory markers to identify CMV infected children with increased risk for disease have not been identified. This study utilizes viral whole-genome next generation-sequencing (NGS) of specimens from congenitally infected infants to explore viral diversity and specific viral variants that may be associated with symptomatic infection and SNHL. Methods CMV DNA from urine specimens of 30 infants (17 asymptomatic, 13 symptomatic) was target enriched and next generation sequenced resulting in 93% coverage of the CMV genome allowing analysis of viral diversity. Results Variant frequency distribution was compared between children with symptomatic and asymptomatic cCMV and those with (n = 13) and without (n = 17) hearing loss. The CMV genes UL48A, UL88, US19 and US22 were found to have an increase in nucleotide diversity in symptomatic children; while UL57, UL20, UL104, US14, UL115, and UL35 had an increase in diversity in children with hearing loss. An analysis of single variant differences between symptomatic and asymptomatic children found UL55 to have the highest number, while the most variants associated with SNHL were in the RL11 gene family. In asymptomatic infants with SNHL, mutations were observed more frequently in UL33 and UL20. Conclusion CMV genomes from infected newborns can be mapped to 93% of the genome at a depth allowing accurate and reproducible analysis of polymorphisms for variant and gene discovery that may be linked to symptomatic and hearing loss outcomes.
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Affiliation(s)
- G Clement Dobbins
- Department of Pediatrics, The University of Alabama School of Medicine, CHB 116, 1600 6th Avenue South, Birmingham, AL, USA.
| | - Amit Patki
- Department of Biostatistics, The University of Alabama School of Public Health, Birmingham, AL, USA
| | - Dongquan Chen
- Informatics Institute, The University of Alabama at Birmingham, Birmingham, AL, USA.,Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hemant K Tiwari
- Department of Biostatistics, The University of Alabama School of Public Health, Birmingham, AL, USA
| | - Curtis Hendrickson
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - William J Britt
- Department of Pediatrics, The University of Alabama School of Medicine, CHB 116, 1600 6th Avenue South, Birmingham, AL, USA.,Informatics Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Karen Fowler
- Department of Pediatrics, The University of Alabama School of Medicine, CHB 116, 1600 6th Avenue South, Birmingham, AL, USA
| | - Jake Y Chen
- Informatics Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Suresh B Boppana
- Department of Pediatrics, The University of Alabama School of Medicine, CHB 116, 1600 6th Avenue South, Birmingham, AL, USA.,Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shannon A Ross
- Department of Pediatrics, The University of Alabama School of Medicine, CHB 116, 1600 6th Avenue South, Birmingham, AL, USA. .,Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA.
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18
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Abstract
Herpes simplex virus (HSV) causes invasive disease in half of infected neonates, resulting in significant mortality and permanent cognitive morbidity. The factors that contribute to invasive disease are not understood. This study revealed diversity among HSV isolates from infected neonates and detected the first associations between viral genetic variations and clinical disease manifestations. We found that viruses isolated from newborns with encephalitis showed enhanced spread in culture. These viruses contained protein-coding variations not found in viruses causing noninvasive disease. Many of these variations were found in proteins known to impact neurovirulence and viral spread between cells. This work advances our understanding of HSV diversity in the neonatal population and how it may impact disease outcome. More than 14,000 neonates are infected with herpes simplex virus (HSV) annually. Approximately half display manifestations limited to the skin, eyes, or mouth (SEM disease). The rest develop invasive infections that spread to the central nervous system (CNS disease or encephalitis) or throughout the infected neonate (disseminated disease). Invasive HSV disease is associated with significant morbidity and mortality, but the viral and host factors that predispose neonates to these forms are unknown. To define viral diversity within the infected neonatal population, we evaluated 10 HSV-2 isolates from newborns with a range of clinical presentations. To assess viral fitness independently of host immune factors, we measured viral growth characteristics in cultured cells and found diverse in vitro phenotypes. Isolates from neonates with CNS disease were associated with larger plaque size and enhanced spread, with the isolates from cerebrospinal fluid (CSF) exhibiting the most robust growth. We sequenced complete viral genomes of all 10 neonatal viruses, providing new insights into HSV-2 genomic diversity in this clinical setting. We found extensive interhost and intrahost genomic diversity throughout the viral genome, including amino acid differences in more than 90% of the viral proteome. The genes encoding glycoprotein G (gG; US4), glycoprotein I (gI; US7), and glycoprotein K (gK; UL53) and viral proteins UL8, UL20, UL24, and US2 contained variants that were found in association with CNS isolates. Many of these viral proteins are known to contribute to cell spread and neurovirulence in mouse models of CNS disease. This report represents the first application of comparative pathogen genomics to neonatal HSV disease. IMPORTANCE Herpes simplex virus (HSV) causes invasive disease in half of infected neonates, resulting in significant mortality and permanent cognitive morbidity. The factors that contribute to invasive disease are not understood. This study revealed diversity among HSV isolates from infected neonates and detected the first associations between viral genetic variations and clinical disease manifestations. We found that viruses isolated from newborns with encephalitis showed enhanced spread in culture. These viruses contained protein-coding variations not found in viruses causing noninvasive disease. Many of these variations were found in proteins known to impact neurovirulence and viral spread between cells. This work advances our understanding of HSV diversity in the neonatal population and how it may impact disease outcome. Podcast: A podcast concerning this article is available.
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19
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Abstract
Bacterial, viral, and parasitic pathogens add significant morbidity and even mortality to pregnancy-with adverse effects extending to both the gravida and the newborn. Three herpesviruses deserve considerable attention given the effects of perinatal infection on obstetric outcomes, specifically maternal and neonatal morbidity. In the following review, we will provide a description of cytomegalovirus, herpes simplex virus, and varicella zoster virus. For each viral pathogen, we will describe the epidemiology, natural history, screening and diagnosis modalities, treatments, and implications for antepartum care. Furthermore, we will highlight future directions of work in reducing the morbidities associated with these viral pathogens.
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20
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Giraud T, Koskella B, Laine AL. Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution. Mol Ecol 2018; 26:1703-1710. [PMID: 28409900 DOI: 10.1111/mec.14091] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 02/14/2017] [Accepted: 03/02/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Anna-Liisa Laine
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
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21
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Higher Expectations for a Vaccine To Prevent Congenital Cytomegalovirus Infection. J Virol 2018; 92:92/15/e00764-18. [PMID: 30018143 DOI: 10.1128/jvi.00764-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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22
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Sackman AM, Pfeifer SP, Kowalik TF, Jensen JD. On the Demographic and Selective Forces Shaping Patterns of Human Cytomegalovirus Variation within Hosts. Pathogens 2018; 7:pathogens7010016. [PMID: 29382090 PMCID: PMC5874742 DOI: 10.3390/pathogens7010016] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 02/08/2023] Open
Abstract
Human cytomegalovirus (HCMV) is a member of the β -herpesvirus subfamily within Herpesviridae that is nearly ubiquitous in human populations, and infection generally results only in mild symptoms. However, symptoms can be severe in immunonaive individuals, and transplacental congenital infection of HCMV can result in serious neurological sequelae. Recent work has revealed much about the demographic and selective forces shaping the evolution of congenitally transmitted HCMV both on the level of hosts and within host compartments, providing insight into the dynamics of congenital infection, reinfection, and evolution of HCMV with important implications for the development of effective treatments and vaccines.
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Affiliation(s)
- Andrew M Sackman
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA.
| | - Susanne P Pfeifer
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA.
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA.
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA.
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Impacts of Genome-Wide Analyses on Our Understanding of Human Herpesvirus Diversity and Evolution. J Virol 2017; 92:JVI.00908-17. [PMID: 29046445 PMCID: PMC5730764 DOI: 10.1128/jvi.00908-17] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Until fairly recently, genome-wide evolutionary dynamics and within-host diversity were more commonly examined in the context of small viruses than in the context of large double-stranded DNA viruses such as herpesviruses. The high mutation rates and more compact genomes of RNA viruses have inspired the investigation of population dynamics for these species, and recent data now suggest that herpesviruses might also be considered candidates for population modeling. High-throughput sequencing (HTS) and bioinformatics have expanded our understanding of herpesviruses through genome-wide comparisons of sequence diversity, recombination, allele frequency, and selective pressures. Here we discuss recent data on the mechanisms that generate herpesvirus genomic diversity and underlie the evolution of these virus families. We focus on human herpesviruses, with key insights drawn from veterinary herpesviruses and other large DNA virus families. We consider the impacts of cell culture on herpesvirus genomes and how to accurately describe the viral populations under study. The need for a strong foundation of high-quality genomes is also discussed, since it underlies all secondary genomic analyses such as RNA sequencing (RNA-Seq), chromatin immunoprecipitation, and ribosome profiling. Areas where we foresee future progress, such as the linking of viral genetic differences to phenotypic or clinical outcomes, are highlighted as well.
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Johnston C, Magaret A, Roychoudhury P, Greninger AL, Reeves D, Schiffer J, Jerome KR, Sather C, Diem K, Lingappa JR, Celum C, Koelle DM, Wald A. Dual-strain genital herpes simplex virus type 2 (HSV-2) infection in the US, Peru, and 8 countries in sub-Saharan Africa: A nested cross-sectional viral genotyping study. PLoS Med 2017; 14:e1002475. [PMID: 29281620 PMCID: PMC5744910 DOI: 10.1371/journal.pmed.1002475] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/20/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Quantitative estimation of the extent to which the immune system's protective effect against one herpes simplex virus type 2 (HSV-2) infection protects against infection with additional HSV-2 strains is important for understanding the potential for HSV-2 vaccine development. Using viral genotyping, we estimated the prevalence of HSV-2 dual-strain infection and identified risk factors. METHODS AND FINDINGS People with and without HIV infection participating in HSV-2 natural history studies (University of Washington Virology Research Clinic) and HIV prevention trials (HIV Prevention Trials Network 039 and Partners in Prevention HSV/HIV Transmission Study) in the US, Africa, and Peru with 2 genital specimens each containing ≥105 copies herpes simplex virus DNA/ml collected a median of 5 months apart (IQR: 2-11 months) were included. It is unlikely that 2 strains would be detected in the same sample simultaneously; therefore, 2 samples were required to detect dual-strain infection. We identified 85 HSV-2 SNPs that, in aggregate, could determine whether paired HSV-2 strains were the same or different with >90% probability. These SNPs were then used to create a customized high-throughput array-based genotyping assay. Participants were considered to be infected with more than 1 strain of HSV-2 if their samples differed by ≥5 SNPs between the paired samples, and dual-strain infection was confirmed using high-throughput sequencing (HTS). We genotyped pairs of genital specimens from 459 people; 213 (46%) were men, the median age was 34 years (IQR: 27-44), and 130 (28%) were HIV seropositive. Overall, 272 (59%) people were from the US, 59 (13%) were from Peru, and 128 (28%) were from 8 countries in Africa. Of the 459 people, 18 (3.9%) met the criteria for dual-strain infection. HTS and phylogenetic analysis of paired specimens confirmed shedding of 2 distinct HSV-2 strains collected at different times in 17 pairs, giving an estimated dual-strain infection prevalence of 3.7% (95% CI = 2.0%-5.4%). Paired samples with dual-strain infection differed by a median of 274 SNPs in the UL_US region (range 129-413). Matching our observed dual-strain infection frequency to simulated data of varying prevalences and allowing only 2 samples per person, we inferred the true prevalence of dual-strain infection to be 7%. In multivariable analysis, controlling for HIV status and continent of origin, people from Africa had a higher risk for dual-strain infection (risk ratio [RR] = 9.20, 95% CI = 2.05-41.32), as did people who were HIV seropositive (RR = 4.06, 95% CI = 1.42-11.56). CONCLUSIONS HSV-2 dual-strain infection was detected in 3.7% of paired samples from individual participants, and was more frequent among people with HIV infection. Simulations suggest that the true prevalence of dual-strain infection is 7%. Our data indicate that naturally occurring immunity to HSV-2 may be protective against infection with a second strain. This study is limited by the inability to determine the timing of acquisition of the second strain.
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Affiliation(s)
- Christine Johnston
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| | - Amalia Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Alexander L. Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Daniel Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Joshua Schiffer
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Cassandra Sather
- Genomics and Bioinformatics Resource, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Kurt Diem
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Jairam R. Lingappa
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Connie Celum
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - David M. Koelle
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Benaroya Research Institute, Seattle, Washington, United States of America
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
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Affiliation(s)
- Philip E Pellett
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, Michigan
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